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*: recursive bump for jpeg -> libjpeg-turbo switch
*: recursive bump for default Kerberos implementation switch
*: recursive bump for icu 77 and libxml2 2.14
(math/R) revert to 4.4.2, newone will be put on wip
(math/R) Updated 4.4.2 to 4.4.3
CHANGES IN R 4.4.3:
INSTALLATION:
* R can be installed using C23 (for example with '-std=gnu23'
or '-std=gnu2x') with recent compilers including 'gcc'
12-14, Apple 'clang' 15-16, LLVM 'clang' 17-20 and Intel
'icx' 2024.2.
It can be installed with the upcoming (at the time of
writing) 'gcc' 15, which defaults to C23.
C-LEVEL FACILITIES:
* The functions 'R_strtod' and 'R_atof' now allow hexadecimal
constants without an exponent, for compatibility with their
C99 versions (PR#18805).
UTILITIES:
* 'R CMD build' and 'R CMD check' now allow reference output
for demo scripts ('demo/<demo>.Rout.save' files) to be
shipped with the package, as proposed by Torsten Hothorn in
PR#18816.
BUG FIXES:
* 'kappa(A, exact=TRUE)' for singular 'A' returns 'Inf' more
generally, fixing PR#18817 reported by Mikael Jagan.
* Fixed URLs of the sun spots ('sunspot.month' etc) data sets
and mention future changes due to recalibration.
* The parser now accepts hexadecimal constants with a decimal
point without an exponent (taken as 'p0') as documented in
'?NumericConstants' (PR#18819).
* 'rbind()' now works correctly when inputs include a raw
vector and a logical, integer or double vector - previously
the inclusion of the latter was garbled.
* 'smooth.spline()' checks validity of its arguments
'df.offset' and 'penalty': it could segfault if they were
'NULL'.
* 'isGeneric(<primitive>, fdef=*, getName=TRUE)' now also
returns the name instead of just 'TRUE', fixing PR#18829
reported by Mikael Jagan.
* 'isGeneric(fdef = print)' now works, fixing PR#18369 thanks
to Mikael Jagan.
* 'sort(x, method = "qsort")' made illegal accesses when 'x'
has length 0.
* 'dir.create()' is protected against being passed an empty
string as its 'path' argument.
* Silent integer overflow could occur in the 'exact'
computations for 'fisher.test()' for unrealistic inputs:
this is now an error.
* Some invalid C-level memory accesses are avoided for
'loglin(, margin = NULL)'.
'loglin(, param = TRUE)' no longer gives an error in corner
cases such as a one-dimensional input.
* 'dev.capabilities() $ events' now reports '"Idle"' if the
device provides it, fixing PR#18836, thanks to Trevor Davis.
* 'arima(.., seasonal = <wrong-vector>)' correctly errors now,
ditto for 'arima0()', thanks to Norbert Kuder's report on
the R-devel list.
* 'binomial(<link>)$linkinv(eta)' and '.. $mu.eta(eta)' now
also work for '"logit"' link when 'is.integer(eta)'.
* 'as.roman(x)' now should work platform independently, also
for, e.g., 'x = "IIIII"' (= V) and 'x = "IIIIII"' (= VI).
* 'R CMD Rd2pdf' works again on an installed package directory
containing LaTeX help (from option '--latex'), thanks to a
report by Peter Ruckdeschel.
R: move API depends line closer to the corresponding buildlink3.mk
math/R: supply custom LDFLAGS, so that libR.so is picked up. Resolves build problem on NetBSD/amd64 (and probably many more). Thanks to wiz@ for the fix, ref. tech-pkg@.
math/R: on NetBSD, disable the ntohl / htonl dance.
These are already declared at the point in the code it's used,
and on macppc it causes build failure, and probably also on other
big-endian targets.
There still appears to be rpath issues, libR.so is installed in
${PREFIX}/lib/R/lib/, but that directory is not in rpath of other
libs or executables, so this does not install, at least not on
macppc at the moment.
Bump PKGREVISION.
*: recursive bump for pango requiring fontconfig 2.15
*: recursive bump for icu 76 shlib major version bump
*: revbump for icu downgrade
(math/R) Updated 4.4.1 to 4.4.2
CHANGES IN R 4.4.2:
C-LEVEL FACILITIES:
* The S-compatibility macros 'F77_COM' and 'F77_COMDECL'
defined in header 'R_ext/RS.h' are deprecated and will be
removed shortly. We could find no record of their use.
BUG FIXES:
* Mathlib function 'lgammacor(x)' no longer warns about
underflow to zero for large 'x'.
* Text widths and heights were incorrectly reported by the
Quartz device if the drawing context didn't exist yet
(typically when drawing off-screen to a window that is yet
to appear, see PR#18591).
* The Quartz device could segfault in cases where paths with
spaces are used in the new glyph drawing API. Thanks to
Tomek Gieorgijewski (PR#18758).
* On macOS in R CRAN builds, it is again possible to read
little-endian UTF-16 text with a BOM from a connection using
'encoding="UTF-16"'. Users building R from source should
avoid using the system 'libiconv' in macOS 14.1 and later.
* 'methods'' internal '.requirePackage()' now re-enables
primitive method dispatch when needed; thanks to Ivan Krylov
for demystifying CRAN package check failures on the R-devel
mailing list.
*: recursive bump for icu 76.1 shlib bump
(math/R) Updated 4.4.0 to 4.4.1
R CMD Rdconv --type=txt /tmp/math/R/work/R-4.4.1/doc/NEWS.Rd | head -70
CHANGES IN R 4.4.1:
C-LEVEL FACILITIES:
* Functions 'R_atof' and 'R_strtod' declared in header
'R_ext/Utils.h' are now documented in 'Writing R Extensions'
and so formally part of the API.
* The non-API entry points 'Rf_setSVector', 'Rf_StringFalse',
'Rf_StringTrue' and 'Rf_isBlankString' have been added to
those reported by 'R CMD check'.
* The new function 'Rf_allocLang' is now available. This
provides an alternative to the idiom of calling
'Rf_allocList' followed by 'SET_TYPEOF'.
UTILITIES:
* 'R CMD check' now reports as warnings what 'gfortran' calls
'Fortran 2018 deleted features', all of which have long been
marked as 'obsolescent' and some of which were deleted in
Fortran 2008 or earlier. Fortran compilers are no longer
required to support these.
BUG FIXES:
* 'as.numeric()', 'scan()', 'type.convert()' and other places
which use the internal C function 'R_strtod' now require a
_non-empty_ digit sequence in a decimal or binary exponent.
This aligns with the C/POSIX standard for 'strtod' and with
'?NumericConstants'.
* 'as.data.frame(m, make.names=NA)' now works correctly for a
matrix 'm' with 'NA''s in row names.
* The error message from '<POSIXlt>[["hour"]]' and similar now
mentions '*[[, "hour"]]', as wished for in PR#17409 and
proposed by Michael Chirico.
* 'qbinom()' and potentially 'qpois()', 'qnbinom()', no longer
sometimes fail accurate inversion (of 'pbinom()', etc),
thanks to Christopher Chang's report and patch in PR#18711.
* The internal help server on Windows can again serve requests
sent in quick succession, fixing a regression in R 4.4.0.
* 'debugcall(<S3Generic>())' now also works when a
corresponding S4-generic version is in the 'methods' cache
(PR#18143).
* Package 'tools'' 'toTitleCase(ch0)' now returns
'character(0)' when 'ch0' is of zero length; fixing
PR#18724, reported by David Hugh Jones.
* 'R CMD check' is no longer broken (without a check result
and no explanation in '00check.log') for a package which
declares an invalid 'VignetteBuilder' in 'DESCRIPTION' but
has no vignettes.
revbump after icu and protobuf updates
(math/R) Updated 4.3.3. to 4.4.0
NEWS for R version 4.4.0 (2024-04-24)
CHANGES IN R 4.4.0
SIGNIFICANT USER-VISIBLE CHANGES:
* Startup banners, R --version, sessionInfo() and R CMD check no longer report
(64-bit) as part of the platform as this is almost universal – the increasingly rare
32-bit platforms will still report (32-bit).
On Windows, ditto for window titles.
* is.atomic(NULL) now returns FALSE, as NULL is not an atomic vector.
Strict back-compatibility would replace is.atomic(foo) by (is.null(foo) ||
is.atomic(foo)) but should happen only sparingly.
NEW FEATURES:
* The confint() methods for "glm" and "nls" objects have been copied to the
stats package. Previously, they were stubs which called versions in package MASS.
The MASS namespace is no longer loaded if you invoke (say) confint(glmfit).
Further, the "glm" method for profile() and the plot() and pairs() methods
for class "profile" have been copied from MASS to stats. (profile.nls() and
plot.profile.nls() were already in stats.)
* The confint() and profile methods for "glm" objects have gained a possibility to
do profiling based on the Rao Score statistic in addition to the default Likelihood
Ratio. This is controlled by a new test = argument.
* The pairs() method for "profile" objects has been extended with a
which = argument to allow plotting only a subset of the
parameters.
* The "glm" method for anova() computes test statistics and p-values
by default, using a chi-squared test or an F test depending on whether
the dispersion is fixed or free. Test statistics can be suppressed by
giving argument test a false logical value.
* In setRepositories() the repositories can be set using their names
via name = instead of index ind =.
* methods() and .S3methods() gain a all.names option for the (rare)
case where functions starting with a ‘.’ should be included.
* Serializations can now be interrupted (e.g., by Ctrl-C on a
Unix-alike) if they take too long, e.g., from save.image(), thanks to
suggestions by Ivan Krylov and others on R-devel.
* New startup option ‘--max-connections’ to set the maximum number of
simultaneous connections for the session. Defaults to 128 as before:
allowed values up to 4096 (but resource limits may in practice
restrict to smaller values).
* R on Windows (since Windows 10 2004) now uses the new Segment Heap
allocator. This may improve performance of some memory-intensive
applications.
* When R packages are built, typically by R CMD build <pkg>, the new
--user=<build_user> option overrides the (internally determined) user
name, currently Sys.info()["user"] or LOGNAME. This is a (modified)
fulfillment of Will Landau’s suggestion in PR#17530.
* tools::testInstalledBasic() gets new optional arguments outDir and
testSrcdir, e.g., allowing to use it in a builddir != srcdir setup,
and in standard “binary” Windows installation if a source ‘tests/’
folder is present.
* range(<DT_with_Inf>, finite = TRUE) now work for objects of class
"Date", "POSIXct", and "POSIXlt" with infinite entries, analogously to
range.default(), as proposed by Davis Vaughan on R-devel. Other
range()-methods can make use of new function .rangeNum().
* New .internalGenerics object complementing .S3PrimitiveGenerics, for
documentation and low-level book-keeping.
* grid() now invisibly returns the x- and y- coordinates at which the
grid-lines were drawn.
* norm(., type) now also works for complex matrices.
* kappa(., exact = TRUE, norm = *) now works for all norms and also
for complex matrices. In symmetric / triangular cases, the new
argument uplo = "U" | "L" allows the upper or lower triangular part to
be specified.
* memDecompress(type = "unknown") recognizes compression in the
default ‘zlib’ format as used by memCompress(type = "gzip").
* memCompress() and memDecompress() will use the libdeflate library
(https: //github.com/ebiggers/libdeflate) if installed. This uses the
same type of compression for type = "gzip" but is 1.5-2x faster than
the system libz library on some common platforms: the speed-up may
depend on the library version.
* diff() for objects of class "Date", "POSIXct", and "POSIXlt" accepts
a units argument passed via ....
* Dynamic help now does a much better job of rendering package
‘DESCRIPTION’ metadata.
* Rprof() gains an event argument and support for elapsed (real) time
profiling on Unix (PR#18076).
* filled.contour() gains a key.border argument.
* tools::update_pkg_po() gets arguments pot_make and mo_make for not
re-making the corresponding files, and additionally a verbose
argument.
* Hexadecimal string colour specifications are now accepted in short
form, so, for example, we can use "#123", which is equivalent to
"#112233". Thanks to MikeFC for the original idea and Ella Kaye,
Malcolm Barrett, George Stagg, and Hanne Oberman for the patch.
* Plain-text help shows \var markup by angle brackets.
* The new experimental primitive function declare() is intended to
eventually allow information about R code to be communicated to the
interpreter, compiler, and code analysis tools. The syntax for
declarations is still being developed.
* Functions psmirnov(), qsmirnov() and rsmirnov() in package stats
have had argument two.sided renamed to alternative, to take into
account that the permutation distributions of the one-sided statistics
can be different in the case of ties. Consequence of PR#18582.
* sort() is now an implicit S4 generic in methods.
* Formatting and printing, format(z), print(z), of complex vectors z
no longer zap relatively small real or imaginary parts to zero, fixing
PR#16752. This is an API change, as it was documented previously to
round real and imaginary parts together on purpose, producing nicer
looking output. As mentioned, e.g. in the PR, this change is
compatible with many other “R-like” programming environments. We have
simplified the internal code and now basically format the real and
imaginary parts independently of each other.
* New experimental functions Tailcall() and Exec() to support writing
stack-spaceefficient recursive functions.
* Where characters are attempted to be plotted by pdf(), postscript()
and xfig() which are not in the selected 8-bit character set (most
often Latin-1) and the R session is using a UTF-8 locale, the warning
messages will show the UTF-8 character rather than its bytes and one
dot will be substituted per character rather than per byte.
(Platforms whose iconv() does transliteration silently plot the
transliteration.) In a UTF-8 locale some transliterations are now
done with a warning (e.g., dashes and Unicode minus to hyphen,
ligatures are expanded, permille (‘‰’) is replaced by ‘o/oo’),
although the OS may have got there first. These are warnings as they
will continue to be replaced by dots in earlier versions of R.
* The matrix multiplication functions crossprod() and tcrossprod() are
now also primitive and S3 generic, as %*% had become in R 4.3.0.
* source() and example() have a new optional argument catch.aborts
which allows continued evaluation of the R code after an error.
* The non-Quartz tiff() devices allow additional types of compression
if supported by the platform’s ‘libtiff’ library.
* The list of base and recommended package names is now provided by
tools::standard_package_names().
* cairo_pdf() and cairo_ps() default to onefile = TRUE to closer match
pdf() and postscript().
* New option catch.script.errors provides a documented way to catch
errors and then continue in non-interactive use.
* L %||% R newly in base is an expressive idiom for the phrases
if(!is.null(L)) L else R or if(is.null(L)) R else L.
* The return value from warnings() now always inherits from "warnings"
as documented, now also in the case of no warnings where it
previously returned NULL.
* as.complex("1i") now returns 0 + 1i instead of NA with a warning.
* z <- c(NA, 1i) now keeps the imaginary part Im(z[1]) == 0, no longer
coercing to NA_complex_. Similarly, cumsum(z) correctly sums real and
imaginary parts separately, i.e., without “crosstalk” in case of NAs.
* On Alpine Linux iconv() now maps "latin2", "latin-2", "latin9" and "latin-9"
to encoding names the OS knows about (case-insensitively).
* iconv(sub = "Unicode") now always zero-pads to four (hex) digits,
rather than to 4 or 8. (This seems to have become the convention
once Unicode restricted the number of Unicode points to 221 − 1
and so will never need more than 6 digits.)
* NCOL(NULL) now returns 0 instead of 1, for consistency with cbind().
* The information for the Euro glyph missing from the Adobe ‘.afm’
files for the Courier, Helvetica and Times families has been copied
from their URW equivalents – this will improve vertical centring in
the pdf() and postscript() devices.
* The included BLAS sources have been updated to those shipped with
LAPACK version 3.12.0. The changes are almost entirely cosmetic.
* The included LAPACK sources have been updated to version 3.12.0 and some further
double-complex routines added.
* There are new font families for the 2014–5 URW 2.0 fonts (see ?pdf)
which are included in recent versions of Ghostscript. These have font
widths for most Greek glyphs and a few others which were missing from
the original versions (whose font families remain available for
reproducibility, although Ghostscript-based viewers will render using
the 2.0 versions).
* Improve the large-n efficiency of as.matrix(<dist>), thanks an R
contributors effort, notably by Tim Taylor and Heather Turner, see
PR#18660.
* The default and numeric methods of all.equal() get a check.class option.
* zapsmall() gets new optional arguments, function mFUN and min.d, for
extra flexibility; fulfills a wish in PR#18199. Also, it is now an
implicit S4 generic in package methods.
* The Rd filter for aspell() gains an ignore argument.
* New generic function sort_by(), primarily useful for the data.frame
method which can be used to sort rows of a data frame by one or more
columns.
* The icence headers for the RPC code in ‘src/extra/xdr’ have been updated to use
the GPL-compatible licence published by Oracle America in 2010.
* New function pkg2HTML() in tools to create single-page HTML reference manuals for
R packages.
* The byte code evaluator now uses less C stack space for recursive
calls to bytecompiled functions. It also makes more of an effort to
avoid allocations for scalar return values.
* New completion option backtick (disabled by default) allows
non-syntactic completions to be wrapped in backquotes. This is
currently only useful for Jupyter notebooks via the IRkernel package,
and may cause problems for other backends.
*: recursive bump for gnutls p11-kit option (existing installations need the bl3.mk included, but it's now only optionally included)
(math/R) Updated 4.3.2 to 4.3.3
CHANGES IN R 4.3.3:
NEW FEATURES:
* 'iconv()' now fixes up variant encoding names such as
'"utf8"' case-insensitively.
DEPRECATED AND DEFUNCT:
* The legacy 'encoding = "MacRoman"' is deprecated in 'pdf()'
and 'postscript()': support was incomplete in earlier
versions of R.
BUG FIXES:
* Arguments are now properly forwarded to methods on S4
generics with ... in the middle of their formal arguments.
This was broken for the case when a method introduced an
argument but did not include ... in its own formals. Thanks
to Herv<c3><a9> Pag<c3><a8>s for the report PR#18538.
* Some invalid 'file' arguments to 'pictex()', 'postscript()'
and 'xfig()' opened a file called 'NA' rather than throw an
error. These included 'postscript(NULL)' (which some people
expected to work like 'pdf(NULL)').
* Passing 'filename = NA' to 'svg()', 'cairo_pdf()',
'cairo_ps()' or the Cairo-based bitmap devices opened a file
called 'NA': it now throws an error.
* 'quartz(file = NA)' opened a file called 'NA', including
when used as a Quartz-based bitmap device. It now gives an
error.
* 'rank(<long vector>)' now works, fixing PR#18617, thanks to
Ilia Kats.
* 'seq.int()' did not adequately check its 'length.out'
argument.
* 'match(<POSIXct>, .)' is correct again for differing time
zones, ditto for '"POSIXlt"', fixing PR#18618 reported by
Bastian Klein.
* 'drop.terms(*, dropx = <0-length>)' now works, fixing
PR#18563 as proposed by Mikael Jagan.
* 'drop.terms(*)' keeps ' + offset(.)' terms when it should,
PR#18565, and 'drop.terms()' no longer makes up a response,
PR#18566, fixing both bugs thanks to Mikael Jagan.
* 'getS3method("t", "test")' no longer finds the 't.test()'
function, fixing PR#18627.
* 'pdf()' and 'postscript()' support for the documented Adobe
encodings '"Greek"' and '"Cyrilllic"' was missing (although
the corresponding Windows' codepages could be used).
* Computations of glyph metric information for 'pdf()' and
'postscript()' did not take into account that
transliteration could replace one character by two or more
(only seen on macOS 14) and typically warned that the
information was not known.
* 'rank(x)' no longer overflows during integer addition, when
computing rank average for largish but not-yet long vector
'x', fixing PR#18630, thanks to Ilia Kats.
* 'list.files()' on Windows now returns also files with names
longer that 260 bytes (the Windows limit is 260 characters).
Previously, some file names particularly with 'East Asian'
characters were omitted.
* 'cov2cor(<0 x 0>)' now works, fixing PR#18423 thanks to
Mikael Jagan and Elin Waring.
* 'cov2cor(<negative diagonal>)' and similar now give one
warning instead of two, with better wording, fixing PR#18424
thanks to Mikael Jagan.
* 'tools'':: startDynamicHelp()' now ensures 'port' is in
proper range, fixing PR#18645.
* 'pbeta(x, a,b)' is correct now for 'x'=0 or 1 in the
boundary cases where 'a' or 'b' or both are 0, fixing
PR#18672 thanks to Michael Fay.
* 'pmatch(x, table)' for large 'table', also called for data
frame row selection, 'dfrm[nm, ]', is now interruptible,
fixing PR#18656.
* 'predict(<rank-deficient lm>, newdata=*)' fix computing of
'nbasis', see Russ Lenth's comment 29 in PR#16158.
* Added a work-around for a bug in macOS 14.3.1 and higher
which prevents R plots in the Quartz Cocoa device from
updating on screen.
*: bump for cairo buildlink3.mk change lzo was made an option
R: fix dealing with conflict with NetBSD function strtoi() Just rename the C level function strtoi() to not conflict with the NetBSD function. Don't also change the name of the R level funstion.
(math/R) Updated 4.2.3 to 4.3.2 with remedy for strtoi
- pkgsrc side change
strtoi function conflicted with NetBSD function. but it was
referenced in the same file. Now it is referenced at various places.
So it is renamed into strtoiR (All the strings for now) by SUBST,
thus including do_strtoi.
(patches/patch-src_main_character.c is dropped)
- upstream info
CHANGES IN R 4.3.2:
NEW FEATURES:
* The default initialization of the '"repos"' option from the
'repositories' file at startup can be skipped by setting
environment variable 'R_REPOSITORIES' to 'NULL' such that
'getOption("repos")' is empty if not set elsewhere.
* 'qr.X()' is now an implicit S4 generic in 'methods'.
* 'iconv(to = "ASCII//TRANSLIT")' is emulated using
substitution on platforms which do not support it (notably
Alpine Linux). This should give a human-readable conversion
in ASCII on all platforms (rather than 'NA_character_').
* 'trans3d()' gains options 'continuous' and 'verbose'
addressing the problem of possible "wrap around" when
projecting too long curves, as reported by Achim Zeileis in
PR#18537.
* 'tools::showNonASCII()' has been rewritten to work better on
macOS 14 (which has a changed implementation of 'iconv()').
* 'tiff(type = "quartz")' (the default on macOS) now warns if
'compression' is specified: it continues to be ignored.
INSTALLATION on a UNIX-ALIKE:
* There is some support for building with Intel's LLVM-based
compilers on 'x86_64' Linux, such as (C) 'icx', (C++) 'ipcx'
and (Fortran) 'ifx' from oneAPI 2023.x.y.
* There is support for using LLVM's 'flang-new' as the Fortran
compiler from LLVM 16.0.x (preferably 17.0.0 or later).
UTILITIES:
* 'R CMD check' reports the use of the Fortran 90 random
number generator 'RANDOM_NUMBER()' and the subroutines to
initialize it.
'Writing R Extensions' has example code to use R's RNGs from
Fortran.
BUG FIXES:
* 'substr(x, n, L) <- cc' now works (more) correctly for
multibyte UTF-8 strings 'x' when 'L > nchar(x)', thanks to a
report and patch by 'Architect 95'.
* 'contrib.url(character())' now returns 0-length
'character()' as documented, which also avoids spurious
warnings from 'available.packages()' et al. in the edge case
of an empty vector of repository URLs.
* 'readChar(., 4e8)' no longer fails, thanks to Kodi Arfer's
report (PR#18557).
* 'lapply(<list>, as.data.frame)' no longer warns falsely for
some base vector components.
* Communication between parent and child processes in the
'multicore' part of 'parallel' could fail on platforms that
do not support an arbitrarily large payload in system
functions 'read()'/'write()' on pipes (seen on macOS where a
restriction to 'INT_MAX' bytes is documented, without doing
a partial read unlike Linux). The payload is now split into
1Gb chunks to avoid that problem. (PR#18571)
* 'qqplot(x,y, conf.level=.)' gives better confidence bounds
when 'length(x) != length(y)', thanks to Alexander Ploner's
report and patch proposal (PR#18557).
* 'norm(<0-length>, "2")' now gives zero instead of an error,
as all the other norm types, thanks to Mikael Jagan's
PR#18542.
* Build-stage Rd macros \packageAuthor and \packageMaintainer
now process 'Authors@R', fixing 'NA' results when the
package 'DESCRIPTION' omits 'Author' and 'Maintainer'
fields.
* Formatting and printing complex numbers could give things
like '0.1683-0i' because of rounding error: '-0i' is now
replaced by '+0i'.
* 'postscript()' refused to accept a 'title' comment
containing the letter "W" (PR#18599).
* 'isoreg(c(1,Inf))' signals an error instead of segfaulting,
fixing PR#18603.
* 'tiff(type = "Xlib")' was only outputting the last page of
multi-page plots.
* 'tools::latexToUtf8()' again knows about '\~{n}' and other
letters with tilde, fixing a regression in R 4.3.0, and
about '\^{i}' as an alternative to '\^{\i}' (similarly with
other accents). Furthermore, LaTeX codes for accented I
letters are now correctly converted, also fixing related
mistakes in 'tools::encoded_text_to_latex()'.
* 'tar(*, tar = "internal")' no longer creates out-of-spec tar
files in the very rare case of user or group names longer
than 32 bytes, fixing PR#17871 with thanks to Ivan Krylov.
* When using the "internal" timezone datetime code, adding a
fraction of a second no longer adds one second, fixing
PR#16856 from a patch by Ivan Krylov.
* 'tools::checkRd()' no longer produces spurious notes about
"unnecessary braces" from multi-line Rd results of \Sexpr
macros.
CHANGES IN R 4.3.1:
C-LEVEL FACILITIES:
* The C-level API version of R's 'integrate()', 'Rdqags()' in
'Applic.h', now returns the correct number of integrand
evaluations 'neval', fixing PR#18515 reported and diagnosed
by Stephen Wade.
* The C prototypes for LAPACK calls 'dspgv' and 'dtptrs' in
'R_exts/Lapack.h' had one too many and one too few character
length arguments - but this has not caused any known issues.
To get the corrected prototypes, include
#include <Rconfig.h> // for PR18534fixed
#ifdef PR18534fixed
# define usePR18534fix 1
#endif
#include <R_exts/Lapack.h>
in your C/C++ code (PR#18534).
INSTALLATION:
* Many of the checks of esoteric Internet operations and those
using unreliable external sites have been moved to a new
target that is not run by default and primarily intended for
the core developers. To run them use
cd tests; make test-Internet-dev
BUG FIXES:
* '.S3methods()', typically called from 'methods()', again
marks methods from package 'base' as 'visible'.
Also, the visibility of non-'base' methods is again
determined by the method's presence in 'search()'.
* 'tools::Rdiff()' is now more robust against invalid strings,
fixing installation tests on Windows without Rtools
installed (PR#18530).
* Fix (new) bug in 'hcl.colors(2, *)', by Achim Zeileis
(PR#18523).
* 'head(., <illegal>)' and 'tail(..)' now produce more useful
'"Error in ...."' error messages, fixing PR#18362.
* Package code syntax on Windows is checked in UTF-8 when
UTF-8 is the native encoding.
* 'na.contiguous(x)' now also returns the first run, when it
is at the beginning and there is a later one of the same
length; reported to R-devel, including a fix, by Georgi
Boshnakov. Further, by default, it modifies only an
existing 'attr(*,"tsp")' but otherwise no longer sets one.
* 'chol(<not pos.def>, pivot = <T|F>)' now gives a correct
error or warning message (depending on 'pivot'), thanks to
Mikael Jagan's (PR#18541).
CHANGES IN R 4.3.0:
SIGNIFICANT USER-VISIBLE CHANGES:
* Calling '&&' or '||' with LHS or (if evaluated) RHS of
length greater than one is now always an error, with a
report of the form
'length = 4' in coercion to 'logical(1)'
Environment variable '_R_CHECK_LENGTH_1_LOGIC2_' no longer
has any effect.
NEW FEATURES:
* The included BLAS sources have been updated to those shipped
with LAPACK version 3.10.1. (This caused some
platform-dependent changes to package check output.) And
then to the sources from LAPACK version 3.11.0 (with changes
only to double complex subroutines).
* The included LAPACK sources have been updated to include the
four Fortran 90 routines rather than their Fortran 77
predecessors. This may give some different signs in SVDs or
eigendecompositions.. (This completes the transition to
LAPACK 3.10.x begun in R 4.2.0.)
* The LAPACK sources have been updated to version 3.11.0. (No
new subroutines have been added, so this almost entirely bug
fixes: Those fixes do affect some computations with 'NaN's,
including R's 'NA'.)
* The parser now signals _classederrors, notably in case of
the pipe operator '|>'. The error object and message now
give line and column numbers, mostly as proposed and
provided by Duncan Murdoch in PR#18328.
* 'toeplitz()' is now generalized for asymmetric cases, with a
'toeplitz2()' variant.
* 'xy.coords()' and 'xyz.coords()' and consequently, e.g.,
'plot(x,y, log = "y")' now signal a _classedwarning about
negative values of y (where 'log(.)' is 'NA'). Such a
warning can be specifically suppressed or caught otherwise.
* Regular expression functions now check more thoroughly
whether their inputs are valid strings (in their encoding,
e.g. in UTF-8).
* The performance of 'grep()', 'sub()', 'gsub()' and
'strsplit()' has been improved, particularly with 'perl =
TRUE' and 'fixed = TRUE'. Use of 'useBytes = TRUE' for
performance reasons should no longer be needed and is
discouraged: it may lead to incorrect results.
* 'apropos()' gains an argument 'dot_internals' which is used
by the completion ('help(rcompgen)') engine to also see
'base' internals such as '.POSIXct()'.
* Support in 'tools::Rdiff()' for comparing uncompressed PDF
files is further reduced - see its help page.
* 'qqplot(x, y, ...)' gains 'conf.level' and 'conf.args'
arguments for computing and plotting a confidence band for
the treatment function transforming the distribution of 'x'
into the distribution of 'y ' (Switzer, 1976, _Biometrika_).
Contributed by Torsten Hothorn.
* Performance of 'package_dependencies()' has been improved
for cases when the number of dependencies is large.
* Strings newly created by 'gsub()', 'sub()' and 'strsplit()',
when any of the inputs is marked as '"bytes"', are also
marked as '"bytes"'. This reduces the risk of creating
invalid strings and accidental substitution of bytes deemed
invalid.
* Support for 'readLines(encoding = "bytes")' has been added
to allow processing special text files byte-by-byte, without
creating invalid strings.
* 'iconv(from = "")' now takes into account any declared
encoding of the input elements and uses it in preference to
the native encoding. This reduces the risk of accidental
creation of invalid strings, particularly when different
elements of the input have different encoding (including
'"bytes"').
* Package repositories in 'getOption("repos")' are now
initialized from the 'repositories' file when 'utils' is
loaded (if not already set, e.g., in '.Rprofile'). (From a
report and patch proposal by Gabriel Becker in PR#18405.)
* 'compactPDF()' gets a 'verbose' option.
* 'type.convert()' and hence 'read.table()' get new option
'tryLogical = TRUE' with back compatible default. When set
to false, converts '"F"' or '"T"' columns to character.
* Added new unit prefixes '"R"' and '"Q"' for abbreviating
(unrealistically large) sizes beyond 10^{27} in 'standard =
"SI"', thanks to Henrik Bengtsson's PR#18435.
* 'as.data.frame()''s default method now also works fine with
atomic objects inheriting from classes such as '"roman"',
'"octmode"' and '"hexmode"', such fulfilling the wish of
PR#18421, by Benjamin Feakins.
* The 'as.data.frame.vector()' utility now errors for
wrong-length 'row.names'. It warned for almost six years,
with "Will be an error!".
* 'sessionInfo()' now also contains 'La_version()' and reports
codepage and timezone when relevant, in both 'print()' and
'toLatex()' methods which also get new option 'tzone' for
displaying timezone information when 'locale = FALSE'.
* New function 'R_compiled_by()' reports the C and Fortran
compilers used to build R, if known.
* 'predict(<lm>, newdata = *)' no longer unnecessarily creates
an 'offset' of all '0's.
* 'solve()' for complex inputs now uses argument 'tol' and by
default checks for 'computational singularity' (as it long
has done for numeric inputs).
* 'predict(<rank-deficient lm>, newdata=*)' now obeys a new
argument 'rankdeficient', with new default '"warnif"',
warning only if there are non-estimable cases in 'newdata'.
Other options include 'rankdeficient = "NA"', predicting
'NA' for non-estimable 'newdata' cases. This addresses
PR#15072 by Russ Lenth and is based on his original proposal
and discussions in PR#16158 also by David Firth and Elin
Waring. Still somewhat experimental.
* 'Rgui' console implementation now works better with the
'NVDA' screen reader when the full blinking cursor is
selected. The underlying improvements in cursor handling
may help also other screen readers on Windows.
* The drop-field control in GraphApp can now be left with the
TAB key and all controls can be navigated in the reverse
order using the Shift+TAB key, improving accessibility of
the 'Rgui' configuration editor.
* 'qnorm(<very large negative>, log.p=TRUE)' is now fully
accurate (instead of to "only" minimally five digits).
* 'demo(error.catching)' now also shows off 'withWarnings()'
and 'tryCatchWEMs()'.
* As an experimental feature the placeholder '_' can now also
be used in the 'rhs' of a forward pipe '|>' expression as
the first argument in an extraction call, such as '_$coef'.
More generally, it can be used as the head of a chain of
extractions, such as '_$coef[[2]]'.
* Spaces in the environment variable used to choose the R
session's temporary directory ('TMPDIR', 'TMP' and 'TEMP'
are tried in turn) are now fatal. (On Windows the 'short
path' version of the path is tried and used if that does not
contain a space.)
* 'all.equal.numeric()' gets a new optional switch 'giveErr'
to return the numeric error as attribute. Relatedly,
'stopifnot(all.equal<some>(a, b, ..))' is as "smart" now, as
'stopifnot(all.equal(....))' has been already, thus allowing
customized 'all.equal<Some>()' wrappers.
* R on Windows is now able to work with path names longer than
260 characters when these are enabled in the system
(requires at least Windows 10 version 1607). Packages
should be updated to work with long paths as well, instead
of assuming 'PATH_MAX' to be the maximum length. Custom
front-ends and applications embedding R need to update their
manifests if they wish to allow this feature. See
<https://blog.r-project.org/2023/03/07/path-length-limit-on-windows>
for more information.
* 'Object not found' and 'Missing argument' errors now give a
more accurate error context. Patch provided by Lionel Henry
in PR#18241.
* The '@' operator is now an S3 generic. Based on
contributions by Tomasz Kalinowski in PR#18482.
* New generic 'chooseOpsMethod()' provides a mechanism for
objects to resolve cases where two suitable methods are
found for an Ops Group Generic. This supports experimenting
with alternative object systems. Based on contributions by
Tomasz Kalinowski in PR#18484.
* 'inherits(x, what)' now accepts values other than a simple
character vector for argument 'what'. A new generic,
'nameOfClass()', is called to resolve the class name from
'what'. This supports experimenting with alternative object
systems. Based on contributions by Tomasz Kalinowski in
PR#18485.
* Detection of BLAS/LAPACK in use ('sessionInfo()') with
FlexiBLAS now reports the current backend.
* The '"data.frame"' method for 'subset()' now warns about
extraneous arguments, typically catching the use of '='
instead of '==' in the 'subset' expression.
* Calling 'a:b' when numeric 'a' or 'b' is longer than one may
now be made into an error by setting environment variable
'_R_CHECK_LENGTH_COLON_' to a true value, along the proposal
in PR#18419 by Henrik Bengtsson.
* 'density(x, weights = *)' now warns if automatic bandwidth
selection happens without using 'weights'; new optional
'warnWbw' may suppress the warning. Prompted by Christoph
Dalitz' PR#18490 and its discussants.
* 'rm(list = *)' is faster and more readable thanks to Kevin
Ushey's PR#18492.
* The 'plot.lm()' function no longer produces a normal Q-Q
plot for GLMs. Instead it plots a half-normal Q-Q plot of
the absolute value of the standardized deviance residuals.
* The 'print()' method for class '"summary.glm"' no longer
shows summary statistics for the deviance residuals by
default. Its optional argument 'show.residuals' can be used
to show them if required.
* The 'tapply()' function now accepts a data frame as its 'X'
argument, and allows 'INDEX' to be a formula in that case.
'by.data.frame()' similarly allows 'INDICES' to be a
formula.
* The performance of 'df[j] <- value' (including for missing
'j') and 'write.table(df)' has been improved for data frames
'df' with a large number of columns. (Thanks to Gabriel
Becker's PR#18500, PR#18503 and discussants, prompted by a
report from Toby Dylan Hocking on the R-devel mailing list.)
* The matrix multiply operator '%*%' is now an S3 generic,
belonging to new group generic 'matrixOps'. From Tomasz
Kalinowski's contribution in PR#18483.
* New function 'array2DF()' to convert arrays to data frames,
particularly useful for the list arrays created by
'tapply()'.
DATES and TIMES:
* On platforms where (non-UTC) datetimes before 1902 (or
before 1900 as with system functions on recent macOS) are
guessed by extrapolating time zones from 1902-2037, there is
a warning at the first use of extrapolation in a session.
(As all time zones post 2037 are extrapolation, we do not
warn on those.)
* (Platforms using '--with-internal-tzone', including Windows
and by default macOS). How years are printed in dates or
date-times can be controlled by environment variable
'R_PAD_YEARS_BY_ZERO'. The default remains to pad to 4
digits by zeroes, but setting value 'no' gives no padding
(as used by default by 'glibc').
* 'strftime()' tries harder to determine the offset for the
'"%z"' format, and succeeds on the mainstream R platforms.
* 'strftime()' has a limit of 2048 bytes on the string
produced - attempting to exceed this is an error.
(Previously it silently truncated at 255 bytes.)
* 'sessionInfo()' records (and by default prints) the system
time zone as part of the locale information. Also, the
source (system/internal) of the date-time conversion and
printing functions.
* Objects of class '"POSIXlt"' created in this version of R
always have 11 components: component 'zone' is always set,
and component 'gmtoff' is set for times in UTC and usually
set on the (almost all) platforms which have C-level
support, otherwise is 'NA'.
* There are comprehensive validity checks on the structure of
objects of class '"POSIXlt"' when converting (including
formatting and printing). (This avoids mis-conversions of
hand-crafted objects.)
* There is some support for using the native date-time
routines on macOS: this is only viable on recent versions
(e.g. 12.6 and 13) and does get wrong some historical
changes (before 1900, during WWII). Use of
'--with-internal-tzone' remains the default.
* 'as.POSIXct(<numeric>)' and 'as.POSIXlt(.)' (without
specifying 'origin') now work. So does
'as.Date(<numeric>)'.
* 'as.Date.POSIXct(., tz)' now treats several 'tz' values,
notably '"GMT"' as equivalent to '"UTC"', proposed and
improved by Michael Chirico and Joshua Ulrich in PR#17674.
* Experimental 'balancePOSIXlt()' utility allows using
"ragged" and or out-of-range '"POSIXlt"' objects more
correctly, e.g., in subsetting and subassignments. Such
objects are now documented.
More experimentally, a '"POSIXlt"' object may have an
attribute '"balanced"' indicating if it is known to be
filled or fully balanced.
* Functions 'axis.Date()' and 'axis.POSIXct()' are rewritten
to gain better default tick locations and better default
formats by using 'prettyDate()'. Thanks to Swetlana
Herbrandt.
* The mapping of Windows' names for time zones to IANA's
'Olson' names has been updated. When ICU is available (it
is by default), it is used to get a mapping for the current
region set in Windows. This can be overridden by setting
environment variable 'TZ' to the desired Olson name - see
'OlsonNames()' for those currently available.
GRAPHICS:
* The graphics engine version, 'R_GE_version', has been bumped
to '16' and so packages that provide graphics devices should
be reinstalled.
* The 'grDevices' and 'grid' packages have new functions for
rendering typeset glyphs, primarily:
'grDevices::glyphInfo()' and 'grid::grid.glyph()'.
Rendering of typeset glyphs is only supported so far on the
Cairo-based graphics devices and on the 'pdf()' and
'quartz()' devices.
* The defined behaviour for '"clear"' and '"source"'
compositing operators (via 'grid::grid.group()') has been
changed (to align better with simple interpretation of
original Porter-Duff definitions).
* Support for gradients, patterns, clipping paths, masks,
groups, compositing operators, and affine transformations
has been added to the 'quartz()' device.
INSTALLATION on a UNIX-ALIKE:
* A system installation of generic LAPACK 3.10.0 or later will
be preferred to the version in the R sources.
'configure' option '--with-lapack=no' (equivalently
'--without-lapack') forces compilation of the internal
LAPACK sources.
If '--with-lapack' is not specified, a system 'liblapack' is
looked for and used if it reports version 3.10.0 or later
and does not contain BLAS routines.
Packages using LAPACK will need to be reinstalled if this
changes to using an external library.
* On 'aarch64' Linux platforms using GCC, 'configure' now
defaults to '-fPIC' (instead of '-fpic'), as desired in
PR#18326.
* 'configure' now checks conversion of datetimes between
'POSIXlt' and 'POSIXct' around year 2020. Failure (which
has been seen on platforms missing 'tzdata') is fatal.
* If 'configure' option '--with-valgrind-instrumentation' is
given value '1' or '2', option
'--with-system-valgrind-headers' is now the default and
ignored (with a warning). It is highly recommended that the
system headers are installed alongside 'valgrind': they are
part of its packaging on some Linux distributions and
packaged separately (e.g. in the 'valgrind-devel' RPM) on
others. 'configure' will give a warning if they are not
found.
The system headers will be required in a future release of R
to build with 'valgrind' instrumentation.
* 'libcurl' 8.x is now accepted by 'configure': despite a
change in major version number it changes neither API nor
ABI.
INSTALLATION on WINDOWS:
* The makefiles and installer scripts for Windows have been
tailored to 'Rtools43', an update of the 'Rtools42'
toolchain. It is based on 'gcc' 12 and newer versions of
MinGW-W64, binutils and libraries. At this time R-devel can
still be built using Rtools42 without changes, but when
R-devel is installed via the installer, it will by default
look for Rtools43.
* Old make targets 'rsync-extsoft' and 32-bit ones that are no
longer needed have been removed.
* Default builds (including for packages) no longer select
C99. Thus the C standard used is the default for the
compiler, which for the toolchain in 'Rtools43' is C17.
(This is consistent with Unix builds.)
PACKAGE INSTALLATION:
* The default C++ standard has been changed to C++17 where
available (which it is on all currently checked platforms):
if not C++14 or C++11 is used if available otherwise C++ is
not supported.
* 'USE_FC_LEN_T' is the default: this uses the correct
(compiler-dependent) prototypes for Fortran BLAS/LAPACK
routines called from C/C++, and requires adjustment of many
such calls - see 'Writing R Extensions' <c2><a7>6.6.1.
* There is initial support for C++23 as several compilers are
now supporting '-std=c++23' or '-std=c++2b' or similar. As
for C++20, there no additional 'configure' checks for C++23
features beyond a check that the compiler reports a
'__cplusplus' value greater than that in the C++20 standard.
C++ feature tests should be used.
* There is support for a package to indicate the version of
the C standard which should be used to compile it, and for
the installing user to specify this. In most cases R
defaults to the C compiler's default standard which is C17
(a `bug-fix' of C11) - earlier versions of R or compilers
may have defaulted to C99.
Current options are:
USE_C17 Use a standard that is at most C17. The intention
is to allow legacy packages to still be installed when
later C standards become the default, including packages
using new keywords as identifiers or with K&R-style
function declarations. This will use C17 if available,
falling back to C11.
USE_C90 Use the C90 (aka C89) standard. (As that standard
did not require compilers to identify that version, all
we can verify is that the compiler does not claim to be
using a later standard. It may accept C99 features -
for example 'clang' accepts // to make comments.)
USE_C99 Use the C99 standard. This should be rarely needed -
it avoids the few new features of C11/C17 which can be
useful if a package assumes them if C17 is specified and
they are not implemented.
USE_C23 Use C23 (or in future, later). Compiler/library
support for C23 is still being implemented, but LLVM
clang from 15.0.0 and the upcoming GCC 13 have quite
extensive support.
These can be specified as part of the 'SystemRequirements'
field in the package's 'DESCRIPTION' file or _viaoptions
'--use-C17' and so on of 'R CMD INSTALL' and 'R CMD SHLIB'.
For further details see "Writing R Extensions" <c2><a7>1.2.5.
* (Windows) A 'src/Makefile.ucrt' or 'src/Makefile.win' file
is now included after 'R_HOME/etcR_ARCH/Makeconf' and so no
longer needs to include that file itself. Installation of a
package with such a file now uses a site 'Makevars' file in
the same way as a package with a 'src/Makevars.win' file
would.
* 'configure' is now passed crucial variables such as 'CC' and
'CFLAGS' in its environment, as many packages were not
setting them (as documented in 'Writing R Extensions' <c2><a7>1.2).
This has most effect where 'configure' is used to compile
parts of the package - most often by 'cmake' or 'libtool'
which obfuscate the actual compile commands used.
Also used for 'configure.win' and 'configure.ucrt' on
Windows.
FORTRAN FLAGS:
* The flag '-fno-optimize-sibling-calls' is no longer forced
for 'gfortran' 7 and later. It should no longer be needed
now using 'hidden' character-length arguments when calling
BLAS/LAPACK routines from C/C++ is the default even for
packages. (Unless perhaps packages call Fortran code from
C/C++ without using R's headers and without allowing for
these arguments.)
C-LEVEL FACILITIES:
* The deprecated S-compatibility macros 'DOUBLE_*' in
'R_ext/Constants.h' (included by 'R.h') have been removed.
* The deprecated legacy typedefs of 'Sint' and 'Sfloat' in
header 'R.h' are no longer defined, and that header no
longer includes header 'limits.h' from C nor 'climits' from
C++.
* New macro 'CAD5R()' is provided in 'Rinternals.h' and used
in a few places in the R sources.
* ALTREP now supports 'VECSXP' vectors. Contributed by Gabor
Csardi in PR#17620.
* The 'Rcomplex' definition (in header 'R_ext/Complex.h') has
been extended to prevent possible mis-compilation when
interfacing with Fortran (PR#18430). The new definition
causes compiler warnings with static initializers such as
'{1, 2}', which can be changed to '{.r=1, .i=2}'.
Using the new definition from C++ depends on compiler
extensions supporting C features that have not been
incorporated into the C++ standards but are available in
'g++' and 'clang++': this may result in C++ compiler
warnings but these have been worked around for recent
versions of common compilers (GCC, Apple/LLVM clang, Intel).
It is intended to change the inclusion of header
'R_ext/Complex.h' by other R headers, so C/C++ code files
which make use of 'Rcomplex' should include that header
explicitly.
UTILITIES:
* 'R CMD check' does more checking of package '.Rd' files,
warning about invalid email addresses and (some) invalid
URIs and noting empty '\item' labels in description lists.
* 'R CMD check' now also reports problems when reading package
news in md (file 'NEWS.md') and (optionally) plain text
(file 'NEWS') formats.
* '_R_CHECK_TIMINGS_' defaults to a value from the environment
even for 'R CMD check --as-cran'; this allows for
exceptionally fast or slow platforms.
It now applies to checking PDF and HTML versions of the
manuals, and 'checking CRAN incoming feasibility'.
* 'R CMD check' can optionally (but included in '--as-cran')
check whether HTML math rendering _viaKaTeX works for the
package '.Rd' files.
* Non-interactive debugger invocations can be trapped by
setting the environment variable
'_R_CHECK_BROWSER_NONINTERACTIVE_' to a true value. This is
enabled by 'R CMD check --as-cran' to detect the use of
leftover 'browser()' statements in the package.
* The use of 'sprintf' and 'vsprintf' from C/C++ has been
deprecated in macOS 13 and is a known security risk. 'R CMD
check' now reports (on all platforms) if their use is found
in compiled code: replace by 'snprintf' or 'vsnprintf'
respectively. [*NB:* whether such calls get compiled into
the package is platform-dependent.]
* Where recorded at installation, 'R CMD check' reports the C
and Fortran compilers used to build R.
It reports the OS in use (if known, as given by 'osVersion')
as well as that R was built for.
It notes if a C++ standard was specified which is older than
the current default: many packages have used C++11 to mean
'not C++98' - as C++11 is the minimum supported since R
4.0.0, that specification can probably be removed.
* 'R CMD INSTALL' reports the compilers (and on macOS, the
SDK) used, and this is copied to the output of 'R CMD
check'.
Where a C++ standard is specified, it is reported.
* 'R CMD check''s 'checking compilation flags in Makevars' has
been relaxed to accept the use of flags such as '-std=f2008'
in 'PKG_FFLAGS'.
* 'tools::buildVignettes()' has a new argument 'skip', which
is used by 'R CMD check' to skip (and note) vignettes with
unavailable '\VignetteDepends' (PR#18318).
* New generic '.AtNames()' added to enable class-specific
completions after '@'. The formerly internal function
'findMatches()' is now exported, mainly for use in methods
for '.DollarNames()' and '.AtNames()'.
DEPRECATED AND DEFUNCT:
* 'default.stringsAsFactors()' is defunct.
* Calling 'as.data.frame.<class>()' directly (for 12 atomic
classes) is going to be formally deprecated, currently
activated by setting the environment variable
'_R_CHECK_AS_DATA_FRAME_EXPLICIT_METHOD_' to non-empty,
which also happens in 'R CMD check --as-cran'.
BUG FIXES:
* Hashed 'environment's with sizes less than 5 can now grow.
(Reported to R-devel by Duncan Garmonsway.)
* 'as.character(<Rd>, deparse = TRUE)' failed to re-escape
curly braces in LaTeX-like text. (Reported by Hadley
Wickham in PR#18324.)
* 'library()' now passes its 'lib.loc' argument when requiring
'Depends' packages; reported (with fix) in PR#18331 by
Mikael Jagan.
* 'R CMD Stangle': improved message about 'Output' files.
* 'head(x, n)' and 'tail(x, n)' now signal an error if 'n' is
not numeric, instead of incidentally "working" sometimes
returning all of 'x'. Reported and discussed by Colin Fay,
in PR#18357.
* The '"lm"' method for 'summary()' now gives the correct
F-statistic when the model contains an offset. Reported in
PR#18008.
* 'C()' and '`contrasts<-`()' now preserve factor level names
when given a function object (as opposed a function name
which did preserve names). Reported in PR#17616.
* 'c(a = 1, 2)[[]]' no longer matches '2' but rather signals a
_classederror. Reported and analysed by Davis Vaughan in
PR#18367, a duplicate of PR#18004, by Jan Meis et al. For
consistency, 'NULL[[]]' is also erroneous now. 'x[[]] <- v'
gives an error of the same class '"MissingSubscriptError"'.
* The 'relist()' function of 'utils' now supports 'NULL'
elements in the skeleton (PR#15854).
* 'ordered(levels = *)' (missing 'x') now works analogously to
'factor(, ordered=TRUE)'; reported (with fix) by Achim
Zeileis in PR#18389.
* User-defined Rd macro definitions can now span multiple
lines, thanks to a patch from Duncan Murdoch. Previously,
the Rd parser silently ignored everything after the first
line.
* Plain-text help ('tools::Rd2txt()') now preserves an initial
blank line for text following description list items.
* 'tools::Rd2HTML()' and 'tools::Rd2latex()' no longer split
\arguments and \value lists at Rd comments.
* 'tools::Rd2latex()' now correctly handles optional text
outside \items of argument lists as well as bracketed text
at the beginning of sections, e.g., \value{[NULL]}.
* 'as.character(<POSIXt>)' now behaves more in line with the
methods for atomic vectors such as numbers, and is no longer
influenced by 'options()'. Ditto for
'as.character(<Date>)'. The 'as.character()' method gets
arguments 'digits' and 'OutDec' with defaults _not_
depending on 'options()'. Use of 'as.character(*, format =
.)' now warns.
* Similarly, the 'as.character.hexmode()' and '*.octmode()'
methods also behave as 'good citizen' methods and back
compatibility option 'keepStr = TRUE'.
* The 'as.POSIXlt(<POSIXlt>)' and 'as.POSIXct(<POSIXct>)'
default methods now do obey their 'tz' argument, also in
this case.
* 'as.POSIXlt(<Date>)' now does apply a 'tz' (time zone)
argument, as does 'as.POSIXct()'; partly suggested by Roland
Fu<c3><9f> on the R-devel mailing list.
* 'as.Date.POSIXlt(x)' now also works when the list components
are of unequal length, aka "partially filled" or "ragged".
* 'expand.model.frame()' looked up variables in the wrong
environment when applied to models fitted without 'data'.
Reported in PR#18414.
* 'time()' now (also) uses the 'ts.eps = getOption("ts.eps")'
argument and thus by default rounds values very close to the
start (or end) of a year. Based on a proposal by Andre<c3><af> V.
Kostyrka on R-help.
* Printing of a 'factanal()' result with just one factor and
'sort = TRUE' now works regularly, fixing PR#17863 by
Timothy Bates, thanks to the 'R Contributors' working group.
* Printing 0-length objects of class '"factor"', '"roman"',
'"hexmode"', '"octmode"', '"person"', '"bibentry"', or
'"citation"' now prints something better, one of which fixes
PR#18422, reported by Benjamin Feakins.
* 'Sys.timezone()' queries 'timedatectl' only if 'systemd' is
loaded; addressing a report by Jan Gorecki in PR#17421.
* The formula method of 'cor.test()' had scoping problems when
'environment(formula)' was not the calling environment;
reported with a patch proposal by Mao Kobayashi in PR#18439.
* 'attach()' of an environment with active bindings now
preserves the active bindings. Reported by Kevin Ushey in
PR#18425.
* BLAS detection now works also with system-provided libraries
not available as regular files. This fixes detection of the
Accelerate framework on macOS since Big Sur. Reported by
David Novgorodsky.
* 'download.file()' gives a helpful error message in case of
an invalid 'download.file.method' option, thanks to Colin
Fay's report in PR#18455.
* Sporadic crashes of 'Rterm' when using completion have been
fixed.
* 'Rprof()' is now more reliable. A livelock in thread
initialization with too short sampling interval has been
fixed on macOS. A deadlock in using the C runtime has been
fixed on Windows. A potential deadlock has been prevented
on Unix.
* Cursor placement in 'Rgui' now works even after a
fixed-width font is selected.
* Mandatory options ('options()') are now set on startup so
that saving and restoring them always works (PR#18372).
* Package installation, 'R CMD INSTALL' or
'install.packages(*)', now parses each of the '<pkg>/R/*.R'
files individually instead of first concatenating and then
'parse()'ing the large resulting file. This allows parser
or syntax errors to be diagnosed with correct file names and
line numbers, thanks to Simon Dedman's report and Bill
Dunlap's patch in PR#17859.
This _doesrequire syntactically self contained R source
files now, fixing another inadvertent bug.
* 'predict.lm(<model with offset>)' now finds the offset in
the correct environment, thanks to Andr<c3><a9> Gillibert's report
and patch in PR#18456.
* 'getInitial(<formula>)' now finds the 'selfStart' model in
the correct environment. (Reported by Ivan Krylov in
PR#18368.)
* Fix for possible segfault when using recently-added graphics
features, such as gradients, clipping paths, masks, and
groups with 'pdf(file=NULL)'.
* 'class(m) <- class(m)' no longer changes a matrix 'm' by
adding a class _attribute_.
* 'packageDate(pkg)' now only warns once if there is no 'pkg'.
* When 'ts()' creates a multivariate time series, '"mts"', it
also inherits from '"array"' now, and 'is.mts()' is
documented _andstricter.
* 'Rd2txt()' now preserves line breaks of \verb Rd content and
from duplicated \cr. The former also fixes the rendering of
verbatim output from Rd \Sexpr in plain-text help.
* 'uniroot(f, interval)' should no longer wrongly converge
_outsidethe interval in some cases where 'abs(f(x)) ==
Inf' for an 'x' at the interval boundary, thanks to posts by
Ben Bolker and Serguei Sokol on R-devel.
* Vectorized alpha handling in palette functions such as in
'gray()', 'rainbow()', or 'hcl.colors()' works correctly
now, thanks to Achim Zeileis' report and patch in PR#18476.
* Formatting and 'print()'ing of 'bibentry' objects has
dropped the deprecated 'citation.bibtex.max' argument, such
that the 'bibtex' argument's default for 'print.bibentry()'
depends directly on the 'citation.bibtex.max' option,
whereas in 'format.bibentry()' the option no longer applies.
* Attempting to use a character string naming a foreign
function entry point in a foreign function call in a package
will now signal an error if the packages has called
'R_forceSymbols' to specify that symbols must be used.
* An error in 'table()' could permanently set
'options(warn=2)' promoting all subsequent warnings to
errors.
* The 'sigma()' function gave misleading results for binary
GLMs. A new method for objects of class '"glm"' returns the
square root of the estimate of the dispersion parameter
using the same calculation as 'summary.glm()'.
* 'bs()' and 'ns()' in the (typical) case of automatic knot
construction, when some of the supposedly inner knots
coincide with boundary knots, now moves them inside (with a
warning), building on PR#18442 by Ben Bolker.
* 'R CMD' on Windows now skips the site profile with
'--no-site-file' and '--vanilla' even when 'R_PROFILE' is
set (PR#18512, from Kevin Ushey).
math/R: update from 4.2.0 to patch release 4.2.3 (current upstream is 4.3.2)
Only the small update because of freeze. 4.2.0 is just outdated, 4.2.3 is from
March this year, 4.3.2 available since end of October.
CHANGES IN R 4.2.3:
C-LEVEL FACILITIES:
* The definition of DL_FUNC in R_ext/Rdynload.h has been changed to
be fully C-compliant. This means that functions loaded _via_ for
example R_GetCCallable need to be cast to an appropriate type if
they have any arguments.
* .Machine has a new element sizeof.time_t to identify old systems
with a 32-bit type and hence a limited range of date-times (and
limited support for dates millions of years from present).
PACKAGE INSTALLATION:
* (Windows) The default C++ standard had accidentally been left at
C++11 when it was changed to C++14 on Unix.
BUG FIXES:
* As "POSIXlt" objects may be "partially filled" and their list
components meant to be recycled, length() now is the length of
the longest component.
* as.POSIXlt.Date() could underflow for dates in the far past (more
than half a million years BCE).
* as.Date.POSIXlt(x) would return "1970-01-01" instead of NA in R
4.2.2, e.g., for
x <- as.POSIXlt(c("2019-01-30","2001-1-1"))
x$mon <- c(0L, NA); as.Date(x)
* R CMD check failed to apply enabled _R_CHECK_SUGGESTS_ONLY_ to
examples and vignettes (regression in R 4.2.0).
* R CMD check did not re-build vignettes in separate processes by
default (regression in R 4.2.0).
* Running examples from HTML documentation now restores previous
knitr settings and options (PR#18420).
* Quartz: fonts are now located using Core Graphics API instead of
deprecated ATS which is no longer supported in the macOS 13 SDK
(PR#18426). This also addresses an issue where the currently
used font in the Quartz device context was not correctly
retained.
* (Windows) Math symbols in text drawing functions are again
rendered correctly (PR#18440). This fixes a regression in R
4.2.1 caused by a fix in PR#18382 which uncovered an issue in
GraphApp due to which the symbol charset was not used with TT
Symbol font face.
* (Windows) Installing a package with a src/Makefile.{win,ucrt}
file includes ~/.R/Makevars.win64 in the search for user
makevars, as documented in "R Installation and Administration"
and done for packages with a src/Makevars.{win,ucrt} file.
* format(<POSIXlt_w/_unbalanced_sec>, "....%OS<n>") with n > 0 no
longer accidentally uses the unbalanced seconds, thanks to
Suharto Anggono's report (including patch) in PR#18448.
* solve.default(a, b) works around issues with some versions of
LAPACK when a contains NA or NaN values.
* When UseMethod() cannot dispatch, it no longer segfaults
producing the error message in case of a long class(), thanks to
Joris Vankerschaver's report (including patch) in PR#18447.
* When example(foo, ..) produces graphics on an interactive device
it needs to open itself, it now leaves devAskNewPage() unchanged
even when it was FALSE, thus fixing a 14 years old '<FIXME>'.
* packageDescription() again catches errors from encoding
conversions. This also fixes broken packageVersion() in C locale
on systems where iconv does not support transliteration.
CHANGES IN R 4.2.2:
NEW FEATURES:
* tools::Rdiff(useDiff = TRUE) checks for the presence of an
external diff command and switches to useDiff = FALSE if none is
found. This allows R CMD Rdiff to always work.
* On Windows, environment variable R_LIBCURL_SSL_REVOKE_BEST_EFFORT
can be used to switch to only 'best-effort' SSL certificate
revocation checks with the default "libcurl" download method.
This reduces security, but may be needed for downloads to work
with MITM proxies (PR#18379).
* (macOS) The run-time check for libraries from XQuartz for X11 and
Tcl/Tk no longer uses otool from the Apple Developer Tools
(PR#18400).
* The LaTeX style for producing the PDF manuals, Rd.sty, now loads
the standard amsmath, amsfonts and amssymb packages for greater
coverage of math commands in the Rd \eqn and \deqn macros. The
\mathscr LaTeX command is also provided (via the mathrsfs
package, if available, or the amsfonts bundle otherwise),
fulfilling the wish of PR#18398.
* (Windows) The default format of readClipboard() and
writeClipboard() has been changed to 13 (CF_UNICODETEXT).
INSTALLATION on a UNIX-ALIKE:
* The PDF manuals (if built) can be compacted by the new target
make compact-pdf (at the top level or in directory doc/manual).
* There is now configure support for LLVM clang 15 on Linux, which
defaults to position-independent (PIE) executables whereas
gfortran does not.
* Many small changes to ease compilation (and suppress warnings)
with LLVM clang 15.
BUG FIXES:
* Rscript -e would fail if stdin were closed (Reported by Henrik
Bengtsson.)
* qt(*, log.p=TRUE) in outer tails no longer produces NaN in its
final steps, thus fixing PR#18360.
* tools::Rd2latex() now escapes hashes and ampersands when writing
URLs, fixing LaTeX errors with such URLs in \tabular.
* When isGeneric(f, fdef=*) is used with mismatching names, the
warning is better understandable; reported (with fix) in PR#18370
by Gabe Becker.
* poly(x, n) now works again (and is now documented) when x is a
"Date" or "POSIXct" object, or of another class while fulfilling
mode(x) == "numeric". This also enables poly(x, *, raw=TRUE) for
such variables. Reported by Michael Chirico to R-devel.
* write.table(), write.csv() and write.csv2() restore their
numerical precision (internal equivalent of digits = 15) after an
interrupt (PR#18384).
* One can now read also byte FF from a clipboard connection
(PR#18385).
* source("") and source(character()) now give more helpful error
messages.
* R CMD check --as-cran set _R_CHECK_TIMINGS_ too late to have the
intended effect.
* as.POSIXlt(x) now also works with very large dates x, fixing
PR#18401 reported by Hannes M"uhleisen.
* Files can now be extracted even from very large zip archives
(PR#18390, thanks to Martin Jakt).
* Non-finite objects of class "POSIXlt" are now correctly coerced
to classes "Date" and "POSIXct"; following up on the extension to
format() them correctly.
* Added methods for is.finite(), is.infinite() and is.nan() for
"POSIXlt" date-time objects.
BUG FIXES on Windows:
* Non-ASCII characters are now properly displayed on Windows in
windows created using GraphApp via e.g. winDialogString thanks to
a workaround for an at least surprising Windows behavior with
UTF-8 as the system encoding (PR#18382).
* Find and replace operations work again in the script editor in
Rgui on Windows.
* Computation of window size based on requested client size in
GraphApp when running in a multi-byte locale on Windows has been
fixed (regression in R 4.2.0 for users of systems where R 4.1
used a single-byte locale). Rgui again respects the number of
console rows and columns given in Rconsole file.
* Rterm support for Alt+xxx sequences has been fixed to produce the
corresponding character (only) once. This fixes pasting text with
tilde on Italian keyboard (PR#18391).
CHANGES IN R 4.2.1:
NEW FEATURES:
* New function utils::findCRANmirror() to find out if a CRAN mirror
has been selected, otherwise fallback to the main site. This
behaves in the same way as tools::CRAN_package_db() and is
intended for packages wishing to access CRAN for purposes other
than installing packages.
The need for this was shown by a day when the main CRAN website
was offline and a dozen or so packages which had its URL
hardcoded failed their checks.
INSTALLATION on a UNIX-ALIKE:
* The libraries searched for by --with-blas (without a value) now
include BLIS (after OpenBLAS but before ATLAS). And on macOS,
the Accelerate framework (after ATLAS). (This is patterned after
the AX_BLAS macro from the Autoconf Archive.)
* The included LAPACK sources have been updated to 3.10.1.
UTILITIES:
* The (full path to) the command tidy to be used for HTML
validation can be set by environment variable R_TIDYCMD.
* Setting environment variable _R_CHECK_RD_VALIDATE_RD2HTML_ to a
false value will override R CMD check --as-cran and turn off HTML
validation. This provides a way to circumvent a problematic
tidy.
The 2006 version that ships with macOS is always skipped.
C-LEVEL FACILITIES:
* The undocumented legacy declarations of Sint, Sfloat, SINT_MAX
and SINT_MIN in header R.h are deprecated.
BUG FIXES:
* fisher.test(d) no longer segfaults for "large" d; fixing PR#18336
by preventing/detecting an integer overflow reliably.
* tar(., files=*) now produces correctly the warning about invalid
UID or GID of files, fixing PR#18344, reported by Martin Morgan.
* tk_choose.files() with multi = FALSE misbehaved on paths
containing spaces (PR#18334) (regression introduced in R 4.0.0).
* sort(x, partial = ind, *) now works correctly notably for the
non-default na.last = FALSE or TRUE, fixing PR#18335 reported by
James Edwards.
* Environment variable _R_CHECK_XREFS_REPOSITORIES_ is only used
for checking .Rd cross-references in R CMD check (as documented)
and not for other uses looking for a CRAN mirror.
* The search for a CRAN mirror when checking packages now uses
getOption("repos") if that specifies a CRAN mirror, even when it
does not also specify all three Bioconductor repositories (as was
previously required).
* The HTML code generated by tools::Rd2HTML() has been improved to
pass tidy 5.8.0.
BUG FIXES on Windows:
* Writing to a clipboard connection works again, fixing a
regression in R 4.2.0 (PR#18332). Re-using a closed clipboard
connection no longer issues a spurious warning about an ignored
encoding argument.
* C function getlocale no longer attempts to query an unsupported
category from the OS, even when requested at R level, which may
cause crashes when R 4.2.0 (which uses UCRT) is embedded
(reported by Kevin Ushey).
* Accent keys now work in GraphApp Unicode windows, which are used
by Rgui whenever running in a multibyte locale (so also in UTF-8,
hence fixing a regression in R 4.2.0 for users of systems where R
4.1 used a single-byte locale).
* Completion in Rgui now works also with non-ASCII characters.
* Rgui no longer truncates usage information with --help.
* Text injection from external applications via SendInput now works
in GraphApp Unicode windows, fixing a regression in R 4.2.0 for
Rgui users of systems where R 4.1 used a single-byte locale but R
4.2.0 uses UTF-8.
* Performance of txtProgressBar() in Rgui when running in a
multi-byte locale has been improved (fixing a performance
regression in R 4.2.0 for users of systems where R 4.1 used a
single-byte locale).
* The script editor in Rgui now works also on systems using UTF-8
as the native encoding. Users of the script editor have to
convert their scripts with non-ASCII characters to UTF-8 before
reading them in R 4.2.1 or newer (on recent Windows where UTF-8
is used). This fixes a regression in R 4.2.0, which prevented
some operations with scripts when they contained non-ASCII
characters.
*: recursive bump for cairo dependency changes
*: revebump for new brotli option for freetype2 Addresses PR 57693
*: recursive bump for icu 74.1
*: bump for openssl 3
recursive revbump for tiff update
R: Limit the NLS disabling to NetBSD-only. Disabling NLS is actively harmful on other platforms, and this builds perfectly fine with pkgsrc gettext.
math/R: Unbreak build on macOS > 12 R 4.2.0 uses a deprecated function Set MACOSX_DEPLOYMENT_TARGET=12.0 for temporary fix on macOS 13+
(math/R) As an interim fix, --disable-nls (gettext-0.22 problem)
Mass-change BUILD_DEPENDS to TOOL_DEPENDS outside mk/. Almost all uses, if not all of them, are wrong, according to the semantics of BUILD_DEPENDS (packages built for target available for use _by_ tools at build-time) and TOOL_DEPEPNDS (packages built for host available for use _as_ tools at build-time). No change to BUILD_DEPENDS as used correctly inside buildlink3. As proposed on tech-pkg: https://mail-index.netbsd.org/tech-pkg/2023/06/03/msg027632.html
revbump after textproc/icu update
*: Recursive revbup from graphics/freetype2
*: recursive bump for tiff shlib major bump
*: bump PKGREVISION for libunistring shlib major bump
math/R: use ../../mk/atomic64.mk for 64-bit atomics. R itself doesn't need this, but some modules might, e.g. R-s2. Bump PKGREVISION.
*: recursive bump for perl 5.36
Update to 4.2.0 Upstream changelog please visit: https://stat.ethz.ch/pipermail/r-announce/2022/000683.html
R: remove superfluous "-Wl," in configure patch Bump PKGREVISION. Fix some pkglint while here.
math/R: fix compiler flags embedded within Makeconf
The R package installs the file lib/R/etc/Makeconf, which is intended
to be used by R packages that themselves compile programs. This
feature is rarely used, but the math/R-nimble package is an example of
one that does. For this to work, the compiler flags embedded within
Makeconf must be compatible with the system compiler. At least on
MacOS, this is not the case by default, and so nimble compilations
fail. This substitutes ${COMPILER_RPATH_FLAG} into configure.ac, so
that it is used when creating Makeconf. Since neither R itself nor
most R packages compile other programs, Makeconf is generally not used
and this fix will have no impact.
Update to 4.1.3
Upstream changes:
CHANGES IN R 4.1.3:
NEW FEATURES:
* The default version of Bioconductor has been changed to 3.14.
(This is used by setRepositories and the menus in GUIs.)
UTILITIES:
* R CMD check --as-cran has a workaround for a bug in versions of
file up to at least 5.41 which mis-identify DBF files last
changed in 2022 as executables.
C-LEVEL FACILITIES:
* The legacy S-compatibility macros SINGLE_* in R_ext/Constants.h
(included by R.h) are deprecated and will be removed in R 4.2.0.
BUG FIXES:
* Initialization of self-starting nls() models with initialization
functions following the pre-R-4.1.0 API (without the ...
argument) works again for now, with a deprecation warning.
* Fixed quoting of ~autodetect~ in Java setting defaults to avoid
inadvertent user lookup due to leading ~, reported in PR#18231 by
Harold Gutch.
* substr(., start, stop) <- v now treats _negative_ stop values
correctly. Reported with a patch in PR#18228 by Brodie Gaslam.
* Subscripting an array x without dimnames by a
length(dim(x))-column character matrix gave "random" non-sense,
now an error; reported in PR#18244 by Mikael Jagan.
* ...names() now matches names(list(...)) closely, fixing PR#18247.
* all.equal(*, scale = s) now works as intended when length(s) > 1,
partly thanks to Michael Chirico's PR#18272.
* print(x) for long vectors x now also works for named atomic
vectors or lists and prints the correct number when reaching the
getOption("max.print") limit; partly thanks to a report and
proposal by Hugh Parsonage to the R-devel list.
* all.equal(<selfStart>, *) no longer signals a deprecation
warning.
* reformulate(*, response=r) gives a helpful error message now when
length(r) > 1, thanks to Bill Dunlap's PR#18281.
* Modifying globalCallingHandlers inside withCallingHandlers() now
works or fails correctly, thanks to Henrik Bengtsson's PR#18257.
* hist(<Date>, breaks = "days") and hist(<POSIXt>, breaks = "secs")
no longer fail for inputs of length 1.
* qbeta(.001, .9, .009) and similar cases now converge correctly
thanks to Ben Bolker's report in PR#17746.
* window(x, start, end) no longer wrongly signals "'start' cannot
be after 'end'", fixing PR#17527 and PR#18291.
* data() now checks that its (rarely used) list argument is a
character vector - a couple of packages passed other types and
gave incorrect results.
* which() now checks its arr.ind argument is TRUE rather coercing
to logical and taking the first element - which gave incorrect
results in package code.
* model.weights() and model.offset() more carefully extract their
model components, thanks to Ben Bolker and Tim Taylor's R-devel
post.
* list.files(recursive = TRUE) now shows all broken symlinks
(previously, some of them may have been omitted, PR#18296).
revbump for icu and libffi
R: Fix PLIST.Darwin yet again. Add a comment to the Makefile to hopefully avoid macOS users constantly being broken on every update.
Update to 4.1.2
Upstream changes:
CHANGES IN R 4.1.2:
C-LEVEL FACILITIES:
* The workaround in headers R.h and Rmath.h (using namespace std;)
for the Oracle Developer Studio compiler is no longer needed now
C++11 is required so has been removed. A couple more usages of
log() (which should have been std::log()) with an int argument
are reported on Solaris.
* The undocumented limit of 4095 bytes on messages from the
S-compatibility macros PROBLEM and MESSAGE is now documented and
longer messages will be silently truncated rather than
potentially causing segfaults.
* If the R_NO_SEGV_HANDLER environment variable is non-empty, the
signal handler for SEGV/ILL/BUS signals (which offers recovery
user interface) is not set. This allows more reliable debugging
of crashes that involve the console.
DEPRECATED AND DEFUNCT:
* The legacy S-compatibility macros PROBLEM, MESSAGE, ERROR, WARN,
WARNING, RECOVER, ... are deprecated and will be hidden in R
4.2.0. R's native interface of Rf_error and Rf_warning has long
been preferred.
BUG FIXES:
* .mapply(F, dots, .) no longer segfaults when dots is not a list
and uses match.fun(F) as always documented; reported by Andrew
Simmons in PR#18164.
* hist(<Date>, ...) and hist(<POSIXt>, ...) no longer pass
arguments for rect() (such as col and density) to axis().
(Thanks to Sebastian Meyer's PR#18171.)
* \Sexpr{ch} now preserves Encoding(ch). (Thanks to report and
patch by Jeroen Ooms in PR#18152.)
* Setting the RNG to "Marsaglia-Multicarry" e.g., by RNGkind(), now
warns in more places, thanks to Andr'e Gillibert's report and
patch in PR#18168.
* gray(numeric(), alpha=1/2) no longer segfaults, fixing PR#18183,
reported by Till Krenz.
* Fixed dnbinom(x, size=<very_small>, .., log=TRUE) regression,
reported by Martin Morgan.
* as.Date.POSIXlt(x) now keeps names(x), thanks to Davis Vaughan's
report and patch in PR#18188.
* model.response() now strips an "AsIs" class typically, thanks to
Duncan Murdoch's report and other discussants in PR#18190.
* try() is considerably faster in case of an error and long call,
as e.g., from some do.call(). Thanks to Alexander Kaever's
suggestion posted to R-devel.
* qqline(y = <object>) such as y=I(.), now works, see also
PR#18190.
* Non-integer mgp par() settings are now handled correctly in
axis() and mtext(), thanks to Mikael Jagan and Duncan Murdoch's
report and suggestion in PR#18194.
* formatC(x) returns length zero character() now, rather than ""
when x is of length zero, as documented, thanks to Davis
Vaughan's post to R-devel.
* removeSource(fn) now retains (other) attributes(fn).
revbump for boost-libs
Update to 4.1.1
Upstream changes:
CHANGES IN R 4.1.1:
NEW FEATURES:
* require(pkg, quietly = TRUE) is quieter and in particular does
not warn if the package is not found.
DEPRECATED AND DEFUNCT:
* Use of ftp:// URIs should be regarded as deprecated, with
on-going support confined to method = "libcurl" and not routinely
tested. (Nowadays no major browser supports them.)
* The non-default method = "internal" is deprecated for http:// and
ftp:// URIs for both download.file and url.
* On Windows, method = "wininet" is deprecated for http://,
https:// and ftp:// URIs for both download.file and url. (A
warning is only given for ftp://.)
For ftp:// URIs the default method is now "libcurl" if available
(which it is on CRAN builds).
method = "wininet" remains the default for http:// and https://
URIs but if libcurl is available, using method = "libcurl" is
preferred.
INSTALLATION:
* make check now works also without a LaTeX installation. (Thanks
to Sebastian Meyer's PR#18103.)
BUG FIXES:
* make check-devel works again in an R build configured with
--without-recommended-packages.
* qnbinom(p, size, mu) for large size/mu is correct now in a range
of cases (PR#18095); similarly for the (size, prob)
parametrization of the negative binomial. Also qpois() and
qbinom() are better and or faster for extreme cases. The
underlying C code has been modularized and is common to all four
cases of discrete distributions.
* gap.axis is now part of the axis() arguments which are passed
from bxp(), and hence boxplot(). (Thanks to Martin Smith's
report and suggestions in PR#18109.)
* .First and .Last can again be set from the site profile.
* seq.int(from, to, *) and seq.default(..) now work better in large
range cases where from-to is infinite where the two boundaries
are finite.
* all.equal(x,y) now returns TRUE correctly also when several
entries of abs(x) and abs(y) are close to .Machine$double.xmax,
the largest finite numeric.
* model.frame() now clears the object bit when removing the class
attribute of a value via na.action (PR#18100).
* charClass() now works with multi-character strings on Windows
(PR#18104, fixed by Bill Dunlap).
* encodeString() on Solaris now works again in Latin-1 encoding on
characters represented differently in UTF-8. Support for
surrogate pairs on Solaris has been improved.
* file.show() on Windows now works with non-ASCII path names
representable in the current native encoding (PR#18132).
* Embedded R on Windows can now find R home directory via the
registry even when installed only for the current user
(PR#18135).
* pretty(x) with finite x now returns finite values also in the
case where the extreme x values are close in size to the maximal
representable number .Machine$double.xmax.
Also, it's been tweaked for very small ranges and when a boundary
is close (or equal) to zero; e.g., pretty(c(0,1e-317)) no longer
has negative numbers, currently still warning about a very small
range, and pretty(2^-(1024 - 2^-1/(c(24,10)))) is more accurate.
* The error message for not finding vignette files when weaving has
correct file sizes now. (Thanks to Sebastian Meyer's PR#18154.)
* dnbinom(20, <large>, 1) now correctly gives 0, and similar cases
are more accurate with underflow precaution. (Reported by
Francisco Vera Alcivar in PR#18072.)
math/R: use our BLAS This used to not actaully honour our BLAS choice, the usage of BLAS_LIBS was missing.
Update to 4.1.0
Upstream changes:
CHANGES IN R 4.1.0:
FUTURE DIRECTIONS:
* It is planned that the 4.1.x series will be the last to support
32-bit Windows, with production of binary packages for that
series continuing until early 2023.
SIGNIFICANT USER-VISIBLE CHANGES:
* Data set esoph in package datasets now provides the correct
numbers of controls; previously it had the numbers of cases added
to these. (Reported by Alexander Fowler in PR#17964.)
NEW FEATURES:
* www.omegahat.net is no longer one of the repositories known by
default to setRepositories(). (Nowadays it only provides source
packages and is often unavailable.)
* Function package_dependencies() (in package tools) can now use
different dependency types for direct and recursive dependencies.
* The checking of the size of tarball in R CMD check --as-cran
<pkg> may be tweaked via the new environment variable
_R_CHECK_CRAN_INCOMING_TARBALL_THRESHOLD_, as suggested in
PR#17777 by Jan Gorecki.
* Using c() to combine a factor with other factors now gives a
factor, an ordered factor when combining ordered factors with
identical levels.
* apply() gains a simplify argument to allow disabling of
simplification of results.
* The format() method for class "ftable" gets a new option justify.
(Suggested by Thomas Soeiro.)
* New ...names() utility. (Proposed by Neal Fultz in PR#17705.)
* type.convert() now warns when its as.is argument is not
specified, as the help file always said it _should_. In that
case, the default is changed to TRUE in line with its change in
read.table() (related to stringsAsFactor) in R 4.0.0.
* When printing list arrays, classed objects are now shown _via_
their format() value if this is a short enough character string,
or by giving the first elements of their class vector and their
length.
* capabilities() gets new entry "Rprof" which is TRUE when R has
been configured with the equivalent of --enable-R-profiling (as
it is by default). (Related to Michael Orlitzky's report
PR#17836.)
* str(xS4) now also shows extraneous attributes of an S4 object
xS4.
* Rudimentary support for vi-style tags in rtags() and R CMD rtags
has been added. (Based on a patch from Neal Fultz in PR#17214.)
* checkRdContents() is now exported from tools; it and also
checkDocFiles() have a new option chkInternal allowing to check
Rd files marked with keyword "internal" as well. The latter can
be activated for R CMD check via environment variable
_R_CHECK_RD_INTERNAL_TOO_.
* New functions numToBits() and numToInts() extend the raw
conversion utilities to (double precision) numeric.
* Functions URLencode() and URLdecode() in package utils now work
on vectors of URIs. (Based on patch from Bob Rudis submitted
with PR#17873.)
* path.expand() can expand ~user on most Unix-alikes even when
readline is not in use. It tries harder to expand ~, for example
should environment variable HOME be unset.
* For HTML help (both dynamic and static), Rd file links to help
pages in external packages are now treated as references to
topics rather than file names, and fall back to a file link only
if the topic is not found in the target package. The earlier rule
which prioritized file names over topics can be restored by
setting the environment variable _R_HELP_LINKS_TO_TOPICS_ to a
false value.
* c() now removes NULL arguments before dispatching to methods,
thus simplifying the implementation of c() methods, _but_ for
back compatibility keeps NULL when it is the first argument.
(From a report and patch proposal by Lionel Henry in PR#17900.)
* Vectorize()'s result function's environment no longer keeps
unneeded objects.
* Function ...elt() now propagates visibility consistently with
..n. (Thanks to Lionel Henry's PR#17905.)
* capture.output() no longer uses non-standard evaluation to
evaluate its arguments. This makes evaluation of functions like
parent.frame() more consistent. (Thanks to Lionel Henry's
PR#17907.)
* packBits(bits, type="double") now works as inverse of
numToBits(). (Thanks to Bill Dunlap's proposal in PR#17914.)
* curlGetHeaders() has two new arguments, timeout to specify the
timeout for that call (overriding getOption("timeout")) and TLS
to specify the minimum TLS protocol version to be used for
https:// URIs (_inter alia_ providing a means to check for sites
using deprecated TLS versions 1.0 and 1.1).
* For nls(), an optional constant scaleOffset may be added to the
denominator of the relative offset convergence test for cases
where the fit of a model is expected to be exact, thanks to a
proposal by John Nash. nls(*, trace=TRUE) now also shows the
convergence criterion.
* Numeric differentiation _via_ numericDeriv() gets new optional
arguments eps and central, the latter for taking central divided
differences. The latter can be activated for nls() via
nls.control(nDcentral = TRUE).
* nls() now passes the trace and control arguments to getInitial(),
notably for all self-starting models, so these can also be fit in
zero-noise situations via a scaleOffset. For this reason, the
initial function of a selfStart model must now have ... in its
argument list.
* bquote(splice = TRUE) can now splice expression vectors with
attributes: this makes it possible to splice the result of
parse(keep.source = TRUE). (Report and patch provided by Lionel
Henry in PR#17869.)
* textConnection() gets an optional name argument.
* get(), exists(), and get0() now signal an error if the first
argument has length greater than 1. Previously additional
elements were silently ignored. (Suggested by Antoine Fabri on
R-devel.)
* R now provides a shorthand notation for creating functions, e.g.
\(x) x + 1 is parsed as function(x) x + 1.
* R now provides a simple native forward pipe syntax |>. The
simple form of the forward pipe inserts the left-hand side as the
first argument in the right-hand side call. The pipe
implementation as a syntax transformation was motivated by
suggestions from Jim Hester and Lionel Henry.
* all.equal(f, g) for functions now by default also compares their
environment(.)s, notably via new all.equal method for class
function. Comparison of nls() fits, e.g., may now need
all.equal(m1, m2, check.environment = FALSE).
* .libPaths() gets a new option include.site, allowing to _not_
include the site library. (Thanks to Dario Strbenac's suggestion
and Gabe Becker's PR#18016.)
* Lithuanian translations are now available. (Thanks to Rimantas
Zakauskas.)
* names() now works for DOTSXP objects. On the other hand, in
R-lang, the R language manual, we now warn against relying on the
structure or even existence of such dot-dot-dot objects.
* all.equal() no longer gives an error on DOTSXP objects.
* capabilities("cairo") now applies only to the file-based devices
as it is now possible (if very unusual) to build R with Cairo
support for those but not for X11().
* There is optional support for tracing the progress of
loadNamespace() - see its help.
* (Not Windows.) l10n_info() reports an additional element, the
name of the encoding as reported by the OS (which may differ from
the encoding part (if any) of the result from
Sys.getlocale("LC_CTYPE").
* New function gregexec() which generalizes regexec() to find _all_
disjoint matches and well as all substrings corresponding to
parenthesized subexpressions of the given regular expression.
(Contributed by Brodie Gaslam.)
* New function charClass() in package utils to query the
wide-character classification functions in use (such as
iswprint).
* The names of quantile()'s result no longer depend on the global
getOption("digits"), but quantile() gets a new optional argument
digits = 7 instead.
* grep(), sub(), regexp and variants work considerably faster for
long factors with few levels. (Thanks to Michael Chirico's
PR#18063.)
* Provide grouping of x11() graphics windows within a window
manager such as Gnome or Unity; thanks to a patch by Ivan Krylov
posted to R-devel.
* The split() method for class data.frame now allows the f argument
to be specified as a formula.
* sprintf now warns on arguments unused by the format string.
* New palettes "Rocket" and "Mako" for hcl.colors() (approximating
palettes of the same name from the 'viridisLite' package).
Contributed by Achim Zeileis.
* The base environment and its namespace are now locked (so one can
no longer add bindings to these or remove from these).
* Rterm handling of multi-byte characters has been improved,
allowing use of such characters when supported by the current
locale.
* Rterm now accepts ALT+ +xxxxxxxx sequences to enter Unicode
characters as hex digits.
* Environment variable LC_ALL on Windows now takes precedence over
LC_CTYPE and variables for other supported categories, matching
the POSIX behaviour.
* duplicated() and anyDuplicated() are now optimized for integer
and real vectors that are known to be sorted via the ALTREP
framework. Contributed by Gabriel Becker via PR#17993.
GRAPHICS:
* The graphics engine version, R_GE_version, has been bumped to 14
and so packages that provide graphics devices should be
reinstalled.
* Graphics devices should now specify deviceVersion to indicate
what version of the graphics engine they support.
* Graphics devices can now specify deviceClip. If TRUE, the
graphics engine will never perform any clipping of output itself.
The clipping that the graphics engine does perform (for both
canClip = TRUE and canClip = FALSE) has been improved to avoid
producing unnecessary artifacts in clipped output.
* The grid package now allows gpar(fill) to be a linearGradient(),
a radialGradient(), or a pattern(). The viewport(clip) can now
also be a grob, which defines a clipping path, and there is a new
viewport(mask) that can also be a grob, which defines a mask.
These new features are only supported so far on the Cairo-based
graphics devices and on the pdf() device.
* (Not Windows.) A warning is given when a Cairo-based type is
specified for a png(), jpeg(), tiff() or bmp() device but Cairo
is unsupported (so type = "Xlib" is tried instead).
* grSoftVersion() now reports the versions of FreeType and
FontConfig if they are used directly (not _via_ Pango), as is
most commonly done on macOS.
C-LEVEL FACILITIES:
* The _standalone_ libRmath math library and R's C API now provide
log1pexp() again as documented, and gain log1mexp().
INSTALLATION on a UNIX-ALIKE:
* configure checks for a program pkgconf if program pkg-config is
not found. These are now only looked for on the path (like
almost all other programs) so if needed specify a full path to
the command in PKG_CONFIG, for example in file config.site.
* C99 function iswblank is required - it was last seen missing ca
2003 so the workaround has been removed.
* There are new configure options --with-internal-iswxxxxx,
--with-internal-towlower and --with-internal-wcwidth which allows
the system functions for wide-character classification,
case-switching and width (wcwidth and wcswidth) to be replaced by
internal ones. The first has long been used on macOS, AIX (and
Windows) but this enables it to be unselected there and selected
for other platforms (it is the new default on Solaris). The
second is new in this version of R and is selected by default on
macOS and Solaris. The third has long been the default and
remains so as it contains customizations for East Asian
languages.
System versions of these functions are often minimally
implemented (sometimes only for ASCII characters) and may not
cover the full range of Unicode points: for example Solaris (and
Windows) only cover the Basic Multilingual Plane.
* Cairo installations without X11 are more likely to be detected by
configure, when the file-based Cairo graphics devices will be
available but not X11(type = "cairo").
* There is a new configure option --with-static-cairo which is the
default on macOS. This should be used when only static cairo
(and where relevant, Pango) libraries are available.
* Cairo-based graphics devices on platforms without Pango but with
FreeType/FontConfig will make use of the latter for font
selection.
LINK-TIME OPTIMIZATION on a UNIX-ALIKE:
* Configuring with flag --enable-lto=R now also uses LTO when
installing the recommended packages.
* R CMD INSTALL and R CMD SHLIB have a new flag --use-LTO to use
LTO when compiling code, for use with R configured with
--enable-lto=R. For R configured with --enable-lto, they have
the new flag --no-use-LTO.
Packages can opt in or out of LTO compilation _via_ a UseLTO
field in the DESCRIPTION file. (As usual this can be overridden
by the command-line flags.)
BUILDING R on Windows:
* for GCC >= 8, FC_LEN_T is defined in config.h and hence character
lengths are passed from C to Fortran in _inter alia_ BLAS and
LAPACK calls.
* There is a new text file src/gnuwin32/README.compilation, which
outlines how C/Fortran code compilation is organized and
documents new features:
* R can be built with Link-Time Optimization with a suitable
compiler - doing so with GCC 9.2 showed several
inconsistencies which have been corrected.
* There is support for cross-compiling the C and Fortran code
in R and standard packages on suitable (Linux) platforms.
This is mainly intended to allow developers to test later
versions of compilers - for example using GCC 9.2 or 10.x has
detected issues that GCC 8.3 in Rtools40 does not.
* There is experimental support for cross-building R packages
with C, C++ and/or Fortran code.
* The R installer can now be optionally built to support a single
architecture (only 64-bit or only 32-bit).
PACKAGE INSTALLATION:
* The default C++ standard has been changed to C++14 where
available (which it is on all currently checked platforms): if
not (as before) C++11 is used if available otherwise C++ is not
supported.
Packages which specify C++11 will still be installed using C++11.
C++14 compilers may give deprecation warnings, most often for
std::random_shuffle (deprecated in C++14 and removed in C++17).
Either specify C++11 (see 'Writing R Extensions') or modernize
the code and if needed specify C++14. The latter has been
supported since R 3.4.0 so the package's DESCRIPTION would need
to include something like
Depends: R (>= 3.4)
PACKAGE INSTALLATION on Windows:
* R CMD INSTALL and R CMD SHLIB make use of their flag --use-LTO
when the LTO_OPT make macro is set in file etc/${R_ARCH}/Makeconf
or in a personal/site Makevars file. (For details see 'Writing R
Extensions' SS4.5.)
This provides a valuable check on code consistency. It does work
with GCC 8.3 as in Rtools40, but that does not detect everything
the CRAN checks with current GCC do.
PACKAGE INSTALLATION on macOS:
* The default personal library directory on builds with
--enable-aqua (including CRAN builds) now differs by CPU type,
one of
~/Library/R/x86_64/x.y/library
~/Library/R/arm64/x.y/library
This uses the CPU type R (and hence the packages) were built for,
so when a x86_64 build of R is run under Rosetta emulation on an
arm64 Mac, the first is used.
UTILITIES:
* R CMD check can now scan package functions for bogus return
statements, which were possibly intended as return() calls (wish
of PR#17180, patch by Sebastian Meyer). This check can be
activated via the new environment variable
_R_CHECK_BOGUS_RETURN_, true for --as-cran.
* R CMD build omits tarballs and binaries of previous builds from
the top-level package directory. (PR#17828, patch by Sebastian
Meyer.)
* R CMD check now runs sanity checks on the use of LazyData, for
example that a data directory is present and that
LazyDataCompression is not specified without LazyData and has a
documented value. For packages with large LazyData databases
without specifying LazyDataCompression, there is a reference to
the code given in 'Writing R Extensions' SS1.1.6 to test the
choice of compression (as in all the CRAN packages tested a
non-default method was preferred).
* R CMD build removes LazyData and LazyDataCompression fields from
the DESCRIPTION file of packages without a data directory.
ENCODING-RELATED CHANGES:
* The parser now treats \Unnnnnnnn escapes larger than the upper
limit for Unicode points (\U10FFFF) as an error as they cannot be
represented by valid UTF-8.
Where such escapes are used for outputting non-printable
(including unassigned) characters, 6 hex digits are used (rather
than 8 with leading zeros). For clarity, braces are used, for
example \U{0effff}.
* The parser now looks for non-ASCII spaces on Solaris (as
previously on most other OSes).
* There are warnings (including from the parser) on the use of
unpaired surrogate Unicode points such as \uD834. (These cannot
be converted to valid UTF-8.)
* Functions nchar(), tolower(), toupper() and chartr() and those
using regular expressions have more support for inputs with a
marked Latin-1 encoding.
* The character-classification functions used (by default) to
replace the system iswxxxxx functions on Windows, macOS and AIX
have been updated to Unicode 13.0.0.
The character-width tables have been updated to include new
assignments in Unicode 13.0.0.
* The code for evaluating default (extended) regular expressions
now uses the same character-classification functions as the rest
of R (previously they differed on Windows, macOS and AIX).
* There is a build-time option to replace the system's
wide-character wctrans C function by tables shipped with R: use
configure option --with-internal-towlower or (on Windows)
-DUSE_RI18N_CASE in CFLAGS when building R. This may be needed
to allow tolower() and toupper() to work with Unicode characters
beyond the Basic Multilingual Plane where not supported by system
functions (e.g. on Solaris where it is the new default).
* R is more careful when truncating UTF-8 and other multi-byte
strings that are too long to be printed, passed to the system or
libraries or placed into an internal buffer. Truncation will no
longer produce incomplete multibyte characters.
DEPRECATED AND DEFUNCT:
* Function plclust() from the package stats and
package.dependencies(), pkgDepends(), getDepList(),
installFoundDepends(), and vignetteDepends() from package tools
are defunct.
* Defunct functions checkNEWS() and readNEWS() from package tools
and CRAN.packages() from utils have been removed.
* R CMD config CXXCPP is defunct (it was deprecated in R 3.6.2).
* parallel::detectCores() drops support for Irix (retired in 2013).
* The LINPACK argument to chol.default(), chol2inv(),
solve.default() and svd() has been defunct since R 3.1.0. It was
silently ignored up to R 4.0.3 but now gives an error.
* Subsetting/indexing, such as ddd[*] or ddd$x on a DOTSXP
(dot-dot-dot) object ddd has been disabled; it worked by accident
only and was undocumented.
BUG FIXES:
* Many more C-level allocations (mainly by malloc and strdup) are
checked for success with suitable alternative actions.
* Bug fix for replayPlot(); this was turning off graphics engine
display list recording if a recorded plot was replayed in the
same session. The impact of the bug became visible if resize the
device after replay OR if attempted another savePlot() after
replay (empty display list means empty screen on resize or empty
saved plot).
* R CMD check etc now warn when a package exports non-existing S4
classes or methods, also in case of no "methods" presence.
(Reported by Alex Bertram; reproducible example and patch by
Sebastian Meyer in PR#16662.)
* boxplot() now also accepts calls for labels such as ylab, the
same as plot(). (Reported by Marius Hofert.)
* The help page for xtabs() now correctly states that addNA is
setting na.action = na.pass among others. (Reported as PR#17770
by Thomas Soeiro.)
* The R CMD check <pkg> gives a longer and more comprehensible
message when DESCRIPTION misses dependencies, e.g., in Imports:.
(Thanks to the contributors of PR#17179.)
* update.default() now calls the generic update() on the formula to
work correctly for models with extended formulas. (As reported
and suggested by Neal Fultz in PR#17865.)
* The horizontal position of leaves in a dendrogram is now correct
also with center = FALSE. (PR#14938, patch from Sebastian
Meyer.)
* all.equal.POSIXt() no longer warns about and subsequently ignores
inconsistent "tzone" attributes, but describes the difference in
its return value (PR#17277). This check can be disabled _via_
the new argument check.tzone = FALSE as suggested by Sebastian
Meyer.
* as.POSIXct() now populates the "tzone" attribute from its tz
argument when x is a logical vector consisting entirely of NA
values.
* x[[2^31]] <- v now works. (Thanks to the report and patch by
Suharto Anggono in PR#17330.)
* In log-scale graphics, axis() ticks and label positions are now
computed more carefully and symmetrically in their range,
typically providing _more_ ticks, fulfilling wishes in PR#17936.
The change really corresponds to an improved axisTicks() (package
grDevices), potentially influencing grid and lattice, for
example.
* qnorm(<very large negative>, log.p=TRUE) is now correct to at
least five digits where it was catastrophically wrong,
previously.
* sum(df) and similar "Summary"- and "Math"-group member functions
now work for data frames df with logical columns, notably also of
zero rows. (Reported to R-devel by Martin "b706".)
* unsplit() had trouble with tibbles due to unsound use of rep(NA,
len)-indexing, which should use NA_integer_ (Reported to R-devel
by Mario Annau.)
* pnorm(x, log.p = TRUE) underflows to -Inf slightly later.
* show(<hidden S4 generic>) prints better and without quotes for
non-hidden S4 generics.
* read.table() and relatives treated an "NA" column name as missing
when check.names = FALSE PR#18007.
* Parsing strings containing UTF-16 surrogate pairs such as
"\uD834\uDD1E" works better on some (uncommon) platforms.
sprintf("%X", utf8ToInt("\uD834\uDD1E")) should now give "1D11E"
on all platforms.
* identical(x,y) is no longer true for differing DOTSXP objects,
fixing PR#18032.
* str() now works correctly for DOTSXP and related exotics, even
when these are doomed.
Additionally, it no longer fails for lists with a class and
"irregular" method definitions such that e.g. lapply(*) will
necessarily fail, as currently for different igraph objects.
* Too long lines in environment files (e.g. Renviron) no longer
crash R. This limit has been increased to 100,000 bytes.
(PR#18001.)
* There is a further workaround for FreeType giving incorrect
italic font faces with cairo-based graphics devices on macOS.
* add_datalist(*, force = TRUE) (from package tools) now actually
updates an existing data/datalist file for new content. (Thanks
to a report and patch by Sebastian Meyer in PR#18048.)
* cut.Date() and cut.POSIXt() could produce an empty last interval
for breaks = "months" or breaks = "years". (Reported as PR#18053
by Christopher Carbone.)
* Detection of the encoding of 'regular' macOS locales such as
en_US (which is UTF-8) had been broken by a macOS change:
fortunately these are now rarely used with en_US.UTF-8 being
preferred.
* sub() and gsub(pattern, repl, x, *) now keep attributes of x such
as names() also when pattern is NA (PR#18079).
* Time differences ("difftime" objects) get a replacement and a
rep() method to keep "units" consistent. (Thanks to a report and
patch by Nicolas Bennett in PR#18066.)
* The \RdOpts macro, setting defaults for \Sexpr options in an Rd
file, had been ineffective since R 2.12.0: it now works again.
(Thanks to a report and patch by Sebastian Meyer in PR#18073.)
* mclapply and pvec no longer accidentally terminate parallel
processes started before by mcparallel or related calls in
package parallel (PR#18078).
* grep and other functions for evaluating (extended) regular
expressions handle in Unicode also strings not explicitly flagged
UTF-8, but flagged native when running in UTF-8 locale.
* Fixed a crash in fifo implementation on Windows (PR#18031).
* Binary mode in fifo on Windows is now properly detected from
argument open (PR#15600, PR#18031).
*: recursive bump for perl 5.34
revbump for boost-libs
(math/R) Ignore the warnings from autoreconf
math/blas, math/lapack: Install interchangeable BLAS system Install the new interchangeable BLAS system created by Thomas Orgis, currently supporting Netlib BLAS/LAPACK, OpenBLAS, cblas, lapacke, and Apple's Accelerate.framework. This system allows the user to select any BLAS implementation without modifying packages or using package options, by setting PKGSRC_BLAS_TYPES in mk.conf. See mk/blas.buildlink3.mk for details. This commit should not alter behavior of existing packages as the system defaults to Netlib BLAS/LAPACK, which until now has been the only supported implementation. Details: Add new mk/blas.buildlink3.mk for inclusion in dependent packages Install compatible Netlib math/blas and math/lapack packages Update math/blas and math/lapack MAINTAINER approved by adam@ OpenBLAS, cblas, and lapacke will follow in separate commits Update direct dependents to use mk/blas.buildlink3.mk Perform recursive revbump
Update to 4.0.3
CHANGES IN R 4.0.3:
NEW FEATURES:
* On platforms using configure option --with-internal-tzcode,
additional values "internal" and (on macOS only) "macOS" are
accepted for the environment variable TZDIR. (See ?TZDIR.)
On macOS, "macOS" is used by default if the system timezone
database is a newer version than that in the R installation.
* When install.packages(type = "source") fails to find a package in
a repository it mentions package versions which are excluded by
their R version requirement and links to hints on why a package
might not be found.
* The default value for options("timeout") can be set from
enviromnent variable R_DEFAULT_INTERNET_TIMEOUT, still defaulting
to 60 (seconds) if that is not set or invalid.
This may be needed when child R processes are doing downloads,
for example during the installation of source packages which
download jars or other forms of data.
LINK-TIME OPTIMIZATION on a UNIX-ALIKE:
* There is now support for parallelized Link-Time Optimization
(LTO) with GCC and for 'thin' LTO with clang _via_ setting the
LTO macro.
* There is support for setting a different LTO flag for the Fortran
compiler, including to empty when mixing clang and gfortran (as
on macOS). See file config.site.
* There is a new LTO_LD macro to set linker options for LTO
compilation, for example to select an alternative linker or to
parallelize thin LTO.
DEPRECATED AND DEFUNCT:
* The LINPACK argument to chol.default(), chol2inv(),
solve.default() and svd() has been defunct since R 3.1.0. Using
it now gives a warning which will become an error in R 4.1.0.
BUG FIXES:
* The code mitigating stack overflow with PCRE regexps on very long
strings is enabled for PCRE2 < 10.30 also when JIT is enabled,
since stack overflows have been seen in that case.
* Fix to correctly show the group labels in dotchart() (which where
lost in the ylab improvement for R 4.0.0).
* addmargins(*, ..) now also works when fn() is a local function,
thanks to bug report and patch PR#17124 from Alex Bertram.
* rank(x) and hence sort(x) now work when x is an object (as per
is.object(x)) of type "raw" _and_ provides a valid `[` method,
e.g., for gmp::as.bigz(.) numbers.
* chisq.test(*, simulate.p.value=TRUE) and r2dtable() now work
correctly for large table entries (in the millions). Reported by
Sebastian Meyer and investigated by more helpers in PR#16184.
* Low-level socket read/write operations have been fixed to
correctly signal communication errors. Previously, such errors
could lead to a segfault due to invalid memory access. Reported
and debugged by Dmitriy Selivanov in PR#17850.
* quantile(x, pr) works more consistently for pr values slightly
outside [0,1], thanks to Suharto Anggono's PR#17891.
Further, quantile(x, prN, names=FALSE) now works even when prN
contains NAs, thanks to Anggono's PR#17892. Ditto for ordered
factors or Date objects when type = 1 or 3, thanks to PR#17899.
* Libcurl-based internet access, including curlGetHeaders(), was
not respecting the "timeout" option. If this causes
unanticipated timeouts, consider increasing the default by
setting R_DEFAULT_INTERNET_TIMEOUT.
* as.Date(<char>) now also works with an initial "", thanks to
Michael Chirico's PR#17909.
* isS3stdGeneric(f) now detects an S3 generic also when it it is
trace()d, thanks to Gabe Becker's PR#17917.
* R_allocLD() has been fixed to return memory aligned for long
double type PR#16534.
* fisher.test() no longer segfaults when called again after its
internal stack has been exceeded PR#17904.
* Accessing a long vector represented by a compact integer sequence
no longer segfaults (reported and debugged by Hugh Parsonage).
* duplicated() now works also for strings with multiple encodings
inside a single vector PR#17809.
* phyper(11, 15, 0, 12, log.p=TRUE) no longer gives NaN; reported
as PR#17271 by Alexey Stukalov.
* Fix incorrect calculation in logLik.nls() PR#16100, patch from
Sebastian Meyer.
* A very old bug could cause a segfault in model.matrix() when
terms involved logical variables. Part of PR#17879.
* model.frame.default() allowed data = 1, leading to involuntary
variable capture (rest of PR#17879).
* tar() no longer skips non-directory files, thanks to a patch by
Sebastian Meyer, fixing the remaining part of PR#16716.
*: bump PKGREVISION for perl-5.32.
*: revbump after fontconfig bl3 changes (libuuid removal)
R: update to 4.0.2
CHANGES IN R 4.0.0:
SIGNIFICANT USER-VISIBLE CHANGES:
* Packages need to be (re-)installed under this version (4.0.0) of
R.
* matrix objects now also inherit from class "array", so e.g.,
class(diag(1)) is c("matrix", "array"). This invalidates code
incorrectly assuming that class(matrix_obj)) has length one.
S3 methods for class "array" are now dispatched for matrix
objects.
* There is a new syntax for specifying _raw_ character constants
similar to the one used in C++: r"(...)" with ... any character
sequence not containing the sequence )". This makes it easier to
write strings that contain backslashes or both single and double
quotes. For more details see ?Quotes.
* R now uses a stringsAsFactors = FALSE default, and hence by
default no longer converts strings to factors in calls to
data.frame() and read.table().
A large number of packages relied on the previous behaviour and
so have needed/will need updating.
* The plot() S3 generic function is now in package base rather than
package graphics, as it is reasonable to have methods that do not
use the graphics package. The generic is currently re-exported
from the graphics namespace to allow packages importing it from
there to continue working, but this may change in future.
Packages which define S4 generics for plot() should be
re-installed and package code using such generics from other
packages needs to ensure that they are imported rather than rely
on their being looked for on the search path (as in a namespace,
the base namespace has precedence over the search path).
See ${PREFIX}/lib/R/doc/NEWS for full changes.
revbump after updating security/nettle
revbump after boost update
R: dependency tex-ifluatex,tex-xetex -> tex-iftex (commented out)
librsvg: update bl3.mk to remove libcroco in rust case recursive bump for the dependency change
*: recursive bump for libffi
all: migrate homepages from http to https pkglint -r --network --only "migrate" As a side-effect of migrating the homepages, pkglint also fixed a few indentations in unrelated lines. These and the new homepages have been checked manually.
*: Recursive revision bump for openssl 1.1.1.
math/R: omit unknown configure option --with-libiconv-prefix
*: Recursive revbump from devel/boost-libs
R: drop maintainership
math/R: remove unknown configure arguments
Recursive revbump from boost-1.71.0
Update to 3.6.1
Upstream changes:
CHANGES IN R 3.6.1:
INSTALLATION on a UNIX-ALIKE:
* The default detection of the shell variable libNN is overridden
for derivatives of Debian Linux, some of which have started to
have a /usr/lib64 directory. (E.g. Ubuntu 19.04.) As before, it
can be specified in config.site.
UTILITIES:
* R CMD config knows the values of AR and RANLIB, often set for LTO
builds.
DEPRECATED AND DEFUNCT:
* The use of a character vector with .Fortran() is formally
deprecated and gives a non-portability warning. (It has long
been strongly discouraged in 'Writing R Extensions'.)
BUG FIXES:
* On Windows, GUI package installation via menuInstallPkgs() works
again, thanks to Len Weil's and Duncan Murdoch's PR#17556.
* R CMD check on data() fixing PR#17558 thanks to Duncan Murdoch.
* quasi(*, variance = list(..)) now works more efficiently, and
should work in all cases fixing PR#17560. Further, quasi(var =
mu(1-mu)) and quasi(var = "mu ^ 3") now work, and quasi(variance
= "log(mu)") now gives a correct error message.
* Creation of lazy loading database during package installation is
again robust to Rprofile changing the current working directory
(PR#17559).
* boxplot(y ~ f, horizontal=TRUE) now produces correct x- and
y-labels.
* rbind.data.frame() allows to keep <NA> levels from factor columns
(PR#17562) via new option factor.exclude.
Additionally, it works in one more case with matrix-columns which
had been reported on 2017-01-16 by Krzysztof Banas.
* Correct messaging in C++ pragma checks in tools code for R CMD
check, fixing PR#17566 thanks to Xavier Robin.
* print()ing and auto-printing no longer differs for functions with
a user defined print.function, thanks to Bill Dunlap's report.
* On Windows, writeClipboard(.., format = <n>) now does correctly
pass format to the underlying C code, thanks to a bug report
(with patch) by Jenny Bryan.
* as.data.frame() treats 1D arrays the same as vectors, PR#17570.
* Improvements in smoothEnds(x, *) working with NAs (towards
runmed() working in that case, in the next version of R).
* vcov(glm(<quasi>), dispersion = *) works correctly again, fixing
PR#17571 thanks to Pavel Krivitsky.
* R CMD INSTALL of binary packages on Windows now works also with
per-directory locking.
* R CMD INSTALL and install.packages() on Windows are now more
robust against a locked file in an earlier installation of the
package to be installed. The default value of option
install.lock on Windows has been changed to TRUE.
* On Unix alikes (when readline is active), only expand tilde (~)
file names starting with a tilde, instead of almost all tildes.
* In R documentation (*.Rd) files, \item [..] is no longer treated
specially when rendered in LaTeX and hence pdf, but rather shows
the brackets in all cases.
Bump PKGREVISIONs for perl 5.30.0
*: recursive bump for nettle 3.5.1
Recursive revbump from boost-1.70.0
R: Skip wrkref checks for Makeconf.
R: Requires pkg-config to detect cairo correctly.
Update to 3.6.0
Upstream changes:
CHANGES IN R 3.6.0:
SIGNIFICANT USER-VISIBLE CHANGES:
* Serialization format version 3 becomes the default for
serialization and saving of the workspace (save(), serialize(),
saveRDS(), compiler::cmpfile()). Serialized data in format 3
cannot be read by versions of R prior to version 3.5.0.
Serialization format version 2 is still supported and can be
selected by version = 2 in the save/serialization functions. The
default can be changed back for the whole R session by setting
environment variables R_DEFAULT_SAVE_VERSION and
R_DEFAULT_SERIALIZE_VERSION to 2. For maximal
back-compatibility, files vignette.rds and partial.rdb generated
by R CMD build are in serialization format version 2, and resave
by default produces files in serialization format version 2
(unless the original is already in format version 3).
* The default method for generating from a discrete uniform
distribution (used in sample(), for instance) has been changed.
This addresses the fact, pointed out by Ottoboni and Stark, that
the previous method made sample() noticeably non-uniform on large
populations. See PR#17494 for a discussion. The previous method
can be requested using RNGkind() or RNGversion() if necessary for
reproduction of old results. Thanks to Duncan Murdoch for
contributing the patch and Gabe Becker for further assistance.
The output of RNGkind() has been changed to also return the
'kind' used by sample().
NEW FEATURES:
* Sys.setFileTime() has been vectorized so arguments path and time
of length greater than one are now supported.
* axis() gets new option gap.axis = NA for specifying a
multiplication factor for the minimal "gap" (distance) between
axis labels drawn. Its default is 1 for labels _parallel_ to the
axis, and 0.25 for perpendicular ones.
Perpendicular labels no longer overlap, fixing bug PR#17384.
* The default method of plot() gains new arguments xgap.axis = NA
and ygap.axis = NA to be passed to the x- and y- axis(..,
gap.axis=*) calls.
* removeSource() now works not only for functions but also for some
language objects.
* as.call(), rep.int(), rep_len() and nchar() dispatch internally.
* is(object, class2) looks for class2 in the calling namespace
after looking in the namespace of class(object).
* extendrange(.., f) with a length-2 f now extends separately to
the left and the right.
* lengths() dispatches internally to S4 methods.
* download.file() on Windows now uses URLdecode() to determine the
file extension, and uses binary transfer (mode = "wb") also for
file extension .rds.
The help page for download.file() now contains the same
information on all platforms.
* Setting C locale for collation _via_ environment variables LC_ALL
and LC_COLLATE and _via_ a call to Sys.setlocale() now takes
precedence over environment variable R_ICU_LOCALE.
* There is a new function, nullfile(), to give the file name of the
null system device (e.g., /dev/null) on the current platform.
* There are two new options, keep.parse.data and
keep.parse.data.pkgs, which control whether parse data are
included into sources when keep.source or keep.source.pkgs is
TRUE. By default, keep.parse.data.pkgs is now FALSE, which
changes previous behavior and significantly reduces space and
time overhead when sources are kept when installing packages.
* In rapply(x, ..), x can also be "list-like" and of length >=
2^{31}.
* trimws() gets new optional whitespace argument, allowing more
extensive definitions of "space", such as including Unicode
spaces (as wished in PR#17431).
* weighted.mean() no longer coerces the weights to a double/numeric
vector, since sum() now handles integer overflow. This makes
weighted.mean() more polymorphic and endomorphic, but be aware
that the results are no longer guaranteed to be a vector of type
double.
* When loading namespaces, S3 method registrations which overwrite
previous registrations are now noted by default (using
packageStartupMessage()).
* compiler::cmpfile() gains a version argument, for use when the
output file should be saved in serialization format 2.
* The axis labeling in the default method of pairs() may now be
toggled by new options horOdd and verOdd.
* (Not Windows nor macOS.) Package tcltk now supports an
environment variable R_DONT_USE_TK which if set disables Tk
initialization. This is intended for use to circumvent errors in
loading the package, e.g. with recent Linux running under an
address sanitizer.
* The numeric method of all.equal() gets optional arguments countEQ
and formatFUN. If countEQ is true, the mean error is more
sensible when many entries are *eq*ual.
* outer(x,y, FUN = "*") is more efficient using tcrossprod(u,v)
instead of u %*% t(v).
* vcov(<mlm>) is more efficient via new optional arguments in
summary.mlm().
* The default method of summary() gets an option to choose the
_kind_ of quantile()s to use; wish of PR#17438.
* Fitting multiple linear models _via_ lm() does work with _matrix_
offsets, as suggested in PR#17407.
* The new functions mem.maxVSize() and mem.maxMSize() allow the
maximal size of the vector heap and the maximal number of nodes
allowed in the current R process to be queried and set.
* news() gains support for NEWS.md files.
* An effort has been started to have our reference manuals, i.e.,
all help pages. show platform-independent information (rather
than Windows or Unix-alike specifics visible only on that
platform). Consequently, the Windows version of X11() / x11()
got identical formal arguments to the Unix one.
* sessionInfo()$running has been factored out in a new variable
osVersion.
* slice.index() now also works for multi-dimensional margins.
* untar() used with an external tar command assumes this supports
decompression including xz and automagically detecting the
compression type. This has been true of all mainstream
implementations since 2009 (for GNU tar, since version 1.22):
older implementations are still supported _via_ the new argument
support_old_tars whose default is controlled by environment
variable R_SUPPORT_OLD_TARS. (It looks like NetBSD and OpenBSD
have 'older' tar commands for this purpose.)
* The new function asplit() allow splitting an array or matrix by
its margins.
* New functions errorCondition() and warningCondition() provide a
convenient way to create structured error and warning objects.
.Deprecated() now signals a warning of class "deprecatedWarning",
and .Defunct() now signals an error of class "defunctError".
* Many 'package not found' errors are now signaled as errors of
class "packageNotFoundError".
* As an experimental feature, when loadNamespace() fails because
the requested package is not available the error is initially
signaled with a retry_loadNamespace restart available. This
allows a calling handler to try to install the package and
continue.
* S3method() directives in NAMESPACE can now also be used to
perform _delayed_ S3 method registration.
* Experimentally, setting environment variable
_R_CHECK_LENGTH_1_LOGIC2_ will lead to warnings (or errors if the
variable is set to a 'true' value) when && or || encounter and
use arguments of length more than one.
* Added "lines" and "chars" coordinate systems to grconvertX() and
grconvertY().
* getOption() is more efficient notably for the rare case when
called with two arguments, from several contributors in PR#17394.
* In .col(dim) and .row(dim), dim now may also be an integer-valued
"double".
* sQuote() and dQuote() get an explicit q argument with obvious
default instead of using getOption("fancyQuotes") implicitly and
unconditionally.
* unzip() can list archives with comments and with spaces in file
names even using an external unzip command.
* Command line completion has a new setting rc.settings(dots =
FALSE) to remove ... from the list of possible function
arguments.
* library() no longer checks packages with compiled code match
R.version$platform. loadNamespace() never has, and increasingly
the 'canonical name' does not reflect the important
characteristics of compiled code.
* The primitive functions drop() and unclass() now avoid
duplicating their data for atomic vectors that are large enough,
by returning ALTREP wrapper objects with adjusted attributes.
R-level assignments to change attributes will also use wrapper
objects to avoid duplicating data for larger atomic vectors. R
functions like structure() and unname() will therefore not
duplicate data in these settings. Generic vectors as produced by
list() are not yet covered by this optimization but may be in due
course.
* In formals(), envir becomes an optional argument instead of being
hardwired.
* Instead of signalling an error for an invalid S4 object x, str(x)
now gives a warning and subsequently still shows most parts of x,
e.g., when slots are missing.
* gamma(x) and lgamma(x) no longer warn when correctly returning
Inf or underflowing to zero. This helps maximum likelihood and
similar computations.
* convertColor() is now vectorized, so a lot faster for converting
many colours at once. The new argument vectorized to
colorConverter() ensures that non-vectorized colour converters
still work. (Thanks to Brodie Gaslam.)
* download.file() and url() get new argument headers for custom
HTTP headers, e.g., allowing to perform basic http
authentication, thanks to a patch contributed by G'abor Cs'ardi.
* File-based connection functions file(), gzfile(), bzfile() and
xzfile() now signal an error when used on a directory.
* For approx(), splinefun() _etc_, a new setting ties =
c("ordered", <fun>) allows skipping the sorting and still treat
ties.
* format(x) gives a more user friendly error message in the case
where no method is defined. A minimal method is provided in
format.default(x) when isS4(x) is true.
* which(x) now also works when x is a long vector, thanks to
Suharto Anggono's PR#17201. *NB*: this may return a double
result, breaking the previous guarantee of an integer result.
* seq.default() is more careful to return an integer (as opposed to
double) result when its arguments are large and/or classed
objects; see comment #9 of Suharto Anggono's PR#17497.
* The plot() method for lm and glm fits, plot.lm(), gains a new
option iter.smooth with a default of 0 for binomial fits, no
longer down-weighting when smoothing the residuals.
* zip() passes its list of files _via_ standard input to the
external command when too long for the command line (on some
platforms).
* data() gains an overwrite argument.
* t.test() now also returns the standard error (in list component
stderr).
* model.matrix(*, contrasts.arg = CC) now warns about invalid
contrasts.args.
* Performance of substr() and substring() has been improved.
* stopifnot() has been simplified thanks to Suharto Anggono's
proposals to become considerably faster for cheap expressions.
* The default 'user agent' has been changed when accessing http://
and https:// sites using libcurl. (A site was found which caused
libcurl to infinite-loop with the previous default.)
* sessionInfo() now also contains RNGkind() and prints it when it
differs from the default; based on a proposal and patch by Gabe
Becker in PR#17535. Also, RNGversion(getRversion()) works
directly.
* library() and require() now allow more control over handling
search path conflicts when packages are attached. The policy is
controlled by the new conflicts.policy option.
* barplot() gets a formula method, thanks to a patch proposal by
Arni Magnusson in PR#17521.
* pmax() and pmin(x) now also work for long vectors, thanks to
Suharto Anggono's PR#17533.
* bxp() now warns when omitting duplicated arguments.
* New hcl.colors() function to provide wide range of HCL-based
colour palettes with much better perceptual properties than the
existing RGB/HSV-based palettes like rainbow().
Also a new hcl.pals() function to list available palette names
for hcl.colors().
Contributed by Achim Zeileis.
* The default colours for image() and filled.contour() are now
based on hcl.colors().
* The palette-generating functions rainbow(), gray.colors(), etc.
get a new rev argument to facilitate reversing the order of
colors.
* New str2lang() and str2expression() as streamlined versions of
parse(text=., keep.source=FALSE) allow to abstract typical call
constructions, e.g., in formula manipulations. (Somewhat
experimental)
* Add update_PACKAGES() for incrementally updating a package
repository index, instead of rebuilding the index from scratch.
Thanks to Gabe Becker in PR#17544 for the patch, based on part of
his switchr package.
INSTALLATION on a UNIX-ALIKE:
* The options selected for the C++ compiler default to the C++11
standard if supported, otherwise to the C++98 standard.
* Visibility macros such as C_VISIBILITY can now be user-set
(including to empty), e.g. in config.site.
* Macro FCLIBS, which has sometimes been needed on Solaris, has
been renamed to FCLIBS_XTRA.
* Macro F77 is always set to the value of FC, so the latter should
be set to user-select the Fortran compiler for both fixed-form
and free-form Fortran. In particular, gfortran is now the first
choice for F77, not f95.
Macros FFLAGS and FCFLAGS remain distinct to allow for a compiler
which needs a flag to select free- or fixed-form Fortran (most
use the source-file extension to choose: .f is fixed-form and
.f90 and .f95 are free-form).
If only one of them is set, its value is used for both.
* The special-casing of CFLAGS, CXXFLAGS and FFLAGS for Intel
compilers on Linux has been removed: we do not have recent
experience but the generic defaults now chosen are the same as
those previously special-cased for x86_64.
If necessary, override the defaults on the configure command line
or in file config.site.
* Long-untested configure support for HP-UX and very old versions
of Linux has been removed.
* configure --with-blas (without specifying a value) includes
OpenBLAS in its search (before ATLAS and a generic BLAS). This
follows recent versions of the ax_blas autoconf macro.
* The configure macro MAKEINFO has been updated to TEXI2ANY.
* Support for make install-strip has been enhanced.
PACKAGE INSTALLATION:
* Source package installation is by default 'staged': the package
is installed into a temporary location under the final library
directory and moved into place once the installation is complete.
The benefit is that partially-installed packages are hidden from
other R sessions.
The overall default is set by environment variable
R_INSTALL_STAGED. R CMD INSTALL has new options --staged-install
and --no-staged-install, and packages can use the StagedInstall
field in their DESCRIPTION file to opt out. (That opt-out is a
temporary measure which may be withdrawn in future.)
Staged installation requires either --pkglock or --lock, one of
which is used by default.
* The interpretation of source code with extension .f is changing.
Previously this denoted FORTRAN 77 code, but current compilers no
longer have a FORTRAN 77 mode and interpret it as 'fixed-form'
Fortran 90 (or later where supported) code. Extensions .f90 and
.f95 continue to indicate 'free-form' Fortran code.
Legal FORTRAN 77 code is also legal fixed-form Fortran 9x;
however this change legitimizes the use of later features, in
particular to replace features marked 'obsolescent' in Fortran 90
and 'deleted' in Fortran 2018 which gfortran 8.x and later warn
about.
* Packages containing files in the src directory with extensions
.f90 or .f95 are now linked using the C or C++ compiler rather
than the Fortran 9x compiler. This is consistent with fixed-form
Fortran code and allows mixing of C++ and free-form Fortran on
most platforms.
Consequentially, a package which includes free-form Fortran 9x
code which uses OpenMP should include SHLIB_OPENMP_CFLAGS (or the
CXXFLAGS version if they also include C++ code) in PKG_LIBS
rather than SHLIB_OPENMP_FCFLAGS - fortunately on almost all
current platforms they are the same flag.
* Macro PKG_FFLAGS will be used for the compilation of both
fixed-form and free-form Fortran code unless PKG_FCFLAGS is also
set (in src/Makevars or src/Makevars.win).
* The make macro F_VISIBILITY is now preferred for both fixed-form
and free-form Fortran, for use in src/Makevars and similar.
* R CMD INSTALL gains a new option --strip which (where supported)
strips installed shared object(s): this can also be achieved by
setting the environment variable _R_SHLIB_STRIP_ to a true value.
The new option --strip-lib attempts stripping of static and
shared libraries installed under lib.
These are most useful on platforms using GNU binutils (such as
Linux) and compiling with -g flags.
* There is more support for installing UTF-8-encoded packages in a
strict Latin-1 locale (and probably for other Latin locales):
non-ASCII comments in R code (and NAMESPACE files) are worked
around better.
UTILITIES:
* R CMD check now optionally checks makefiles for correct and
portable use of the SHLIB_OPENMP_*FLAGS macros.
* R CMD check now evaluates \Sexpr{} expressions (including those
in macros) before checking the contents of Rd files and so
detects issues both in evaluating the expressions and in the
expanded contents.
* R CMD check now lists missing packages separated by commas and
with regular quotes such as to be useful as argument in calling
install.packages(c(..)); from a suggestion by Marcel Ramos.
* tools::Rd2latex() now uses UTF-8 as its default output encoding.
* R CMD check now checks line endings of files with extension .hpp
and those under inst/include. The check now includes that a
non-empty file is terminated with a newline.
R CMD build will correct line endings in such files.
* R CMD check now tries re-building all vignettes rather than
stopping at the first error: whilst doing so it adds 'bookmarks'
to the log. By default (see the 'R Internals' manual) it
re-builds each vignette in a separate process.
It now checks for duplicated vignette titles (also known as
'index entries'): they are used as hyperlinks on CRAN package
pages and so do need to be unique.
* R CMD check has more comprehensive checks on the data directory
and the functioning of data() in a package.
* R CMD check now checks autoconf-generated configure files have
their corresponding source files, including optionally attempting
to regenerate them on platforms with autoreconf.
* R CMD build has a new option --compression to select the
compression used for the tarball.
* R CMD build now removes src/*.mod files on all platforms.
C-LEVEL FACILITIES:
* New pointer protection C functions R_PreserveInMSet and
R_ReleaseFromMSet have been introduced to replace UNPROTECT_PTR,
which is not safe to mix with UNPROTECT (and with
PROTECT_WITH_INDEX). Intended for use in parsers only.
* NAMEDMAX has been raised to 7 to allow further protection of
intermediate results from (usually ill-advised) assignments in
arguments to BUILTIN functions. Properly written package code
should not be affected.
* R_unif_index is now considered to be part of the C API.
* R_GetCurrentEnv() allows C code to retrieve the current
environment.
DEPRECATED AND DEFUNCT:
* Argument compressed of untar() is deprecated - it is only used
for external tar commands which increasingly for extraction
auto-detect compression and ignore their zjJ flags.
* var(f) and hence sd(f) now give an error for factor arguments;
they gave a deprecation warning since R 3.2.3, PR#16564.
* Package tools' vignetteDepends() has been deprecated (it called a
function deprecated since Feb 2016), being partly replaced by
newly exported vignetteInfo().
* The f77_f2c script has been removed: it no longer sufficed to
compile the .f files in R.
* The deprecated legacy support of make macros such as CXX1X has
been removed: use the CXX11 forms instead.
* Make macro F77_VISIBILITY is deprecated in favour of
F_VISIBILITY.
* Make macros F77, FCPIFCPLAGS and SHLIB_OPENMP_FCFLAGS are
deprecated in favour of FC, FPICFLAGS and SHLIB_OPENMP_FFLAGS
respectively.
* $.data.frame had become an expensive version of the default
method, so has been removed. (Thanks to Radford Neal for picking
this up and to Duncan Murdoch for providing a patch.)
BUG FIXES:
* replayPlot(r) now also works in the same R session when r has
been "reproduced" from serialization, typically after saving to
and reading from an RDS file.
* substr() and substring() now signal an error when the input is
invalid UTF-8.
* file.copy() now works also when its argument to is of length
greater than one.
* mantelhaen.test() no longer suffers from integer overflow in
largish cases, thanks to Ben Bolker's PR#17383.
* Calling setGeneric("foo") in a package no longer fails when the
enclosing environment of the implicit generic foo() is
.GlobalEnv.
* untar(file("<some>.tar.gz"), *) now gives a better error message,
suggesting to use gzfile() instead.
* Method dispatch uses more relevant environments when looking up
class definitions.
* The documentation for identify() incorrectly claimed that the
indices of identified points were returned in the order that the
points were selected. identify() now has a new argument order to
allow the return value to include the order in which points were
identified; the documentation has been updated. Reported by
Richard Rowe and Samuel Granjeaud.
* order(...., decreasing=c(TRUE, FALSE)) could fail in some cases.
Reported from StackOverflow via Karl Nordstr"om.
* User macros in Rd files now accept empty and multi-line
arguments.
* Changes in print.*(), thanks to Lionel Henry's patches in
PR#17398:
* Printing lists, pairlists or attributes containing calls with
S3 class no longer evaluate those.
* Printing S4 objects within lists and pairlists dispatches
with show() rather than print(), as with auto-printing.
* The indexing tags (names or [[<n>]]) of recursive data
structures are now printed correctly in complex cases.
* Arguments supplied to print() are now properly forwarded to
methods when printing lists, pairlists or attributes
containing S3 objects.
* The print parameters are now preserved when printing S3
objects or deparsing symbols and calls. Previously, printing
lists containing S3 objects or expressions would reset these
parameters.
* Printing lists, pairlists or attributes containing functions
now uses srcref attributes if present.
* Calling install.packages() with a length zero pkgs argument now
is a no-op (PR#17422).
* unlist(x) now returns a correct factor when x is a nested list
with factor leaves, fixing PR#12572 and PR#17419.
* The documentation help(family) gives more details about the aic
component, thanks to Ben Bolker's prompting.
* The documentation for attributes and `attributes<-` now gives x
as name of the first and main argument which the implementation
has been requiring, fixing PR#17434. For consistency, the first
argument name is also changed from obj to x for
`mostattributes<-`.
* strwidth() now uses par("font") as default font face (PR#17352).
* plot(<table>, log="x") no longer warns about log.
* The print() method for "htest" objects now formats the test
statistic and parameter directly and hence no longer rounds to
units _before_ the decimal point. Consequently, printing of
t.test() results with a small number of digits now shows
non-large df's to the full precision (PR#17444).
* kruskal.test() and fligner.test() no longer erroneously insist on
numeric g group arguments (PR#16719).
* Printing a news db via the browser now does a much better job
(PR#17433).
* print.aov() missed column names in the multivariate case due to
misspelling (reported by Chris Andrews).
* axis() now creates valid at locations also for small subnormal
number ranges in log scale plots.
* format.POSIXlt() now also recycles the zone and gmtoff list
components to full length when needed, and its internal C code
detects have_zone in more cases. In some cases, this changes its
output to become compatible with format.POSIXct().
* On Windows, detectCores() in package parallel now detects
processors in all processor groups, not just the group R is
running in (impacts particularly systems with more than 64
logical processors). Reported by Arunkumar Srinivasan.
* On Windows, socketSelect() would hang with more than 64 sockets,
and hence parallel::clusterApplyLB() would hang with more than 64
workers. Reported by Arunkumar Srinivasan.
* as(1L, "double") now does coerce (PR#17457).
* lm.influence(), influence.measures(), rstudent() etc now work
(more) correctly for multivariate models ("mlm"), thanks to
(anonymous) stackoverflow remarks.
* sample.int(2.9, *, replace=TRUE) again behaves as documented and
as in R < 3.0.0, namely identically to sample.int(2, ..).
* Fixes to convertColor() for chromatic adaptation; thanks to
Brodie Gaslam PR#17473.
* Using \Sexpr[stage=install]{..} to create an Rd section no longer
gives a warning in R CMD check; problem originally posted by
G'abor Cs'ardi, then reported as PR#17479 with a partial patch by
Duncan Murdoch.
* Parse data now include a special node for equal assignment.
* split.default() no longer relies on [[<-(), so it behaves as
expected when splitting an object by a factor with the empty
string as one of its levels. Thanks to Brad Friedman for the
report.
* Line numbers in messages about .Rd files are now more reliable,
thanks to a patch from Duncan Murdoch.
* In the numeric method for all.equal(), a numeric scale argument
is now checked to be positive and allowed to be of length > 1.
(The latter worked originally and with a warning in recent
years).
* Deferred string conversions now record the OutDec option setting
when not equal to the default. Reported by Michael Sannella.
* When y is numeric and f a factor, plot(y ~ f) nicely uses "y" and
"f" as y- and x-labels. The more direct boxplot(y ~ f) now does
too. The new argument ann = FALSE may be used to suppress these.
* Subassignment to no/empty rows of a data frame is more consistent
and typically a no-op in all cases instead of sometimes an error;
part of Emil Bode's PR#17483.
* Calls like formatC(*, zero.print = "< 0.001") no longer give an
error and are further improved via new optional argument
replace.zero. Reported by David Hugh-Jones.
* methods::formalArgs("<fn>") now finds the same function as
formals("<fn>"), fixing Emil Bode's PR#17499.
* The methods package better handles duplicated class names across
packages.
* The default method of seq() now avoids integer overflow, thanks
to the report and "cumsum" patch of Suharto Anggono's PR#17497.
* sub() no longer loses encodings for non-ASCII replacements
(PR#17509).
* Fix for rotated raster image on X11 device. (Partial fix for
PR#17148; thanks to Mikko Korpela).
* formula(model.frame(frml, ..)) now returns frml in all cases,
thanks to Bill Dunlap. The previous behavior is available as
DF2formula(<model.frame>).
* ar.ols() also returns scalar var.pred in univariate case
(PR#17517).
* normalizePath() now treats NA path as non-existent and normalizes
it to NA. file.access() treats NA file name as non-existent.
file.edit() and connection functions such as file() now treat NA
file names as errors.
* The internal regularize.values() auxiliary of approx(),
splinefun() etc now warns again when there are ties and the
caller did not specify ties. Further, it no longer duplicates x
and y unnecessarily when x is already sorted (PR#17515).
* strtoi("", base) now gives NA on all platforms, following its
documentation. Reported by Michael Chirico.
* In the definition of an S4 class, prototype elements are checked
against the slots of the class, with giving a prototype for an
undefined slot now being an error. (Reported by Bill Dunlap.)
* From setClassUnion(), if environment variable
_R_METHODS_SHOW_CHECKSUBCLASSES is set to true, the internal
.checkSubclasses() utility prints debugging info to see where it
is used.
* max.col(m) with an m of zero columns now returns integer NA
(instead of 1).
* axTicks() no longer returns small "almost zero" numbers (in
exponential format) instead of zero, fixing Ilario Gelmetti's
PR#17534.
* isSymmetric(matrix(0, dimnames=list("A","b"))) is FALSE again, as
always documented.
* The cairo_pdf graphics device (and other Cairo-based devices) now
clip correctly to the right and bottom border.
There was an off-by-one-pixel bug, reported by Lee Kelvin.
* as.roman(3) <= 2:4 and all other comparisons now work, as do
group "Summary" function calls such as max(as.roman(sample(20)))
and as.roman(NA). (Partly reported by Bill Dunlap in PR#17542.)
* reformulate("x", response = "sin(y)") no longer produces extra
back quotes, PR#17359, and gains new optional argument env.
* When reading console input from stdin with re-encoding (R
--encoding=enc < input) the code on a Unix-alike now ensures that
each converted input line is terminated with a newline even if
re-encoding fails.
* as.matrix.data.frame() now produces better strings from logicals,
thanks to PR#17548 from Gabe Becker.
* The S4 generic signature of rowSums(), rowMeans(), colSums() and
colMeans() is restricted to "x".
* match(x, tab) now works for long _character_ vectors x, thanks to
PR#17552 by Andreas Kersting.
* Class unions are unloaded when their namespace is unloaded
(PR#17531, adapted from a patch by Brodie Gaslam).
* selectMethod() is robust to ANY-truncation of method signatures
(thanks to Herve Pages for the report).
Update to 3.5.3
Upstream changes:
CHANGES IN R 3.5.3:
INSTALLATION on a UNIX-ALIKE:
* Detection of flags for C++98/11/14/17 has been improved: in
particular if CXX??STD is set, it is tried first with no
additional flags.
PACKAGE INSTALLATION:
* New macro F_VISIBILITY as an alternative to F77_VISIBILITY. This
will become the preferred form in R 3.6.0.
BUG FIXES:
* writeLines(readLines(fnam), fnam) now works as expected, thanks
to Peter Meissner's PR#17528.
* setClassUnion() no longer warns, but uses message() for now, when
encountering "non local" subclasses of class members.
* stopifnot(exprs = T) no longer fails.
Update to 3.5.2
Upstream changes:
CHANGES IN R 3.5.2:
PACKAGE INSTALLATION:
* New macro CXX_VISIBILITY analogous to C_VISIBILITY (which several
packages have been misusing for C++ code) for the default C++
compiler (but not necessarily one used for non-default C++
dialects like C++14).
TESTING:
* The random number generator tests in tests/p-r-random-tests.R no
longer fail occasionally as they now randomly sample from
"certified" random seeds.
BUG FIXES:
* The "glm" method of drop1() miscalculated the score test
(test="Rao") when the model contained an offset.
* Linear multiple empty models such as lm(y ~ 0) now have a
correctly dimensioned empty coefficient matrix; reported by Brett
Presnell.
* vcov(<empty mlm>) and hence confint() now work (via a consistency
change in summary.lm()).
* confint(<multiple lm()>) now works correctly; reported on R-devel
by Steven Pav.
* quade.test() now also works correctly when its arguments are not
yet sorted along groups, fixing PR#15842.
* Installation on a Unix-alike tries harder to link to the pthread
library where required (rather than relying on OpenMP to provide
it: configuring with --disable-openmp was failing on some Linux
systems).
* The data.frame method for print(x) is fast now also for large
data frames x and got an optional argument max, thanks to
suggestions by Juan Telleria.
* hist() no longer integer overflows in very rare cases, fixing
PR#17450.
* untar() ignored a character compressed argument: however many
external tar programs ignore the flags which should have been set
and automagically choose the compression type, and if appropriate
gzip or bzip2 compression would have been chosen from the magic
header of the tarball.
* zapsmall(x) now works for more "number-like" objects.
* The tools-internal function called from R CMD INSTALL now gets a
warnOption = 1 argument and only sets options(warn = warnOption)
when that increases the warning level (PR#17453).
* Analogously, the tools-internal function called from R CMD check
gets a warnOption = 1 argument and uses the larger of that and
getOption("warn"), also allowing to be run with increased warning
level.
* Parse data now have deterministic parent nodes (PR#16041).
* Calling match() with length one x and POSIXlt table gave a
segfault (PR#17459).
* Fork clusters could hang due to a race condition in cluster
initialization (makeCluster()).
* nextn(n) now also works for larger n and no longer loops
infinitely for e.g, n <- 214e7.
* cooks.distance() and rstandard() now work correctly for multiple
linear models ("mlm").
* polym() and corresponding lm() prediction now also work for a
boundary "vector" case fixing PR#17474, reported by Alexandre
Courtiol.
* With a very large number of variables terms() could segfault
(PR#17480).
* cut(rep(0, 7)) now works, thanks to Joey Reid and Benjamin Tyner
(PR#16802).
* download.file(*, method = "curl", cacheOK = FALSE) should work
now on Windows, thanks to Kevin Ushey's patch in PR#17323.
* duplicated(<dataframe with 'f'>) now works, too, thanks to
Andreas Kersting's PR#17485; ditto for anyDuplicated().
* legend(*, cex = 1:2) now works less badly.
* The print() method for POSIXct and POSIXlt now correctly obeys
getOption("max.print"), fixing a long-standing typo, and it also
gets a corresponding optional max argument.
* Unserialization of raw vectors serialized in ASCII representation
now works correctly.
* <data frame>[TRUE, <new>] <- list(c1, c2) now works correctly,
thanks to Suharto Anggono's PR#15362 and Emil Bode's patch in
PR#17504.
* seq.int(*, by=by, length=n) no longer wrongly "drops fractional
parts" when by is integer, thanks to Suharto Anggono's report
PR#17506.
* Buffering is disabled for file() connections to non-regular files
(like sockets), as well as fifo() and pipe() connections. Fixes
PR#17470, reported by Chris Culnane.
revbump for boost 1.69.0
Revbump after cairo 1.16.0 update.
*: Add CTF_SUPPORTED/CTF_FILES_SKIP where necessary.
Recursive revbump from hardbuzz-2.1.1
Recursive bump for perl5-5.28.0
revbump after boost-libs update
R: remove cases for ancient NetBSD versions.
Update to 3.5.1
Upstream changes:
CHANGES IN R 3.5.1
BUG FIXES
file("stdin") is no longer considered seekable.
dput() and dump() are no longer truncating when options(deparse.max.lines = *) is set.
Calls with an S3 class are no longer evaluated when printed, fixing part of PR#17398, thanks to a patch from Lionel Henry.
Allow file argument of Rscript to include space even when it is first on the command line.
callNextMethod() uses the generic from the environment of the calling method. Reported by Hervé Pagès with well documented examples.
Compressed file connections are marked as blocking.
optim(*, lower = c(-Inf, -Inf)) no longer warns (and switches the method), thanks to a suggestion by John Nash.
predict(fm, newdata) is now correct also for models where the formula has terms such as splines::ns(..) or stats::poly(..), fixing PR#17414, based on a patch from Duncan Murdoch.
simulate.lm(glm(*, gaussian(link = <non-default>))) has been corrected, fixing PR#17415 thanks to Alex Courtiol.
unlist(x) no longer fails in some cases of nested empty lists. Reported by Steven Nydick.
qr.coef(qr(<all 0, w/ colnames>)) now works. Reported by Kun Ren.
The radix sort is robust to vectors with >1 billion elements (but long vectors are still unsupported). Thanks to Matt Dowle for the fix.
Terminal connections (e.g., stdin) are no longer buffered. Fixes PR#17432.
deparse(x), dput(x) and dump() now respect c()'s argument names recursive and use.names, e.g., for x <- setNames(0, "recursive"), thanks to Suharto Anggono's PR#17427.
Unbuffered connections now work with encoding conversion. Reported by Stephen Berman.
‘.Renviron’ on Windows with Rgui is again by default searched for in user documents directory when invoked via the launcher icon. Reported by Jeroen Ooms.
printCoefmat() now also works with explicit right=TRUE.
print.noquote() now also works with explicit quote=FALSE.
The default method for pairs(.., horInd=*, verInd=*) now gets the correct order, thanks to reports by Chris Andrews and Gerrit Eichner. Additionally, when horInd or verInd contain only a subset of variables, all the axes are labeled correctly now.
agrep("..|..", .., fixed=FALSE) now matches when it should, thanks to a reminder by Andreas Kolter.
str(ch) now works for more invalid multibyte strings.
Update to 3.5.0
Upstream changes:
CHANGES IN R 3.5.0
SIGNIFICANT USER-VISIBLE CHANGES
All packages are by default byte-compiled on installation. This makes the installed packages larger (usually marginally so) and may affect the format of messages and tracebacks (which often exclude .Call and similar).
NEW FEATURES
factor() now uses order() to sort its levels, rather than sort.list(). This allows factor() to support custom vector-like objects if methods for the appropriate generics are defined. It has the side effect of making factor() succeed on empty or length-one non-atomic vector(-like) types (e.g., "list"), where it failed before.
diag() gets an optional names argument: this may require updates to packages defining S4 methods for it.
chooseCRANmirror() and chooseBioCmirror() no longer have a useHTTPS argument, not needed now all R builds support https:// downloads.
New summary() method for warnings() with a (somewhat experimental) print() method.
(methods package.) .self is now automatically registered as a global variable when registering a reference class method.
tempdir(check = TRUE) recreates the tempdir() directory if it is no longer valid (e.g. because some other process has cleaned up the ‘/tmp’ directory).
New askYesNo() function and "askYesNo" option to ask the user binary response questions in a customizable but consistent way. (Suggestion of PR#17242.)
New low level utilities ...elt(n) and ...length() for working with ... parts inside a function.
isTRUE() is more tolerant and now true in
x <- rlnorm(99)
isTRUE(median(x) == quantile(x)["50%"])
New function isFALSE() defined analogously to isTRUE().
The default symbol table size has been increased from 4119 to 49157; this may improve the performance of symbol resolution when many packages are loaded. (Suggested by Jim Hester.)
line() gets a new option iter = 1.
Reading from connections in text mode is buffered, significantly improving the performance of readLines(), as well as scan() and read.table(), at least when specifying colClasses.
order() is smarter about picking a default sort method when its arguments are objects.
available.packages() has two new arguments which control if the values from the per-session repository cache are used (default true, as before) and if so how old cached values can be to be used (default one hour).
These arguments can be passed from install.packages(), update.packages() and functions calling that: to enable this available.packages(), packageStatus() and download.file() gain a ... argument.
packageStatus()'s upgrade() method no longer ignores its ... argument but passes it to install.packages().
installed.packages() gains a ... argument to allow arguments (including noCache) to be passed from new.packages(), old.packages(), update.packages() and packageStatus().
factor(x, levels, labels) now allows duplicated labels (not duplicated levels!). Hence you can map different values of x to the same level directly.
Attempting to use names<-() on an S4 derivative of a basic type no longer emits a warning.
The list method of within() gains an option keepAttrs = FALSE for some speed-up.
system() and system2() now allow the specification of a maximum elapsed time (‘timeout’).
debug() supports debugging of methods on any object of S4 class "genericFunction", including group generics.
Attempting to increase the length of a variable containing NULL using length()<- still has no effect on the target variable, but now triggers a warning.
type.convert() becomes a generic function, with additional methods that operate recursively over list and data.frame objects. Courtesy of Arni Magnusson (PR#17269).
lower.tri(x) and upper.tri(x) only needing dim(x) now work via new functions .row() and .col(), so no longer call as.matrix() by default in order to work efficiently for all kind of matrix-like objects.
print() methods for "xgettext" and "xngettext" now use encodeString() which keeps, e.g. "\n", visible. (Wish of PR#17298.)
package.skeleton() gains an optional encoding argument.
approx(), spline(), splinefun() and approxfun() also work for long vectors.
deparse() and dump() are more useful for S4 objects, dput() now using the same internal C code instead of its previous imperfect workaround R code. S4 objects now typically deparse perfectly, i.e., can be recreated identically from deparsed code.
dput(), deparse() and dump() now print the names() information only once, using the more readable (tag = value) syntax, notably for list()s, i.e., including data frames.
These functions gain a new control option "niceNames" (see .deparseOpts()), which when set (as by default) also uses the (tag = value) syntax for atomic vectors. On the other hand, without deparse options "showAttributes" and "niceNames", names are no longer shown also for lists. as.character(list( c (one = 1))) now includes the name, as as.character(list(list(one = 1))) has always done.
m:n now also deparses nicely when m > n.
The "quoteExpressions" option, also part of "all", no longer quote()s formulas as that may not re-parse identically. (PR#17378)
If the option setWidthOnResize is set and TRUE, R run in a terminal using a recent readline library will set the width option when the terminal is resized. Suggested by Ralf Goertz.
If multiple on.exit() expressions are set using add = TRUE then all expressions will now be run even if one signals an error.
mclapply() gets an option affinity.list which allows more efficient execution with heterogeneous processors, thanks to Helena Kotthaus.
The character methods for as.Date() and as.POSIXlt() are more flexible via new arguments tryFormats and optional: see their help pages.
on.exit() gains an optional argument after with default TRUE. Using after = FALSE with add = TRUE adds an exit expression before any existing ones. This way the expressions are run in a first-in last-out fashion. (From Lionel Henry.)
On Windows, file.rename() internally retries the operation in case of error to attempt to recover from possible anti-virus interference.
Command line completion on :: now also includes lazy-loaded data.
If the TZ environment variable is set when date-time functions are first used, it is recorded as the session default and so will be used rather than the default deduced from the OS if TZ is subsequently unset.
There is now a [ method for class "DLLInfoList".
glm() and glm.fit get the same singular.ok = TRUE argument that lm() has had forever. As a consequence, in glm(*, method = <your_own>), user specified methods need to accept a singular.ok argument as well.
aspell() gains a filter for Markdown (‘.md’ and ‘.Rmd’) files.
intToUtf8(multiple = FALSE) gains an argument to allow surrogate pairs to be interpreted.
The maximum number of DLLs that can be loaded into R e.g. via dyn.load() has been increased up to 614 when the OS limit on the number of open files allows.
Sys.timezone() on a Unix-alike caches the value at first use in a session: inter alia this means that setting TZ later in the session affects only the current time zone and not the system one.
Sys.timezone() is now used to find the system timezone to pass to the code used when R is configured with --with-internal-tzcode.
When tar() is used with an external command which is detected to be GNU tar or libarchive tar (aka bsdtar), a different command-line is generated to circumvent line-length limits in the shell.
system(*, intern = FALSE), system2() (when not capturing output), file.edit() and file.show() now issue a warning when the external command cannot be executed.
The “default” ("lm" etc) methods of vcov() have gained new optional argument complete = TRUE which makes the vcov() methods more consistent with the coef() methods in the case of singular designs. The former (back-compatible) behavior is given by vcov(*, complete = FALSE).
coef() methods (for lm etc) also gain a complete = TRUE optional argument for consistency with vcov().
For "aov", both coef() and vcov() methods remain back-compatibly consistent, using the other default, complete = FALSE.
attach(*, pos = 1) is now an error instead of a warning.
New function getDefaultCluster() in package parallel to get the default cluster set via setDefaultCluster().
str(x) for atomic objects x now treats both cases of is.vector(x) similarly, and hence much less often prints "atomic". This is a slight non-back-compatible change producing typically both more informative and shorter output.
write.dcf() gets optional argument useBytes.
New, partly experimental packageDate() which tries to get a valid "Date" object from a package ‘DESCRIPTION’ file, thanks to suggestions in PR#17324.
tools::resaveRdaFiles() gains a version argument, for use when packages should remain compatible with earlier versions of R.
ar.yw(x) and hence by default ar(x) now work when x has NAs, mostly thanks to a patch by Pavel Krivitsky in PR#17366. The ar.yw.default()'s AIC computations have become more efficient by using determinant().
New warnErrList() utility (from package nlme, improved).
By default the (arbitrary) signs of the loadings from princomp() are chosen so the first element is non-negative.
If --default-packages is not used, then Rscript now checks the environment variable R_SCRIPT_DEFAULT_PACKAGES. If this is set, then it takes precedence over R_DEFAULT_PACKAGES. If default packages are not specified on the command line or by one of these environment variables, then Rscript now uses the same default packages as R. For now, the previous behavior of not including methods can be restored by setting the environment variable R_SCRIPT_LEGACY to yes.
When a package is found more than once, the warning from find.package(*, verbose=TRUE) lists all library locations.
POSIXt objects can now also be rounded or truncated to month or year.
stopifnot() can be used alternatively via new argument exprs which is nicer and useful when testing several expressions in one call.
The environment variable R_MAX_VSIZE can now be used to specify the maximal vector heap size. On macOS, unless specified by this environment variable, the maximal vector heap size is set to the maximum of 16GB and the available physical memory. This is to avoid having the R process killed when macOS over-commits memory.
sum(x) and sum(x1,x2,..,x<N>) with many or long logical or integer vectors no longer overflows (and returns NA with a warning), but returns double numbers in such cases.
Single components of "POSIXlt" objects can now be extracted and replaced via [ indexing with 2 indices.
S3 method lookup now searches the namespace registry after the top level environment of the calling environment.
Arithmetic sequences created by 1:n, seq_along, and the like now use compact internal representations via the ALTREP framework. Coercing integer and numeric vectors to character also now uses the ALTREP framework to defer the actual conversion until first use.
Finalizers are now run with interrupts suspended.
merge() gains new option no.dups and by default suffixes the second of two duplicated column names, thanks to a proposal by Scott Ritchie (and Gabe Becker).
scale.default(x, center, scale) now also allows center or scale to be “numeric-alike”, i.e., such that as.numeric(.) coerces them correctly. This also eliminates a wrong error message in such cases.
par*apply and par*applyLB gain an optional argument chunk.size which allows to specify the granularity of scheduling.
Some as.data.frame() methods, notably the matrix one, are now more careful in not accepting duplicated or NA row names, and by default produce unique non-NA row names. This is based on new function .rowNamesDF(x, make.names = *) <- rNms where the logical argument make.names allows to specify how invalid row names rNms are handled. .rowNamesDF() is a “workaround” compatible default.
R has new serialization format (version 3) which supports custom serialization of ALTREP framework objects. These objects can still be serialized in format 2, but less efficiently. Serialization format 3 also records the current native encoding of unflagged strings and converts them when de-serialized in R running under different native encoding. Format 3 comes with new serialization magic numbers (RDA3, RDB3, RDX3). Format 3 can be selected by version = 3 in save(), serialize() and saveRDS(), but format 2 remains the default for all serialization and saving of the workspace. Serialized data in format 3 cannot be read by versions of R prior to version 3.5.0.
The "Date" and “date-time” classes "POSIXlt" and "POSIXct" now have a working `length<-` method, as wished in PR#17387.
optim(*, control = list(warn.1d.NelderMead = FALSE)) allows to turn off the warning when applying the default "Nelder-Mead" method to 1-dimensional problems.
matplot(.., panel.first = .) etc now work, as log becomes explicit argument and ... is passed to plot() unevaluated, as suggested by Sebastian Meyer in PR#17386.
Interrupts can be suspended while evaluating an expression using suspendInterrupts. Subexpression can be evaluated with interrupts enabled using allowInterrupts. These functions can be used to make sure cleanup handlers cannot be interrupted.
R 3.5.0 includes a framework that allows packages to provide alternate representations of basic R objects (ALTREP). The framework is still experimental and may undergo changes in future R releases as more experience is gained. For now, documentation is provided in https://svn.r-project.org/R/branches/ALTREP/ALTREP.html.
UTILITIES
install.packages() for source packages now has the possibility to set a ‘timeout’ (elapsed-time limit). For serial installs this uses the timeout argument of system2(): for parallel installs it requires the timeout utility command from GNU coreutils.
It is now possible to set ‘timeouts’ (elapsed-time limits) for most parts of R CMD check via environment variables documented in the ‘R Internals’ manual.
The ‘BioC extra’ repository which was dropped from Bioconductor 3.6 and later has been removed from setRepositories(). This changes the mapping for 6–8 used by setRepositories(ind=).
R CMD check now also applies the settings of environment variables _R_CHECK_SUGGESTS_ONLY_ and _R_CHECK_DEPENDS_ONLY_ to the re-building of vignettes.
R CMD check with environment variable _R_CHECK_DEPENDS_ONLY_ set to a true value makes test-suite-management packages available and (for the time being) works around a common omission of rmarkdown from the VignetteBuilder field.
INSTALLATION on a UNIX-ALIKE
Support for a system Java on macOS has been removed — install a fairly recent Oracle Java (see ‘R Installation and Administration’ §C.3.2).
configure works harder to set additional flags in SAFE_FFLAGS only where necessary, and to use flags which have little or no effect on performance.
In rare circumstances it may be necessary to override the setting of SAFE_FFLAGS.
C99 functions expm1, hypot, log1p and nearbyint are now required.
configure sets a -std flag for the C++ compiler for all supported C++ standards (e.g., -std=gnu++11 for the C++11 compiler). Previously this was not done in a few cases where the default standard passed the tests made (e.g. clang 6.0.0 for C++11).
C-LEVEL FACILITIES
‘Writing R Extensions’ documents macros MAYBE_REFERENCED, MAYBE_SHARED and MARK_NOT_MUTABLE that should be used by package C code instead NAMED or SET_NAMED.
The object header layout has been changed to support merging the ALTREP branch. This requires re-installing packages that use compiled code.
‘Writing R Extensions’ now documents the R_tryCatch, R_tryCatchError, and R_UnwindProtect functions.
NAMEDMAX has been raised to 3 to allow protection of intermediate results from (usually ill-advised) assignments in arguments to BUILTIN functions. Package C code using SET_NAMED may need to be revised.
DEPRECATED AND DEFUNCT
Sys.timezone(location = FALSE) is defunct, and is ignored (with a warning).
methods:::bind_activation() is defunct now; it typically has been unneeded for years.
The undocumented ‘hidden’ objects .__H__.cbind and .__H__.rbind in package base are deprecated (in favour of cbind and rbind).
The declaration of pythag() in ‘Rmath.h’ has been removed — the entry point has not been provided since R 2.14.0.
BUG FIXES
printCoefmat() now also works without column names.
The S4 methods on Ops() for the "structure" class no longer cause infinite recursion when the structure is not an S4 object.
nlm(f, ..) for the case where f() has a "hessian" attribute now computes LL' = H + µI correctly. (PR#17249).
An S4 method that “rematches” to its generic and overrides the default value of a generic formal argument to NULL no longer drops the argument from its formals.
Rscript can now accept more than one argument given on the #! line of a script. Previously, one could only pass a single argument on the #! line in Linux.
Connections are now written correctly with encoding "UTF-16LE". (PR#16737).
Evaluation of ..0 now signals an error. When ..1 is used and ... is empty, the error message is more appropriate.
(Windows mainly.) Unicode code points which require surrogate pairs in UTF-16 are now handled. All systems should properly handle surrogate pairs, even those systems that do not need to make use of them. (PR#16098)
stopifnot(e, e2, ...) now evaluates the expressions sequentially and in case of an error or warning shows the relevant expression instead of the full stopifnot(..) call.
path.expand() on Windows now accepts paths specified as UTF-8-encoded character strings even if not representable in the current locale. (PR#17120)
line(x, y) now correctly computes the medians of the left and right group's x-values and in all cases reproduces straight lines.
Extending S4 classes with slots corresponding to special attributes like dim and dimnames now works.
Fix for legend() when fill has multiple values the first of which is NA (all colours used to default to par(fg)). (PR#17288)
installed.packages() did not remove the cached value for a library tree that had been emptied (but would not use the old value, just waste time checking it).
The documentation for installed.packages(noCache = TRUE) incorrectly claimed it would refresh the cache.
aggregate(<data.frame>) no longer uses spurious names in some cases. (PR#17283)
object.size() now also works for long vectors.
packageDescription() tries harder to solve re-encoding issues, notably seen in some Windows locales. This fixes the citation() issue in PR#17291.
poly(<matrix>, 3) now works, thanks to prompting by Marc Schwartz.
readLines() no longer segfaults on very large files with embedded '\0' (aka ‘nul’) characters. (PR#17311)
ns() (package splines) now also works for a single observation. interpSpline() gives a more friendly error message when the number of points is less than four.
dist(x, method = "canberra") now uses the correct definition; the result may only differ when x contains values of differing signs, e.g. not for 0-1 data.
methods:::cbind() and methods:::rbind() avoid deep recursion, thanks to Suharto Anggono via PR#17300.
Arithmetic with zero-column data frames now works more consistently; issue raised by Bill Dunlap.
Arithmetic with data frames gives a data frame for ^ (which previously gave a numeric matrix).
pretty(x, n) for large n or large diff(range(x)) now works better (though it was never meant for large n); internally it uses the same rounding fuzz (1e-10) as seq.default() — as it did up to 2010-02-03 when both were 1e-7.
Internal C-level R_check_class_and_super() and hence R_check_class_etc() now also consider non-direct super classes and hence return a match in more cases. This e.g., fixes behaviour of derived classes in package Matrix.
Reverted unintended change in behavior of return calls in on.exit expressions introduced by stack unwinding changes in R 3.3.0.
Attributes on symbols are now detected and prevented; attempt to add an attribute to a symbol results in an error.
fisher.test(*, workspace = <n>) now may also increase the internal stack size which allows larger problem to be solved, fixing PR#1662.
The methods package no longer directly copies slots (attributes) into a prototype that is of an “abnormal” (reference) type, like a symbol.
The methods package no longer attempts to call length<-() on NULL (during the bootstrap process).
The methods package correctly shows methods when there are multiple methods with the same signature for the same generic (still not fully supported, but at least the user can see them).
sys.on.exit() is now always evaluated in the right frame. (From Lionel Henry.)
seq.POSIXt(*, by = "<n> DSTdays") now should work correctly in all cases and is faster. (PR#17342)
.C() when returning a logical vector now always maps values other than FALSE and NA to TRUE (as documented).
Subassignment with zero length vectors now coerces as documented (PR#17344).
Further, x <- numeric(); x[1] <- character() now signals an error ‘replacement has length zero’ (or a translation of that) instead of doing nothing.
(Package parallel.) mclapply(), pvec() and mcparallel() (when mccollect() is used to collect results) no longer leave zombie processes behind.
R CMD INSTALL <pkg> now produces the intended error message when, e.g., the LazyData field is invalid.
as.matrix(dd) now works when the data frame dd contains a column which is a data frame or matrix, including a 0-column matrix/d.f. .
mclapply(X, mc.cores) now follows its documentation and calls lapply() in case mc.cores = 1 also in the case mc.preschedule is false. (PR#17373)
aggregate(<data.frame>, drop=FALSE) no longer calls the function on <empty> parts but sets corresponding results to NA. (Thanks to Suharto Anggono's patches in PR#17280).
The duplicated() method for data frames is now based on the list method (instead of string coercion). Consequently unique() is better distinguishing data frame rows, fixing PR#17369 and PR#17381. The methods for matrices and arrays are changed accordingly.
Calling names() on an S4 object derived from "environment" behaves (by default) like calling names() on an ordinary environment.
read.table() with a non-default separator now supports quotes following a non-whitespace character, matching the behavior of scan().
parLapplyLB and parSapplyLB have been fixed to do load balancing (dynamic scheduling). This also means that results of computations depending on random number generators will now really be non-reproducible, as documented.
Indexing a list using dollar and empty string (l$"") returns NULL.
Using \usage{ data(<name>, package="<pkg>") } no longer produces R CMD check warnings.
match.arg() more carefully chooses the environment for constructing default choices, fixing PR#17401 as proposed by Duncan Murdoch.
Deparsing of consecutive ! calls is now consistent with deparsing unary - and + calls and creates code that can be reparsed exactly; thanks to a patch by Lionel Henry in PR#17397. (As a side effect, this uses fewer parentheses in some other deparsing involving ! calls.)
[R logo] CHANGES IN R 3.4.4
NEW FEATURES
Sys.timezone() tries more heuristics on Unix-alikes and so is more likely to succeed (especially on Linux). For the slowest method, a warning is given recommending that TZ is set to avoid the search.
The version of LAPACK included in the sources has been updated to 3.8.0 (for the routines used by R, a very minor bug-fix change).
parallel::detectCores(logical = FALSE) is ignored on Linux systems, since the information is not available with virtualized OSes.
INSTALLATION on a UNIX-ALIKE
configure will use pkg-config to find the flags to link to jpeg if available (as it should be for the recently-released jpeg-9c and libjpeg-turbo). (This amends the code added in R 3.3.0 as the module name in jpeg-9c is not what that tested for.)
DEPRECATED AND DEFUNCT
Sys.timezone(location = FALSE) (which was a stop-gap measure for Windows long ago) is deprecated. It no longer returns the value of environment variable TZ (usually a location).
Legacy support of make macros such as CXX1X is formally deprecated: use the CXX11 forms instead.
BUG FIXES
power.prop.test() now warns when it cannot solve the problem, typically because of impossible constraints. (PR#17345)
removeSource() no longer erroneously removes NULL in certain cases, thanks to Dénes Tóth.
nls(`NO [mol/l]` ~ f(t)) and nls(y ~ a) now work. (Partly from PR#17367)
R CMD build checks for GNU cp rather than assuming Linux has it. (PR#17370 says ‘Alpine Linux’ does not.)
Non-UTF-8 multibyte character handling fixed more permanently (PR#16732).
sum(<large ints>, <stuff>) is more consistent. (PR#17372)
rf() and rbeta() now also work correctly when ncp is not scalar, notably when (partly) NA. (PR#17375)
is.na(NULL) no longer warns. (PR#16107)
R CMD INSTALL now correctly sets C++ compiler flags when all source files are in sub-directories of ‘src’.
revbump for boost-libs update
Recursive bump for new fribidi dependency in pango.
Recursive bumps for fontconfig and libzip dependency changes.
math/R: Use the Accelerate framework if it is available This package was already using libblas from the Accelerate framework on Darwin through /usr/lib/libblas.dylib. This change makes it explicit and removes unnecessary dependencies on math/blas and math/lapack. Bump PKGREVISION.
Revbump after boost update
- Update to 3.4.3
Upstream changes:
CHANGES IN R 3.4.3:
INSTALLATION on a UNIX-ALIKE:
* A workaround has been added for the changes in location of
time-zone files in macOS 10.13 'High Sierra' and again in
10.13.1, so the default time zone is deduced correctly from the
system setting when R is configured with --with-internal-tzcode
(the default on macOS).
* R CMD javareconf has been updated to recognize the use of a Java
9 SDK on macOS.
BUG FIXES:
* raw(0) & raw(0) and raw(0) | raw(0) again return raw(0) (rather
than logical(0)).
* intToUtf8() converts integers corresponding to surrogate code
points to NA rather than invalid UTF-8, as well as values larger
than the current Unicode maximum of 0x10FFFF. (This aligns with
the current RFC3629.)
* Fix calling of methods on S4 generics that dispatch on ... when
the call contains ....
* Following Unicode 'Corrigendum 9', the UTF-8 representations of
U+FFFE and U+FFFF are now regarded as valid by utf8ToInt().
* range(c(TRUE, NA), finite = TRUE) and similar no longer return
NA. (Reported by Lukas Stadler.)
* The self starting function attr(SSlogis, "initial") now also
works when the y values have exact minimum zero and is slightly
changed in general, behaving symmetrically in the y range.
* The printing of named raw vectors is now formatted nicely as for
other such atomic vectors, thanks to Lukas Stadler.
R: update to 3.4.2
CHANGES IN R 3.4.2:
NEW FEATURES:
* Setting the LC_ALL category in Sys.setlocale() invalidates any
cached locale-specific day/month names and the AM/PM indicator
for strptime() (as setting LC_TIME has since R 3.1.0).
* The version of LAPACK included in the sources has been updated to
3.7.1, a bug-fix release.
* The default for tools::write_PACKAGES(rds_compress=) has been
changed to "xz" to match the compression used by CRAN.
* c() and unlist() are now more efficient in constructing the
names(.) of their return value, thanks to a proposal by Suharto
Anggono. (PR#17284)
CHANGES IN R 3.4.0:
SIGNIFICANT USER-VISIBLE CHANGES:
* (Unix-alike) The default methods for download.file() and url()
now choose "libcurl" except for file:// URLs. There will be
small changes in the format and wording of messages, including in
rare cases if an issue is a warning or an error. For example,
when HTTP re-direction occurs, some messages refer to the final
URL rather than the specified one.
Those who use proxies should check that their settings are
compatible (see ?download.file: the most commonly used forms work
for both "internal" and "libcurl").
* table() has been amended to be more internally consistent and
become back compatible to R <= 2.7.2 again. Consequently,
table(1:2, exclude = NULL) no longer contains a zero count for
<NA>, but useNA = "always" continues to do so.
* summary.default() no longer rounds, but its print method does
resulting in less extraneous rounding, notably of numbers in the
ten thousands.
* factor(x, exclude = L) behaves more rationally when x or L are
character vectors. Further, exclude = <factor> now behaves as
documented for long.
* Arithmetic, logic (&, |) and comparison (aka 'relational', e.g.,
<, ==) operations with arrays now behave consistently, notably
for arrays of length zero.
Arithmetic between length-1 arrays and longer non-arrays had
silently dropped the array attributes and recycled. This now
gives a warning and will signal an error in the future, as it has
always for logic and comparison operations in these cases (e.g.,
compare matrix(1,1) + 2:3 and matrix(1,1) < 2:3).
* The JIT ('Just In Time') byte-code compiler is now enabled by
default at its level 3. This means functions will be compiled on
first or second use and top-level loops will be compiled and then
run. (Thanks to Tomas Kalibera for extensive work to make this
possible.)
For now, the compiler will not compile code containing explicit
calls to browser(): this is to support single stepping from the
browser() call.
JIT compilation can be disabled for the rest of the session using
compiler::enableJIT(0) or by setting environment variable
R_ENABLE_JIT to 0.
* xtabs() works more consistently with NAs, also in its result no
longer setting them to 0. Further, a new logical option addNA
allows to count NAs where appropriate. Additionally, for the
case sparse = TRUE, the result's dimnames are identical to the
default case's.
* Matrix products now consistently bypass BLAS when the inputs have
NaN/Inf values. Performance of the check of inputs has been
improved. Performance when BLAS is used is improved for
matrix/vector and vector/matrix multiplication (DGEMV is now used
instead of DGEMM).
One can now choose from alternative matrix product
implementations _via_ options(matprod = ). The "internal"
implementation is not optimized for speed but consistent in
precision with other summations in R (using long double
accumulators where available). "blas" calls BLAS directly for
best speed, but usually with undefined behavior for inputs with
NaN/Inf.
NEW FEATURES:
* User errors such as integrate(f, 0:1, 2) are now caught.
* Add signature argument to debug(), debugonce(), undebug() and
isdebugged() for more conveniently debugging S3 and S4 methods.
(Based on a patch by Gabe Becker.)
* Add utils::debugcall() and utils::undebugcall() for debugging the
function that would be called by evaluating the given expression.
When the call is to an S4 generic or standard S3 generic,
debugcall() debugs the method that would be dispatched. A number
of internal utilities were added to support this, most notably
utils::isS3stdGeneric(). (Based on a patch by Gabe Becker.)
And many more - see the NEWS file for details.
R: pkgsrc changes PkgSrc changes: * On Darwin, use Aqua interface instead of X11 * Cairo support also requires Pango * Allow Cairo with other backends, not only X11 (e.g. to make it work on Darwin)
math/R: better fix for fbsd Also move fixes from configure to configure.ac m4/R.m4 fix by @joerg Oked @joerg
math/R: fix build on fbsd cpow and clog are not implemented on FreeBSD and the configure checks only emit warnings instead of errors. Ok@ markd
Revbump for boost update
Recursive revbump from boost update
Update to 3.3.3
Upstream changes:
CHANGES IN R 3.3.3
NEW FEATURES
Changes when redirection of a http:// URL to a https:// URL is encountered:
The internal methods of download.file() and url() now report that they cannot follow this (rather than failing silently).
(Unix-alike) download.file(method = "auto") (the default) re-tries with method = "libcurl".
(Unix-alike) url(method = "default") with an explicit open argument re-tries with method = "libcurl". This covers many of the usages, e.g. readLines() with a URL argument.
INSTALLATION on a UNIX-ALIKE
The configure check for the zlib version is now robust to versions longer than 5 characters, including 1.2.11.
UTILITIES
Environmental variable _R_CHECK_TESTS_NLINES_ controls how R CMD check reports failing tests (see §8 of the ‘R Internals’ manual).
DEPRECATED AND DEFUNCT
(C-level Native routine registration.) The undocumented styles field of the components of R_CMethodDef and R_FortranMethodDef is deprecated.
BUG FIXES
vapply(x, *) now works with long vectors x. (PR#17174)
isS3method("is.na.data.frame") and similar are correct now. (PR#17171)
grepRaw(<long>, <short>, fixed = TRUE) now works, thanks to a patch by Mikko Korpela. (PR#17132)
Package installation into a library where the package exists via symbolic link now should work wherever Sys.readlink() works, resolving PR#16725.
"Cincinnati" was missing an "n" in the precip dataset.
Fix buffer overflow vulnerability in pdf() when loading an encoding file. Reported by Talos (TALOS-2016-0227).
getDLLRegisteredRoutines() now produces its warning correctly when multiple DLLs match, thanks to Matt Dowle's PR#17184.
Sys.timezone() now returns non-NA also on platforms such as Ubuntu 14.04.5 LTS, thanks to Mikko Korpela's PR#17186.
format(x) for an illegal "POSIXlt" object x no longer segfaults.
methods(f) now also works for f "(" or "{".
(Windows only) dir.create() did not check the length of the path to create, and so could overflow a buffer and crash R. (PR#17206)
On some systems, very small hexadecimal numbers in hex notation would underflow to zero. (PR#17199)
pmin() and pmax() now work again for ordered factors and 0-length S3 classed objects, thanks to Suharto Anggono's PR#17195 and PR#17200.
bug.report() did not do any validity checking on a package's BugReports field. It now ignores an empty field, removes leading whitespace and only attempts to open http:// and https:// URLs, falling back to emailing the maintainer.
Bandwidth selectors bw.ucv() and bw.SJ() gave incorrect answers or incorrectly reported an error (because of integer overflow) for inputs longer than 46341. Similarly for bw.bcv() at length 5793.
Another possible integer overflow is checked and may result in an error report (rather than an incorrect result) for much longer inputs (millions for a smooth distribution).
findMethod() failed if the active signature had expanded beyond what a particular package used. (Example with packages XR and XRJulia on CRAN.)
qbeta() underflowed too early in some very asymmetric cases. (PR#17178)
R CMD Rd2pdf had problems with packages with non-ASCII titles in ‘.Rd’ files (usually the titles were omitted).
Revbump after boost update
Update to 3.3.2
Upstream changes:
CHANGES IN R 3.3.2:
NEW FEATURES:
* extSoftVersion() now reports the version (if any) of the readline
library in use.
* The version of LAPACK included in the sources has been updated to
3.6.1, a bug-fix release including a speedup for the
non-symmetric case of eigen().
* Use options(deparse.max.lines=) to limit the number of lines
recorded in .Traceback and other deparsing activities.
* format(<AsIs>) looks more regular, also for non-character atomic
matrices.
* abbreviate() gains an option named = TRUE.
* The online documentation for package methods is extensively
rewritten. The goals are to simplify documentation for basic
use, to note old features not recommended and to correct
out-of-date information.
* Calls to setMethod() no longer print a message when creating a
generic function in those cases where that is natural: S3
generics and primitives.
INSTALLATION and INCLUDED SOFTWARE:
* Versions of the readline library >= 6.3 had been changed so that
terminal window resizes were not signalled to readline: code has
been added using a explicit signal handler to work around that
(when R is compiled against readline >= 6.3). (PR#16604)
* configure works better with Oracle Developer Studio 12.5.
UTILITIES:
* R CMD check reports more dubious flags in files
src/Makevars[.in], including -w and -g.
* R CMD check has been set up to filter important warnings from
recent versions of gfortran with -Wall -pedantic: this now
reports non-portable GNU extensions such as out-of-order
declarations.
* R CMD config works better with paths containing spaces, even
those of home directories (as reported by Ken Beath).
DEPRECATED AND DEFUNCT:
* Use of the C/C++ macro NO_C_HEADERS is deprecated (no C headers
are included by R headers from C++ as from R 3.3.0, so it should
no longer be needed).
BUG FIXES:
* The check for non-portable flags in R CMD check could be stymied
by src/Makevars files which contained targets.
* (Windows only) When using certain desktop themes in Windows 7 or
higher, Alt-Tab could cause Rterm to stop accepting input.
(PR#14406; patch submitted by Jan Gleixner.)
* pretty(d, ..) behaves better for date-time d (PR#16923).
* When an S4 class name matches multiple classes in the S4 cache,
perform a dynamic search in order to obey namespace imports.
This should eliminate annoying messages about multiple hits in
the class cache. Also, pass along the package from the
ClassExtends object when looking up superclasses in the cache.
* sample(NA_real_) now works.
* Packages using non-ASCII encodings in their code did not install
data properly on systems using different encodings.
* merge(df1, df2) now also works for data frames with column names
"na.last", "decreasing", or "method". (PR#17119)
* contour() caused a segfault if the labels argument had length
zero. (Reported by Bill Dunlap.)
* unique(warnings()) works more correctly, thanks to a new
duplicated.warnings() method.
* findInterval(x, vec = numeric(), all.inside = TRUE) now returns
0s as documented. (Reported by Bill Dunlap.)
* (Windows only) R CMD SHLIB failed when a symbol in the resulting
library had the same name as a keyword in the .def file.
(PR#17130)
* pmax() and pmin() now work with (more ?) classed objects, such
as "Matrix" from the Matrix package, as documented for a long
time.
* axis(side, x = D) and hence Axis() and plot() now work correctly
for "Date" and time objects D, even when "time goes backward",
e.g., with decreasing xlim. (Reported by William May.)
* str(I(matrix(..))) now looks as always intended.
* plot.ts(), the plot() method for time series, now respects cex,
lwd and lty. (Reported by Greg Werbin.)
* parallel::mccollect() now returns a named list (as documented)
when called with wait = FALSE. (Reported by Michel Lang.)
* If a package added a class to a class union in another package,
loading the first package gave erroneous warnings about
"undefined subclass".
* c()'s argument use.names is documented now, as belonging to the
(C internal) default method. In "parallel", argument recursive
is also moved from the generic to the default method, such that
the formal argument list of base generic c() is just (...).
* rbeta(4, NA) and similarly rgamma() and rnbinom() now return
NaN's with a warning, as other r<dist>(), and as documented.
(PR#17155)
* Using options(checkPackageLicense = TRUE) no longer requires
acceptance of the licence for non-default standard packages such
as compiler. (Reported by Mikko Korpela.)
* split(<very_long>, *) now works even when the split off parts are
long. (PR#17139)
* min() and max() now also work correctly when the argument list
starts with character(0). (PR#17160)
* Subsetting very large matrices (prod(dim(.)) >= 2^31) now works
thanks to Michael Schubmehl's PR#17158.
* bartlett.test() used residual sums of squares instead of
variances, when the argument was a list of lm objects. (Reported
by Jens Ledet Jensen).
* plot(<lm>, which = *) now correctly labels the contour lines for
the standardized residuals for which = 6. It also takes the
correct p in case of singularities (also for which = 5).
(PR#17161)
* xtabs(~ exclude) no longer fails from wrong scope, thanks to
Suharto Anggono's PR#17147.
* Reference class calls to methods() did not re-analyse previously
defined methods, meaning that calls to methods defined later
would fail. (Reported by Charles Tilford).
* findInterval(x, vec, left.open = TRUE) misbehaved in some cases.
(Reported by Dmitriy Chernykh.)
Revbump post boost update
Override zlib 1.2.5 check in configure, it is not required. Unbreaks NetBSD 7.0 and earlier.
Update to 3.3.1
Upstream changes:
CHANGES IN R 3.3.1:
BUG FIXES:
* R CMD INSTALL and hence install.packages() gave an internal error
installing a package called description from a tarball on a
case-insensitive file system.
* match(x, t) (and hence x %in% t) failed when x was of length one,
and either character and x and t only differed in their Encoding
or when x and t where complex with NAs or NaNs. (PR#16885.)
* unloadNamespace(ns) also works again when ns is a 'namespace', as
from getNamespace().
* rgamma(1,Inf) or rgamma(1, 0,0) no longer give NaN but the
correct limit.
* length(baseenv()) is correct now.
* pretty(d, ..) for date-time d rarely failed when "halfmonth" time
steps were tried (PR#16923) and on 'inaccurate' platforms such as
32-bit windows or a configuration with --disable-long-double; see
comment #15 of PR#16761.
* In text.default(x, y, labels), the rarely(?) used default for
labels is now correct also for the case of a 2-column matrix x
and missing y.
* as.factor(c(a = 1L)) preserves names() again as in R < 3.1.0.
* strtrim(""[0], 0[0]) now works.
* Use of Ctrl-C to terminate a reverse incremental search started
by Ctrl-R in the readline-based Unix terminal interface is now
supported for readline >= 6.3 (Ctrl-G always worked). (PR#16603)
* diff(<difftime>) now keeps the "units" attribute, as subtraction
already did, PR#16940.
CHANGES IN R 3.3.0:
SIGNIFICANT USER-VISIBLE CHANGES:
* nchar(x, *)'s argument keepNA governing how the result for NAs in
x is determined, gets a new default keepNA = NA which returns NA
where x is NA, except for type = "width" which still returns 2,
the formatting / printing width of NA.
* All builds have support for https: URLs in the default methods
for download.file(), url() and code making use of them.
Unfortunately that cannot guarantee that any particular https:
URL can be accessed. For example, server and client have to
successfully negotiate a cryptographic protocol (TLS/SSL, ...)
and the server's identity has to be verifiable _via_ the
available certificates. Different access methods may allow
different protocols or use private certificate bundles: we
encountered a https: CRAN mirror which could be accessed by one
browser but not by another nor by download.file() on the same
Linux machine.
NEW FEATURES:
* The print method for methods() gains a byclass argument.
* New functions validEnc() and validUTF8() to give access to the
validity checks for inputs used by grep() and friends.
* Experimental new functionality for S3 method checking, notably
isS3method().
Also, the names of the R 'language elements' are exported as
character vector tools::langElts.
* str(x) now displays "Time-Series" also for matrix (multivariate)
time-series, i.e. when is.ts(x) is true.
* (Windows only) The GUI menu item to install local packages now
accepts *.tar.gz files as well as *.zip files (but defaults to
the latter).
* New programmeR's utility function chkDots().
* D() now signals an error when given invalid input, rather than
silently returning NA. (Request of John Nash.)
* formula objects are slightly more "first class": e.g., formula()
or new("formula", y ~ x) are now valid. Similarly, for "table",
"ordered" and "summary.table". Packages defining S4 classes with
the above S3/S4 classes as slots should be reinstalled.
* New function strrep() for repeating the elements of a character
vector.
* rapply() preserves attributes on the list when how = "replace".
* New S3 generic function sigma() with methods for extracting the
estimated standard deviation aka "residual standard deviation"
from a fitted model.
* news() now displays R and package news files within the HTML help
system if it is available. If no news file is found, a visible
NULL is returned to the console.
* as.raster(x) now also accepts raw arrays x assuming values in
0:255.
* Subscripting of matrix/array objects of type "expression" is now
supported.
* type.convert("i") now returns a factor instead of a complex value
with zero real part and missing imaginary part.
* Graphics devices cairo_pdf() and cairo_ps() now allow non-default
values of the cairographics 'fallback resolution' to be set.
This now defaults to 300 on all platforms: that is the default
documented by cairographics, but apparently was not used by all
system installations.
* file() gains an explicit method argument rather than implicitly
using getOption("url.method", "default").
* Thanks to a patch from Tomas Kalibera, x[x != 0] is now typically
faster than x[which(x != 0)] (in the case where x has no NAs, the
two are equivalent).
* read.table() now always uses the names for a named colClasses
argument (previously names were only used when colClasses was too
short). (In part, wish of PR#16478.)
* (Windows only) download.file() with default method = "auto" and a
ftps:// URL chooses "libcurl" if that is available.
* The out-of-the box Bioconductor mirror has been changed to one
using https://: use chooseBioCmirror() to choose a http:// mirror
if required.
* The data frame and formula methods for aggregate() gain a drop
argument.
* available.packages() gains a repos argument.
* The undocumented switching of methods for url() on https: and
ftps: URLs is confined to method = "default" (and documented).
* smoothScatter() gains a ret.selection argument.
* qr() no longer has a ... argument to pass additional arguments to
methods.
* [ has a method for class "table".
* It is now possible (again) to replayPlot() a display list
snapshot that was created by recordPlot() in a different R
session.
It is still not a good idea to use snapshots as a persistent
storage format for R plots, but it is now not completely silly to
use a snapshot as a format for transferring an R plot between two
R sessions.
The underlying changes mean that packages providing graphics
devices (e.g., Cairo, RSvgDevice, cairoDevice, tikzDevice) will
need to be reinstalled.
Code for restoring snapshots was contributed by Jeroen Ooms and
JJ Allaire.
Some testing code is available at <URL:
https://github.com/pmur002/R-display-list>.
* tools::undoc(dir = D) and codoc(dir = D) now also work when D is
a directory whose normalizePath()ed version does not end in the
package name, e.g. from a symlink.
* abbreviate() has more support for multi-byte character sets - it
no longer removes bytes within characters and knows about Latin
vowels with accents. It is still only really suitable for (most)
European languages, and still warns on non-ASCII input.
abbreviate(use.classes = FALSE) is now implemented, and that is
more suitable for non-European languages.
* match(x, table) is faster (sometimes by an order of magnitude)
when x is of length one and incomparables is unchanged, thanks to
Peter Haverty (PR#16491).
* More consistent, partly not back-compatible behavior of NA and
NaN coercion to complex numbers, operations less often resulting
in complex NA (NA_complex_).
* lengths() considers methods for length and [[ on x, so it should
work automatically on any objects for which appropriate methods
on those generics are defined.
* The logic for selecting the default screen device on OS X has
been simplified: it is now quartz() if that is available even if
environment variable DISPLAY has been set by the user.
The choice can easily be overridden _via_ environment variable
R_INTERACTIVE_DEVICE.
* On Unix-like platforms which support the getline C library
function, system(*,intern = TRUE) no longer truncates (output)
lines longer than 8192 characters, thanks to Karl Millar.
(PR#16544)
* rank() gains a ties.method = "last" option, for convenience (and
symmetry).
* regmatches(invert = NA) can now be used to extract both
non-matched and matched substrings.
* data.frame() gains argument fix.empty.names; as.data.frame.list()
gets new cut.names, col.names and fix.empty.names.
* plot(x ~ x, *) now warns that it is the same as plot(x ~ 1, *).
* recordPlot() has new arguments load and attach to allow package
names to be stored as part of a recorded plot. replayPlot() has
new argument reloadPkgs to load/attach any package names that
were stored as part of a recorded plot.
* S4 dispatch works within calls to .Internal(). This means
explicit S4 generics are no longer needed for unlist() and
as.vector().
* Only font family names starting with "Hershey" (and not "Her" as
before) are given special treatment by the graphics engine.
* S4 values are automatically coerced to vector (via as.vector)
when subassigned into atomic vectors.
* findInterval() gets a left.open option.
* The version of LAPACK included in the sources has been updated to
3.6.0, including those 'deprecated' routines which were
previously included. _Ca_ 40 double-complex routines have been
added at the request of a package maintainer.
As before, the details of what is included are in
src/modules/lapack/README and this now gives information on
earlier additions.
* tapply() has been made considerably more efficient without
changing functionality, thanks to proposals from Peter Haverty
and Suharto Anggono. (PR#16640)
* match.arg(arg) (the one-argument case) is faster; so is
sort.int(). (PR#16640)
* The format method for object_size objects now also accepts
"binary" units such as "KiB" and e.g., "Tb". (Partly from
PR#16649.)
* Profiling now records calls of the form foo::bar and some similar
cases directly rather than as calls to <Anonymous>. Contributed
by Winston Chang.
* New string utilities startsWith(x, prefix) and endsWith(x,
suffix). Also provide speedups for some grepl("^...",*) uses
(related to proposals in PR#16490).
* Reference class finalizers run at exit, as well as on garbage
collection.
* Avoid parallel dependency on stats for port choice and random
number seeds. (PR#16668)
* The radix sort algorithm and implementation from data.table
(forder) replaces the previous radix (counting) sort and adds a
new method for order(). Contributed by Matt Dowle and Arun
Srinivasan, the new algorithm supports logical, integer (even
with large values), real, and character vectors. It outperforms
all other methods, but there are some caveats (see ?sort).
* The order() function gains a method argument for choosing between
"shell" and "radix".
* New function grouping() returns a permutation that stably
rearranges data so that identical values are adjacent. The
return value includes extra partitioning information on the
groups. The implementation came included with the new radix
sort.
* rhyper(nn, m, n, k) no longer returns NA when one of the three
parameters exceeds the maximal integer.
* switch() now warns when no alternatives are provided.
* parallel::detectCores() now has default logical = TRUE on all
platforms - as this was the default on Windows, this change only
affects Sparc Solaris.
Option logical = FALSE is now supported on Linux and recent
versions of OS X (for the latter, thanks to a suggestion of Kyaw
Sint).
* hist() for "Date" or "POSIXt" objects would sometimes give
misleading labels on the breaks, as they were set to the day
before the start of the period being displayed. The display
format has been changed, and the shift of the start day has been
made conditional on right = TRUE (the default). (PR#16679)
* R now uses a new version of the logo (donated to the R Foundation
by RStudio). It is defined in .svg format, so will resize
without unnecessary degradation when displayed on HTML
pages-there is also a vector PDF version. Thanks to Dirk
Eddelbuettel for producing the corresponding X11 icon.
* New function .traceback() returns the stack trace which
traceback() prints.
* lengths() dispatches internally.
* dotchart() gains a pt.cex argument to control the size of points
separately from the size of plot labels. Thanks to Michael
Friendly and Milan Bouchet-Valat for ideas and patches.
* as.roman(ch) now correctly deals with more diverse character
vectors ch; also arithmetic with the resulting roman numbers
works in more cases. (PR#16779)
* prcomp() gains a new option rank. allowing to directly aim for
less than min(n,p) PC's. The summary() and its print() method
have been amended, notably for this case.
* gzcon() gains a new option text, which marks the connection as
text-oriented (so e.g. pushBack() works). It is still always
opened in binary mode.
* The import() namespace directive now accepts an argument except
which names symbols to exclude from the imports. The except
expression should evaluate to a character vector (after
substituting symbols for strings). See Writing R Extensions.
* New convenience function Rcmd() in package tools for invoking R
CMD tools from within R.
* New functions makevars_user() and makevars_site() in package
tools to determine the location of the user and site specific
Makevars files for customizing package compilation.
UTILITIES:
* R CMD check has a new option --ignore-vignettes for use with
non-Sweave vignettes whose VignetteBuilder package is not
available.
* R CMD check now by default checks code usage (_via_ codetools)
with only the base package attached. Functions from default
packages other than base which are used in the package code but
not imported are reported as undefined globals, with a suggested
addition to the NAMESPACE file.
* R CMD check --as-cran now also checks DOIs in package CITATION
and Rd files.
* R CMD Rdconv and R CMD Rd2pdf each have a new option
--RdMacros=pkglist which allows Rd macros to be specified before
processing.
DEPRECATED AND DEFUNCT:
* The previously included versions of zlib, bzip2, xz and PCRE have
been removed, so suitable external (usually system) versions are
required (see the 'R Installation and Administration' manual).
* The unexported and undocumented Windows-only devices cairo_bmp(),
cairo_png() and cairo_tiff() have been removed. (These devices
should be used as e.g. bmp(type = "cairo").)
* (Windows only) Function setInternet2() has no effect and will be
removed in due course. The choice between methods "internal" and
"wininet" is now made by the method arguments of url() and
download.file() and their defaults can be set _via_ options. The
out-of-the-box default remains "wininet" (as it has been since R
3.2.2).
* [<- with an S4 value into a list currently embeds the S4 object
into its own list such that the end result is roughly equivalent
to using [[<-. That behavior is deprecated. In the future, the
S4 value will be coerced to a list with as.list().
* Package tools' functions package.dependencies(), pkgDepends(),
etc are deprecated now, mostly in favor of package_dependencies()
which is both more flexible and efficient.
INSTALLATION and INCLUDED SOFTWARE:
* Support for very old versions of valgrind (e.g., 3.3.0) has been
removed.
* The included libtool script (generated by configure) has been
updated to version 2.4.6 (from 2.2.6a).
* libcurl version 7.28.0 or later with support for the https
protocol is required for installation (except on Windows).
* BSD networking is now required (except on Windows) and so
capabilities("http/ftp") is always true.
* configure uses pkg-config for PNG, TIFF and JPEG where this is
available. This should work better with multiple installs and
with those using static libraries.
* The minimum supported version of OS X is 10.6 ('Snow Leopard'):
even that has been unsupported by Apple since 2012.
* The configure default on OS X is --disable-R-framework: enable
this if you intend to install under /Library/Frameworks and use
with R.app.
* The minimum preferred version of PCRE has since R 3.0.0 been 8.32
(released in Nov 2012). Versions 8.10 to 8.31 are now deprecated
(with warnings from configure), but will still be accepted until
R 3.4.0.
* configure looks for C functions __cospi, __sinpi and __tanpi and
uses these if cospi _etc_ are not found. (OS X is the main
instance.)
* (Windows) R is now built using gcc 4.9.3. This build will
require recompilation of at least those packages that include C++
code, and possibly others. A build of R-devel using the older
toolchain will be temporarily available for comparison purposes.
During the transition, the environment variable R_COMPILED_BY has
been defined to indicate which toolchain was used to compile R
(and hence, which should be used to compile code in packages).
The COMPILED_BY variable described below will be a permanent
replacement for this.
* (Windows) A make and R CMD config variable named COMPILED_BY has
been added. This indicates which toolchain was used to compile R
(and hence, which should be used to compile code in packages).
PACKAGE INSTALLATION:
* The make macro AWK which used to be made available to files such
as src/Makefile is no longer set.
C-LEVEL FACILITIES:
* The API call logspace_sum introduced in R 3.2.0 is now remapped
as an entry point to Rf_logspace_sum, and its first argument has
gained a const qualifier. (PR#16470)
Code using it will need to be reinstalled.
Similarly, entry point log1pexp also defined in Rmath.h is
remapped there to Rf_log1pexp
* R_GE_version has been increased to 11.
* New API call R_orderVector1, a faster one-argument version of
R_orderVector.
* When R headers such as R.h and Rmath.h are called from C++ code
in packages they include the C++ versions of system headers such
as <cmath> rather than the legacy headers such as <math.h>.
(Headers Rinternals.h and Rinterface.h already did, and inclusion
of system headers can still be circumvented by defining
NO_C_HEADERS, including as from this version for those two
headers.)
The manual has long said that R headers should *not* be included
within an extern "C" block, and almost all the packages affected
by this change were doing so.
* Including header S.h from C++ code would fail on some platforms,
and so gives a compilation error on all.
* The deprecated header Rdefines.h is now compatible with defining
R_NO_REMAP.
* The connections API now includes a function R_GetConnection()
which allows packages implementing connections to convert R
connection objects to Rconnection handles used in the API. Code
which previously used the low-level R-internal getConnection()
entry point should switch to the official API.
BUG FIXES:
* C-level asChar(x) is fixed for when x is not a vector, and it
returns "TRUE"/"FALSE" instead of "T"/"F" for logical vectors.
* The first arguments of .colSums() etc (with an initial dot) are
now named x rather than X (matching colSums()): thus error
messages are corrected.
* A coef() method for class "maov" has been added to allow vcov()
to work with multivariate results. (PR#16380)
* method = "libcurl" connections signal errors rather than
retrieving HTTP error pages (where the ISP reports the error).
* xpdrows.data.frame() was not checking for unique row names; in
particular, this affected assignment to non-existing rows via
numerical indexing. (PR#16570)
* tail.matrix() did not work for zero rows matrices, and could
produce row "labels" such as "[1e+05,]".
* Data frames with a column named "stringsAsFactors" now format and
print correctly. (PR#16580)
* cor() is now guaranteed to return a value with absolute value
less than or equal to 1. (PR#16638)
* Array subsetting now keeps names(dim(.)).
* Blocking socket connection selection recovers more gracefully on
signal interrupts.
* The data.frame method of rbind() construction row.names works
better in borderline integer cases, but may change the names
assigned. (PR#16666)
* (X11 only) getGraphicsEvent() miscoded buttons and missed mouse
motion events. (PR#16700)
* methods(round) now also lists round.POSIXt.
* tar() now works with the default files = NULL. (PR#16716)
* Jumps to outer contexts, for example in error recovery, now make
intermediate jumps to contexts where on.exit() actions are
established instead of trying to run all on.exit() actions before
jumping to the final target. This unwinds the stack gradually,
releases resources held on the stack, and significantly reduces
the chance of a segfault when running out of C stack space. Error
handlers established using withCallingHandlers() and
options("error") specifications are ignored when handling a C
stack overflow error as attempting one of these would trigger a
cascade of C stack overflow errors. (These changes resolve
PR#16753.)
* The spacing could be wrong when printing a complex array.
(Report and patch by Lukas Stadler.)
* pretty(d, n, min.n, *) for date-time objects d works again in
border cases with large min.n, returns a labels attribute also
for small-range dates and in such cases its returned length is
closer to the desired n. (PR#16761) Additionally, it finally
does cover the range of d, as it always claimed.
* tsp(x) <- NULL did not handle correctly objects inheriting from
both "ts" and "mts". (PR#16769)
* install.packages() could give false errors when
options("pkgType") was "binary". (Reported by Jose Claudio
Faria.)
* A bug fix in R 3.0.2 fixed problems with locator() in X11, but
introduced problems in Windows. Now both should be fixed.
(PR#15700)
* download.file() with method = "wininet" incorrectly warned of
download file length difference when reported length was unknown.
(PR#16805)
* diag(NULL, 1) crashed because of missed type checking.
(PR#16853)
Bump PKGREVISION for perl-5.24.0 for everything mentioning perl.
Update to R 3.2.4
3.2.4
NEW FEATURES
install.packages() and related functions now give a more informative
warning when an attempt is made to install a base package.
summary(x) now prints with less rounding when x contains infinite values.
provideDimnames() gets an optional unique argument.
shQuote() gains type = "cmd2" for quoting in cmd.exe in Windows.
The data.frame method of rbind() gains an optional argument stringsAsFactors
(instead of only depending on getOption("stringsAsFactors")).
smooth(x, *) now also works for long vectors.
tools::texi2dvi() has a workaround for problems with the texi2dvi script
supplied by texinfo 6.1.
It extracts more error messages from the LaTeX logs when in emulation mode.
DEPRECATED AND DEFUNCT
Use of SUPPORT_OPENMP from header ‘Rconfig.h’ is deprecated in favour of
the standard OpenMP define _OPENMP.
(This has been the recommendation in the manual for a while now.)
The make macro AWK which is long unused by R itself but recorded in file
‘etc/Makeconf’ is deprecated and will be removed in R 3.3.0.
The C header file ‘S.h’ is no longer documented: its use should be
replaced by ‘R.h’.
3.2.3
NEW FEATURES
Some recently-added Windows time zone names have been added to the
conversion table used to convert these to Olson names. (Including
those relating to changes for Russia in Oct 2014, as in PR#16503.)
(Windows) Compatibility information has been added to the manifests
for ‘Rgui.exe’, ‘Rterm.exe’ and ‘Rscript.exe’. This should allow
win.version() and Sys.info() to report the actual Windows version up
to Windows 10.
Windows "wininet" FTP first tries EPSV / PASV mode rather than only
using active mode (reported by Dan Tenenbaum).
which.min(x) and which.max(x) may be much faster for logical and integer
x and now also work for long vectors.
The ‘emulation’ part of tools::texi2dvi() has been somewhat enhanced,
including supporting quiet = TRUE. It can be selected by texi2dvi =
"emulation".
(Windows) MiKTeX removed its texi2dvi.exe command in Sept 2015:
tools::texi2dvi() tries texify.exe if it is not found.
(Windows only) Shortcuts for printing and saving have been added to
menus in Rgui.exe.
loess(..., iterTrace=TRUE) now provides diagnostics for robustness
iterations, and the print() method for summary(<loess>) shows slightly
more.
The included version of PCRE has been updated to 8.38, a bug-fix release.
View() now displays nested data frames in a more friendly way.
Use OPSYSVARS.
Fix more library install names on Darwin.
Use install_name_tool to fix up Darwin library names. Fixes check-shlib.
Update to 3.2.2
Upstream changes:
CHANGES IN R 3.2.2:
SIGNIFICANT USER-VISIBLE CHANGES:
* It is now easier to use secure downloads from https:// URLs on
builds which support them: no longer do non-default options need
to be selected to do so. In particular, packages can be
installed from repositories which offer https:// URLs, and those
listed by setRepositories() now do so (for some of their
mirrors).
Support for https:// URLs is available on Windows, and on other
platforms if support for libcurl was compiled in and if that
supports the https protocol (system installations can be expected
to do). So https:// support can be expected except on rather old
OSes (an example being OS X 'Snow Leopard', where a non-system
version of libcurl can be used).
(Windows only) The default method for accessing URLs _via_
download.file() and url() has been changed to be "wininet" using
Windows API calls. This changes the way proxies need to be set
and security settings made: there have been some reports of sites
being inaccessible under the new default method (but the previous
methods remain available).
NEW FEATURES:
* cmdscale() gets new option list. for increased flexibility when a
list should be returned.
* configure now supports texinfo version 6.0, which (unlike the
change from 4.x to 5.0) is a minor update. (Wish of PR#16456.)
* (Non-Windows only) download.file() with default method = "auto"
now chooses "libcurl" if that is available and a https:// or
ftps:// URL is used.
* (Windows only) setInternet2(TRUE) is now the default. The
command-line option --internet2 and environment variable
R_WIN_INTERNET2 are now ignored.
Thus by default the "internal" method for download.file() and
url() uses the "wininet" method: to revert to the previous
default use setInternet2(FALSE).
This means that https:// can be read by default by
download.file() (they have been readable by file() and url()
since R 3.2.0).
There are implications for how proxies need to be set (see
?download.file): also, cacheOK = FALSE is not supported.
* chooseCRANmirror() and chooseBioCmirror() now offer HTTPS mirrors
in preference to HTTP mirrors. This changes the interpretation
of their ind arguments: see their help pages.
* capture.output() gets optional arguments type and split to pass
to sink(), and hence can be used to capture messages.
C-LEVEL FACILITIES:
* Header Rconfig.h now defines HAVE_ALLOCA_H if the platform has
the alloca.h header (it is needed to define alloca on Solaris and
AIX, at least: see 'Writing R Extensions' for how to use it).
INSTALLATION and INCLUDED SOFTWARE:
* The libtool script generated by configure has been modified to
support FreeBSD >= 10 (PR#16410).
BUG FIXES:
* The HTML help page links to demo code failed due to a change in R
3.2.0. (PR#16432)
* If the na.action argument was used in model.frame(), the original
data could be modified. (PR#16436)
* getGraphicsEvent() could cause a crash if a graphics window was
closed while it was in use. (PR#16438)
* matrix(x, nr, nc, byrow = TRUE) failed if x was an object of type
"expression".
* strptime() could overflow the allocated storage on the C stack
when the timezone had a non-standard format much longer than the
standard formats. (Part of PR#16328.)
* options(OutDec = s) now signals a warning (which will become an
error in the future) when s is not a string with exactly one
character, as that has been a documented requirement.
* prettyNum() gains a new option input.d.mark which together with
other changes, e.g., the default for decimal.mark, fixes some
format()ting variants with non-default getOption("OutDec") such
as in PR#16411.
* download.packages() failed for type equal to either "both" or
"binary". (Reported by Dan Tenenbaum.)
* The dendrogram method of labels() is much more efficient for
large dendrograms, now using rapply(). (Comment #15 of PR#15215)
* The "port" algorithm of nls() could give spurious errors.
(Reported by Radford Neal.)
* Reference classes that inherited from reference classes in
another package could invalidate methods of the inherited class.
Fixing this requires adding the ability for methods to be
"external", with the object supplied explicitly as the first
argument, named .self. See "Inter-Package Superclasses" in the
documentation.
* readBin() could fail on the SPARC architecture due to alignment
issues. (Reported by Radford Neal.)
* qt(*, df=Inf, ncp=.) now uses the natural qnorm() limit instead
of returning NaN. (PR#16475)
* Auto-printing of S3 and S4 values now searches for print() in the
base namespace and show() in the methods namespace instead of
searching the global environment.
* polym() gains a coefs = NULL argument and returns class "poly"
just like poly() which gets a new simple=FALSE option. They now
lead to correct predict()ions, e.g., on subsets of the original
data.
* rhyper(nn, <large>) now works correctly. (PR#16489)
* ttkimage() did not (and could not) work so was removed. Ditto for
tkimage.cget() and tkimage.configure(). Added two Ttk widgets and
missing subcommands for Tk's image command: ttkscale(),
ttkspinbox(), tkimage.delete(), tkimage.height(),
tkimage.inuse(), tkimage.type(), tkimage.types(),
tkimage.width(). (PR#15372, PR#16450)
* getClass("foo") now also returns a class definition when it is
found in the cache more than once.
Update to 3.2.1
Upstream changes:
CHANGES IN R 3.2.1
NEW FEATURES
utf8ToInt() now checks that its input is valid UTF-8 and returns NA if it is not.
install.packages() now allows type = "both" with repos = NULL if it can infer the type of file.
nchar(x, *) and nzchar(x) gain a new argument keepNA which governs how the result for NAs in x is determined. For the R 3.2.x series, the default remains FALSE which is fully back compatible. From R 3.3.0, the default will change to keepNA = NA and you are advised to consider this for code portability.
news() more flexibly extracts dates from package ‘NEWS.Rd’ files.
lengths(x) now also works (trivially) for atomic x and hence can be used more generally as an efficient replacement of sapply(x, length) and similar.
The included version of PCRE has been updated to 8.37, a bug-fix release.
diag() no longer duplicates a matrix when extracting its diagonal.
as.character.srcref() gains an argument to allow characters corresponding to a range of source references to be extracted.
BUG FIXES
acf() and ccf() now guarantee values strictly in [-1,1] (instead of sometimes very slightly outside). PR#15832.
as.integer("111111111111") now gives NA (with a warning) as it does for the corresponding numeric or negative number coercions. Further, as.integer(M + 0.1) now gives M (instead of NA) when M is the maximal representable integer.
On some platforms nchar(x, "c") and nchar(x, "w") would return values (possibly NA) for inputs which were declared to be UTF-8 but were not, or for invalid strings without a marked encoding in a multi-byte locale, rather than give an error. Additional checks have been added to mitigate this.
apply(a, M, function(u) c(X = ., Y = .)) again has dimnames containing "X" and "Y" (as in R < 3.2.0).
(Windows only) In some cases, the --clean option to R CMD INSTALL could fail. (PR#16178)
(Windows only) choose.files() would occasionally include characters from the result of an earlier call in the result of a later one. (PR#16270)
A change in RSiteSearch() in R 3.2.0 caused it to submit invalid URLs. (PR#16329)
Rscript and command line R silently ignored incomplete statements at the end of a script; now they are reported as parse errors. (PR#16350)
Parse data for very long strings was not stored. (PR#16354)
plotNode(), the workhorse of the plot method for "dendrogram"s is no longer recursive, thanks to Suharto Anggono, and hence also works for deeply nested dendrograms. (PR#15215)
The parser could overflow internally when given numbers in scientific format with extremely large exponents. (PR#16358)
If the CRAN mirror was not set, install.packages(type = "both") and related functions could repeatedly query the user for it. (Part of PR#16362)
The low-level functions .rowSums() etc. did not check the length of their argument, so could segfault. (PR#16367)
The quietly argument of library() is now correctly propagated from .getRequiredPackages2().
Under some circumstances using the internal PCRE when building R fron source would cause external libs such as -llzma to be omitted from the main link.
The .Primitive default methods of the logic operators, i.e., !, & and |, now give correct error messages when appropriate, e.g., for `&`(TRUE) or `!`(). (PR#16385)
cummax(x) now correctly propagates NAs also when x is of type integer and begins with an NA.
summaryRprof() could fail when the profile contained only two records. (PR#16395)
HTML vignettes opened using vignette() did not support links into the rest of the HTML help system. (Links worked properly when the vignette was opened using browseVignettes() or from within the help system.)
arima(*, xreg = .) (for d >= 1) computes estimated variances based on a the number of effective observations as in R version 3.0.1 and earlier. (PR#16278)
slotNames(.) is now correct for "signature" objects (mostly used internally in methods).
On some systems, the first string comparison after a locale change would result in NA.
Fix symbol visibility.
Update the fixwrap substitution to work correctly after the recent libtool changes. Fixes CHECK_WRKREF builds.
Recursive PKGREVISION bump for all packages mentioning 'perl', having a PKGNAME of p5-*, or depending such a package, for perl-5.22.0.
Bump PKGREVISION. * Fix build under NetBSD 6.1.5. Newer texinfo is required. From wen@.
Update to 3.2.0
Changelog:
CHANGES IN 3.2.0:
NEW FEATURES:
* anyNA() gains a recursive argument.
* When x is missing and names is not false (including the default
value), Sys.getenv(x, names) returns an object of class "Dlist"
and hence prints tidily.
* (Windows.) shell() no longer consults the environment variable
SHELL: too many systems have been encountered where it was set
incorrectly (usually to a path where software was compiled, not
where it was installed). R_SHELL, the preferred way to select a
non-default shell, can be used instead.
* Some unusual arguments to embedFonts() can now be specified as
character vectors, and the defaults have been changed
accordingly.
* Functions in the Summary group duplicate less. (PR#15798)
* (Unix-alikes.) system(cmd, input = ) now uses
'shell-execution-environment' redirection, which will be more
natural if cmd is not a single command (but requires a
POSIX-compliant shell). (Wish of PR#15508)
* read.fwf() and read.DIF() gain a fileEncoding argument, for
convenience.
* Graphics devices can add attributes to their description in
.Device and .Devices. Several of those included with R use a
"filepath" attribute.
* pmatch() uses hashing in more cases and so is faster at the
expense of using more memory. (PR#15697)
* pairs() gains new arguments to select sets of variables to be
plotted against each other.
* file.info(, extra_cols = FALSE) allows a minimal set of columns
to be computed on Unix-alikes: on some systems without
properly-configured caching this can be significantly faster with
large file lists.
* New function dir.exists() in package base to test efficiently
whether one or more paths exist and are directories.
* dput() and friends gain new controls hexNumeric and digits17
which output double and complex quantities as, respectively,
binary fractions (exactly, see sprintf("%a")) and as decimals
with up to 17 significant digits.
* save(), saveRDS() and serialize() now support ascii = NA which
writes ASCII files using sprintf("%a") for double/complex
quantities. This is read-compatible with ascii = TRUE but avoids
binary->decimal->binary conversions with potential loss of
precision. Unfortunately the Windows C runtime's lack of C99
compliance means that the format cannot be read correctly there
in R before 3.1.2.
* The default for formatC(decimal.mark =) has been changed to be
getOption("OutDec"); this makes it more consistent with format()
and suitable for use in print methods, e.g. those for classes
"density", "ecdf", "stepfun" and "summary.lm".
getOption("OutDec") is now consulted by the print method for
class "kmeans", by cut(), dendrogram(), plot.ts() and quantile()
when constructing labels and for the report from legend(trace =
TRUE).
(In part, wish of PR#15819.)
* printNum() and hence format() and formatC() give a warning if
big.mark and decimal.mark are set to the same value (period and
comma are not uncommonly used for each, and this is a check that
conventions have not got mixed).
* merge() can create a result which uses long vectors on 64-bit
platforms.
* dget() gains a new argument keep.source which defaults to FALSE
for speed (dput() and dget() are most often used for data objects
where this can make dget() many times faster).
* Packages may now use a file of common macro definitions in their
help files, and may import definitions from other packages.
* A number of macros have been added in the new share/Rd directory
for use in package overview help pages, and promptPackage() now
makes use of them.
* tools::parse_Rd() gains a new permissive argument which converts
unrecognized macros into text. This is used by
utils:::format.bibentry to allow LaTeX markup to be ignored.
* options(OutDec =) can now specify a multi-byte character, e.g.,
options(OutDec = "\u00b7") in a UTF-8 locale.
* is.recursive(x) is no longer true when x is an external pointer,
a weak reference or byte code; the first enables all.equal(x, x)
when x <- getClass(.).
* ls() (aka objects()) and as.list.environment() gain a new
argument sorted.
* The "source" attribute (which has not been added to functions by
R since before R version 2.14.0) is no longer treated as special.
* Function returnValue() has been added to give on.exit() code
access to a function's return value for debugging purposes.
* crossprod(x, y) allows more matrix coercions when x or y are
vectors, now equalling t(x) %*% y in these cases (also reported
by Radford Neal). Similarly, tcrossprod(x,y) and %*% work in
more cases with vector arguments.
* Utility function dynGet() useful for detecting cycles, aka
infinite recursions.
* The byte-code compiler and interpreter include new instructions
that allow many scalar subsetting and assignment and scalar
arithmetic operations to be handled more efficiently. This can
result in significant performance improvements in scalar
numerical code.
* apply(m, 2, identity) is now the same as the matrix m when it has
_named_ row names.
* A new function debuggingState() has been added, allowing to
temporarily turn off debugging.
* example() gets a new optional argument run.donttest and
tools::Rd2ex() a corresponding commentDonttest, with a default
such that example(..) in help examples will run \donttest code
only if used interactively (a change in behaviour).
* rbind.data.frame() gains an optional argument make.row.names, for
potential speedup.
* New function extSoftVersion() to report on the versions of
third-party software in use in this session. Currently reports
versions of zlib, bzlib, the liblzma from xz, PCRE, ICU, TRE and
the iconv implementation.
A similar function grSoftVersion() in package grDevices reports
on third-party graphics software.
Function tcltk::tclVersion() reports the Tcl/Tk version.
* Calling callGeneric() without arguments now works with primitive
generics to some extent.
* vapply(x, FUN, FUN.VALUE) is more efficient notably for large
length(FUN.VALUE); as extension of PR#16061.
* as.table() now allows tables with one or more dimensions of
length 0 (such as as.table(integer())).
* names(x) <- NULL now clears the names of call and ... objects.
* library() will report a warning when an insufficient dependency
version is masking a sufficient one later on the library search
path.
* A new plot() method for class "raster" has been added.
* New check_packages_in_dir_changes() function in package tools for
conveniently analyzing how changing sources impacts the check
results of their reverse dependencies.
* Speed-up from Peter Haverty for ls() and
methods:::.requirePackage() speeding up package loading.
(PR#16133)
* New get0() function, combining exists() and get() in one call,
for efficiency.
* match.call() gains an envir argument for specifying the
environment from which to retrieve the ... in the call, if any;
this environment was wrong (or at least undesirable) when the
definition argument was a function.
* topenv() has been made .Internal() for speedup, based on Peter
Haverty's proposal in PR#16140.
* getOption() no longer calls options() in the main case.
* Optional use of libcurl (version 7.28.0 from Oct 2012 or later)
for Internet access:
* capabilities("libcurl") reports if this is available.
* libcurlVersion() reports the version in use, and other
details of the "libcurl" build including which URL schemes it
supports.
* curlGetHeaders() retrieves the headers for http://, https://,
ftp:// and ftps:// URLs: analysis of these headers can
provide insights into the `existence' of a URL (it might for
example be permanently redirected) and is so used in R CMD
check --as-cran.
* download.file() has a new optional method "libcurl" which
will handle more URL schemes, follow redirections, and allows
simultaneous downloads of multiple URLs.
* url() has a new method "libcurl" which handles more URL
schemes and follows redirections. The default method is
controlled by a new option url.method, which applies also to
the opening of URLs _via_ file() (which happens implicitly in
functions such as read.table.)
* When file() or url() is invoked with a https:// or ftps://
URL which the current method cannot handle, it switches to a
suitable method if one is available.
* (Windows.) The DLLs internet.dll and internet2.dll have been
merged. In this version it is safe to switch (repeatedly)
between the internal and Windows internet functions within an R
session.
The Windows internet functions are still selected by flag
--internet2 or setInternet2(). This can be overridden for an
url() connection _via_ its new method argument.
download.file() has new method "wininet", selected as the default
by --internet2 or setInternet2().
* parent.env<- can no longer modify the parent of a locked
namespace or namespace imports environment. Contributed by Karl
Millar.
* New function isLoadedNamespace() for readability and speed.
* names(env) now returns all the object names of an environment
env, equivalently to ls(env, all.names = TRUE, sorted = FALSE)
and also to the names of the corresponding list,
names(as.list(env, all.names = TRUE)). Note that although
names() returns a character vector, the names have no particular
ordering.
* The memory manager now grows the heap more aggressively. This
reduces the number of garbage collections, in particular while
data or code are loaded, at the expense of slightly increasing
the memory footprint.
* New function trimws() for removing leading/trailing whitespace.
* cbind() and rbind() now consider S4 inheritance during S3
dispatch and also obey deparse.level.
* cbind() and rbind() will delegate recursively to methods::cbind2
(methods::rbind2) when at least one argument is an S4 object and
S3 dispatch fails (due to ambiguity).
* (Windows.) download.file(quiet = FALSE) now uses text rather
than Windows progress bars in non-interactive use.
* New function hsearch_db() in package utils for building and
retrieving the help search database used by help.search(), along
with functions for inspecting the concepts and keywords in the
help search database.
* New function .getNamespaceInfo(), a no-check version of
getNamespaceInfo() mostly for internal speedups.
* The help search system now takes \keyword entries in Rd files
which are not standard keywords (as given in KEYWORDS in the R
documentation directory) as concepts. For standard keyword
entries the corresponding descriptions are additionally taken as
concepts.
* New lengths() function for getting the lengths of all elements in
a list.
* New function toTitleCase() in package tools, tailored to package
titles.
* The matrix methods of cbind() and rbind() allow matrices as
inputs which have 2^31 or more elements. (For cbind(), wish of
PR#16198.)
* The default method of image() has an explicit check for a numeric
or logical matrix (which was always required).
* URLencode() will not by default encode further URLs which appear
to be already encoded.
* BIC(mod) and BIC(mod, mod2) now give non-NA numbers for arima()
fitted models, as nobs(mod) now gives the number of "used"
observations for such models. This fixes PR#16198, quite
differently than proposed there.
* The print() methods for "htest", "pairwise.htest" and
"power.htest" objects now have a digits argument defaulting to (a
function of) getOption("digits"), and influencing all printed
numbers coherently. Unavoidably, this changes the display of
such test results in some cases.
* Code completion for namespaces now recognizes all loaded
namespaces, rather than only the ones that are also attached.
* The code completion mechanism can now be replaced by a
user-specified completer function, for (temporary) situations
where the usual code completion is inappropriate.
* unzip() will now warn if it is able to detect truncation when
unpacking a file of 4GB or more (related to PR#16243).
* methods() reports S4 in addition to S3 methods; output is
simplified when the class argument is used. .S3methods() and
methods::.S4methods() report S3 and S4 methods separately.
* Higher order functions such as the apply functions and Reduce()
now force arguments to the functions they apply in order to
eliminate undesirable interactions between lazy evaluation and
variable capture in closures. This resolves PR#16093.
INSTALLATION and INCLUDED SOFTWARE:
* The \donttest sections of R's help files can be tested by
make check TEST_DONTTEST=TRUE .
* It is possible to request the use of system valgrind headers
_via_ configure option --with-system-valgrind-headers: note the
possible future incompatibility of such headers discussed in the
'R Installation and Administration' manual. (Wish of PR#16068.)
* The included version of liblzma has been updated to xz-utils
5.0.7 (minor bug fixes from 5.0.5).
* configure options --with-system-zlib, --with-system-bzlib and
--with-system-pcre are now the default. For the time being there
is fallback to the versions included in the R sources if no
system versions are found or (unlikely) if they are too old.
Linux users should check that the -devel or -dev versions of
packages zlib, bzip2/libbz2 and pcre as well as
xz-devel/liblzma-dev (or similar names) are installed.
* configure by default looks for the texi2any script from texinfo
5.1 or later, rather than the makeinfo program. (makeinfo is a
link to the Perl script texi2any in texinfo 5.x.)
* R CMD INSTALL gains an option --built-timestamp=STAMP allowing
100% reproducible package building, thanks to Dirk Eddelbuettel.
UTILITIES:
* There is support for testing the \dontrun and \donttest parts of
examples in packages.
tools::testInstalledPackage() accepts new arguments
commentDontrun = FALSE and commentDonttest = FALSE.
R CMD check gains options --run-dontrun and --run-donttest.
* The HTML generated by tools::Rd2HTML() and tools::toHTML()
methods is now 'XHTML 1.0 Strict'.
* The compiler package's utility function setCompilerOptions() now
returns the old values invisibly. The initial optimization level
can also be set with the environment variable
R_COMPILER_OPTIMIZE.
* R CMD build adds a NeedsCompilation field if one is not already
present in the DESCRIPTION file.
* R CMD check gains option --test-dir to specify an alternative set
of tests to run.
* R CMD check will now by default continue with testing after many
types of errors, and will output a summary count of errors at the
end if any have occurred.
* R CMD check now checks that the Title and Description fields are
correctly terminated.
* R CMD check --as-cran now:
* checks a README.md file can be processed: this needs pandoc
installed.
* checks the existence and accessibility of URLs in the
DESCRIPTION, CITATION, NEWS.Rd and README.md files and in the
help files (provided the build has libcurl support).
* reports non-ASCII characters in R source files when there is
no package encoding declared in the DESCRIPTION file.
* reports (apparent) S3 methods exported but not registered.
* reports overwriting registered S3 methods from
base/recommended packages. (Such methods are replaced in the
affected package for the rest of the session, even if the
replacing namespace is unloaded.)
* reports if the Title field does not appear to be in title
case (see 'Writing R Extensions': there may be false
positives, but note that technical words should be
single-quoted and will then be accepted).
Most of these checks can also be selected by environment
variables: see the 'R Internals' manual.
C-LEVEL FACILITIES:
* New C API utility logspace_sum(logx[], n).
* Entry points rbinom_mu, rnbinom_mu and rmultinom are remapped (by
default) to Rf_rbinom_mu etc. This requires packages using them
to be re-installed.
* .C(DUP = FALSE) and .Fortran(DUP = FALSE) are now ignored, so
arguments are duplicated if DUP = TRUE would do so. As their
help has long said, .Call() is much preferred.
* New entry point R_allocLD, like R_alloc but guaranteed to have
sufficient alignment for long double pointers.
* isPairList() now returns TRUE for DOTSXP.
WINDOWS BUILD CHANGES:
A number of changes to the Windows build system are in development.
The following are currently in place.
* Installation using external binary distributions of zlib, bzip2,
liblzma, pcre, libpng, jpeglib and libtiff is now required, and
the build instructions have been revised.
* A new make target rsync-extsoft has been added to obtain copies
of the external libraries from CRAN.
* Building the manuals now requires texi2any from texinfo 5.1 or
later. CRAN binary builds include the manuals, but by default
builds from source will not, and they will be accessed from CRAN.
See the comments in src/gnuwin32/MkRules.dist for how to specify
the location of texi2any.
* (Windows) Changes have been made to support an experimental
Windows toolchain based on GCC 4.9.2. The default toolchain
continues to be based on GCC 4.6.3, as the new toolchain is not
yet stable enough. A change to a new toolchain is expected
during the R 3.2.x lifetime.
PACKAGE INSTALLATION:
* (Windows) The use of macro ZLIB_LIBS in file src/Makevars.win
(which has not been documented for a long time) now requires an
external libz.a to be available (it is part of the 'goodies' used
to compile Windows binary packages). It would be simpler to use
-lz instead.
* The default for option pkgType on platforms using binary packages
is now "both", so source packages will be tried if binary
versions are not available or not up to date.
There are options for what install.packages(type = "both")
(possibly called _via_ update.packages()) will do if compilation
of a source package is desirable: see ?options (under utils).
If you intend not to accept updates as source packages, you
should use update.packages(type = "binary").
DEPRECATED AND DEFUNCT:
* download.file(method = "lynx") is defunct.
* Building R using the included versions of zlib, bzip2, xz and
PCRE is deprecated: these are frozen (bar essential bug-fixes)
and will be removed for R 3.3.0.
* The configure option --with-valgrind-instrumentation=3 has been
withdrawn, as it did not work with recent valgrind headers: it is
now treated as level 2.
* The MethodsList class in package methods had been deprecated in R
2.11.0 and is defunct now. Functions using it are defunct if
they had been deprecated in R 2.11.0, and are deprecated now,
otherwise.
BUG FIXES:
* Fixed two obscure bugs in pairlist subassignment, reported by
Radford Neal as part of pqR issue 16.
* Fixes for bugs in handling empty arguments and argument matching
by name in log().
* all.equal() gains methods for environments and refClasses.
* [<- and [[<- gain S4 data.frame methods to avoid corruption of S4
class information by the S3 methods.
* callNextMethod() should now work within a .local call when ... is
absent from formals(.local).
* dput(pairlist(x)) generates a call to the pairlist constructor
instead of the list constructor.
* Fix missing() when arguments are propagated through ... .
(PR#15707)
* eigen(m) now defaults to symmetric = TRUE even when the dimnames
are asymmetric if the matrix is otherwise symmetric. (PR#16151)
* Fix issues with forwarding ... through callGeneric() and
callNextMethod(). (PR#16141)
* callGeneric() now works after a callNextMethod().
* Subclass information is kept consistent when replacing an
ordinary S4 class with an "old class" _via_ the S4Class argument
to setOldClass(). Thus, for example, a data.frame is valid for a
list argument in the signature, and a factor is valid for vector
arguments.
* In qbeta() the inversion of pbeta() is much more sophisticated.
This works better in corner cases some of which failed completely
previously (PR#15755), or were using too many iterations.
* Auto-printing no longer duplicates objects when printing is
dispatched to a method.
* kmeans(x, k) would fail when nrow(x) >= 42949673. (Comment 6 of
PR#15364)
* 'Abbreviated' locale-specific day and month names could have been
truncated in those rare locales where there are the same as the
full names.
* An irrelevant warning message from updating subclass information
was silenced (the namespace would not be writable in this case).
CHANGES IN R 3.1.3:
NEW FEATURES:
* The internal method of download.file() can now handle files
larger than 2GB on 32-bit builds which support such files (tested
on 32-bit R running on 64-bit Windows).
* kruskal.test() warns on more types of suspicious input.
* The as.dendrogram() method for "hclust" objects gains a check
argument protecting against memory explosion for invalid inputs.
* capabilities() has a new item long.double which indicates if the
build uses a long double type which is longer than double.
* nlm() no longer modifies the callback argument in place (a new
vector is allocated for each invocation, which mimics the
implicit duplication that occurred in R < 3.1.0); note that this
is a change from the previously documented behavior. (PR#15958)
* icuSetCollate() now accepts locale = "ASCII" which uses the basic
C function strcmp and so collates strings byte-by-byte in
numerical order.
* sessionInfo() tries to report the OS version in use (not just
that compiled under, and including details of Linux
distributions).
* model.frame() (used by lm() and many other modelling functions)
now warns when it drops contrasts from factors. (Wish of
PR#16119)
* install.packages() and friends now accept the value type =
"binary" as a synonym for the native binary type on the platform
(if it has one).
* Single source or binary files can be supplied for
install.packages(type = "both") and the appropriate type and
repos = NULL will be inferred.
* New function pcre_config() to report on some of the configuration
options of the version of PCRE in use. In particular, this
reports if regular expressions using \p{xx} are supported.
* (Windows.) download.file(cacheOK = FALSE) is now supported when
internet2.dll is used.
* browseURL() has been updated to work with Firefox 36.0 which has
dropped support for the -remote interface.
INSTALLATION and INCLUDED SOFTWARE:
* The included version of PCRE has been updated to 8.36.
* configure accepts MAKEINFO=texi2any as another way to ensure
texinfo 5.x is used when both 5.x and 4.x are installed.
UTILITIES:
* R CMD check now checks the packages used in \donttest sections of
the examples are specified in the DESCRIPTION file. (These are
needed to run the examples interactively.)
* R CMD check checks for the undeclared use of GNU extensions in
Makefiles, and for Makefiles with a missing final linefeed.
R CMD build will correct line endings in all Makefiles, not just
those in the src directory.
* R CMD check notes uses of library() and require() in package
code: see the section 'Suggested packages' of 'Writing R
Extensions' for good practice.
DEPRECATED AND DEFUNCT:
* The configure option --with-valgrind-instrumentation=3 is
deprecated and will be removed in R 3.2.0.
BUG FIXES:
* (Windows.) Rscript.exe was missing a manifest specifying the
modern style for common controls (e.g., the download progress
bar).
* If a package had extra documentation files but no vignette, the
HTML help system produced an empty index page.
* The parser now gives an error if a null character is included in
a string using Unicode escapes. (PR#16046)
* qr.Q() failed on complex arguments due to pre-3.0(!) typo.
(PR#16054)
* abs() failed with named arguments when the argument was complex.
(PR#16047)
* "noquote" objects may now be used as columns in dataframes.
(PR#15997)
* Some values with extremely long names were printed incorrectly.
(PR#15999)
* Extremely large exponents on zero expressed in scientific
notation (e.g. 0.0e50000) could give NaN. (PR#15976)
* download.file() reported downloaded sizes as 0KB if less than
1MB, only for R 3.1.2 and only on big-endian platforms.
* prompt() did not escape percent signs in the automatically
generated usage section of help files.
* drop.terms() dropped some of the attributes of the object it was
working with. (PR#16029)
* (Windows.) The command completion in Rgui.exe messed up the
console. (PR#15791)
* (Windows.) The choose.files() command returned a blank string
when the user asked for a single file but cancelled the request.
(PR#16074)
* Math2 S4 group generics failed to correctly dispatch "structure"-
and "nonStructure"-derived classes.
* loadNamespace() imposed undocumented restrictions on the
versionCheck parameter. (Reported by Geoff Lee.)
* Rare over-runs detected by AddressSanitizer in substr() and its
replacement version have been avoided.
_Inter alia_ that fix gives the documented behaviour for
substr(x, 1, 2) <- "" (subsequently reported as PR#16214).
* Loading packages incorrectly defining an S4 generic followed by a
function of the same name caused an erroneous cyclic namespace
dependency error.
* Declared vignette encodings are now always passed to the vignette
engine.
* Port Tomas Kalibera's fix from R-devel that restores the
loadMethod() fast path, effectively doubling the speed of S4
dispatch.
* power.t.test() and power.prop.test() now make use of the
extendInt option of uniroot() and hence work in more extreme
cases. (PR#15792)
* If a package was updated and attached when its namespace was
already loaded, it could end up with parts from one version and
parts from the other. (PR#16120)
* tools:::.Rdconv() didn't accept --encoding= due to a typo.
(PR#16121)
* Unix-alike builds without a suitable makeinfo were documented to
link the missing HTML manuals to CRAN, but did not.
* save(*, ascii=TRUE) and load() now correctly deal with NaN's.
(PR#16137)
* split.Date() retains fractional representations while avoiding
incomplete class propagation.
* R_ext/Lapack.h had not been updated for changes made by LAPACK to
the argument lists of its (largely internal) functions dlaed2 and
dlaed3. (PR#16157)
* RShowDoc("NEWS", "txt") had not been updated for the layout
changes of R 3.1.0.
* The xtfrm() method for class "Surv" has been corrected and its
description expanded.
* mode(x) <- y would incorrectly evaluate x before changing its
mode. (PR#16215)
* besselJ(1, 2^64) and besselY(..) now signal a warning, returning
NaN instead of typically segfaulting. (Issue 3 of PR#15554)
* HTML conversion of \href markup in .Rd files did not remove the
backslash from \% and so gave an invalid URL. In a related
change, the \ escape is now required in such URLs.
CHANGES IN R 3.1.2:
NEW FEATURES:
* embedFonts() now defaults to format = "ps2write" for .ps and .eps
files. This is available in Ghostscript 9.x (since 2010) whereas
the previous default, format = "pswrite", was removed in
Ghostscript 9.10.
* For consistency with [dpqr]norm(), [dp]lnorm(sdlog = 0) model a
point mass at exp(mulog) rather than return NaN (for an error).
* capabilities() now reports if ICU is compiled in for use for
collation (it is only actually used if a suitable locale is set
for collation, and never for a C locale).
* (OS X only.) Package tcltk checks when loaded if it is linked
against the CRAN X11-based Tcl/Tk and if so that the Tcl/Tk
component and the X11 libraries are installed. This allows more
informative error messages to be given advising the installation
of the missing component or of XQuartz.
The X11() device and X11-based versions of the data editor and
viewer (invoked by edit() and View() for data frames and matrices
from command-line R) check that the X11 libraries are installed
and if not advises installing XQuartz.
* icuSetCollate() allows locale = "default", and locale = "none" to
use OS services rather than ICU for collation.
Environment variable R_ICU_LOCALE can be used to set the default
ICU locale, in case the one derived from the OS locale is
inappropriate (this is currently necessary on Windows).
* New function icuGetCollate() to report on the ICU collation
locale in use (if any).
* utils::URLencode() was updated to use unreserved and reserved
characters from RFC 3986 (<URL:
http://tools.ietf.org/html/rfc3986>) instead of RFC 1738.
* unique(warnings()) and c(warnings()) are now supported.
* The Bioconductor 'version' used by setRepositories() now defaults
to 3.0. (It can be set at runtime _via_ environment variable
R_BIOC_VERSION.)
* Omegahat is no longer listed as providing Windows binary
packages, e.g. by setRepositories(). It has no binary packages
available for R 3.1.x and those for earlier versions were 32-bit
only.
INSTALLATION and INCLUDED SOFTWARE:
* The configure script reports on the more important
capabilities/options which will not be compiled in.
More types of external BLAS are recognized by name in that
report.
* When building R as a shared library, the -L${R_HOME}/lib${R_ARCH}
flag is placed earlier in the link commands used during
installation and when packages are installed: this helps ensure
that the current build has priority if an R shared library has
already been installed by e.g. install-libR in a library
mentioned in LDFLAGS (and not in 'your system's library
directory' as documented). (Wish of PR#15790.)
* LaTeX package upquote is no longer required for R's use of
inconsolata.
* (Windows only) If both 32- and 64-bit versions of R are
installed, the bin/R.exe and bin/Rscript.exe executables now run
64-bit R. (To run 32-bit R, overwrite these files with copies of
bin/i386/Rfe.exe.)
UTILITIES:
* Running R CMD check with _R_CHECK_DEPENDS_ONLY_ true now makes
the VignetteBuilder packages available even if they are listed in
Suggests, since they are needed to recognise and process
non-Sweave vignettes.
* R CMD check now reports empty importFrom declarations in a
NAMESPACE file, as these are common errors (writing
importFrom(Pkg) where import(Pkg) was intended).
* R CMD check now by default checks code usage directly on the
package namespace without loading and attaching the package and
its suggests and enhances. For good practice with packages in
the Suggests field, see SS1.1.3.1 of 'Writing R Extensions'. For
use of lazy-data objects in the package's own code, see ?data.
BUG FIXES:
* dmultinom() did not handle non-finite probabilities correctly.
* prettyNum(x, zero.print=*) now also works when x contains NAs.
* A longstanding bug exhibited by nlminb() on Windows was traced to
a compiler bug in gcc 4.6.3; a workaround has been put in place.
(PR#15244 and PR#15914).
* Rendering of \command in HTML versions of help pages has been
improved: this is particularly evident on the help page for
INSTALL.
* as.hexmode(x) and as.octmode(x) now behave correctly for some
numeric x, e.g., c(NA, 1) or c(1, pi).
* drop1() failed if the scope argument had no variables to drop.
(PR#15935)
* edit() (and hence fix()) failed if an object had a non-character
attribute named "source" (an attribute that had been used in R
prior to version 2.14.0).
* callGeneric() could fail if the generic had ... as a formal
argument. (PR#15937).
* Forking in package parallel called C entry point exit in the
child. This was unsafe (_exit should have been called), and
could flush stdin of the main R process (seen most often on
Solaris).
As good practice, stdout is now flushed before forking a child.
* R objects such as list(`a\b` = 1) now print correctly.
* getAnywhere("C_pbinom") now returns correctly a single object
(rather than unlisting it).
* The confint() method for nls() fits failed it these has specified
parameter limits despite using an algorithm other than "port".
(PR#15960)
* Subclassing an S4 class failed if the class required arguments to
the generator, through its initialize() method.
* removeSource() did not properly handle expressions containing
arguments that were supplied as missing, e.g. x[i,]. (PR#15957)
* as.environment(list()) now works, and as.list() of such an
environment is now the same as list().
* Several tcltk functions failed when run in unusual environments.
(PR#15970)
* options(list()) now works (trivially). (PR#15979)
* merge(<dendrogram>, ..) now works correctly for two `independent'
dendrograms (PR#15648), and still compatibly via adjust = "auto"
e.g. for two branches of an existing dendrogram.
* The plot method for "hclust" objects gets an optional argument
check; When that is true (the default) it checks more carefully
for valid input.
* (Windows only) If a user chose to install 64 bit R but not 32 bit
R, the bin/R and bin/Rscript executables failed to run.
(PR#15981)
* Various possible buffer overruns have been prevented, and missed
memory protection added. (PR#15990)
* Rscript no longer passes --args to R when there are no extra
("user") arguments.
* objects like getClass("refClass")@prototype now print() and str()
without error.
* identical() now also looks at the S4 bit.
* hist(x, breaks) is more robust in adding a small fuzz to few
breaks when some are very large. (PR#15988)
* sub() and gsub() did not handle regular expressions like "\s{2,}"
properly if the text contained NA or non-ascii elements in a
UTF-8 locale. Part of this was due to a bug in the TRE library.
(PR#16009)
* RShowDoc("NEWS") now displays the PDF version.
* Matrices and arrays with last dimension zero did not print at all
or incompletely. (PR#16012)
* plot.histogram() and hence hist() now respect the xaxs, yaxs and
lab graphics parameters. (PR#16021)
* bw.SJ(x) and other bw.*() no longer segfault when x contains
non-finite values. (PR#16024)
* R CMD Rd2pdf unintentionally ignored its --os option.
* The internal method of download.file() was not reporting file
sizes and progress correctly on files larger than 2GB (inherited
from libxml2). This is corrected for 64-bit builds (32-bit
platforms may not support such files, but where possible will be
supported in future versions of R).
* Work around a bug in OS X Yosemite where key environment
variables may be duplicated causing issues in subprocesses. The
duplicates are now removed on R startup (via Rprofile).
(PR#16042)
* Adjust X11 auto-launch detection in DISPLAY on OS X to recognize
latest XQuartz.
Recursive revbump following MesaLib update, categories g through n.
Remove pkgviews: don't set PKG_INSTALLATION_TYPES in Makefiles.
Replace WRAPPER_BINDIR reference with real path in generated file.
Update R to 3.1.1
NEW FEATURES:
* When attach() reports conflicts, it does so compatibly with
library() by using message().
* R CMD Sweave no longer cleans any files by default, compatibly
with versions of R prior to 3.1.0. There are new options
--clean, --clean=default and --clean=keepOuts.
* tools::buildVignette() and tools::buildVignettes() with clean =
FALSE no longer remove any created files. buildvignette() gains
a keep argument for more cleaning customization.
* The Bioconductor 'version' used by setRepositories() can now be
set by environment variable R_BIOC_VERSION at runtime, not just
when R is installed. (It has been stated that Bioconductor will
switch from 'version' 2.14 to 'version' 3.0 during the lifetime
of the R 3.1 series.)
* Error messages from bugs in embedded Sexpr code in Sweave
documents now report the source location.
* type.convert(), read.table() and similar read.*() functions get a
new numerals argument, specifying how numeric input is converted
when its conversion to double precision loses accuracy. The
default value, "allow.loss" allows accuracy loss, as in R
versions before 3.1.0.
* For some compilers, integer addition could overflow without a
warning. R's internal code for both integer addition and
subtraction is more robust now.
* The function determining the default number of knots for
smooth.spline() is now exported, as .nknots.smspl().
* dbeta(, a,b), pbeta(), qbeta() and rbeta() are now defined also
for a = 0, b = 0, or infinite a and b (where they typically
returned NaN before).
* Many package authors report that the RStudio graphics device does
not work correctly with their package's use of dev.new(). The
new option dev.new(noRStudioGD = TRUE) replaces the RStudio
override by the default device as selected by R itself, still
respecting environment variables R_INTERACTIVE_DEVICE and
R_DEFAULT_DEVICE.
* readRDS() now returns visibly.
* Modifying internal logical scalar constants now results in an
error instead of a warning.
* install.packages(repos = NULL) now accepts http:// or ftp:// URLs
of package archives as well as file paths, and will download as
required. In most cases repos = NULL can be deduced from the
extension of the URL.
* The warning when using partial matching with the $ operator on
data frames is now only given when
options("warnPartialMatchDollar") is TRUE.
* Package help requests like package?foo now try the package foo
whether loaded or not.
* General help requests now default to trying all loaded packages,
not just those on the search path.
* Added a new function promptImport(), to generate a help page for
a function that was imported from another package (and presumably
re-exported, or help would not be needed).
Bump for perl-5.20.0. Do it for all packages that * mention perl, or * have a directory name starting with p5-*, or * depend on a package starting with p5- like last time, for 5.18, where this didn't lead to complaints. Let me know if you have any this time.
Recursive revbump from x11/pixman Fix PR pkg/48777
Update to R 3.1.0
NEW FEATURES:
* type.convert() (and hence by default read.table()) returns a
character vector or factor when representing a numeric input as a
double would lose accuracy. Similarly for complex inputs.
If a file contains numeric data with unrepresentable numbers of
decimal places that are intended to be read as numeric, specify
colClasses in read.table() to be "numeric".
* tools::Rdiff(useDiff = FALSE) is closer to the POSIX definition
of diff -b (as distinct from the description in the man pages of
most systems).
* New function anyNA(), a version of any(is.na(.)) which is fast
for atomic vectors, based on a proposal by Tim Hesterberg.
* arrayInd(*, useNames = TRUE) and, analogously, which(*, arr.ind =
TRUE) now make use of names(.dimnames) when available.
* is.unsorted() now also works for raw vectors.
* The "table" method for as.data.frame() (also useful as
as.data.frame.table()) now passes sep and base arguments to
provideDimnames().
* uniroot() gets new optional arguments, notably extendInt,
allowing to auto-extend the search interval when needed. The
return value has an extra component, init.it.
* switch(f, ...) now warns when f is a factor, as this typically
happens accidentally where the useR meant to pass a character
string, but f is treated as integer (as always documented).
* The parser has been modified to use less memory.
* The way the unary operators (+ - !) handle attributes is now more
consistent. If there is no coercion, all attributes (including
class) are copied from the input to the result: otherwise only
names, dims and dimnames are.
* colorRamp() and colorRampPalette() now allow non-opaque colours
and a ramp in opacity via the new argument alpha = TRUE.
(Suggested by Alberto Krone-Martins, but optionally as there are
existing uses which expect only RGB values.)
* grid.show.layout() and grid.show.viewport() get an optional vp.ex
argument.
* There is a new function find_gs_cmd() in the tools package to
locate a GhostScript executable. (This is an enhanced version of
a previously internal function there.)
* object.size() gains a format() method.
* There is a new family, "ArialMT", for the pdf() and postscript()
devices. This will only be rendered correctly on viewers which
have access to Monotype TrueType fonts (which are sometimes
requested by journals).
* The text and PDF news files, including NEWS and NEWS.2, have been
moved to the doc directory.
* combn(x, simplify = TRUE) now gives a factor result for factor
input x (previously user error).
* Added utils::fileSnapshot() and utils::changedFiles() functions
to allow snapshots and comparison of directories of files.
* make.names(names, unique=TRUE) now tries to preserve existing
names.
* New functions cospi(x), sinpi(x), and tanpi(x), for more accurate
computation of cos(pi*x), etc, both in R and the C API. Using
these gains accuracy in some cases, e.g., inside lgamma() or
besselI().
* print.table(x, zero.print = ".") now also has an effect when x is
not integer-valued.
* There is more support to explore the system's idea of time-zone
names. Sys.timezone() tries to give the current system setting
by name (and succeeds at least on Linux, OS X, Solaris and
Windows), and OlsonNames() lists the names in the system's Olson
database. Sys.timezone(location = FALSE) gives the previous
behaviour.
* Platforms with a 64-bit time_t type are allowed to handle
conversions between the "POSIXct" and "POSIXlt" classes for
date-times outside the 32-bit range (before 1902 or after 2037):
the existing workarounds are used on other platforms. (Note that
time-zone information for post-2037 is speculative at best, and
the OS services are tested for known errors and so not used on OS
X.)
Currently time_t is usually long and hence 64-bit on Unix-alike
64-bit platforms: however it several cases the time-zone database
is 32-bit. On R for Windows it is 64-bit (for both architectures
as from this version).
* The "save.defaults" option can include a value for
compression_level.
* colSums() and friends now have support for arrays and data-frame
columns with 2^31 or more elements.
* as.factor() is faster when f is an unclassed integer vector (for
example, when called from tapply()).
* fft() now works with longer inputs, from the 12 million
previously supported up to 2 billion.
* Complex svd() now uses LAPACK subroutine ZGESDD, the complex
analogue of the routine used for the real case.
* Sweave now outputs .tex files in UTF-8 if the input encoding is
declared to be UTF-8, regardless of the local encoding. The
UTF-8 encoding may now be declared using a LaTeX comment
containing the string %\SweaveUTF8 on a line by itself.
* file.copy() gains a copy.date argument.
* Printing of date-times will make use of the time-zone
abbreviation in use at the time, if known. For example, for
Paris pre-1940 this could be LMT, PMT, WET or WEST. To enable
this, the "POSIXlt" class has an optional component "zone"
recording the abbreviation for each element.
For platforms which support it, there is also a component
"gmtoff" recording the offset from GMT where known.
* (On Windows, by default on OS X and optionally elsewhere.) The
system C function strftime has been replaced by a more
comprehensive version with closer conformance to the POSIX 2008
standard.
* dnorm(x, log = FALSE) is more accurate (but somewhat slower) for
|x| > 5.
* Some versions of the tiff() device have further compression
options.
* read.table(), readLines() and scan() have a new argument to
influence the treatment of embedded nuls.
* Avoid duplicating the right hand side values in complex
assignments when possible. This reduces copying of replacement
values in expressions such as Z$a <- a0 and ans[[i]] <- tmp: some
package code has relied on there being copies.
Also, a number of other changes to reduce copying of objects; all
contributed by or based on suggestions by Michael Lawrence.
* The fast argument of KalmanLike(), KalmanRun() and
KalmanForecast() has been replaced by update, which instead of
updating mod in place, optionally returns the updated model in an
attribute "mod" of the return value.
* arima() and makeARIMA() get a new optional argument SSinit,
allowing the choice of a different *s*tate *s*pace initialization
which has been observed to be more reliable close to
non-stationarity.
* warning() has a new argument noBreaks., to simplify
post-processing of output with options(warn = 1).
* pushBack() gains an argument encoding, to support reading of
UTF-8 characters using scan(), read.table() and related functions
in a non-UTF-8 locale.
* all.equal.list() gets a new argument use.names which by default
labels differing components by names (if they match) rather than
by integer index. Saved R output in packages may need to be
updated.
* The methods for all.equal() and attr.all.equal() now have
argument check.attributes after ... so it cannot be partially nor
positionally matched (as it has been, unintentionally).
A side effect is that some previously undetected errors of
passing empty arguments (no object between commas) to all.equal()
are detected and reported.
There are explicit checks that check.attributes is logical,
tolerance is numeric and scale is NULL or numeric. This catches
some unintended positional matching.
The message for all.equal.numeric() reports a "scaled difference"
only for scale != 1.
* all.equal() now has a "POSIXt" method replacing the "POSIXct"
method.
* The "Date" and "POSIXt" methods of seq() allows by = "quarter"
for completeness (by = "3 months" always worked).
* file.path() removes any trailing separator on Windows, where they
are invalid (although sometimes accepted). This is intended to
enhance the portability of code written by those using POSIX file
systems (where a trailing / can be used to confine path matching
to directories).
* New function agrepl() which like grepl() returns a logical
vector.
* fifo() is now supported on Windows.
* sort.list(method = "radix") now allows negative integers
* Some functionality of print.ts() is now available in
.preformat.ts() for more modularity.
* mcparallel() gains an option detach = TRUE which allows execution
of code independently of the current session. It is based on a
new estranged = TRUE argument to mcfork() which forks child
processes such that they become independent of the parent
process.
* The pdf() device omits circles and text at extremely small sizes,
since some viewers were failing on such files.
* The rightmost break for the "months", "quarters" and "years"
cases of hist.POSIXlt() has been increased by a day.
* The handling of DF[i,] <- a where i is of length 0 is improved.
* hclust() gains a new method "ward.D2" which implements Ward's
method correctly. The previous "ward" method is "ward.D" now,
with the old name still working. Thanks to research and
proposals by Pierre Legendre.
* The sunspot.month dataset has been amended and updated from the
official source, whereas the sunspots and sunspot.year datasets
will remain immutable. The documentation and source links have
been updated correspondingly.
* The summary() method for "lm" fits warns if the fit is
essentially perfect, as most of the summary may be computed
inaccurately (and with platform-dependent values).
Programmers who use summary() in order to extract just a
component which will be reliable (e.g. $cov.unscaled) should wrap
their calls in suppressWarnings().
Update to R 3.0.3. update from wen heping. CHANGES IN R 3.0.3: NEW FEATURES: * On Windows there is support for making .texi manuals using texinfo 5.0 or later: the setting is in file src/gnuwin32/MkRules.dist. A packaging of the Perl script and modules for texinfo 5.2 has been made available at <URL: http://www.stats.ox.ac.uk/pub/Rtools/>. * write.table() now handles matrices of 2^31 or more elements, for those with large amounts of patience and disc space. * There is a new function, La_version(), to report the version of LAPACK in use. * The HTML version of 'An Introduction to R' now has links to PNG versions of the figures. * There is some support to produce manuals in ebook formats. (See doc/manual/Makefile. Suggested by Mauro Cavalcanti.) * On a Unix-alike Sys.timezone() returns NA if the environment variable TZ is unset, to distinguish it from an empty string which on some OSes means the UTC time zone. * The backtick may now be escaped in strings, to allow names containing them to be constructed, e.g. `\``. * read.table(), readLines() and scan() now warn when an embedded nul is found in the input. * KalmanForecast(fast = FALSE) is now the default, and the help contains an example of how fast = TRUE can be used in this version. (The usage will change in 3.1.0.) * strptime() now checks the locale only when locale-specific formats are used and caches the locale in use: this can halve the time taken on OSes with slow system functions (e.g. OS X). * strptime() and the format() methods for classes "POSIXct", "POSIXlt" and "Date" recognize strings with marked encodings: this allows, for example, UTF-8 French month names to be read on (French) Windows. * iconv(to = "utf8") is now accepted on all platforms (some implementations did already, but GNU libiconv did not: however converted strings were not marked as being in UTF-8). The official name, "UTF-8" is still preferred. * available.packages() is better protected against corrupt metadata files. * Finalizers are marked to be run at garbage collection, but run only at a somewhat safer later time (when interrupts are checked). This circumvents some problems with finalizers running arbitrary code during garbage collection (the known instances being running options() and (C-level) path.expand() re-entrantly).
Set USE_GCC_RUNTIME=yes for packages which build shared libraries but do not use libtool to do so. This is required to correctly depend upon a gcc runtime package (e.g. gcc47-libs) when using USE_PKGSRC_GCC_RUNTIME.
Pass --disable-openmp on Darwin. With changes to g95 and tk, this package finally builds.
Update to R 3.0.2 * The NEWS files have been re-organized. This file contains news for R >= 3.0.0: news for the 0.x.y, 1.x.y and 2.x.y releases is in files NEWS.0, NEWS.1 and NEWS.2. The latter files are now installed when R is installed. An HTML version of news from 2.10.0 to 2.15.3 is available as doc/html/NEWS.2.html. * sum() for integer arguments now uses an integer accumulator of at least 64 bits and so will be more accurate in the very rare case that a cumulative sum exceeds 2^53 (necessarily summing more than 4 million elements). * The example() and tools::Rd2ex() functions now have parameters to allow them to ignore \dontrun markup in examples. (Suggested by Peter Solymos.) * str(x) is considerably faster for very large lists, or factors with 100,000 levels, the latter as in PR#15337. * col2rgb() now converts factors to character strings not integer codes (suggested by Bryan Hanson). * tail(warnings()) now works, via the new `[` method. * There is now support for the LaTeX style file zi4.sty which has in some distributions replaced inconsolata.sty. * unlist(x) now typically returns all non-list xs unchanged, not just the "vector" ones. Consequently, format(lst) now also works when the list lst has non-vector elements. * The tools::getVignetteInfo() function has been added to give information about installed vignettes. * New assertCondition(), etc. utilities in tools, useful for testing. * Profiling now records non-inlined calls from byte-compiled code to BUILTIN functions. * Various functions in stats and elsewhere that use non-standard evaluation are now more careful to follow the namespace scoping rules. E.g. stats::lm() can now find stats::model.frame() even if stats is not on the search path or if some package defines a function of that name. * If an invalid/corrupt .Random.seed object is encountered in the workspace it is ignored with a warning rather than giving an error. (This allows R itself to rely on a working RNG, e.g. to choose a random port.) * seq() and seq.int() give more explicit error messages if called with invalid (e.g. NaN) inputs. * When parse() finds a syntax error, it now makes partial parse information available up to the location of the error. (Request of Reijo Sund.) * Methods invoked by NextMethod() had a different dynamic parent to the generic. This was causing trouble where S3 methods invoked via lazy evaluation could lose track of their generic. (PR#15267) * Code for the negative binomial distribution now treats the case size == 0 as a one-point distribution at zero. * abbreviate() handles without warning non-ASCII input strings which require no abbreviation. * read.dcf() no longer has a limit of 8191 bytes per line. (Wish of PR#15250.) * formatC(x) no longer copies the class of x to the result, to avoid misuse creating invalid objects as in PR#15303. A warning is given if a class is discarded. * Dataset npk has been copied from MASS to allow more tests to be run without recommended packages being installed. * The initialization of the regression coefficients for non-degenerate differenced models in arima() has been changed and in some examples avoids a local maximum. (PR#15396) * termplot() now has an argument transform.x to control the display of individual terms in the plot. (PR#15329) * format() now supports digits = 0, to display nsmall decimal places. * There is a new read-only par() parameter called "page", which returns a logical value indicating whether the next plot.new() call will start a new page. * Processing Sweave and Rd documents to PDF now renders backticks * utils::modifyList() gets a new argument keep.null allowing NULL components in the replacement to be retained, instead of causing corresponding components to be deleted. * tools::pkgVignettes() gains argument check; if set to TRUE, it will warn when it appears a vignette requests a non-existent vignette engine.
Revbump after updating tcl/tk.
Update to R 3.0.1 Changes: many new features and bug fixes. See NEWS file for details.
* .include "../../devel/readline/buildlink3.mk" with USE_GNU_READLINE=yes are replaced with .include "../../devel/readline/buildlink3.mk", and USE_GNU_READLINE are removed, * .include "../../devel/readline/buildlink3.mk" without USE_GNU_READLINE are replaced with .include "../../mk/readline.buildlink3.mk".
Bump PKGREVISION for libXft changes for NetBSD native X support on NetBSD 6, requested by tron.
Try to fix the fallout caused by the fix for PR pkg/47882. Part 3: Recursively bump package revisions again after the "freetype2" and "fontconfig" handling was fixed.
Bump freetype2 and fontconfig dependencies to current pkgsrc versions, to address issues with NetBSD-6(and earlier)'s fontconfig not being new enough for pango. While doing that, also bump freetype2 dependency to current pkgsrc version. Suggested by tron in PR 47882
Bump all packages for perl-5.18, that a) refer 'perl' in their Makefile, or b) have a directory name of p5-*, or c) have any dependency on any p5-* package Like last time, where this caused no complaints.
Install info files. Bump PKGREVISION. Fixes PR pkg/47391
Recursive bump for png-1.6.
Revbump after graphics/jpeg and textproc/icu
Update to 2.15.1
Approved by wiz@
Upstream changes:
CHANGES IN R VERSION 2.15.1:
NEW FEATURES:
o source() now uses withVisible() rather than
.Internal(eval.with.vis). This sometimes alters tracebacks
slightly.
o install.packages("pkg_version.tgz") on Mac OS X now has sanity
checks that this is actually a binary package (as people have
tried it with incorrectly named source packages).
o splineDesign() and spline.des() in package splines have a new
option sparse which can be used for efficient construction of a
sparse B-spline design matrix (_via_ Matrix).
o norm() now allows type = "2" (the 'spectral' or 2-norm) as well,
mainly for didactical completeness.
o pmin() and pmax()) now also work when one of the inputs is of
length zero and others are not, returning a zero-length vector,
analogously to, say, +.
o colorRamp() (and hence colorRampPalette()) now also works for the
boundary case of just one color when the ramp is flat.
o qqline() has new optional arguments distribution, probs and
qtype, following the example of lattice's panel.qqmathline().
o .C() gains some protection against the misuse of character vector
arguments. (An all too common error is to pass character(N),
which initializes the elements to "", and then attempt to edit
the strings in-place, sometimes forgetting to terminate them.)
o Calls to the new function globalVariables() in package utils
declare that functions and other objects in a package should be
treated as globally defined, so that CMD check will not note
them.
o print(packageDescription(*)) trims the Collate field by default.
o The included copy of zlib has been updated to version 1.2.7.
o A new option "show.error.locations" has been added. When set to
TRUE, error messages will contain the location of the most recent
call containing source reference information. (Other values are
supported as well; see ?options.)
o The NA warning messages from e.g. pchisq() now report the call to
the closure and not that of the .Internal.
o Added Polish translations by <c5><81>ukasz Daniel.
PERFORMANCE IMPROVEMENTS:
o In package parallel, makeForkCluster() and the multicore-based
functions use native byte-order for serialization (deferred from
2.15.0).
o lm.fit(), lm.wfit(), glm.fit() and lsfit() do less copying of
objects, mainly by using .Call() rather than .Fortran().
o .C() and .Fortran() do less copying: arguments which are raw,
logical, integer, real or complex vectors and are unnamed are not
copied before the call, and (named or not) are not copied after
the call. Lists are no longer copied (they are supposed to be
used read-only in the C code).
o tabulate() makes use of .C(DUP = FALSE) and hence does not copy
bin. (Suggested by Tim Hesterberg.) It also avoids making a
copy of a factor argument bin.
o Other functions (often or always) doing less copying include
cut(), dist(), the complex case of eigen(), hclust(), image(),
kmeans(), loess(), stl() and svd(LINPACK = TRUE).
o There is less copying when using primitive replacement functions
such as names(), attr() and attributes().
DEPRECATED AND DEFUNCT:
o The converters for use with .C() (see ?getCConverterDescriptions)
are deprecated: use the .Call() interface instead. There are no
known examples (they were never fully documented).
UTILITIES:
o For R CMD check, a few people have reported problems with
junctions on Windows (although they were tested on Windows 7, XP
and Server 2008 machines and it is unknown under what
circumstances the problems occur). Setting the environment
variable R_WIN_NO_JUNCTIONS to a non-empty value (e.g. in
~/.R/check.Renviron) will force copies to be used instead.
INSTALLATION:
o R CMD INSTALL with _R_CHECK_INSTALL_DEPENDS_ set to a true value
(as done by R CMD check --as-cran) now restricts the packages
available when lazy-loading as well as when test-loading (since
packages such as ETLUtils and agsemisc had top-level calls to
library() for undeclared packages).
This check is now also available on Windows.
C-LEVEL FACILITIES:
o C entry points mkChar and mkCharCE now check that the length of
the string they are passed does not exceed 2^31-1 bytes: they
used to overflow with unpredictable consequences.
o C entry points R_GetCurrentSrcref and R_GetSrcFilename have been
added to the API to allow debuggers access to the source
references on the stack.
WINDOWS-SPECIFIC CHANGES:
o Windows-specific changes will now be announced in this file
(NEWS). Changes up and including R 2.15.0 remain in the CHANGES
file.
o There are two new environment variables which control the
defaults for command-line options.
If R_WIN_INTERNET2 is set to a non-empty value, it is as if
--internet2 was used.
If R_MAX_MEM_SIZE is set, it gives the default memory limit if
--max-mem-size is not specified: invalid values being ignored.
BUG FIXES:
o lsfit() lost the names from the residuals.
o More cases in which merge() could create a data frame with
duplicate column names now give warnings. Cases where names
specified in by match multiple columns are errors.
o Nonsense uses such as seq(1:50, by = 5) (from package plotrix)
and seq.int(1:50, by = 5) are now errors.
o The residuals in the 5-number summary printed by summary() on an
"lm" object are now explicitly labelled as weighted residuals
when non-constant weights are present. (Wish of PR#14840.)
o tracemem() reported that all objects were copied by .C() or
.Fortran() whereas only some object types were ever copied.
It also reported and marked as copies _some_ transformations such
as rexp(n, x): it no longer does so.
o The plot() method for class "stepfun" only used the optional xval
argument to compute xlim and not the points at which to plot (as
documented). (PR#14864)
o Names containing characters which need to be escaped were not
deparsed properly. (PR#14846)
o Trying to update (recommended) packages in R_HOME/library without
write access is now dealt with more gracefully. Further, such
package updates may be skipped (with a warning), when a newer
installed version is already going to be used from .libPaths().
(PR#14866)
o hclust() is now fast again (as up to end of 2003), with a
different fix for the "median"/"centroid" problem. (PR#4195).
o get_all_vars() failed when the data came entirely from vectors in
the global environment. (PR#14847)
o R CMD check with _R_CHECK_NO_RECOMMENDED_ set to a true value (as
done by the --as-cran option) could issue false errors if there
was an indirect dependency on a recommended package.
o formatC() uses the C entry point str_signif which could write
beyond the length allocated for the output string.
o Missing default argument added to implicit S4 generic for
backsolve(). (PR#14883)
o Some bugs have been fixed in handling load actions that could
fail to export assigned items or generate spurious warnings in
CMD check on loading.
o For tiff(type = "windows"), the numbering of per-page files
except the last was off by one.
o On Windows, loading package stats (which is done for a default
session) would switch line endings on stdout and stderr from CRLF
to LF. This affected Rterm and R CMD BATCH.
o On Windows, the compatibility function x11() had not kept up with
changes to windows(), and issued warnings about bad parameters.
(PR#14880)
o On Windows, the Sys.glob() function did not handle UNC paths as
it was designed to try to do. (PR#14884)
o In package parallel, clusterApply() and similar failed to handle
a (pretty pointless) length-1 argument. (PR#14898)
o Quartz Cocoa display reacted asynchronously to dev.flush() which
means that the redraw could be performed after the plot has been
already modified by subsequent code. The redraw is now done
synchronously in dev.flush() to allow animations without sleep
cycles.
o Source locations reported in traceback() were incorrect when
byte-compiled code was on the stack.
o plogis(x, lower = FALSE, log.p = TRUE) no longer underflows early
for large x (e.g. 800).
o ?Arithmetic's "1 ^ y and y ^ 0 are 1, _always_" now also applies
for integer vectors y.
o X11-based pixmap devices like png(type = "Xlib") were trying to
set the cursor style, which triggered some warnings and hangs.
o Code executed by the built-in HTTP server no longer allows other
HTTP clients to re-enter R until the current worker evaluation
finishes, to prevent cascades.
o The plot() and Axis() methods for class "table" now respect
graphical parameters such as cex.axis. (Reported by Martin
Becker.)
o Under some circumstances package.skeleton() would give out
progress reports that could not be translated and so were
displayed by question marks. Now they are always in English.
(This was seen for CJK locales on Windows, but may have occurred
elsewhere.)
o The evaluator now keeps track of source references outside of
functions, e.g. when source() executes a script.
o The replacement method for window() now works correctly for
multiple time series of class "mts". (PR#14925)
o is.unsorted() gave incorrect results on non-atomic objects such
as data frames. (Reported by Matthew Dowle.)
o The value returned by tools::psnice() for invalid pid values was
not always NA as documented.
o Closing an X11() window while locator() was active could abort
the R process.
o getMethod(f, sig) produced an incorrect error message in some
cases when f was not a string).
o Using a string as a "call" in an error condition with
options(showErrorCalls=TRUE) could cause a segfault. (PR#14931)
o The string "infinity" allowed by C99 was not accepted as a
numerical string value by e.g. scan() and as.character().
(PR#14933)
o In legend(), setting some entries of lwd to NA was inconsistent
(depending on the graphics device) in whether it would suppress
those lines; now it consistently does so. (PR#14926)
o by() failed for a zero-row data frame. (Reported by Weiqiang
Qian)
o Yates correction in chisq.test() could be bigger than the terms
it corrected, previously leading to an infinite test statistic in
some corner cases which are now reported as NaN.
o xgettext() and related functions sometimes returned items that
were not strings for translation. (PR#14935)
o plot(<lm>, which=5) now correctly labels the factor level
combinations for the special case where all h[i,i] are the same.
(PR#14837)
CHANGES IN R VERSION 2.15.0:
SIGNIFICANT USER-VISIBLE CHANGES:
o The behaviour of unlink(recursive = TRUE) for a symbolic link to
a directory has changed: it now removes the link rather than the
directory contents (just as rm -r does).
On Windows it no longer follows reparse points (including
junctions and symbolic links).
NEW FEATURES:
o Environment variable RD2DVI_INPUTENC has been renamed to
RD2PDF_INPUTENC.
o .Deprecated() becomes a bit more flexible, getting an old
argument.
o Even data-only packages without R code need a namespace and so
may need to be installed under R 2.14.0 or later.
o assignInNamespace() has further restrictions on use apart from at
top-level, as its help page has warned. Expect it to be disabled
from programmatic use in the future.
o system() and system2() when capturing output report a non-zero
status in the new "status" attribute.
o kronecker() now has an S4 generic in package methods on which
packages can set methods. It will be invoked by X %x% Y if
either X or Y is an S4 object.
o pdf() accepts forms like file = "|lpr" in the same way as
postscript().
o pdf() accepts file = NULL. This means that the device does NOT
create a PDF file (but it can still be queried, e.g., for font
metric info).
o format() (and hence print()) on "bibentry" objects now uses
options("width") to set the output width.
o legend() gains a text.font argument. (Suggested by Tim Paine,
PR#14719.)
o nchar() and nzchar() no longer accept factors (as integer
vectors). (Wish of PR#6899.)
o summary() behaves slightly differently (or more precisely, its
print() method does). For numeric inputs, the number of NAs is
printed as an integer and not a real. For dates and datetimes,
the number of NAs is included in the printed output (the latter
being the wish of PR#14720).
The "data.frame" method is more consistent with the default
method: in particular it now applies zapsmall() to
numeric/complex summaries.
o The number of items retained with options(warn = 0) can be set by
options(nwarnings=).
o There is a new function assignInMyNamespace() which uses the
namespace of the function it is called from.
o attach() allows the default name for an attached file to be
overridden.
o bxp(), the work horse of boxplot(), now uses a more sensible
default xlim in the case where at is specified differently from
1:n, see the discussion on R-devel, <URL:
https://stat.ethz.ch/pipermail/r-devel/2011-November/062586.html>.
o New function paste0(), an efficient version of paste(*, sep=""),
to be used in many places for more concise (and slightly more
efficient) code.
o Function setClass() in package methods now returns, invisibly, a
generator function for the new class, slightly preferred to
calling new(), as explained on the setClass help page.
o The "dendrogram" method of str() now takes its default for
last.str from option str.dendrogram.last.
o New simple fitted() method for "kmeans" objects.
o The traceback() function can now be called with an integer
argument, to display a current stack trace. (Wish of PR#14770.)
o setGeneric() calls can be simplified when creating a new generic
function by supplying the default method as the def argument.
See ?setGeneric.
o serialize() has a new option xdr = FALSE which will use the
native byte-order for binary serializations. In scenarios where
only little-endian machines are involved (these days, close to
universal) and (un)serialization takes an appreciable amount of
time this may speed up noticeably transferring data between
systems.
o The internal (un)serialization code is faster for long vectors,
particularly with XDR on some platforms. (Based on a suggested
patch by Michael Spiegel.)
o For consistency, circles with zero radius are omitted by points()
and grid.circle(). Previously this was device-dependent, but
they were usually invisible.
o NROW(x) and NCOL(x) now work whenever dim(x) looks appropriate,
e.g., also for more generalized matrices.
o PCRE has been updated to version 8.30.
o The internal R_Srcref variable is now updated before the browser
stops on entering a function. (Suggestion of PR#14818.)
o There are 'bare-bones' functions .colSums(), .rowSums(),
.colMeans() and .rowMeans() for use in programming where ultimate
speed is required.
o The formerly internal function .package_dependencies() from
package tools for calculating (recursive) (reverse) dependencies
on package databases has been renamed to package_dependencies()
and is now exported.
o There is a new function optimHess() to compute the (approximate)
Hessian for an optim() solution if hessian = TRUE was forgotten.
o .filled.contour() is a 'bare-bones' function to add a
filled-contour rectangular plot to an already prepared plot
region.
o The stepping in debugging and single-step browsing modes has
changed slightly: now left braces at the start of the body are
stepped over for if statements as well as for for and while
statements. (Wish of PR#14814.)
o library() no longer warns about a conflict with a function from
package:base if the function has the same code as the base one
but with a different environment. (An example is Matrix::det().)
o When deparsing very large language objects, as.character() now
inserts newlines after each line of approximately 500 bytes,
rather than truncating to the first line.
o New function rWishart() generates Wishart-distributed random
matrices.
o Packages may now specify actions to be taken when the package is
loaded (setLoadActions()).
o options(max.print = Inf) and similar now give an error (instead
of warnings later).
o The "difftime" replacement method of units tries harder to
preserve other attributes of the argument. (Wish of PR#14839.)
o poly(raw = TRUE) no longer requires more unique points than the
degree. (Requested by John Fox.)
PACKAGE parallel:
o There is a new function mcmapply(), a parallel version of
mapply(), and a wrapper mcMap(), a parallel version of Map().
o A default cluster can be registered by the new function
setDefaultCluster(): this will be used by default in functions
such as parLapply().
o clusterMap() has a new argument .scheduling to allow the use of
load-balancing.
o There are new load-balancing functions parLapplyLB() and
parSapplyLB().
o makePSOCKCluster() has a new option useXDR = FALSE which can be
used to avoid byte-shuffling for serialization when all the nodes
are known to be little-endian (or all big-endian).
PACKAGE INSTALLATION:
o Non-ASCII vignettes without a declared encoding are no longer
accepted.
o C/C++ code in packages is now compiled with -NDEBUG to mitigate
against the C/C++ function assert being called in production use.
Developers can turn this off during package development with
PKG_CPPFLAGS = -UNDEBUG.
o R CMD INSTALL has a new option --dsym which on Mac OS X (Darwin)
dumps the symbols alongside the .so file: this is helpful when
debugging with valgrind (and especially when installing packages
into R.framework). [This can also be enabled by setting the
undocumented environment variable PKG_MAKE_DSYM, since R 2.12.0.]
o R CMD INSTALL will test loading under all installed
sub-architectures even for packages without compiled code, unless
the flag --no-multiarch is used. (Pure R packages can do things
which are architecture-dependent: in the case which prompted
this, looking for an icon in a Windows R executable.)
o There is a new option install.packages(type = "both") which tries
source packages if binary packages are not available, on those
platforms where the latter is the default.
o The meaning of install.packages(dependencies = TRUE) has changed:
it now means to install the essential dependencies of the named
packages plus the Suggests, but only the essential dependencies
of dependencies. To get the previous behaviour, specify
dependencies as a character vector.
o R CMD INSTALL --merge-multiarch is now supported on OS X and
other Unix-alikes using multiple sub-architectures.
o R CMD INSTALL --libs-only now by default does a test load on
Unix-alikes as well as on Windows: suppress with --no-test-load.
UTILITIES:
o R CMD check now gives a warning rather than a note if it finds
inefficiently compressed datasets. With bzip2 and xz compression
having been available since R 2.10.0, it only exceptionally makes
sense to not use them.
The environment variable _R_CHECK_COMPACT_DATA2_ is no longer
consulted: the check is always done if _R_CHECK_COMPACT_DATA_ has
a true value (its default).
o Where multiple sub-architectures are to be tested, R CMD check
now runs the examples and tests for all the sub-architectures
even if one fails.
o R CMD check can optionally report timings on various parts of the
check: this is controlled by environment variable
_R_CHECK_TIMINGS_ documented in 'Writing R Extensions'. Timings
(in the style of R CMD BATCH) are given at the foot of the output
files from running each test and the R code in each vignette.
o There are new options for more rigorous testing by R CMD check
selected by environment variables - see the 'Writing R
Extensions' manual.
o R CMD check now warns (rather than notes) on undeclared use of
other packages in examples and tests: increasingly people are
using the metadata in the DESCRIPTION file to compute information
about packages, for example reverse dependencies.
o The defaults for some of the options in R CMD check (described in
the 'R Internals' manual) have changed: checks for unsafe and
.Internal() calls and for partial matching of arguments in R
function calls are now done by default.
o R CMD check has more comprehensive facilities for checking
compiled code and so gives fewer reports on entry points linked
into .so/.dll files from libraries (including C++ and Fortran
runtimes).
Checking compiled code is now done on FreeBSD (as well as the
existing supported platforms of Linux, Mac OS X, Solaris and
Windows).
o R CMD build has more options for --compact-vignettes: see R CMD
build --help.
o R CMD build has a new option --md5 to add an MD5 file (as done by
CRAN): this is used by R CMD INSTALL to check the integrity of
the distribution.
If this option is not specified, any existing (and probably
stale) MD5 file is removed.
DEPRECATED AND DEFUNCT:
o R CMD Rd2dvi is now defunct: use R CMD Rd2pdf.
o Options such --max-nsize, --max-vsize and the function
mem.limits() are now defunct. (Options --min-nsize and
--min-vsize remain available.)
o Use of library.dynam() without specifying all the first three
arguments is now disallowed.
Use of an argument chname in library.dynam() including the
extension .so or .dll (which was never allowed according to the
help page) is defunct. This also applies to
library.dynam.unload() and to useDynLib directives in NAMESPACE
files.
o The internal functions .readRDS() and .saveRDS() are now defunct.
o The off-line help() types "postscript" and "ps" are defunct.
o Sys.putenv(), replaced and deprecated in R 2.5.0, is finally
removed.
o Some functions/objects which have been defunct for five or more
years have been removed completely. These include .Alias(),
La.chol(), La.chol2inv(), La.eigen(), Machine(), Platform(),
Version, codes(), delay(), format.char(), getenv(), httpclient(),
loadURL(), machine(), parse.dcf(), printNoClass(), provide(),
read.table.url(), restart(), scan.url(), symbol.C(), symbol.For()
and unix().
o The ENCODING argument to .C() is deprecated. It was intended to
smooth the transition to multi-byte character strings, but can be
replaced by the use of iconv() in the rare cases where it is
still needed.
INSTALLATION:
o Building with a positive value of --with-valgrind-instrumentation
now also instruments logical, complex and raw vectors.
C-LEVEL FACILITIES:
o Passing R objects other than atomic vectors, functions, lists and
environments to .C() is now deprecated and will give a warning.
Most cases (especially NULL) are actually coding errors. NULL
will be disallowed in future.
.C() now passes a pairlist as a SEXP to the compiled code. This
is as was documented, but pairlists were in reality handled
differently as a legacy from the early days of R.
o call_R and call_S are deprecated. They still exist in the
headers and as entry points, but are no longer documented and
should not be used for new code.
BUG FIXES:
o str(x, width) now obeys its width argument also for function
headers and other objects x where deparse() is applied.
o The convention for x %/% 0L for integer-mode x has been changed
from 0L to NA_integer_. (PR#14754)
o The exportMethods directive in a NAMESPACE file now exports S4
generics as necessary, as the extensions manual said it does.
The manual has also been updated to be a little more informative
on this point.
It is now required that there is an S4 generic (imported or
created in the package) when methods are to be exported.
o Reference methods cannot safely use non-exported entries in the
namespace. We now do not do so, and warn in the documentation.
o The namespace import code was warning when identical S4 generic
functions were imported more than once, but should not (reported
by Brian Ripley, then Martin Morgan).
o merge() is no longer allowed (in some ways) to create a data
frame with duplicate column names (which confused PR#14786).
o Fixes for rendering raster images on X11 and Windows devices when
the x-axis or y-axis scale is reversed.
o getAnywhere() found S3 methods as seen from the utils namespace
and not from the environment from which it was called.
o selectMethod(f, sig) would not return inherited group methods
when caching was off (as it is by default).
o dev.copy2pdf(out.type = "cairo") gave an error. (PR#14827)
o Virtual classes (e.g., class unions) had a NULL prototype even if
that was not a legal subclass. See ?setClassUnion.
o The C prototypes for zdotc and zdotu in R_ext/BLAS.h have been
changed to the more modern style rather than that used by f2c.
(Patch by Berwin Turlach.)
o isGeneric() produced an error for primitives that can not have
methods.
o .C() or .Fortran() had a lack-of-protection error if the
registration information resulted in an argument being coerced to
another type.
o boxplot(x=x, at=at) with non finite elements in x and non integer
at could not generate a warning but failed.
o heatmap(x, symm=TRUE, RowSideColors=*) no longer draws the colors
in reversed order.
o predict(<ar>) was incorrect in the multivariate case, for p >= 2.
o print(x, max=m) is now consistent when x is a "Date"; also the
"reached ... max.print .." messages are now consistently using
single brackets.
o Closed the <li> tag in pages generated by Rd2HTML(). (PR#14841.)
o Axis tick marks could go out of range when a log scale was used.
(PR#14833.)
o Signature objects in methods were not allocated as S4 objects
(caused a problem with trace() reported by Martin Morgan).
Bump PKGREVISION as fix to mk/compiler/g95.mk means that correct FC value is now stored in R/etc/Makeconf meaning that R can now build modules outside of pkgsrc context.
Bump all packages that use perl, or depend on a p5-* package, or are called p5-*. I hope that's all of them.
Pullup ticket #3927 - requested by tron
graphics/cairo: build fix
Revisions pulled up:
- archivers/ark/Makefile 1.9
- archivers/file-roller/Makefile 1.121
- audio/albumplayer/Makefile 1.22
- audio/amarok-kde3/Makefile 1.28
- audio/amarok/Makefile 1.115
- audio/ario/Makefile 1.23
- audio/audacious-plugins/Makefile 1.34
- audio/audacious/Makefile 1.28
- audio/audacious/buildlink3.mk 1.20
- audio/audacity/Makefile 1.78
- audio/aumix-gtk/Makefile 1.18
- audio/bmp-esound/Makefile 1.30
- audio/bmp-flac/Makefile 1.13
- audio/bmp-mac/Makefile 1.19
- audio/bmp-musepack/Makefile 1.27
- audio/bmp-pulse/Makefile 1.17
- audio/bmp-scrobbler/Makefile 1.15
- audio/bmp/Makefile 1.49
- audio/bmp/buildlink3.mk 1.23
- audio/bmpx/Makefile 1.48
- audio/bsl/Makefile 1.17
- audio/buzztard/Makefile 1.21
- audio/easytag/Makefile 1.76
- audio/exaile/Makefile 1.34
- audio/gbemol/Makefile 1.18
- audio/gimmix/Makefile 1.24
- audio/gkrellm-volume/Makefile 1.41
- audio/glurp/Makefile 1.28
- audio/gmp3info/Makefile 1.40
- audio/gmpc-albumview/Makefile 1.12
- audio/gmpc-lastfm/Makefile 1.11
- audio/gmpc-lyrics/Makefile 1.12
- audio/gmpc-lyricwiki/Makefile 1.14
- audio/gmpc-magnatune/Makefile 1.16
- audio/gmpc-mdcover/Makefile 1.11
- audio/gmpc-tagedit/Makefile 1.12
- audio/gmpc/Makefile 1.53
- audio/gmpc/buildlink3.mk 1.17
- audio/gnome-vfs-cdda/Makefile 1.20
- audio/gqmpeg-devel/Makefile 1.39
- audio/gtick/Makefile 1.26
- audio/gtkpod/Makefile 1.46
- audio/hydrogen/Makefile 1.31
- audio/jack-rack/Makefile 1.25
- audio/libcanberra/Makefile 1.26
- audio/libcanberra/buildlink3.mk 1.16
- audio/libgpod/Makefile 1.29
- audio/libgpod/buildlink3.mk 1.15
- audio/liblastfm/Makefile 1.22
- audio/liblastfm/buildlink3.mk 1.14
- audio/libvisual-bmp/Makefile 1.31
- audio/libvisual-plugins/Makefile 1.35
- audio/libvisual0.2-plugins/Makefile 1.18
- audio/liteamp/Makefile 1.52
- audio/mp3diags/Makefile 1.29
- audio/mp3splt-gtk/Makefile 1.14
- audio/muse/Makefile 1.42
- audio/padevchooser/Makefile 1.23
- audio/paman/Makefile 1.19
- audio/paprefs/Makefile 1.20
- audio/pavucontrol/Makefile 1.22
- audio/pavumeter/Makefile 1.20
- audio/pulseaudio/Makefile 1.60
- audio/py-musique/Makefile 1.35
- audio/qjackctl/Makefile 1.20
- audio/rhythmbox/Makefile 1.98
- audio/sfxr/Makefile 1.13
- audio/snd/Makefile 1.70
- audio/solfege/Makefile 1.39
- audio/sonata/Makefile 1.30
- audio/sound-juicer/Makefile 1.55
- audio/streamtuner/Makefile 1.58
- audio/streamtuner/buildlink3.mk 1.27
- audio/sweep/Makefile 1.55
- audio/terminatorx/Makefile 1.32
- audio/timidity/Makefile 1.85
- audio/xfce4-mixer/Makefile 1.40
- audio/xfce4-xmms-plugin/Makefile 1.28
- audio/xfce4-xmms-plugin/buildlink3.mk 1.32
- biology/chemtool/Makefile 1.41
- biology/gnome-chemistry-utils/Makefile 1.14
- biology/openbabel/Makefile 1.10
- cad/boolean/Makefile 1.57
- cad/geda/Makefile 1.79
- cad/gerbv/Makefile 1.50
- cad/gsmc/Makefile 1.26
- cad/gtk2-wcalc/Makefile 1.18
- cad/gtkwave/Makefile 1.43
- cad/gwave/Makefile 1.47
- cad/librecad/Makefile 1.10
- cad/openscad/Makefile 1.13
- cad/pcb/Makefile 1.63
- cad/transcalc/Makefile 1.33
- chat/empathy/Makefile 1.42
- chat/empathy/buildlink3.mk 1.20
- chat/finch/Makefile 1.45
- chat/gajim/Makefile 1.15
- chat/gg2/Makefile 1.43
- chat/gnomeicu/Makefile 1.83
- chat/gossip/Makefile 1.79
- chat/konversation/Makefile 1.48
- chat/libpurple/Makefile 1.46
- chat/libpurple/buildlink3.mk 1.34
- chat/msn-pecan/Makefile 1.21
- chat/pidgin-facebookchat/Makefile 1.28
- chat/pidgin-icb/Makefile 1.24
- chat/pidgin-latex/Makefile 1.27
- chat/pidgin-libnotify/Makefile 1.20
- chat/pidgin-otr/Makefile 1.30
- chat/pidgin-sametime/Makefile 1.32
- chat/pidgin-silc/Makefile 1.35
- chat/pidgin/Makefile 1.45
- chat/pidgin/buildlink3.mk 1.31
- chat/psi/Makefile 1.69
- chat/spectrum/Makefile 1.23
- chat/telepathy-farsight/Makefile 1.26
- chat/telepathy-farsight/buildlink3.mk 1.20
- chat/telepathy-mission-control/Makefile 1.20
- chat/telepathy-mission-control/buildlink3.mk 1.15
- chat/xchat-systray-integration/Makefile 1.30
- chat/xchat/Makefile 1.79
- comms/asterisk10/Makefile 1.30
- comms/asterisk18/Makefile 1.48
- comms/efax-gtk/Makefile 1.59
- comms/gnome-pilot/Makefile 1.71
- comms/gnome-pilot/buildlink3.mk 1.44
- comms/jpilot-syncmal/Makefile 1.54
- comms/jpilot/Makefile 1.83
- comms/jpilot/buildlink3.mk 1.26
- comms/multisync-gui/Makefile 1.22
- converters/tex2rtf/Makefile 1.36
- databases/gourmet/Makefile 1.30
- databases/gq/Makefile 1.53
- databases/gramps/Makefile 1.60
- databases/gramps2/Makefile 1.57
- databases/gramps3/Makefile 1.35
- databases/gtkdbfeditor/Makefile 1.8
- databases/libgnomedb/Makefile 1.87
- databases/libgnomedb/buildlink3.mk 1.40
- databases/mergeant/Makefile 1.79
- databases/mysql-workbench/Makefile 1.17
- databases/p5-RRD-Simple/Makefile 1.14
- databases/pgadmin3/Makefile 1.30
- databases/rrdtool/Makefile 1.99
- databases/rrdtool/buildlink3.mk 1.35
- databases/ruby-rrdtool/Makefile 1.7
- devel/GConf-ui/Makefile 1.23
- devel/GConf-ui/buildlink3.mk 1.16
- devel/SDL_Pango/Makefile 1.15
- devel/SDL_Pango/buildlink3.mk 1.12
- devel/anjuta/Makefile 1.93
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- x11/lablgtk/buildlink3.mk 1.22
- x11/libX11/Makefile 1.28
- x11/libdesktop-agnostic/Makefile 1.10
- x11/libdesktop-agnostic/buildlink3.mk 1.7
- x11/libgnomekbd/Makefile 1.37
- x11/libunique/Makefile 1.21
- x11/libunique/buildlink3.mk 1.15
- x11/libunique3/Makefile 1.9
- x11/libxcb/buildlink3.mk 1.3
- x11/libxfce4gui/Makefile 1.41
- x11/libxfce4gui/buildlink3.mk 1.40
- x11/libxfce4menu/Makefile 1.11
- x11/libxfce4menu/buildlink3.mk 1.13
- x11/libxfce4util/Makefile 1.27
- x11/matchbox-panel-manager/Makefile 1.24
- x11/mlterm/Makefile 1.72
- x11/nucleo/Makefile 1.29
- x11/nucleo/buildlink3.mk 1.24
- x11/p5-Alien-wxWidgets/Makefile 1.20
- x11/p5-Wx-Perl-ProcessStream/Makefile 1.19
- x11/p5-Wx/Makefile 1.24
- x11/p5-Wx/buildlink3.mk 1.15
- x11/p5-gtk2/Makefile 1.49
- x11/p5-gtk2/buildlink3.mk 1.16
- x11/py-gnome2-desktop/Makefile 1.67
- x11/py-gnome2-desktop/buildlink3.mk 1.21
- x11/py-gnome2-extras/Makefile 1.57
- x11/py-gnome2-extras/buildlink3.mk 1.32
- x11/py-gnome2/Makefile 1.86
- x11/py-gnome2/buildlink3.mk 1.41
- x11/py-gtk2/Makefile 1.87
- x11/py-gtk2/buildlink3.mk 1.40
- x11/py-gtksourceview/Makefile 1.24
- x11/py-kde4/Makefile 1.14
- x11/py-kiwi/Makefile 1.22
- x11/py-qt4-qscintilla/Makefile 1.22
- x11/py-qt4-qscintilla/buildlink3.mk 1.16
- x11/py-qt4/Makefile 1.54
- x11/py-vte/Makefile 1.11
- x11/py-vte/buildlink3.mk 1.11
- x11/py-wxWidgets/Makefile 1.39
- x11/py-wxWidgets/buildlink3.mk 1.33
- x11/qt4-creator/Makefile 1.15
- x11/qt4-docs/Makefile 1.23
- x11/qt4-libs/Makefile 1.78
- x11/qt4-libs/buildlink3.mk 1.34
- x11/qt4-mng/Makefile 1.17
- x11/qt4-mysql/Makefile 1.26
- x11/qt4-pgsql/Makefile 1.34
- x11/qt4-qdbus/Makefile 1.28
- x11/qt4-qdbus/buildlink3.mk 1.17
- x11/qt4-qscintilla/Makefile 1.21
- x11/qt4-qscintilla/buildlink3.mk 1.15
- x11/qt4-sqlite3/Makefile 1.29
- x11/qt4-tiff/Makefile 1.26
- x11/qt4-tools/Makefile 1.54
- x11/qt4-tools/buildlink3.mk 1.24
- x11/qwt-qt4/Makefile 1.20
- x11/qwt-qt4/buildlink3.mk 1.17
- x11/qwt6-qt4/Makefile 1.5
- x11/qwt6-qt4/buildlink3.mk 1.4
- x11/qwtplot3d-qt4/Makefile 1.15
- x11/qwtplot3d-qt4/buildlink3.mk 1.15
- x11/rep-gtk2/Makefile 1.22
- x11/rox-session/Makefile 1.31
- x11/ruby-gnome2-gtk/Makefile 1.36
- x11/ruby-gnome2-gtk/buildlink3.mk 1.21
- x11/ruby-gnome2-gtksourceview2/Makefile 1.25
- x11/ruby-gnome2-vte/Makefile 1.28
- x11/ruby-wxruby/Makefile 1.8
- x11/sakura/Makefile 1.10
- x11/startup-notification/Makefile 1.26
- x11/startup-notification010/Makefile 1.3
- x11/tint2/Makefile 1.19
- x11/vte/Makefile 1.92
- x11/vte/buildlink3.mk 1.33
- x11/vte029/Makefile 1.4
- x11/vte029/buildlink3.mk 1.4
- x11/wxGTK24/Makefile 1.22
- x11/wxGTK24/buildlink3.mk 1.25
- x11/wxGTK26-contrib/Makefile 1.15
- x11/wxGTK26-contrib/buildlink3.mk 1.18
- x11/wxGTK26/Makefile 1.18
- x11/wxGTK26/buildlink3.mk 1.17
- x11/wxGTK28-contrib/Makefile 1.18
- x11/wxGTK28-contrib/buildlink3.mk 1.18
- x11/wxGTK28/Makefile 1.26
- x11/wxGTK28/buildlink3.mk 1.19
- x11/wxhaskell/Makefile 1.38
- x11/x11vnc/Makefile 1.43
- x11/xcb-util-image/Makefile 1.2
- x11/xcb-util-keysyms/Makefile 1.2
- x11/xcb-util-renderutil/Makefile 1.2
- x11/xcb-util-wm/Makefile 1.2
- x11/xcb-util/Makefile 1.9
- x11/xcb-util036/Makefile 1.2
- x11/xdialog/Makefile 1.34
- x11/xfce4-clipman-plugin/Makefile 1.27
- x11/xfce4-clipman-plugin/buildlink3.mk 1.31
- x11/xfce4-desktop/Makefile 1.48
- x11/xfce4-exo/Makefile 1.23
- x11/xfce4-exo/buildlink3.mk 1.18
- x11/xfce4-eyes-plugin/Makefile 1.15
- x11/xfce4-eyes-plugin/buildlink3.mk 1.17
- x11/xfce4-gtk2-engine/Makefile 1.24
- x11/xfce4-notes-plugin/Makefile 1.29
- x11/xfce4-notes-plugin/buildlink3.mk 1.33
- x11/xfce4-panel/Makefile 1.51
- x11/xfce4-panel/buildlink3.mk 1.38
- x11/xfce4-places-plugin/Makefile 1.18
- x11/xfce4-places-plugin/buildlink3.mk 1.20
- x11/xfce4-screenshooter-plugin/Makefile 1.15
- x11/xfce4-screenshooter-plugin/buildlink3.mk 1.17
- x11/xfce4-session/Makefile 1.39
- x11/xfce4-session/buildlink3.mk 1.34
- x11/xfce4-settings/Makefile 1.18
- x11/xfce4-terminal/Makefile 1.25
- x11/xfce4-utils/Makefile 1.46
- x11/xlockmore/Makefile 1.98
- x11/xlsclients/Makefile 1.8
- x11/xpad/Makefile 1.41
- x11/xplanet/Makefile 1.59
- x11/xscreensaver-demo/Makefile 1.47
- x11/xvidcap-gtk2/Makefile 1.23
- x11/xwininfo/Makefile 1.8
- x11/zenity/Makefile 1.71
-------------------------------------------------------------------
Module Name: pkgsrc
Committed By: tron
Date: Tue Oct 2 07:39:30 UTC 2012
Modified Files:
pkgsrc/graphics/cairo: Makefile buildlink3.mk options.mk
Log Message:
The "cairo" package needs at least version 1.6 of the "libxcb" library.
Set the minimum version accordingly. The package now uses "libxcb" from
"pkgsrc" under Mac OS X Snow Leopard which fixes the build.
Bump package revision because of the dependence change.
To generate a diff of this commit:
cvs rdiff -u -r1.104 -r1.105 pkgsrc/graphics/cairo/Makefile
cvs rdiff -u -r1.42 -r1.43 pkgsrc/graphics/cairo/buildlink3.mk
cvs rdiff -u -r1.7 -r1.8 pkgsrc/graphics/cairo/options.mk
-------------------------------------------------------------------
Module Name: pkgsrc
Committed By: tron
Date: Tue Oct 2 12:09:42 UTC 2012
Modified Files:
pkgsrc/graphics/cairo: buildlink3.mk options.mk
pkgsrc/multimedia/vlc: Makefile
pkgsrc/multimedia/vlc10: Makefile
pkgsrc/multimedia/vlc2: Makefile
pkgsrc/multimedia/xine-lib: Makefile
pkgsrc/pkgtools/x11-links: Makefile
pkgsrc/x11/libX11: Makefile
pkgsrc/x11/libxcb: buildlink3.mk
pkgsrc/x11/startup-notification: Makefile
pkgsrc/x11/startup-notification010: Makefile
pkgsrc/x11/xcb-util: Makefile
pkgsrc/x11/xcb-util-image: Makefile
pkgsrc/x11/xcb-util-keysyms: Makefile
pkgsrc/x11/xcb-util-renderutil: Makefile
pkgsrc/x11/xcb-util-wm: Makefile
pkgsrc/x11/xcb-util036: Makefile
pkgsrc/x11/xlsclients: Makefile
pkgsrc/x11/xwininfo: Makefile
Log Message:
Increase the minium required version of the "x11/libxcb" package to 1.6.
There are at least two packages ("graphics/cairo" and "x11/xlsclients")
which require this. And we definitely want to avoid the situation where
both the based and "pkgsrc" version get used at the same time.
Bump all the packages which use the "x11/libxcb" package except the two
which already require version 1.6. For those package remove the manually
set minimum required version.
Change discussed with Thomas Klausner in private e-mail.
To generate a diff of this commit:
cvs rdiff -u -r1.43 -r1.44 pkgsrc/graphics/cairo/buildlink3.mk
cvs rdiff -u -r1.8 -r1.9 pkgsrc/graphics/cairo/options.mk
cvs rdiff -u -r1.139 -r1.140 pkgsrc/multimedia/vlc/Makefile
cvs rdiff -u -r1.20 -r1.21 pkgsrc/multimedia/vlc10/Makefile
cvs rdiff -u -r1.12 -r1.13 pkgsrc/multimedia/vlc2/Makefile
cvs rdiff -u -r1.105 -r1.106 pkgsrc/multimedia/xine-lib/Makefile
cvs rdiff -u -r1.134 -r1.135 pkgsrc/pkgtools/x11-links/Makefile
cvs rdiff -u -r1.27 -r1.28 pkgsrc/x11/libX11/Makefile
cvs rdiff -u -r1.2 -r1.3 pkgsrc/x11/libxcb/buildlink3.mk
cvs rdiff -u -r1.25 -r1.26 pkgsrc/x11/startup-notification/Makefile
cvs rdiff -u -r1.2 -r1.3 pkgsrc/x11/startup-notification010/Makefile
cvs rdiff -u -r1.8 -r1.9 pkgsrc/x11/xcb-util/Makefile
cvs rdiff -u -r1.1 -r1.2 pkgsrc/x11/xcb-util-image/Makefile
cvs rdiff -u -r1.1 -r1.2 pkgsrc/x11/xcb-util-keysyms/Makefile
cvs rdiff -u -r1.1 -r1.2 pkgsrc/x11/xcb-util-renderutil/Makefile
cvs rdiff -u -r1.1 -r1.2 pkgsrc/x11/xcb-util-wm/Makefile
cvs rdiff -u -r1.1 -r1.2 pkgsrc/x11/xcb-util036/Makefile
cvs rdiff -u -r1.7 -r1.8 pkgsrc/x11/xlsclients/Makefile
cvs rdiff -u -r1.7 -r1.8 pkgsrc/x11/xwininfo/Makefile
-------------------------------------------------------------------
Module Name: pkgsrc
Committed By: tron
Date: Tue Oct 2 12:17:10 UTC 2012
Modified Files:
pkgsrc/pkgtools/x11-links: Makefile buildlink3.mk
Log Message:
Increase version number to 0.71 instead of bumping the revision. Also
increase the minimum required version to 0.71.
To generate a diff of this commit:
cvs rdiff -u -r1.135 -r1.136 pkgsrc/pkgtools/x11-links/Makefile
cvs rdiff -u -r1.43 -r1.44 pkgsrc/pkgtools/x11-links/buildlink3.mk
-------------------------------------------------------------------
Module Name: pkgsrc
Committed By: tron
Date: Tue Oct 2 17:12:24 UTC 2012
Modified Files:
pkgsrc/archivers/ark: Makefile
pkgsrc/archivers/file-roller: Makefile
pkgsrc/audio/albumplayer: Makefile
pkgsrc/audio/amarok: Makefile
pkgsrc/audio/amarok-kde3: Makefile
pkgsrc/audio/ario: Makefile
pkgsrc/audio/audacious: Makefile buildlink3.mk
pkgsrc/audio/audacious-plugins: Makefile
pkgsrc/audio/audacity: Makefile
pkgsrc/audio/aumix-gtk: Makefile
pkgsrc/audio/bmp: Makefile buildlink3.mk
pkgsrc/audio/bmp-esound: Makefile
pkgsrc/audio/bmp-flac: Makefile
pkgsrc/audio/bmp-mac: Makefile
pkgsrc/audio/bmp-musepack: Makefile
pkgsrc/audio/bmp-pulse: Makefile
pkgsrc/audio/bmp-scrobbler: Makefile
pkgsrc/audio/bmpx: Makefile
pkgsrc/audio/bsl: Makefile
pkgsrc/audio/buzztard: Makefile
pkgsrc/audio/easytag: Makefile
pkgsrc/audio/exaile: Makefile
pkgsrc/audio/gbemol: Makefile
pkgsrc/audio/gimmix: Makefile
pkgsrc/audio/gkrellm-volume: Makefile
pkgsrc/audio/glurp: Makefile
pkgsrc/audio/gmp3info: Makefile
pkgsrc/audio/gmpc: Makefile buildlink3.mk
pkgsrc/audio/gmpc-albumview: Makefile
pkgsrc/audio/gmpc-lastfm: Makefile
pkgsrc/audio/gmpc-lyrics: Makefile
pkgsrc/audio/gmpc-lyricwiki: Makefile
pkgsrc/audio/gmpc-magnatune: Makefile
pkgsrc/audio/gmpc-mdcover: Makefile
pkgsrc/audio/gmpc-tagedit: Makefile
pkgsrc/audio/gnome-vfs-cdda: Makefile
pkgsrc/audio/gqmpeg-devel: Makefile
pkgsrc/audio/gtick: Makefile
pkgsrc/audio/gtkpod: Makefile
pkgsrc/audio/hydrogen: Makefile
pkgsrc/audio/jack-rack: Makefile
pkgsrc/audio/libcanberra: Makefile buildlink3.mk
pkgsrc/audio/libgpod: Makefile buildlink3.mk
pkgsrc/audio/liblastfm: Makefile buildlink3.mk
pkgsrc/audio/libvisual-bmp: Makefile
pkgsrc/audio/libvisual-plugins: Makefile
pkgsrc/audio/libvisual0.2-plugins: Makefile
pkgsrc/audio/liteamp: Makefile
pkgsrc/audio/mp3diags: Makefile
pkgsrc/audio/mp3splt-gtk: Makefile
pkgsrc/audio/muse: Makefile
pkgsrc/audio/padevchooser: Makefile
pkgsrc/audio/paman: Makefile
pkgsrc/audio/paprefs: Makefile
pkgsrc/audio/pavucontrol: Makefile
pkgsrc/audio/pavumeter: Makefile
pkgsrc/audio/pulseaudio: Makefile
pkgsrc/audio/py-musique: Makefile
pkgsrc/audio/qjackctl: Makefile
pkgsrc/audio/rhythmbox: Makefile
pkgsrc/audio/sfxr: Makefile
pkgsrc/audio/snd: Makefile
pkgsrc/audio/solfege: Makefile
pkgsrc/audio/sonata: Makefile
pkgsrc/audio/sound-juicer: Makefile
pkgsrc/audio/streamtuner: Makefile buildlink3.mk
pkgsrc/audio/sweep: Makefile
pkgsrc/audio/terminatorx: Makefile
pkgsrc/audio/timidity: Makefile
pkgsrc/audio/xfce4-mixer: Makefile
pkgsrc/audio/xfce4-xmms-plugin: Makefile buildlink3.mk
pkgsrc/biology/chemtool: Makefile
pkgsrc/biology/gnome-chemistry-utils: Makefile
pkgsrc/biology/openbabel: Makefile
pkgsrc/cad/boolean: Makefile
pkgsrc/cad/geda: Makefile
pkgsrc/cad/gerbv: Makefile
pkgsrc/cad/gsmc: Makefile
pkgsrc/cad/gtk2-wcalc: Makefile
pkgsrc/cad/gtkwave: Makefile
pkgsrc/cad/gwave: Makefile
pkgsrc/cad/librecad: Makefile
pkgsrc/cad/openscad: Makefile
pkgsrc/cad/pcb: Makefile
pkgsrc/cad/transcalc: Makefile
pkgsrc/chat/empathy: Makefile buildlink3.mk
pkgsrc/chat/finch: Makefile
pkgsrc/chat/gajim: Makefile
pkgsrc/chat/gg2: Makefile
pkgsrc/chat/gnomeicu: Makefile
pkgsrc/chat/gossip: Makefile
pkgsrc/chat/konversation: Makefile
pkgsrc/chat/libpurple: Makefile buildlink3.mk
pkgsrc/chat/msn-pecan: Makefile
pkgsrc/chat/pidgin: Makefile buildlink3.mk
pkgsrc/chat/pidgin-facebookchat: Makefile
pkgsrc/chat/pidgin-icb: Makefile
pkgsrc/chat/pidgin-latex: Makefile
pkgsrc/chat/pidgin-libnotify: Makefile
pkgsrc/chat/pidgin-otr: Makefile
pkgsrc/chat/pidgin-sametime: Makefile
pkgsrc/chat/pidgin-silc: Makefile
pkgsrc/chat/psi: Makefile
pkgsrc/chat/spectrum: Makefile
pkgsrc/chat/telepathy-farsight: Makefile buildlink3.mk
pkgsrc/chat/telepathy-mission-control: Makefile buildlink3.mk
pkgsrc/chat/xchat: Makefile
pkgsrc/chat/xchat-systray-integration: Makefile
pkgsrc/comms/asterisk10: Makefile
pkgsrc/comms/asterisk18: Makefile
pkgsrc/comms/efax-gtk: Makefile
pkgsrc/comms/gnome-pilot: Makefile buildlink3.mk
pkgsrc/comms/jpilot: Makefile buildlink3.mk
pkgsrc/comms/jpilot-syncmal: Makefile
pkgsrc/comms/multisync-gui: Makefile
pkgsrc/converters/tex2rtf: Makefile
pkgsrc/databases/gourmet: Makefile
pkgsrc/databases/gq: Makefile
pkgsrc/databases/gramps: Makefile
pkgsrc/databases/gramps2: Makefile
pkgsrc/databases/gramps3: Makefile
pkgsrc/databases/gtkdbfeditor: Makefile
pkgsrc/databases/libgnomedb: Makefile buildlink3.mk
pkgsrc/databases/mergeant: Makefile
pkgsrc/databases/mysql-workbench: Makefile
pkgsrc/databases/p5-RRD-Simple: Makefile
pkgsrc/databases/pgadmin3: Makefile
pkgsrc/databases/rrdtool: Makefile buildlink3.mk
pkgsrc/databases/ruby-rrdtool: Makefile
pkgsrc/devel/GConf-ui: Makefile buildlink3.mk
pkgsrc/devel/SDL_Pango: Makefile buildlink3.mk
pkgsrc/devel/anjuta: Makefile
pkgsrc/devel/at-spi: Makefile buildlink3.mk
pkgsrc/devel/automoc4: Makefile
pkgsrc/devel/blib: Makefile buildlink3.mk
pkgsrc/devel/boa-constructor: Makefile
pkgsrc/devel/coconut: Makefile
pkgsrc/devel/compizconfig-backend-gconf: Makefile
pkgsrc/devel/cppcheck: Makefile
pkgsrc/devel/cutter: Makefile
pkgsrc/devel/dconf-editor: Makefile
pkgsrc/devel/devhelp: Makefile buildlink3.mk
pkgsrc/devel/distccmon-gnome: Makefile
pkgsrc/devel/distccmon-gtk: Makefile
pkgsrc/devel/eric4: Makefile
pkgsrc/devel/ethos: Makefile buildlink3.mk
pkgsrc/devel/frama-c: Makefile
pkgsrc/devel/gconfmm: Makefile buildlink3.mk
pkgsrc/devel/gdl: Makefile buildlink3.mk
pkgsrc/devel/geany: Makefile
pkgsrc/devel/glade: Makefile
pkgsrc/devel/glade3: Makefile buildlink3.mk
pkgsrc/devel/gmtk: Makefile buildlink3.mk
pkgsrc/devel/gnome-build: Makefile buildlink3.mk
pkgsrc/devel/gobject-introspection: Makefile
pkgsrc/devel/gps: Makefile
pkgsrc/devel/gst-plugins0.10-pango: Makefile
pkgsrc/devel/guile-gnome: Makefile
pkgsrc/devel/kdesdk4: Makefile
pkgsrc/devel/kdevelop4: Makefile
pkgsrc/devel/kdevplatform: Makefile
pkgsrc/devel/kdiff3: Makefile
pkgsrc/devel/libbonoboui: Makefile buildlink3.mk
pkgsrc/devel/libcompizconfig: Makefile
pkgsrc/devel/libdbusmenu-qt: Makefile buildlink3.mk
pkgsrc/devel/libextractor: Makefile
pkgsrc/devel/libgail-gnome: Makefile buildlink3.mk
pkgsrc/devel/libglade: Makefile buildlink3.mk
pkgsrc/devel/libglademm: Makefile buildlink3.mk
pkgsrc/devel/libgnome: Makefile buildlink3.mk
pkgsrc/devel/libgnomemm: Makefile buildlink3.mk
pkgsrc/devel/libgnomeui: Makefile buildlink3.mk
pkgsrc/devel/libgnomeuimm: Makefile buildlink3.mk
pkgsrc/devel/libgweather: Makefile buildlink3.mk
pkgsrc/devel/libpeas: Makefile buildlink3.mk
pkgsrc/devel/libsexy: Makefile buildlink3.mk
pkgsrc/devel/libsexymm: Makefile buildlink3.mk
pkgsrc/devel/libview: Makefile buildlink3.mk
pkgsrc/devel/libwnck: Makefile buildlink3.mk
pkgsrc/devel/mono-tools: Makefile
pkgsrc/devel/monodevelop: Makefile buildlink3.mk
pkgsrc/devel/monodevelop-database: Makefile
pkgsrc/devel/monotone-viz: Makefile
pkgsrc/devel/p5-Gnome2: Makefile
pkgsrc/devel/p5-Gtk2-GladeXML: Makefile
pkgsrc/devel/p5-Wx-Perl-DataWalker: Makefile
pkgsrc/devel/p5-pango: Makefile buildlink3.mk
pkgsrc/devel/pango: Makefile buildlink3.mk
pkgsrc/devel/pangomm: Makefile buildlink3.mk
pkgsrc/devel/py-compizconfig: Makefile
pkgsrc/devel/py-gobject: Makefile
pkgsrc/devel/py-gobject-shared: Makefile
pkgsrc/devel/py-gobject3: Makefile
pkgsrc/devel/qconf: Makefile
pkgsrc/devel/qjson: Makefile
pkgsrc/devel/qtscriptgenerator: Makefile buildlink3.mk
pkgsrc/devel/rapidsvn: Makefile
pkgsrc/devel/ruby-gnome2-pango: Makefile buildlink3.mk
pkgsrc/devel/scintilla: Makefile buildlink3.mk
pkgsrc/devel/swt: Makefile
pkgsrc/devel/valide: Makefile
pkgsrc/devel/xfce4-dev-tools: Makefile
pkgsrc/devel/xfconf: Makefile
pkgsrc/devel/xulrunner: Makefile buildlink3.mk
pkgsrc/devel/xulrunner10: Makefile buildlink3.mk
pkgsrc/devel/xulrunner192: Makefile buildlink3.mk
pkgsrc/editors/Sigil: Makefile
pkgsrc/editors/TeXmacs-devel: Makefile
pkgsrc/editors/abiword: Makefile
pkgsrc/editors/abiword-plugins: Makefile
pkgsrc/editors/beaver: Makefile
pkgsrc/editors/conglomerate: Makefile
pkgsrc/editors/dasher: Makefile
pkgsrc/editors/emacs: Makefile
pkgsrc/editors/emacs-snapshot: Makefile
pkgsrc/editors/emacs22: Makefile
pkgsrc/editors/emacs24: Makefile
pkgsrc/editors/gconf-editor: Makefile
pkgsrc/editors/gedit: Makefile buildlink3.mk
pkgsrc/editors/gedit-python: Makefile
pkgsrc/editors/gedit3: Makefile
pkgsrc/editors/gedit3-spell: Makefile
pkgsrc/editors/ghex: Makefile
pkgsrc/editors/gice: Makefile
pkgsrc/editors/gobby: Makefile
pkgsrc/editors/gtranslator: Makefile
pkgsrc/editors/gummi: Makefile
pkgsrc/editors/kate: Makefile
pkgsrc/editors/kile: Makefile
pkgsrc/editors/leafpad: Makefile
pkgsrc/editors/lyx: Makefile
pkgsrc/editors/medit: Makefile
pkgsrc/editors/mlview: Makefile
pkgsrc/editors/notecase: Makefile
pkgsrc/editors/p5-Padre: Makefile
pkgsrc/editors/p5-Wx-Scintilla: Makefile
pkgsrc/editors/poedit: Makefile
pkgsrc/editors/qgoogletranslator: Makefile
pkgsrc/editors/scite: Makefile
pkgsrc/editors/tea: Makefile
pkgsrc/editors/texmaker: Makefile
pkgsrc/editors/texworks: Makefile
pkgsrc/editors/tomboy: Makefile
pkgsrc/editors/vim-gtk2: Makefile
pkgsrc/editors/xfce4-mousepad: Makefile
pkgsrc/editors/xournal: Makefile
pkgsrc/emulators/blinkensim: Makefile
pkgsrc/emulators/bochs: Makefile
pkgsrc/emulators/e-uae: Makefile
pkgsrc/emulators/fuse: Makefile
pkgsrc/emulators/gambatte: Makefile
pkgsrc/emulators/gens: Makefile
pkgsrc/emulators/gpsim: Makefile
pkgsrc/emulators/gpsim-devel: Makefile buildlink3.mk
pkgsrc/emulators/gpsim-oscilloscope: Makefile
pkgsrc/emulators/gpsim-ptyusart: Makefile
pkgsrc/emulators/mame: Makefile
pkgsrc/emulators/mess: Makefile
pkgsrc/emulators/nestopia: Makefile
pkgsrc/emulators/snes9x-gtk: Makefile
pkgsrc/emulators/tme: Makefile
pkgsrc/emulators/uae: Makefile
pkgsrc/emulators/vice: Makefile
pkgsrc/emulators/xnp2: Makefile
pkgsrc/emulators/yabause: Makefile
pkgsrc/filesystems/fuse-pod: Makefile
pkgsrc/finance/gkrellm-stock: Makefile
pkgsrc/finance/gnucash: Makefile
pkgsrc/fonts/fntsample: Makefile
pkgsrc/fonts/fontforge: Makefile
pkgsrc/fonts/gbdfed: Makefile
pkgsrc/fonts/gucharmap: Makefile buildlink3.mk
pkgsrc/games/atomix: Makefile
pkgsrc/games/blinken: Makefile
pkgsrc/games/bluemoon: Makefile
pkgsrc/games/ccgo: Makefile
pkgsrc/games/crack-attack: Makefile
pkgsrc/games/crossfire-client-gtk2: Makefile
pkgsrc/games/dopewars: Makefile
pkgsrc/games/eboard: Makefile
pkgsrc/games/flightgear: Makefile
pkgsrc/games/freeciv-client: Makefile
pkgsrc/games/frozen-bubble: Makefile
pkgsrc/games/gamazons: Makefile
pkgsrc/games/gbrainy: Makefile
pkgsrc/games/gcompris: Makefile
pkgsrc/games/genecys-client: Makefile
pkgsrc/games/gnome-games: Makefile
pkgsrc/games/gnome-mastermind: Makefile
pkgsrc/games/grhino: Makefile
pkgsrc/games/gtetrinet: Makefile
pkgsrc/games/gtkballs: Makefile
pkgsrc/games/gtklevel9: Makefile
pkgsrc/games/gtkmagnetic: Makefile
pkgsrc/games/gturing: Makefile
pkgsrc/games/holtz: Makefile
pkgsrc/games/kanagram: Makefile
pkgsrc/games/kanatest: Makefile
pkgsrc/games/kdegames4: Makefile
pkgsrc/games/kdetoys4: Makefile
pkgsrc/games/khangman: Makefile
pkgsrc/games/kye: Makefile
pkgsrc/games/pioneers: Makefile
pkgsrc/games/pokerth: Makefile
pkgsrc/games/puzzles: Makefile
pkgsrc/games/pytraffic: Makefile
pkgsrc/games/quarry: Makefile
pkgsrc/games/rftg: Makefile
pkgsrc/games/scummvm-tools: Makefile
pkgsrc/games/simgear: Makefile
pkgsrc/games/sirius: Makefile
pkgsrc/games/teg: Makefile
pkgsrc/games/wesnoth: Makefile
pkgsrc/games/wxhugo: Makefile
pkgsrc/games/xcowsay: Makefile
pkgsrc/geography/emerillon: Makefile
pkgsrc/geography/geoclue: Makefile
pkgsrc/geography/libchamplain04: Makefile buildlink3.mk
pkgsrc/geography/libchamplain06: Makefile buildlink3.mk
pkgsrc/geography/libchamplain08: Makefile buildlink3.mk
pkgsrc/geography/mapserver: Makefile
pkgsrc/geography/merkaartor: Makefile
pkgsrc/geography/qgis: Makefile
pkgsrc/geography/qlandkartegt: Makefile
pkgsrc/geography/qlandkartem: Makefile
pkgsrc/geography/viking: Makefile
pkgsrc/graphics/aqsis: Makefile
pkgsrc/graphics/blinkenthemes: Makefile
pkgsrc/graphics/blinkentools: Makefile
pkgsrc/graphics/cairo: Makefile buildlink3.mk
pkgsrc/graphics/cairo-gobject: Makefile buildlink3.mk
pkgsrc/graphics/cairomm: Makefile buildlink3.mk
pkgsrc/graphics/camlimages: Makefile
pkgsrc/graphics/cheese: Makefile
pkgsrc/graphics/cinepaint: Makefile
pkgsrc/graphics/clutter: Makefile buildlink3.mk
pkgsrc/graphics/clutter-box2d: Makefile
pkgsrc/graphics/clutter-cairo: Makefile buildlink3.mk
pkgsrc/graphics/clutter-gtk: Makefile buildlink3.mk
pkgsrc/graphics/clutter-mx: Makefile buildlink3.mk
pkgsrc/graphics/clutter-qt: Makefile
pkgsrc/graphics/clutter08: Makefile buildlink3.mk
pkgsrc/graphics/clutter08-gtk: Makefile buildlink3.mk
pkgsrc/graphics/comix: Makefile
pkgsrc/graphics/darktable: Makefile
pkgsrc/graphics/denemo: Makefile
pkgsrc/graphics/dia: Makefile
pkgsrc/graphics/dia-python: Makefile
pkgsrc/graphics/digikam: Makefile
pkgsrc/graphics/djview4: Makefile
pkgsrc/graphics/eog: Makefile buildlink3.mk
pkgsrc/graphics/eog-plugins: Makefile
pkgsrc/graphics/eog-plugins-map: Makefile
pkgsrc/graphics/eog3: Makefile
pkgsrc/graphics/evas-svg: Makefile
pkgsrc/graphics/extrema: Makefile
pkgsrc/graphics/f-spot: Makefile
pkgsrc/graphics/fotoxx: Makefile
pkgsrc/graphics/frameworks: Makefile
pkgsrc/graphics/geeqie: Makefile
pkgsrc/graphics/gegl: Makefile buildlink3.mk
pkgsrc/graphics/gfract: Makefile
pkgsrc/graphics/gimmage: Makefile
pkgsrc/graphics/gimp: Makefile buildlink3.mk
pkgsrc/graphics/gimp-color-manager: Makefile
pkgsrc/graphics/gimp-exif-browser: Makefile
pkgsrc/graphics/gimp-fix-ca: Makefile
pkgsrc/graphics/gimp-liquid-rescale: Makefile
pkgsrc/graphics/gimp-rawphoto: Makefile
pkgsrc/graphics/gimp-refocus-it: Makefile
pkgsrc/graphics/gimp-resynthesizer: Makefile
pkgsrc/graphics/gimp-ufraw: Makefile
pkgsrc/graphics/gimp2-wideangle: Makefile
pkgsrc/graphics/giram: Makefile
pkgsrc/graphics/gliv: Makefile
pkgsrc/graphics/gmngview: Makefile
pkgsrc/graphics/gnome-icon-theme: Makefile
pkgsrc/graphics/gnuplot: Makefile
pkgsrc/graphics/goocanvas: Makefile buildlink3.mk
pkgsrc/graphics/goocanvasmm: Makefile
pkgsrc/graphics/gpicview: Makefile
pkgsrc/graphics/gqview: Makefile
pkgsrc/graphics/gqview-devel: Makefile
pkgsrc/graphics/graphviz: Makefile
pkgsrc/graphics/gst-plugins0.10-cairo: Makefile
pkgsrc/graphics/gthumb: Makefile
pkgsrc/graphics/gthumb3: Makefile
pkgsrc/graphics/gtkam: Makefile
pkgsrc/graphics/gtkglext: Makefile buildlink3.mk
pkgsrc/graphics/gtkimageview: Makefile
pkgsrc/graphics/guile-cairo: Makefile
pkgsrc/graphics/gwenview: Makefile
pkgsrc/graphics/hugin: Makefile
pkgsrc/graphics/inkscape: Makefile
pkgsrc/graphics/kamera: Makefile
pkgsrc/graphics/kcolorchooser: Makefile
pkgsrc/graphics/kdegraphics-mobipocket: Makefile
pkgsrc/graphics/kdegraphics-strigi-analyzer: Makefile
pkgsrc/graphics/kdegraphics-thumbnailers: Makefile
pkgsrc/graphics/kgamma: Makefile
pkgsrc/graphics/kipi-plugins: Makefile
pkgsrc/graphics/kipi-plugins-calendar-kde3: Makefile
pkgsrc/graphics/kipi-plugins-kde3: Makefile
pkgsrc/graphics/kolourpaint: Makefile
pkgsrc/graphics/koverartist: Makefile
pkgsrc/graphics/kruler: Makefile
pkgsrc/graphics/ksaneplugin: Makefile
pkgsrc/graphics/ksnapshot: Makefile
pkgsrc/graphics/libexif-gtk: Makefile buildlink3.mk
pkgsrc/graphics/libgdiplus: Makefile buildlink3.mk
pkgsrc/graphics/libgnomecanvas: Makefile buildlink3.mk
pkgsrc/graphics/libgnomecanvasmm: Makefile buildlink3.mk
pkgsrc/graphics/libkdcraw: Makefile buildlink3.mk
pkgsrc/graphics/libkexiv2: Makefile
pkgsrc/graphics/libkface: Makefile buildlink3.mk
pkgsrc/graphics/libkipi: Makefile buildlink3.mk
pkgsrc/graphics/libksane: Makefile buildlink3.mk
pkgsrc/graphics/librsvg: Makefile buildlink3.mk
pkgsrc/graphics/libscigraphica: Makefile buildlink3.mk
pkgsrc/graphics/nvtv: Makefile
pkgsrc/graphics/opencv: Makefile
pkgsrc/graphics/osg: Makefile buildlink3.mk
pkgsrc/graphics/p5-Gnome2-Canvas: Makefile buildlink3.mk
pkgsrc/graphics/p5-cairo: Makefile buildlink3.mk
pkgsrc/graphics/p5-clutter: Makefile
pkgsrc/graphics/py-cairo: Makefile buildlink3.mk
pkgsrc/graphics/py-clutter: Makefile buildlink3.mk
pkgsrc/graphics/py-clutter-gtk: Makefile
pkgsrc/graphics/py-goocanvas: Makefile
pkgsrc/graphics/py-gtkglext: Makefile
pkgsrc/graphics/py-matplotlib-gtk2: Makefile
pkgsrc/graphics/qimageblitz: Makefile buildlink3.mk
pkgsrc/graphics/qiv: Makefile
pkgsrc/graphics/qiviewer: Makefile
pkgsrc/graphics/ristretto: Makefile
pkgsrc/graphics/ruby-clutter-cairo: Makefile
pkgsrc/graphics/ruby-clutter-core: Makefile
pkgsrc/graphics/ruby-clutter-gtk: Makefile
pkgsrc/graphics/ruby-gnome2-goocanvas: Makefile
pkgsrc/graphics/ruby-gnome2-rsvg: Makefile
pkgsrc/graphics/ruby-rcairo: Makefile buildlink3.mk
pkgsrc/graphics/sane-frontends: Makefile
pkgsrc/graphics/scidavis: Makefile
pkgsrc/graphics/scigraphica: Makefile
pkgsrc/graphics/shotwell: Makefile
pkgsrc/graphics/shotwell-gtk3: Makefile
pkgsrc/graphics/svgpart: Makefile
pkgsrc/graphics/tuxpaint: Makefile
pkgsrc/graphics/ucview: Makefile
pkgsrc/graphics/unicap: Makefile
pkgsrc/graphics/veusz: Makefile
pkgsrc/graphics/viewnior: Makefile
pkgsrc/graphics/wxsvg: Makefile buildlink3.mk
pkgsrc/graphics/xfce4-icon-theme: Makefile buildlink3.mk
pkgsrc/graphics/xsane: Makefile
pkgsrc/graphics/xzgv: Makefile
pkgsrc/graphics/zphoto: Makefile
pkgsrc/ham/gmfsk: Makefile
pkgsrc/ham/gnuradio-examples: Makefile
pkgsrc/ham/gnuradio-radio-astronomy: Makefile
pkgsrc/ham/gnuradio-wxgui: Makefile buildlink3.mk
pkgsrc/ham/gpredict: Makefile
pkgsrc/ham/grig: Makefile
pkgsrc/ham/xdx: Makefile
pkgsrc/ham/xlog: Makefile
pkgsrc/inputmethod/gcin: Makefile
pkgsrc/inputmethod/gtk-im-libthai: Makefile
pkgsrc/inputmethod/ibus: Makefile
pkgsrc/inputmethod/ibus-chewing: Makefile
pkgsrc/inputmethod/ibus-handwrite: Makefile
pkgsrc/inputmethod/ibus-input-pad: Makefile
pkgsrc/inputmethod/ibus-m17n: Makefile
pkgsrc/inputmethod/ibus-qt: Makefile
pkgsrc/inputmethod/ibus-skk: Makefile
pkgsrc/inputmethod/ibus-t9: Makefile
pkgsrc/inputmethod/ibus-unikey: Makefile
pkgsrc/inputmethod/im-ja: Makefile
pkgsrc/inputmethod/imhangul: Makefile
pkgsrc/inputmethod/imhangul_status_applet: Makefile
pkgsrc/inputmethod/input-pad: Makefile buildlink3.mk
pkgsrc/inputmethod/kasumi: Makefile
pkgsrc/inputmethod/kimera: Makefile
pkgsrc/inputmethod/kimera-tomoe-gtk: Makefile
pkgsrc/inputmethod/m17n-im-config: Makefile buildlink3.mk
pkgsrc/inputmethod/nabi: Makefile
pkgsrc/inputmethod/novel-pinyin: Makefile
pkgsrc/inputmethod/py-input-pad: Makefile
pkgsrc/inputmethod/scim: Makefile buildlink3.mk
pkgsrc/inputmethod/scim-anthy: Makefile
pkgsrc/inputmethod/scim-array: Makefile
pkgsrc/inputmethod/scim-canna: Makefile
pkgsrc/inputmethod/scim-ccinput: Makefile
pkgsrc/inputmethod/scim-chewing: Makefile
pkgsrc/inputmethod/scim-fcitx: Makefile
pkgsrc/inputmethod/scim-hangul: Makefile
pkgsrc/inputmethod/scim-input-pad: Makefile
pkgsrc/inputmethod/scim-m17n: Makefile
pkgsrc/inputmethod/scim-pinyin: Makefile
pkgsrc/inputmethod/scim-prime: Makefile
pkgsrc/inputmethod/scim-python: Makefile
pkgsrc/inputmethod/scim-sinhala: Makefile
pkgsrc/inputmethod/scim-skk: Makefile
pkgsrc/inputmethod/scim-tables: Makefile
pkgsrc/inputmethod/scim-thai: Makefile
pkgsrc/inputmethod/scim-tomoe: Makefile
pkgsrc/inputmethod/scim-uim: Makefile
pkgsrc/inputmethod/scim-unikey: Makefile
pkgsrc/inputmethod/tomoe-gtk: Makefile buildlink3.mk
pkgsrc/inputmethod/uim: Makefile
pkgsrc/inputmethod/uim-tomoe-gtk: Makefile
pkgsrc/lang/basic256: Makefile
pkgsrc/lang/classpath-gui: Makefile
pkgsrc/lang/clisp: Makefile
pkgsrc/lang/coq: Makefile
pkgsrc/lang/kaffe-x11: Makefile
pkgsrc/lang/racket: Makefile
pkgsrc/lang/sablevm-classpath-gui: Makefile
pkgsrc/lang/smalltalk: Makefile
pkgsrc/lang/squeak-vm: Makefile
pkgsrc/mail/akonadi: Makefile buildlink3.mk
pkgsrc/mail/balsa: Makefile
pkgsrc/mail/claws-mail: Makefile
pkgsrc/mail/claws-mail-archive: Makefile
pkgsrc/mail/claws-mail-attachwarner: Makefile
pkgsrc/mail/claws-mail-attremover: Makefile
pkgsrc/mail/claws-mail-cachesaver: Makefile
pkgsrc/mail/claws-mail-dillo-viewer: Makefile
pkgsrc/mail/claws-mail-fetchinfo: Makefile
pkgsrc/mail/claws-mail-gtkhtml: Makefile
pkgsrc/mail/claws-mail-mailmbox: Makefile
pkgsrc/mail/claws-mail-newmail: Makefile
pkgsrc/mail/claws-mail-notification: Makefile
pkgsrc/mail/claws-mail-pgpcore: Makefile buildlink3.mk
pkgsrc/mail/claws-mail-pgpinline: Makefile
pkgsrc/mail/claws-mail-pgpmime: Makefile
pkgsrc/mail/claws-mail-rssyl: Makefile
pkgsrc/mail/claws-mail-smime: Makefile
pkgsrc/mail/claws-mail-spamreport: Makefile
pkgsrc/mail/claws-mail-synce: Makefile
pkgsrc/mail/claws-mail-tnef: Makefile
pkgsrc/mail/claws-mail-vcalendar: Makefile
pkgsrc/mail/evolution: Makefile buildlink3.mk
pkgsrc/mail/evolution-data-server: Makefile
pkgsrc/mail/evolution-exchange: Makefile
pkgsrc/mail/mail-notification: Makefile
pkgsrc/mail/msmtp: Makefile
pkgsrc/mail/netbiff: Makefile
pkgsrc/mail/sylpheed: Makefile
pkgsrc/mail/thunderbird: Makefile
pkgsrc/mail/thunderbird10: Makefile
pkgsrc/math/R: Makefile
pkgsrc/math/analitza: Makefile buildlink3.mk
pkgsrc/math/calcoo: Makefile
pkgsrc/math/cantor: Makefile
pkgsrc/math/cgal: Makefile buildlink3.mk
pkgsrc/math/euler: Makefile
pkgsrc/math/extcalc: Makefile
pkgsrc/math/fityk: Makefile
pkgsrc/math/galculator: Makefile
pkgsrc/math/gcalctool: Makefile
pkgsrc/math/gcalctool-gtk3: Makefile
pkgsrc/math/genius: Makefile
pkgsrc/math/gnumeric: Makefile
pkgsrc/math/gnumeric110: Makefile
pkgsrc/math/grpn: Makefile
pkgsrc/math/gtklife: Makefile
pkgsrc/math/kalgebra: Makefile
pkgsrc/math/kcalc: Makefile
pkgsrc/math/pspp: Makefile
pkgsrc/math/qalculate-bases: Makefile
pkgsrc/math/qalculate-currency: Makefile
pkgsrc/math/qalculate-gtk: Makefile
pkgsrc/math/qalculate-units: Makefile
pkgsrc/math/speedcrunch: Makefile
pkgsrc/math/wxMaxima: Makefile
pkgsrc/meta-pkgs/xfce4: Makefile buildlink3.mk
pkgsrc/meta-pkgs/xfce4-extras: Makefile
pkgsrc/misc/attica: Makefile buildlink3.mk
pkgsrc/misc/blccc: Makefile
pkgsrc/misc/calibre: Makefile
pkgsrc/misc/celestia: Makefile
pkgsrc/misc/deskbar-applet: Makefile
pkgsrc/misc/fbreader: Makefile
pkgsrc/misc/gelemental: Makefile
pkgsrc/misc/gkrellm-flynn: Makefile
pkgsrc/misc/gkrellm-launch: Makefile
pkgsrc/misc/gkrellm-leds: Makefile
pkgsrc/misc/gkrellm-moon: Makefile
pkgsrc/misc/gkrellm-weather: Makefile
pkgsrc/misc/gnome-utils: Makefile
pkgsrc/misc/goffice0.6: Makefile buildlink3.mk
pkgsrc/misc/goffice0.8: Makefile buildlink3.mk
pkgsrc/misc/gok: Makefile
pkgsrc/misc/gperiodic: Makefile
pkgsrc/misc/gwaei: Makefile
pkgsrc/misc/kaccessible: Makefile
pkgsrc/misc/kalzium: Makefile
pkgsrc/misc/kanjipad: Makefile
pkgsrc/misc/kbruch: Makefile
pkgsrc/misc/kcharselect: Makefile
pkgsrc/misc/kchmviewer: Makefile
pkgsrc/misc/kde-wallpapers4: Makefile
pkgsrc/misc/kdeadmin4: Makefile
pkgsrc/misc/kdeartwork4: Makefile
pkgsrc/misc/kdepim-runtime4: Makefile
pkgsrc/misc/kdepim4: Makefile
pkgsrc/misc/kdepimlibs4: Makefile buildlink3.mk
pkgsrc/misc/kdeplasma-addons4: Makefile
pkgsrc/misc/kgeography: Makefile
pkgsrc/misc/kig: Makefile
pkgsrc/misc/kiten: Makefile
pkgsrc/misc/klettres: Makefile
pkgsrc/misc/kmag: Makefile
pkgsrc/misc/kmousetool: Makefile
pkgsrc/misc/kmouth: Makefile
pkgsrc/misc/kremotecontrol: Makefile
pkgsrc/misc/kstars: Makefile
pkgsrc/misc/ktouch: Makefile
pkgsrc/misc/kturtle: Makefile
pkgsrc/misc/kwordquiz: Makefile
pkgsrc/misc/libkdeedu: Makefile buildlink3.mk
pkgsrc/misc/libkgeomap: Makefile buildlink3.mk
pkgsrc/misc/libkvkontakte: Makefile buildlink3.mk
pkgsrc/misc/libreoffice: Makefile
pkgsrc/misc/marble: Makefile buildlink3.mk
pkgsrc/misc/mousetweaks: Makefile
pkgsrc/misc/openoffice3: Makefile
pkgsrc/misc/parley: Makefile
pkgsrc/misc/rocs: Makefile
pkgsrc/misc/stellarium: Makefile
pkgsrc/misc/step: Makefile
pkgsrc/misc/superkaramba: Makefile
pkgsrc/misc/sweeper: Makefile
pkgsrc/misc/tellico: Makefile
pkgsrc/misc/usbprog: Makefile
pkgsrc/misc/vym: Makefile
pkgsrc/misc/xchm: Makefile
pkgsrc/misc/xfce4-weather-plugin: Makefile buildlink3.mk
pkgsrc/misc/yelp: Makefile
pkgsrc/misc/yelp3: Makefile
pkgsrc/misc/zyGrib: Makefile
pkgsrc/multimedia/avidemux: Makefile
pkgsrc/multimedia/clutter-gst: Makefile buildlink3.mk
pkgsrc/multimedia/clutter08-gst: Makefile buildlink3.mk
pkgsrc/multimedia/dvdstyler: Makefile
pkgsrc/multimedia/farsight2: Makefile buildlink3.mk
pkgsrc/multimedia/gecko-mediaplayer: Makefile
pkgsrc/multimedia/gmencoder: Makefile
pkgsrc/multimedia/gmplayer: Makefile
pkgsrc/multimedia/gnash: Makefile
pkgsrc/multimedia/gnome-media: Makefile buildlink3.mk
pkgsrc/multimedia/gnome-mplayer: Makefile
pkgsrc/multimedia/gopchop: Makefile
pkgsrc/multimedia/gst123: Makefile
pkgsrc/multimedia/gxine: Makefile
pkgsrc/multimedia/handbrake: Makefile
pkgsrc/multimedia/hwdecode-demos: Makefile
pkgsrc/multimedia/kdemultimedia4: Makefile
pkgsrc/multimedia/kdenlive: Makefile
pkgsrc/multimedia/kmplayer: Makefile
pkgsrc/multimedia/kmplayer-kde3: Makefile
pkgsrc/multimedia/mkvtoolnix: Makefile
pkgsrc/multimedia/mkvtoolnix-old: Makefile
pkgsrc/multimedia/mlt: Makefile
pkgsrc/multimedia/mplayer-plugin: Makefile
pkgsrc/multimedia/ogle_gui: Makefile
pkgsrc/multimedia/phonon: Makefile buildlink3.mk
pkgsrc/multimedia/phonon-backend-gstreamer: Makefile
pkgsrc/multimedia/pitivi: Makefile
pkgsrc/multimedia/pspvc: Makefile
pkgsrc/multimedia/py-clutter-gst: Makefile
pkgsrc/multimedia/ruby-clutter-gst: Makefile
pkgsrc/multimedia/subtitleeditor: Makefile
pkgsrc/multimedia/swfdec: Makefile buildlink3.mk
pkgsrc/multimedia/swfdec-gnome: Makefile
pkgsrc/multimedia/swfdec-mozilla: Makefile
pkgsrc/multimedia/totem: Makefile buildlink3.mk
pkgsrc/multimedia/totem-browser-plugin: Makefile
pkgsrc/multimedia/totem-nautilus: Makefile
pkgsrc/multimedia/totem-pl-parser: Makefile buildlink3.mk
pkgsrc/multimedia/vlc: Makefile
pkgsrc/multimedia/vlc08: Makefile
pkgsrc/multimedia/vlc10: Makefile
pkgsrc/multimedia/vlc2: Makefile
pkgsrc/multimedia/xfce4-mpc-plugin: Makefile buildlink3.mk
pkgsrc/multimedia/xfmedia: Makefile
pkgsrc/multimedia/xvid4conf: Makefile
pkgsrc/net/Transmission-gui: Makefile
pkgsrc/net/amule: Makefile
pkgsrc/net/avahi: Makefile buildlink3.mk
pkgsrc/net/bug-buddy: Makefile
pkgsrc/net/cacti: Makefile
pkgsrc/net/choqok: Makefile
pkgsrc/net/dc_gui2: Makefile
pkgsrc/net/dcsharp: Makefile
pkgsrc/net/dhcpcd-gtk: Makefile
pkgsrc/net/ed2k-gtk-gui: Makefile
pkgsrc/net/ekiga: Makefile
pkgsrc/net/etherape: Makefile
pkgsrc/net/ettercap: Makefile
pkgsrc/net/filezilla: Makefile
pkgsrc/net/gitso: Makefile
pkgsrc/net/gkrellm-multiping: Makefile
pkgsrc/net/gkrellm-snmp: Makefile
pkgsrc/net/gkrellm-wireless: Makefile
pkgsrc/net/gnome-netstatus: Makefile
pkgsrc/net/gnome-nettool: Makefile
pkgsrc/net/gnome-vfs-smb: Makefile
pkgsrc/net/gssdp: Makefile
pkgsrc/net/gtk-gnutella: Makefile
pkgsrc/net/gtk-vnc: Makefile buildlink3.mk
pkgsrc/net/gupnp-tools: Makefile
pkgsrc/net/jigdo: Makefile
pkgsrc/net/kdenetwork4: Makefile
pkgsrc/net/kmldonkey: Makefile
pkgsrc/net/ktorrent: Makefile
pkgsrc/net/libdmapsharing: Makefile
pkgsrc/net/libktorrent: Makefile buildlink3.mk
pkgsrc/net/logjam: Makefile
pkgsrc/net/mbrowse: Makefile
pkgsrc/net/mldonkey-gui: Makefile
pkgsrc/net/monsoon: Makefile
pkgsrc/net/mtr: Makefile
pkgsrc/net/nagstamon: Makefile
pkgsrc/net/nfdump: Makefile
pkgsrc/net/nmap: Makefile
pkgsrc/net/ntop: Makefile
pkgsrc/net/remmina: Makefile
pkgsrc/net/remmina-plugins: Makefile
pkgsrc/net/tsclient: Makefile
pkgsrc/net/twitux: Makefile
pkgsrc/net/unison: Makefile
pkgsrc/net/unison2.32: Makefile
pkgsrc/net/urlgfe: Makefile
pkgsrc/net/vinagre: Makefile
pkgsrc/net/vino: Makefile
pkgsrc/net/wireshark: Makefile
pkgsrc/net/wistumbler2-gtk: Makefile
pkgsrc/net/xfce4-wavelan-plugin: Makefile buildlink3.mk
pkgsrc/net/xymon: Makefile
pkgsrc/news/pan: Makefile
pkgsrc/parallel/ganglia-monitor-core: Makefile
pkgsrc/parallel/hwloc: Makefile
pkgsrc/pkgtools/gnome-packagekit: Makefile
pkgsrc/pkgtools/packagekit: Makefile
pkgsrc/print/abcm2ps: Makefile
pkgsrc/print/advi: Makefile
pkgsrc/print/diffpdf: Makefile
pkgsrc/print/epdfview: Makefile
pkgsrc/print/evince: Makefile buildlink3.mk
pkgsrc/print/evince-nautilus: Makefile
pkgsrc/print/evince3: Makefile buildlink3.mk
pkgsrc/print/glabels: Makefile
pkgsrc/print/gtklp: Makefile
pkgsrc/print/gutenprint-lib: Makefile
pkgsrc/print/hplip: Makefile
pkgsrc/print/imposter: Makefile
pkgsrc/print/kbibtex: Makefile
pkgsrc/print/libgnomeprint: Makefile buildlink3.mk
pkgsrc/print/libgnomeprintui: Makefile buildlink3.mk
pkgsrc/print/libgxps: Makefile buildlink3.mk
pkgsrc/print/lilypond: Makefile
pkgsrc/print/okular: Makefile
pkgsrc/print/paps: Makefile
pkgsrc/print/poppler-glib: Makefile buildlink3.mk
pkgsrc/print/poppler-qt4: Makefile
pkgsrc/print/printer-applet: Makefile
pkgsrc/print/ruby-gnome2-poppler: Makefile
pkgsrc/print/scribus: Makefile
pkgsrc/print/scribus-qt4: Makefile
pkgsrc/print/xfce4-print: Makefile buildlink3.mk
pkgsrc/security/MyPasswordSafe: Makefile
pkgsrc/security/fprint-demo: Makefile
pkgsrc/security/fwbuilder: Makefile
pkgsrc/security/gnome-keyring: Makefile buildlink3.mk
pkgsrc/security/gnome-keyring-manager: Makefile
pkgsrc/security/gpa: Makefile
pkgsrc/security/gpass: Makefile
pkgsrc/security/honeyd: Makefile
pkgsrc/security/hydra: Makefile
pkgsrc/security/keepassx: Makefile
pkgsrc/security/kgpg: Makefile
pkgsrc/security/ksecrets: Makefile
pkgsrc/security/kwallet: Makefile
pkgsrc/security/libfwbuilder: Makefile buildlink3.mk
pkgsrc/security/openvas-client: Makefile
pkgsrc/security/pinentry-gtk2: Makefile
pkgsrc/security/pinentry-qt4: Makefile
pkgsrc/security/policykit-gnome: Makefile
pkgsrc/security/polkit-qt: Makefile buildlink3.mk
pkgsrc/security/putty: Makefile
pkgsrc/security/qca2: Makefile buildlink3.mk
pkgsrc/security/qca2-gnupg: Makefile
pkgsrc/security/qca2-ossl: Makefile
pkgsrc/security/qoauth: Makefile buildlink3.mk
pkgsrc/security/seahorse: Makefile buildlink3.mk
pkgsrc/security/seahorse-plugins: Makefile
pkgsrc/sysutils/amtterm: Makefile
pkgsrc/sysutils/bacula-qt-console: Makefile
pkgsrc/sysutils/bacula-tray-monitor: Makefile
pkgsrc/sysutils/bacula-wx-console: Makefile
pkgsrc/sysutils/brasero: Makefile buildlink3.mk
pkgsrc/sysutils/brasero-nautilus: Makefile
pkgsrc/sysutils/btpin-qt: Makefile
pkgsrc/sysutils/bubblemon: Makefile
pkgsrc/sysutils/conky: Makefile
pkgsrc/sysutils/dvdisaster: Makefile
pkgsrc/sysutils/filelight: Makefile
pkgsrc/sysutils/gcdmaster: Makefile
pkgsrc/sysutils/gkrellm: Makefile buildlink3.mk
pkgsrc/sysutils/gkrellm-est: Makefile
pkgsrc/sysutils/gnome-commander: Makefile
pkgsrc/sysutils/gnome-device-manager: Makefile
pkgsrc/sysutils/gnome-mount: Makefile buildlink3.mk
pkgsrc/sysutils/gnome-nds-thumbnailer: Makefile
pkgsrc/sysutils/gnome-pkgview: Makefile
pkgsrc/sysutils/gnome-power-manager: Makefile
pkgsrc/sysutils/gnome-settings-daemon: Makefile
pkgsrc/sysutils/gnome-system-monitor: Makefile
pkgsrc/sysutils/gnome-system-tools: Makefile
pkgsrc/sysutils/gnome-vfs: Makefile buildlink3.mk
pkgsrc/sysutils/gnome-vfs-monikers: Makefile
pkgsrc/sysutils/gnome-vfsmm: Makefile buildlink3.mk
pkgsrc/sysutils/gnome-volume-manager: Makefile
pkgsrc/sysutils/grun: Makefile
pkgsrc/sysutils/gst-plugins0.10-gnomevfs: Makefile
pkgsrc/sysutils/gtk-send-pr: Makefile
pkgsrc/sysutils/gvfs: Makefile
pkgsrc/sysutils/k3b: Makefile
pkgsrc/sysutils/k4dirstat: Makefile
pkgsrc/sysutils/kdf: Makefile
pkgsrc/sysutils/kfloppy: Makefile
pkgsrc/sysutils/libgksu: Makefile buildlink3.mk
pkgsrc/sysutils/libnotify: Makefile buildlink3.mk
pkgsrc/sysutils/nautilus: Makefile buildlink3.mk
pkgsrc/sysutils/nautilus-sendto: Makefile
pkgsrc/sysutils/notification-daemon: Makefile
pkgsrc/sysutils/open-vm-tools: Makefile
pkgsrc/sysutils/p5-Gnome2-VFS: Makefile buildlink3.mk
pkgsrc/sysutils/pcmanfm: Makefile
pkgsrc/sysutils/py-notify: Makefile buildlink3.mk
pkgsrc/sysutils/rox: Makefile
pkgsrc/sysutils/screentest: Makefile
pkgsrc/sysutils/strigi: Makefile
pkgsrc/sysutils/virt-manager: Makefile
pkgsrc/sysutils/xcdroast: Makefile
pkgsrc/sysutils/xfce4-appfinder: Makefile
pkgsrc/sysutils/xfce4-battery-plugin: Makefile buildlink3.mk
pkgsrc/sysutils/xfce4-cpugraph-plugin: Makefile buildlink3.mk
pkgsrc/sysutils/xfce4-diskperf-plugin: Makefile buildlink3.mk
pkgsrc/sysutils/xfce4-fsguard-plugin: Makefile buildlink3.mk
pkgsrc/sysutils/xfce4-genmon-plugin: Makefile buildlink3.mk
pkgsrc/sysutils/xfce4-netload-plugin: Makefile buildlink3.mk
pkgsrc/sysutils/xfce4-quicklauncher-plugin: Makefile buildlink3.mk
pkgsrc/sysutils/xfce4-systemload-plugin: Makefile buildlink3.mk
pkgsrc/sysutils/xfce4-thunar: Makefile buildlink3.mk
pkgsrc/sysutils/xfce4-volman: Makefile
pkgsrc/sysutils/xfce4-xarchiver: Makefile buildlink3.mk
pkgsrc/sysutils/xfce4-xkb-plugin: Makefile buildlink3.mk
pkgsrc/textproc/FlightCrew: Makefile
pkgsrc/textproc/OdfConverter: Makefile
pkgsrc/textproc/dikt: Makefile
pkgsrc/textproc/ebview: Makefile
pkgsrc/textproc/gnome-spell: Makefile buildlink3.mk
pkgsrc/textproc/gnome-subtitles: Makefile
pkgsrc/textproc/gtkspell: Makefile buildlink3.mk
pkgsrc/textproc/py-gdick: Makefile
pkgsrc/textproc/soprano: Makefile buildlink3.mk
pkgsrc/textproc/xfce4-dict-plugin: Makefile buildlink3.mk
pkgsrc/time/cairo-clock: Makefile
pkgsrc/time/evolution-webcal: Makefile
pkgsrc/time/gchore: Makefile
pkgsrc/time/gdeskcal: Makefile
pkgsrc/time/gnotime: Makefile
pkgsrc/time/gtodo: Makefile
pkgsrc/time/gtodo-applet: Makefile
pkgsrc/time/hamster-applet: Makefile
pkgsrc/time/ktimer: Makefile
pkgsrc/time/planner: Makefile
pkgsrc/time/rsibreak: Makefile
pkgsrc/time/xfce4-datetime-plugin: Makefile buildlink3.mk
pkgsrc/time/xfce4-orage: Makefile
pkgsrc/time/xfce4-timer-plugin: Makefile buildlink3.mk
pkgsrc/wm/afterstep: Makefile
pkgsrc/wm/awesome: Makefile
pkgsrc/wm/bmpanel2: Makefile
pkgsrc/wm/compiz: Makefile buildlink3.mk
pkgsrc/wm/compiz-fusion-plugins-extra: Makefile
pkgsrc/wm/compiz-fusion-plugins-main: Makefile buildlink3.mk
pkgsrc/wm/e16menuedit2: Makefile
pkgsrc/wm/fluxconf: Makefile
pkgsrc/wm/metacity: Makefile buildlink3.mk
pkgsrc/wm/metisse: Makefile
pkgsrc/wm/openbox: Makefile
pkgsrc/wm/oroborox: Makefile
pkgsrc/wm/sawfish: Makefile
pkgsrc/wm/selectwm: Makefile
pkgsrc/wm/wbar: Makefile
pkgsrc/wm/wmakerconf: Makefile
pkgsrc/wm/xfce4-wm: Makefile
pkgsrc/wm/xfce4-wm-themes: Makefile
pkgsrc/www/amaya: Makefile
pkgsrc/www/ap22-dnssd: Makefile
pkgsrc/www/bluefish: Makefile
pkgsrc/www/browser-bookmarks-menu: Makefile
pkgsrc/www/drivel: Makefile
pkgsrc/www/epiphany: Makefile buildlink3.mk
pkgsrc/www/epiphany-extensions: Makefile
pkgsrc/www/firefox: Makefile
pkgsrc/www/firefox10: Makefile
pkgsrc/www/firefox36: Makefile
pkgsrc/www/gtkhtml314: Makefile
pkgsrc/www/icedtea-web: Makefile
pkgsrc/www/kazehakase: Makefile
pkgsrc/www/kdewebdev4: Makefile
pkgsrc/www/libgtkhtml: Makefile buildlink3.mk
pkgsrc/www/libmediawiki: Makefile buildlink3.mk
pkgsrc/www/liferea: Makefile
pkgsrc/www/liferea-current: Makefile
pkgsrc/www/midori: Makefile
pkgsrc/www/netsurf: Makefile
pkgsrc/www/nspluginwrapper: Makefile
pkgsrc/www/seamonkey: Makefile
pkgsrc/www/webkit-gtk: Makefile buildlink3.mk
pkgsrc/www/webkit-gtk3: Makefile buildlink3.mk
pkgsrc/x11/alacarte: Makefile
pkgsrc/x11/antiright: Makefile
pkgsrc/x11/avant-window-navigator: Makefile
pkgsrc/x11/clisp-gtk2: Makefile
pkgsrc/x11/deskmenu: Makefile
pkgsrc/x11/devilspie: Makefile
pkgsrc/x11/eekboard: Makefile buildlink3.mk
pkgsrc/x11/fast-user-switch-applet: Makefile
pkgsrc/x11/fltk13: Makefile
pkgsrc/x11/ftmenu: Makefile
pkgsrc/x11/gdm: Makefile
pkgsrc/x11/gnome-applets: Makefile
pkgsrc/x11/gnome-control-center: Makefile buildlink3.mk
pkgsrc/x11/gnome-desktop: Makefile buildlink3.mk
pkgsrc/x11/gnome-desktop-sharp: Makefile buildlink3.mk
pkgsrc/x11/gnome-desktop3: Makefile buildlink3.mk
pkgsrc/x11/gnome-mag: Makefile buildlink3.mk
pkgsrc/x11/gnome-panel: Makefile buildlink3.mk
pkgsrc/x11/gnome-screensaver: Makefile
pkgsrc/x11/gnome-session: Makefile
pkgsrc/x11/gnome-sharp: Makefile buildlink3.mk
pkgsrc/x11/gnome-terminal: Makefile
pkgsrc/x11/gnome-themes: Makefile
pkgsrc/x11/gnome-themes-extras: Makefile
pkgsrc/x11/gnopernicus: Makefile
pkgsrc/x11/grandr_applet: Makefile
pkgsrc/x11/gromit: Makefile
pkgsrc/x11/gselt: Makefile
pkgsrc/x11/gtk-sharp: Makefile
pkgsrc/x11/gtk2: Makefile buildlink3.mk
pkgsrc/x11/gtk2+extra: Makefile buildlink3.mk
pkgsrc/x11/gtk2-chtheme: Makefile
pkgsrc/x11/gtk2-engines: Makefile buildlink3.mk
pkgsrc/x11/gtk2-engines-bluecurve: Makefile
pkgsrc/x11/gtk2-engines-murrine: Makefile
pkgsrc/x11/gtk2-theme-switch: Makefile
pkgsrc/x11/gtk3: Makefile buildlink3.mk
pkgsrc/x11/gtkada: Makefile buildlink3.mk
pkgsrc/x11/gtkglarea2: Makefile buildlink3.mk
pkgsrc/x11/gtkmm: Makefile buildlink3.mk
pkgsrc/x11/gtkmm-utils: Makefile buildlink3.mk
pkgsrc/x11/gtksourceview: Makefile buildlink3.mk
pkgsrc/x11/gtksourceview-sharp2: Makefile
pkgsrc/x11/gtksourceview2: Makefile buildlink3.mk
pkgsrc/x11/gtksourceview3: Makefile buildlink3.mk
pkgsrc/x11/gtkterm2: Makefile
pkgsrc/x11/hot-babe: Makefile
pkgsrc/x11/kactivities: Makefile buildlink3.mk
pkgsrc/x11/kde-baseapps4: Makefile
pkgsrc/x11/kde-runtime4: Makefile buildlink3.mk
pkgsrc/x11/kde-workspace4: Makefile buildlink3.mk
pkgsrc/x11/kdelibs4: Makefile buildlink3.mk
pkgsrc/x11/konsole: Makefile
pkgsrc/x11/lablgtk: Makefile buildlink3.mk
pkgsrc/x11/libdesktop-agnostic: Makefile buildlink3.mk
pkgsrc/x11/libgnomekbd: Makefile
pkgsrc/x11/libunique: Makefile buildlink3.mk
pkgsrc/x11/libunique3: Makefile
pkgsrc/x11/libxfce4gui: Makefile buildlink3.mk
pkgsrc/x11/libxfce4menu: Makefile buildlink3.mk
pkgsrc/x11/libxfce4util: Makefile
pkgsrc/x11/matchbox-panel-manager: Makefile
pkgsrc/x11/mlterm: Makefile
pkgsrc/x11/nucleo: Makefile buildlink3.mk
pkgsrc/x11/p5-Alien-wxWidgets: Makefile
pkgsrc/x11/p5-Wx: Makefile buildlink3.mk
pkgsrc/x11/p5-Wx-Perl-ProcessStream: Makefile
pkgsrc/x11/p5-gtk2: Makefile buildlink3.mk
pkgsrc/x11/py-gnome2: Makefile buildlink3.mk
pkgsrc/x11/py-gnome2-desktop: Makefile buildlink3.mk
pkgsrc/x11/py-gnome2-extras: Makefile buildlink3.mk
pkgsrc/x11/py-gtk2: Makefile buildlink3.mk
pkgsrc/x11/py-gtksourceview: Makefile
pkgsrc/x11/py-kde4: Makefile
pkgsrc/x11/py-kiwi: Makefile
pkgsrc/x11/py-qt4: Makefile
pkgsrc/x11/py-qt4-qscintilla: Makefile buildlink3.mk
pkgsrc/x11/py-vte: Makefile buildlink3.mk
pkgsrc/x11/py-wxWidgets: Makefile buildlink3.mk
pkgsrc/x11/qt4-creator: Makefile
pkgsrc/x11/qt4-docs: Makefile
pkgsrc/x11/qt4-libs: Makefile buildlink3.mk
pkgsrc/x11/qt4-mng: Makefile
pkgsrc/x11/qt4-mysql: Makefile
pkgsrc/x11/qt4-pgsql: Makefile
pkgsrc/x11/qt4-qdbus: Makefile buildlink3.mk
pkgsrc/x11/qt4-qscintilla: Makefile buildlink3.mk
pkgsrc/x11/qt4-sqlite3: Makefile
pkgsrc/x11/qt4-tiff: Makefile
pkgsrc/x11/qt4-tools: Makefile buildlink3.mk
pkgsrc/x11/qwt-qt4: Makefile buildlink3.mk
pkgsrc/x11/qwt6-qt4: Makefile buildlink3.mk
pkgsrc/x11/qwtplot3d-qt4: Makefile buildlink3.mk
pkgsrc/x11/rep-gtk2: Makefile
pkgsrc/x11/rox-session: Makefile
pkgsrc/x11/ruby-gnome2-gtk: Makefile buildlink3.mk
pkgsrc/x11/ruby-gnome2-gtksourceview2: Makefile
pkgsrc/x11/ruby-gnome2-vte: Makefile
pkgsrc/x11/ruby-wxruby: Makefile
pkgsrc/x11/sakura: Makefile
pkgsrc/x11/tint2: Makefile
pkgsrc/x11/vte: Makefile buildlink3.mk
pkgsrc/x11/vte029: Makefile buildlink3.mk
pkgsrc/x11/wxGTK24: Makefile buildlink3.mk
pkgsrc/x11/wxGTK26: Makefile buildlink3.mk
pkgsrc/x11/wxGTK26-contrib: Makefile buildlink3.mk
pkgsrc/x11/wxGTK28: Makefile buildlink3.mk
pkgsrc/x11/wxGTK28-contrib: Makefile buildlink3.mk
pkgsrc/x11/wxhaskell: Makefile
pkgsrc/x11/x11vnc: Makefile
pkgsrc/x11/xdialog: Makefile
pkgsrc/x11/xfce4-clipman-plugin: Makefile buildlink3.mk
pkgsrc/x11/xfce4-desktop: Makefile
pkgsrc/x11/xfce4-exo: Makefile buildlink3.mk
pkgsrc/x11/xfce4-eyes-plugin: Makefile buildlink3.mk
pkgsrc/x11/xfce4-gtk2-engine: Makefile
pkgsrc/x11/xfce4-notes-plugin: Makefile buildlink3.mk
pkgsrc/x11/xfce4-panel: Makefile buildlink3.mk
pkgsrc/x11/xfce4-places-plugin: Makefile buildlink3.mk
pkgsrc/x11/xfce4-screenshooter-plugin: Makefile buildlink3.mk
pkgsrc/x11/xfce4-session: Makefile buildlink3.mk
pkgsrc/x11/xfce4-settings: Makefile
pkgsrc/x11/xfce4-terminal: Makefile
pkgsrc/x11/xfce4-utils: Makefile
pkgsrc/x11/xlockmore: Makefile
pkgsrc/x11/xpad: Makefile
pkgsrc/x11/xplanet: Makefile
pkgsrc/x11/xscreensaver-demo: Makefile
pkgsrc/x11/xvidcap-gtk2: Makefile
pkgsrc/x11/zenity: Makefile
Log Message:
Mass recursive bump after the dependence fix of the "cairo" package
requested by Thomas Klausner.
To generate a diff of this commit:
cvs rdiff -u -r1.8 -r1.9 pkgsrc/archivers/ark/Makefile
cvs rdiff -u -r1.120 -r1.121 pkgsrc/archivers/file-roller/Makefile
cvs rdiff -u -r1.21 -r1.22 pkgsrc/audio/albumplayer/Makefile
cvs rdiff -u -r1.114 -r1.115 pkgsrc/audio/amarok/Makefile
cvs rdiff -u -r1.27 -r1.28 pkgsrc/audio/amarok-kde3/Makefile
cvs rdiff -u -r1.22 -r1.23 pkgsrc/audio/ario/Makefile
cvs rdiff -u -r1.27 -r1.28 pkgsrc/audio/audacious/Makefile
cvs rdiff -u -r1.19 -r1.20 pkgsrc/audio/audacious/buildlink3.mk
cvs rdiff -u -r1.33 -r1.34 pkgsrc/audio/audacious-plugins/Makefile
cvs rdiff -u -r1.77 -r1.78 pkgsrc/audio/audacity/Makefile
cvs rdiff -u -r1.17 -r1.18 pkgsrc/audio/aumix-gtk/Makefile
cvs rdiff -u -r1.48 -r1.49 pkgsrc/audio/bmp/Makefile
cvs rdiff -u -r1.22 -r1.23 pkgsrc/audio/bmp/buildlink3.mk
cvs rdiff -u -r1.29 -r1.30 pkgsrc/audio/bmp-esound/Makefile
cvs rdiff -u -r1.12 -r1.13 pkgsrc/audio/bmp-flac/Makefile
cvs rdiff -u -r1.18 -r1.19 pkgsrc/audio/bmp-mac/Makefile
cvs rdiff -u -r1.26 -r1.27 pkgsrc/audio/bmp-musepack/Makefile
cvs rdiff -u -r1.16 -r1.17 pkgsrc/audio/bmp-pulse/Makefile
cvs rdiff -u -r1.14 -r1.15 pkgsrc/audio/bmp-scrobbler/Makefile
cvs rdiff -u -r1.47 -r1.48 pkgsrc/audio/bmpx/Makefile
cvs rdiff -u -r1.16 -r1.17 pkgsrc/audio/bsl/Makefile
cvs rdiff -u -r1.20 -r1.21 pkgsrc/audio/buzztard/Makefile
cvs rdiff -u -r1.75 -r1.76 pkgsrc/audio/easytag/Makefile
cvs rdiff -u -r1.33 -r1.34 pkgsrc/audio/exaile/Makefile
cvs rdiff -u -r1.17 -r1.18 pkgsrc/audio/gbemol/Makefile
cvs rdiff -u -r1.23 -r1.24 pkgsrc/audio/gimmix/Makefile
cvs rdiff -u -r1.40 -r1.41 pkgsrc/audio/gkrellm-volume/Makefile
cvs rdiff -u -r1.27 -r1.28 pkgsrc/audio/glurp/Makefile
cvs rdiff -u -r1.39 -r1.40 pkgsrc/audio/gmp3info/Makefile
cvs rdiff -u -r1.52 -r1.53 pkgsrc/audio/gmpc/Makefile
cvs rdiff -u -r1.16 -r1.17 pkgsrc/audio/gmpc/buildlink3.mk
cvs rdiff -u -r1.11 -r1.12 pkgsrc/audio/gmpc-albumview/Makefile
cvs rdiff -u -r1.10 -r1.11 pkgsrc/audio/gmpc-lastfm/Makefile
cvs rdiff -u -r1.11 -r1.12 pkgsrc/audio/gmpc-lyrics/Makefile
cvs rdiff -u -r1.13 -r1.14 pkgsrc/audio/gmpc-lyricwiki/Makefile
cvs rdiff -u -r1.15 -r1.16 pkgsrc/audio/gmpc-magnatune/Makefile
cvs rdiff -u -r1.10 -r1.11 pkgsrc/audio/gmpc-mdcover/Makefile
cvs rdiff -u -r1.11 -r1.12 pkgsrc/audio/gmpc-tagedit/Makefile
cvs rdiff -u -r1.19 -r1.20 pkgsrc/audio/gnome-vfs-cdda/Makefile
cvs rdiff -u -r1.38 -r1.39 pkgsrc/audio/gqmpeg-devel/Makefile
cvs rdiff -u -r1.25 -r1.26 pkgsrc/audio/gtick/Makefile
cvs rdiff -u -r1.45 -r1.46 pkgsrc/audio/gtkpod/Makefile
cvs rdiff -u -r1.30 -r1.31 pkgsrc/audio/hydrogen/Makefile
cvs rdiff -u -r1.24 -r1.25 pkgsrc/audio/jack-rack/Makefile
cvs rdiff -u -r1.25 -r1.26 pkgsrc/audio/libcanberra/Makefile
cvs rdiff -u -r1.15 -r1.16 pkgsrc/audio/libcanberra/buildlink3.mk
cvs rdiff -u -r1.28 -r1.29 pkgsrc/audio/libgpod/Makefile
cvs rdiff -u -r1.14 -r1.15 pkgsrc/audio/libgpod/buildlink3.mk
cvs rdiff -u -r1.21 -r1.22 pkgsrc/audio/liblastfm/Makefile
cvs rdiff -u -r1.13 -r1.14 pkgsrc/audio/liblastfm/buildlink3.mk
cvs rdiff -u -r1.30 -r1.31 pkgsrc/audio/libvisual-bmp/Makefile
cvs rdiff -u -r1.34 -r1.35 pkgsrc/audio/libvisual-plugins/Makefile
cvs rdiff -u -r1.17 -r1.18 pkgsrc/audio/libvisual0.2-plugins/Makefile
cvs rdiff -u -r1.51 -r1.52 pkgsrc/audio/liteamp/Makefile
cvs rdiff -u -r1.28 -r1.29 pkgsrc/audio/mp3diags/Makefile
cvs rdiff -u -r1.13 -r1.14 pkgsrc/audio/mp3splt-gtk/Makefile
cvs rdiff -u -r1.41 -r1.42 pkgsrc/audio/muse/Makefile
cvs rdiff -u -r1.22 -r1.23 pkgsrc/audio/padevchooser/Makefile
cvs rdiff -u -r1.18 -r1.19 pkgsrc/audio/paman/Makefile
cvs rdiff -u -r1.19 -r1.20 pkgsrc/audio/paprefs/Makefile
cvs rdiff -u -r1.21 -r1.22 pkgsrc/audio/pavucontrol/Makefile
cvs rdiff -u -r1.19 -r1.20 pkgsrc/audio/pavumeter/Makefile
cvs rdiff -u -r1.59 -r1.60 pkgsrc/audio/pulseaudio/Makefile
cvs rdiff -u -r1.34 -r1.35 pkgsrc/audio/py-musique/Makefile
cvs rdiff -u -r1.19 -r1.20 pkgsrc/audio/qjackctl/Makefile
cvs rdiff -u -r1.97 -r1.98 pkgsrc/audio/rhythmbox/Makefile
cvs rdiff -u -r1.12 -r1.13 pkgsrc/audio/sfxr/Makefile
cvs rdiff -u -r1.69 -r1.70 pkgsrc/audio/snd/Makefile
cvs rdiff -u -r1.38 -r1.39 pkgsrc/audio/solfege/Makefile
cvs rdiff -u -r1.29 -r1.30 pkgsrc/audio/sonata/Makefile
cvs rdiff -u -r1.54 -r1.55 pkgsrc/audio/sound-juicer/Makefile
cvs rdiff -u -r1.57 -r1.58 pkgsrc/audio/streamtuner/Makefile
cvs rdiff -u -r1.26 -r1.27 pkgsrc/audio/streamtuner/buildlink3.mk
cvs rdiff -u -r1.54 -r1.55 pkgsrc/audio/sweep/Makefile
cvs rdiff -u -r1.31 -r1.32 pkgsrc/audio/terminatorx/Makefile
cvs rdiff -u -r1.84 -r1.85 pkgsrc/audio/timidity/Makefile
cvs rdiff -u -r1.39 -r1.40 pkgsrc/audio/xfce4-mixer/Makefile
cvs rdiff -u -r1.27 -r1.28 pkgsrc/audio/xfce4-xmms-plugin/Makefile
cvs rdiff -u -r1.31 -r1.32 pkgsrc/audio/xfce4-xmms-plugin/buildlink3.mk
cvs rdiff -u -r1.40 -r1.41 pkgsrc/biology/chemtool/Makefile
cvs rdiff -u -r1.13 -r1.14 pkgsrc/biology/gnome-chemistry-utils/Makefile
cvs rdiff -u -r1.9 -r1.10 pkgsrc/biology/openbabel/Makefile
cvs rdiff -u -r1.56 -r1.57 pkgsrc/cad/boolean/Makefile
cvs rdiff -u -r1.78 -r1.79 pkgsrc/cad/geda/Makefile
cvs rdiff -u -r1.49 -r1.50 pkgsrc/cad/gerbv/Makefile
cvs rdiff -u -r1.25 -r1.26 pkgsrc/cad/gsmc/Makefile
cvs rdiff -u -r1.17 -r1.18 pkgsrc/cad/gtk2-wcalc/Makefile
cvs rdiff -u -r1.42 -r1.43 pkgsrc/cad/gtkwave/Makefile
cvs rdiff -u -r1.46 -r1.47 pkgsrc/cad/gwave/Makefile
cvs rdiff -u -r1.9 -r1.10 pkgsrc/cad/librecad/Makefile
cvs rdiff -u -r1.12 -r1.13 pkgsrc/cad/openscad/Makefile
cvs rdiff -u -r1.62 -r1.63 pkgsrc/cad/pcb/Makefile
cvs rdiff -u -r1.32 -r1.33 pkgsrc/cad/transcalc/Makefile
cvs rdiff -u -r1.41 -r1.42 pkgsrc/chat/empathy/Makefile
cvs rdiff -u -r1.19 -r1.20 pkgsrc/chat/empathy/buildlink3.mk
cvs rdiff -u -r1.44 -r1.45 pkgsrc/chat/finch/Makefile
cvs rdiff -u -r1.14 -r1.15 pkgsrc/chat/gajim/Makefile
cvs rdiff -u -r1.42 -r1.43 pkgsrc/chat/gg2/Makefile
cvs rdiff -u -r1.82 -r1.83 pkgsrc/chat/gnomeicu/Makefile
cvs rdiff -u -r1.78 -r1.79 pkgsrc/chat/gossip/Makefile
cvs rdiff -u -r1.47 -r1.48 pkgsrc/chat/konversation/Makefile
cvs rdiff -u -r1.45 -r1.46 pkgsrc/chat/libpurple/Makefile
cvs rdiff -u -r1.33 -r1.34 pkgsrc/chat/libpurple/buildlink3.mk
cvs rdiff -u -r1.20 -r1.21 pkgsrc/chat/msn-pecan/Makefile
cvs rdiff -u -r1.44 -r1.45 pkgsrc/chat/pidgin/Makefile
cvs rdiff -u -r1.30 -r1.31 pkgsrc/chat/pidgin/buildlink3.mk
cvs rdiff -u -r1.27 -r1.28 pkgsrc/chat/pidgin-facebookchat/Makefile
cvs rdiff -u -r1.23 -r1.24 pkgsrc/chat/pidgin-icb/Makefile
cvs rdiff -u -r1.26 -r1.27 pkgsrc/chat/pidgin-latex/Makefile
cvs rdiff -u -r1.19 -r1.20 pkgsrc/chat/pidgin-libnotify/Makefile
cvs rdiff -u -r1.29 -r1.30 pkgsrc/chat/pidgin-otr/Makefile
cvs rdiff -u -r1.31 -r1.32 pkgsrc/chat/pidgin-sametime/Makefile
cvs rdiff -u -r1.34 -r1.35 pkgsrc/chat/pidgin-silc/Makefile
cvs rdiff -u -r1.68 -r1.69 pkgsrc/chat/psi/Makefile
cvs rdiff -u -r1.22 -r1.23 pkgsrc/chat/spectrum/Makefile
cvs rdiff -u -r1.25 -r1.26 pkgsrc/chat/telepathy-farsight/Makefile
cvs rdiff -u -r1.19 -r1.20 pkgsrc/chat/telepathy-farsight/buildlink3.mk
cvs rdiff -u -r1.19 -r1.20 pkgsrc/chat/telepathy-mission-control/Makefile
cvs rdiff -u -r1.14 -r1.15 \
pkgsrc/chat/telepathy-mission-control/buildlink3.mk
cvs rdiff -u -r1.78 -r1.79 pkgsrc/chat/xchat/Makefile
cvs rdiff -u -r1.29 -r1.30 pkgsrc/chat/xchat-systray-integration/Makefile
cvs rdiff -u -r1.29 -r1.30 pkgsrc/comms/asterisk10/Makefile
cvs rdiff -u -r1.47 -r1.48 pkgsrc/comms/asterisk18/Makefile
cvs rdiff -u -r1.58 -r1.59 pkgsrc/comms/efax-gtk/Makefile
cvs rdiff -u -r1.70 -r1.71 pkgsrc/comms/gnome-pilot/Makefile
cvs rdiff -u -r1.43 -r1.44 pkgsrc/comms/gnome-pilot/buildlink3.mk
cvs rdiff -u -r1.82 -r1.83 pkgsrc/comms/jpilot/Makefile
cvs rdiff -u -r1.25 -r1.26 pkgsrc/comms/jpilot/buildlink3.mk
cvs rdiff -u -r1.53 -r1.54 pkgsrc/comms/jpilot-syncmal/Makefile
cvs rdiff -u -r1.21 -r1.22 pkgsrc/comms/multisync-gui/Makefile
cvs rdiff -u -r1.35 -r1.36 pkgsrc/converters/tex2rtf/Makefile
cvs rdiff -u -r1.29 -r1.30 pkgsrc/databases/gourmet/Makefile
cvs rdiff -u -r1.52 -r1.53 pkgsrc/databases/gq/Makefile
cvs rdiff -u -r1.59 -r1.60 pkgsrc/databases/gramps/Makefile
cvs rdiff -u -r1.56 -r1.57 pkgsrc/databases/gramps2/Makefile
cvs rdiff -u -r1.34 -r1.35 pkgsrc/databases/gramps3/Makefile
cvs rdiff -u -r1.7 -r1.8 pkgsrc/databases/gtkdbfeditor/Makefile
cvs rdiff -u -r1.86 -r1.87 pkgsrc/databases/libgnomedb/Makefile
cvs rdiff -u -r1.39 -r1.40 pkgsrc/databases/libgnomedb/buildlink3.mk
cvs rdiff -u -r1.78 -r1.79 pkgsrc/databases/mergeant/Makefile
cvs rdiff -u -r1.16 -r1.17 pkgsrc/databases/mysql-workbench/Makefile
cvs rdiff -u -r1.13 -r1.14 pkgsrc/databases/p5-RRD-Simple/Makefile
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cvs rdiff -u -r1.12 -r1.13 pkgsrc/graphics/clutter08-gtk/buildlink3.mk
cvs rdiff -u -r1.38 -r1.39 pkgsrc/graphics/comix/Makefile
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cvs rdiff -u -r1.13 -r1.14 pkgsrc/graphics/eog-plugins/Makefile
cvs rdiff -u -r1.15 -r1.16 pkgsrc/graphics/eog-plugins-map/Makefile
cvs rdiff -u -r1.5 -r1.6 pkgsrc/graphics/eog3/Makefile
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cvs rdiff -u -r1.32 -r1.33 pkgsrc/graphics/gmngview/Makefile
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cvs rdiff -u -r1.63 -r1.64 pkgsrc/graphics/gnuplot/Makefile
cvs rdiff -u -r1.19 -r1.20 pkgsrc/graphics/goocanvas/Makefile
cvs rdiff -u -r1.14 -r1.15 pkgsrc/graphics/goocanvas/buildlink3.mk
cvs rdiff -u -r1.21 -r1.22 pkgsrc/graphics/goocanvasmm/Makefile
cvs rdiff -u -r1.7 -r1.8 pkgsrc/graphics/gpicview/Makefile
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cvs rdiff -u -r1.16 -r1.17 pkgsrc/graphics/gst-plugins0.10-cairo/Makefile
cvs rdiff -u -r1.72 -r1.73 pkgsrc/graphics/gthumb/Makefile
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cvs rdiff -u -r1.20 -r1.21 pkgsrc/graphics/gtkimageview/Makefile
cvs rdiff -u -r1.12 -r1.13 pkgsrc/graphics/guile-cairo/Makefile
cvs rdiff -u -r1.56 -r1.57 pkgsrc/graphics/gwenview/Makefile
cvs rdiff -u -r1.28 -r1.29 pkgsrc/graphics/hugin/Makefile
cvs rdiff -u -r1.76 -r1.77 pkgsrc/graphics/inkscape/Makefile
cvs rdiff -u -r1.5 -r1.6 pkgsrc/graphics/kamera/Makefile
cvs rdiff -u -r1.5 -r1.6 pkgsrc/graphics/kcolorchooser/Makefile
cvs rdiff -u -r1.5 -r1.6 pkgsrc/graphics/kdegraphics-mobipocket/Makefile
cvs rdiff -u -r1.5 -r1.6 pkgsrc/graphics/kdegraphics-strigi-analyzer/Makefile
cvs rdiff -u -r1.5 -r1.6 pkgsrc/graphics/kdegraphics-thumbnailers/Makefile
cvs rdiff -u -r1.5 -r1.6 pkgsrc/graphics/kgamma/Makefile
cvs rdiff -u -r1.75 -r1.76 pkgsrc/graphics/kipi-plugins/Makefile
cvs rdiff -u -r1.19 -r1.20 \
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cvs rdiff -u -r1.23 -r1.24 pkgsrc/graphics/kipi-plugins-kde3/Makefile
cvs rdiff -u -r1.5 -r1.6 pkgsrc/graphics/kolourpaint/Makefile
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cvs rdiff -u -r1.5 -r1.6 pkgsrc/graphics/ksaneplugin/Makefile
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cvs rdiff -u -r1.37 -r1.38 pkgsrc/graphics/libexif-gtk/Makefile
cvs rdiff -u -r1.21 -r1.22 pkgsrc/graphics/libexif-gtk/buildlink3.mk
cvs rdiff -u -r1.59 -r1.60 pkgsrc/graphics/libgdiplus/Makefile
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cvs rdiff -u -r1.65 -r1.66 pkgsrc/graphics/libgnomecanvas/Makefile
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cvs rdiff -u -r1.27 -r1.28 pkgsrc/graphics/libgnomecanvasmm/Makefile
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cvs rdiff -u -r1.31 -r1.32 pkgsrc/graphics/libkdcraw/Makefile
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cvs rdiff -u -r1.34 -r1.35 pkgsrc/graphics/libkexiv2/Makefile
cvs rdiff -u -r1.4 -r1.5 pkgsrc/graphics/libkface/Makefile \
pkgsrc/graphics/libkface/buildlink3.mk
cvs rdiff -u -r1.43 -r1.44 pkgsrc/graphics/libkipi/Makefile
cvs rdiff -u -r1.30 -r1.31 pkgsrc/graphics/libkipi/buildlink3.mk
cvs rdiff -u -r1.5 -r1.6 pkgsrc/graphics/libksane/Makefile
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cvs rdiff -u -r1.62 -r1.63 pkgsrc/graphics/librsvg/Makefile
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cvs rdiff -u -r1.25 -r1.26 pkgsrc/graphics/libscigraphica/Makefile
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cvs rdiff -u -r1.21 -r1.22 pkgsrc/graphics/nvtv/Makefile
cvs rdiff -u -r1.28 -r1.29 pkgsrc/graphics/opencv/Makefile
cvs rdiff -u -r1.24 -r1.25 pkgsrc/graphics/osg/Makefile
cvs rdiff -u -r1.16 -r1.17 pkgsrc/graphics/osg/buildlink3.mk
cvs rdiff -u -r1.12 -r1.13 pkgsrc/graphics/p5-Gnome2-Canvas/Makefile \
pkgsrc/graphics/p5-Gnome2-Canvas/buildlink3.mk
cvs rdiff -u -r1.16 -r1.17 pkgsrc/graphics/p5-cairo/Makefile
cvs rdiff -u -r1.8 -r1.9 pkgsrc/graphics/p5-cairo/buildlink3.mk
cvs rdiff -u -r1.20 -r1.21 pkgsrc/graphics/p5-clutter/Makefile
cvs rdiff -u -r1.33 -r1.34 pkgsrc/graphics/py-cairo/Makefile
cvs rdiff -u -r1.16 -r1.17 pkgsrc/graphics/py-cairo/buildlink3.mk
cvs rdiff -u -r1.29 -r1.30 pkgsrc/graphics/py-clutter/Makefile
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cvs rdiff -u -r1.17 -r1.18 pkgsrc/graphics/py-clutter-gtk/Makefile
cvs rdiff -u -r1.24 -r1.25 pkgsrc/graphics/py-goocanvas/Makefile
cvs rdiff -u -r1.24 -r1.25 pkgsrc/graphics/py-gtkglext/Makefile
cvs rdiff -u -r1.32 -r1.33 pkgsrc/graphics/py-matplotlib-gtk2/Makefile
cvs rdiff -u -r1.15 -r1.16 pkgsrc/graphics/qimageblitz/Makefile
cvs rdiff -u -r1.16 -r1.17 pkgsrc/graphics/qimageblitz/buildlink3.mk
cvs rdiff -u -r1.35 -r1.36 pkgsrc/graphics/qiv/Makefile
cvs rdiff -u -r1.6 -r1.7 pkgsrc/graphics/qiviewer/Makefile
cvs rdiff -u -r1.16 -r1.17 pkgsrc/graphics/ristretto/Makefile
cvs rdiff -u -r1.15 -r1.16 pkgsrc/graphics/ruby-clutter-cairo/Makefile
cvs rdiff -u -r1.18 -r1.19 pkgsrc/graphics/ruby-clutter-core/Makefile
cvs rdiff -u -r1.15 -r1.16 pkgsrc/graphics/ruby-clutter-gtk/Makefile
cvs rdiff -u -r1.22 -r1.23 pkgsrc/graphics/ruby-gnome2-goocanvas/Makefile
cvs rdiff -u -r1.35 -r1.36 pkgsrc/graphics/ruby-gnome2-rsvg/Makefile
cvs rdiff -u -r1.27 -r1.28 pkgsrc/graphics/ruby-rcairo/Makefile
cvs rdiff -u -r1.15 -r1.16 pkgsrc/graphics/ruby-rcairo/buildlink3.mk
cvs rdiff -u -r1.54 -r1.55 pkgsrc/graphics/sane-frontends/Makefile
cvs rdiff -u -r1.18 -r1.19 pkgsrc/graphics/scidavis/Makefile
cvs rdiff -u -r1.60 -r1.61 pkgsrc/graphics/scigraphica/Makefile
cvs rdiff -u -r1.36 -r1.37 pkgsrc/graphics/shotwell/Makefile
cvs rdiff -u -r1.8 -r1.9 pkgsrc/graphics/shotwell-gtk3/Makefile
cvs rdiff -u -r1.5 -r1.6 pkgsrc/graphics/svgpart/Makefile
cvs rdiff -u -r1.67 -r1.68 pkgsrc/graphics/tuxpaint/Makefile
cvs rdiff -u -r1.16 -r1.17 pkgsrc/graphics/ucview/Makefile
cvs rdiff -u -r1.19 -r1.20 pkgsrc/graphics/unicap/Makefile
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cvs rdiff -u -r1.7 -r1.8 pkgsrc/graphics/viewnior/Makefile
cvs rdiff -u -r1.30 -r1.31 pkgsrc/graphics/wxsvg/Makefile
cvs rdiff -u -r1.24 -r1.25 pkgsrc/graphics/wxsvg/buildlink3.mk
cvs rdiff -u -r1.19 -r1.20 pkgsrc/graphics/xfce4-icon-theme/Makefile
cvs rdiff -u -r1.29 -r1.30 pkgsrc/graphics/xfce4-icon-theme/buildlink3.mk
cvs rdiff -u -r1.96 -r1.97 pkgsrc/graphics/xsane/Makefile
cvs rdiff -u -r1.53 -r1.54 pkgsrc/graphics/xzgv/Makefile
cvs rdiff -u -r1.24 -r1.25 pkgsrc/graphics/zphoto/Makefile
cvs rdiff -u -r1.45 -r1.46 pkgsrc/ham/gmfsk/Makefile
cvs rdiff -u -r1.30 -r1.31 pkgsrc/ham/gnuradio-examples/Makefile
cvs rdiff -u -r1.24 -r1.25 pkgsrc/ham/gnuradio-radio-astronomy/Makefile
cvs rdiff -u -r1.34 -r1.35 pkgsrc/ham/gnuradio-wxgui/Makefile
cvs rdiff -u -r1.30 -r1.31 pkgsrc/ham/gnuradio-wxgui/buildlink3.mk
cvs rdiff -u -r1.28 -r1.29 pkgsrc/ham/gpredict/Makefile
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cvs rdiff -u -r1.18 -r1.19 pkgsrc/inputmethod/gcin/Makefile
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cvs rdiff -u -r1.20 -r1.21 pkgsrc/inputmethod/ibus/Makefile
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cvs rdiff -u -r1.17 -r1.18 pkgsrc/inputmethod/ibus-handwrite/Makefile
cvs rdiff -u -r1.15 -r1.16 pkgsrc/inputmethod/ibus-input-pad/Makefile
cvs rdiff -u -r1.17 -r1.18 pkgsrc/inputmethod/ibus-m17n/Makefile
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cvs rdiff -u -r1.15 -r1.16 pkgsrc/inputmethod/input-pad/Makefile
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cvs rdiff -u -r1.16 -r1.17 pkgsrc/inputmethod/m17n-im-config/Makefile \
pkgsrc/inputmethod/m17n-im-config/buildlink3.mk
cvs rdiff -u -r1.40 -r1.41 pkgsrc/inputmethod/nabi/Makefile
cvs rdiff -u -r1.16 -r1.17 pkgsrc/inputmethod/novel-pinyin/Makefile
cvs rdiff -u -r1.18 -r1.19 pkgsrc/inputmethod/py-input-pad/Makefile
cvs rdiff -u -r1.17 -r1.18 pkgsrc/inputmethod/scim/Makefile
cvs rdiff -u -r1.14 -r1.15 pkgsrc/inputmethod/scim/buildlink3.mk
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cvs rdiff -u -r1.14 -r1.15 pkgsrc/inputmethod/scim-hangul/Makefile
cvs rdiff -u -r1.13 -r1.14 pkgsrc/inputmethod/scim-input-pad/Makefile
cvs rdiff -u -r1.14 -r1.15 pkgsrc/inputmethod/scim-m17n/Makefile
cvs rdiff -u -r1.13 -r1.14 pkgsrc/inputmethod/scim-pinyin/Makefile
cvs rdiff -u -r1.13 -r1.14 pkgsrc/inputmethod/scim-prime/Makefile
cvs rdiff -u -r1.13 -r1.14 pkgsrc/inputmethod/scim-python/Makefile
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cvs rdiff -u -r1.15 -r1.16 pkgsrc/inputmethod/scim-tomoe/Makefile
cvs rdiff -u -r1.14 -r1.15 pkgsrc/inputmethod/scim-uim/Makefile
cvs rdiff -u -r1.12 -r1.13 pkgsrc/inputmethod/scim-unikey/Makefile
cvs rdiff -u -r1.18 -r1.19 pkgsrc/inputmethod/tomoe-gtk/Makefile
cvs rdiff -u -r1.16 -r1.17 pkgsrc/inputmethod/tomoe-gtk/buildlink3.mk
cvs rdiff -u -r1.65 -r1.66 pkgsrc/inputmethod/uim/Makefile
cvs rdiff -u -r1.18 -r1.19 pkgsrc/inputmethod/uim-tomoe-gtk/Makefile
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cvs rdiff -u -r1.16 -r1.17 pkgsrc/lang/squeak-vm/Makefile
cvs rdiff -u -r1.40 -r1.41 pkgsrc/mail/akonadi/Makefile
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cvs rdiff -u -r1.28 -r1.29 pkgsrc/mail/claws-mail-attremover/Makefile
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cvs rdiff -u -r1.38 -r1.39 pkgsrc/mail/claws-mail-gtkhtml/Makefile
cvs rdiff -u -r1.28 -r1.29 pkgsrc/mail/claws-mail-mailmbox/Makefile
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cvs rdiff -u -r1.31 -r1.32 pkgsrc/mail/claws-mail-notification/Makefile
cvs rdiff -u -r1.26 -r1.27 pkgsrc/mail/claws-mail-pgpcore/Makefile
cvs rdiff -u -r1.17 -r1.18 pkgsrc/mail/claws-mail-pgpcore/buildlink3.mk
cvs rdiff -u -r1.26 -r1.27 pkgsrc/mail/claws-mail-pgpinline/Makefile
cvs rdiff -u -r1.25 -r1.26 pkgsrc/mail/claws-mail-pgpmime/Makefile
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cvs rdiff -u -r1.27 -r1.28 pkgsrc/mail/claws-mail-smime/Makefile
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cvs rdiff -u -r1.28 -r1.29 pkgsrc/mail/claws-mail-synce/Makefile
cvs rdiff -u -r1.26 -r1.27 pkgsrc/mail/claws-mail-tnef/Makefile
cvs rdiff -u -r1.33 -r1.34 pkgsrc/mail/claws-mail-vcalendar/Makefile
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cvs rdiff -u -r1.123 -r1.124 pkgsrc/mail/evolution-data-server/Makefile
cvs rdiff -u -r1.63 -r1.64 pkgsrc/mail/evolution-exchange/Makefile
cvs rdiff -u -r1.68 -r1.69 pkgsrc/mail/mail-notification/Makefile
cvs rdiff -u -r1.41 -r1.42 pkgsrc/mail/msmtp/Makefile
cvs rdiff -u -r1.17 -r1.18 pkgsrc/mail/netbiff/Makefile
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pkgsrc/misc/libkgeomap/buildlink3.mk
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pkgsrc/misc/libkvkontakte/buildlink3.mk
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cvs rdiff -u -r1.21 -r1.22 pkgsrc/multimedia/swfdec-gnome/Makefile
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cvs rdiff -u -r1.59 -r1.60 pkgsrc/multimedia/totem/Makefile
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cvs rdiff -u -r1.24 -r1.25 pkgsrc/multimedia/totem-browser-plugin/Makefile
cvs rdiff -u -r1.28 -r1.29 pkgsrc/multimedia/totem-nautilus/Makefile
cvs rdiff -u -r1.39 -r1.40 pkgsrc/multimedia/totem-pl-parser/Makefile
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cvs rdiff -u -r1.140 -r1.141 pkgsrc/multimedia/vlc/Makefile
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cvs rdiff -u -r1.33 -r1.34 pkgsrc/multimedia/xfmedia/Makefile
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cvs rdiff -u -r1.6 -r1.7 pkgsrc/net/Transmission-gui/Makefile
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cvs rdiff -u -r1.3 -r1.4 pkgsrc/net/libktorrent/Makefile \
pkgsrc/net/libktorrent/buildlink3.mk
cvs rdiff -u -r1.32 -r1.33 pkgsrc/net/logjam/Makefile
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cvs rdiff -u -r1.30 -r1.31 pkgsrc/security/fwbuilder/Makefile
cvs rdiff -u -r1.71 -r1.72 pkgsrc/security/gnome-keyring/Makefile
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cvs rdiff -u -r1.7 -r1.8 pkgsrc/security/qca2-gnupg/Makefile
cvs rdiff -u -r1.21 -r1.22 pkgsrc/security/qca2-ossl/Makefile
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cvs rdiff -u -r1.21 -r1.22 pkgsrc/sysutils/brasero-nautilus/Makefile
cvs rdiff -u -r1.18 -r1.19 pkgsrc/sysutils/btpin-qt/Makefile
cvs rdiff -u -r1.15 -r1.16 pkgsrc/sysutils/bubblemon/Makefile
cvs rdiff -u -r1.4 -r1.5 pkgsrc/sysutils/conky/Makefile
cvs rdiff -u -r1.20 -r1.21 pkgsrc/sysutils/dvdisaster/Makefile
cvs rdiff -u -r1.32 -r1.33 pkgsrc/sysutils/filelight/Makefile
cvs rdiff -u -r1.60 -r1.61 pkgsrc/sysutils/gcdmaster/Makefile
cvs rdiff -u -r1.70 -r1.71 pkgsrc/sysutils/gkrellm/Makefile
cvs rdiff -u -r1.27 -r1.28 pkgsrc/sysutils/gkrellm/buildlink3.mk
cvs rdiff -u -r1.27 -r1.28 pkgsrc/sysutils/gkrellm-est/Makefile
cvs rdiff -u -r1.35 -r1.36 pkgsrc/sysutils/gnome-commander/Makefile
cvs rdiff -u -r1.21 -r1.22 pkgsrc/sysutils/gnome-device-manager/Makefile
cvs rdiff -u -r1.20 -r1.21 pkgsrc/sysutils/gnome-mount/Makefile
cvs rdiff -u -r1.16 -r1.17 pkgsrc/sysutils/gnome-mount/buildlink3.mk
cvs rdiff -u -r1.15 -r1.16 pkgsrc/sysutils/gnome-nds-thumbnailer/Makefile
cvs rdiff -u -r1.44 -r1.45 pkgsrc/sysutils/gnome-pkgview/Makefile
cvs rdiff -u -r1.30 -r1.31 pkgsrc/sysutils/gnome-power-manager/Makefile
cvs rdiff -u -r1.35 -r1.36 pkgsrc/sysutils/gnome-settings-daemon/Makefile
cvs rdiff -u -r1.32 -r1.33 pkgsrc/sysutils/gnome-system-monitor/Makefile
cvs rdiff -u -r1.19 -r1.20 pkgsrc/sysutils/gnome-system-tools/Makefile
cvs rdiff -u -r1.94 -r1.95 pkgsrc/sysutils/gnome-vfs/Makefile
cvs rdiff -u -r1.37 -r1.38 pkgsrc/sysutils/gnome-vfs/buildlink3.mk
cvs rdiff -u -r1.19 -r1.20 pkgsrc/sysutils/gnome-vfs-monikers/Makefile
cvs rdiff -u -r1.36 -r1.37 pkgsrc/sysutils/gnome-vfsmm/Makefile
cvs rdiff -u -r1.26 -r1.27 pkgsrc/sysutils/gnome-vfsmm/buildlink3.mk
cvs rdiff -u -r1.23 -r1.24 pkgsrc/sysutils/gnome-volume-manager/Makefile
cvs rdiff -u -r1.31 -r1.32 pkgsrc/sysutils/grun/Makefile
cvs rdiff -u -r1.32 -r1.33 pkgsrc/sysutils/gst-plugins0.10-gnomevfs/Makefile
cvs rdiff -u -r1.41 -r1.42 pkgsrc/sysutils/gtk-send-pr/Makefile
cvs rdiff -u -r1.45 -r1.46 pkgsrc/sysutils/gvfs/Makefile
cvs rdiff -u -r1.47 -r1.48 pkgsrc/sysutils/k3b/Makefile
cvs rdiff -u -r1.6 -r1.7 pkgsrc/sysutils/k4dirstat/Makefile
cvs rdiff -u -r1.26 -r1.27 pkgsrc/sysutils/kdf/Makefile
cvs rdiff -u -r1.5 -r1.6 pkgsrc/sysutils/kfloppy/Makefile
cvs rdiff -u -r1.21 -r1.22 pkgsrc/sysutils/libgksu/Makefile
cvs rdiff -u -r1.16 -r1.17 pkgsrc/sysutils/libgksu/buildlink3.mk
cvs rdiff -u -r1.22 -r1.23 pkgsrc/sysutils/libnotify/Makefile
cvs rdiff -u -r1.19 -r1.20 pkgsrc/sysutils/libnotify/buildlink3.mk
cvs rdiff -u -r1.125 -r1.126 pkgsrc/sysutils/nautilus/Makefile
cvs rdiff -u -r1.50 -r1.51 pkgsrc/sysutils/nautilus/buildlink3.mk
cvs rdiff -u -r1.32 -r1.33 pkgsrc/sysutils/nautilus-sendto/Makefile
cvs rdiff -u -r1.27 -r1.28 pkgsrc/sysutils/notification-daemon/Makefile
cvs rdiff -u -r1.28 -r1.29 pkgsrc/sysutils/open-vm-tools/Makefile
cvs rdiff -u -r1.14 -r1.15 pkgsrc/sysutils/p5-Gnome2-VFS/Makefile
cvs rdiff -u -r1.13 -r1.14 pkgsrc/sysutils/p5-Gnome2-VFS/buildlink3.mk
cvs rdiff -u -r1.19 -r1.20 pkgsrc/sysutils/pcmanfm/Makefile
cvs rdiff -u -r1.25 -r1.26 pkgsrc/sysutils/py-notify/Makefile
cvs rdiff -u -r1.19 -r1.20 pkgsrc/sysutils/py-notify/buildlink3.mk
cvs rdiff -u -r1.63 -r1.64 pkgsrc/sysutils/rox/Makefile
cvs rdiff -u -r1.26 -r1.27 pkgsrc/sysutils/screentest/Makefile
cvs rdiff -u -r1.22 -r1.23 pkgsrc/sysutils/strigi/Makefile
cvs rdiff -u -r1.3 -r1.4 pkgsrc/sysutils/virt-manager/Makefile
cvs rdiff -u -r1.62 -r1.63 pkgsrc/sysutils/xcdroast/Makefile
cvs rdiff -u -r1.25 -r1.26 pkgsrc/sysutils/xfce4-appfinder/Makefile
cvs rdiff -u -r1.21 -r1.22 pkgsrc/sysutils/xfce4-battery-plugin/Makefile
cvs rdiff -u -r1.18 -r1.19 pkgsrc/sysutils/xfce4-battery-plugin/buildlink3.mk
cvs rdiff -u -r1.24 -r1.25 pkgsrc/sysutils/xfce4-cpugraph-plugin/Makefile
cvs rdiff -u -r1.28 -r1.29 \
pkgsrc/sysutils/xfce4-cpugraph-plugin/buildlink3.mk
cvs rdiff -u -r1.28 -r1.29 pkgsrc/sysutils/xfce4-diskperf-plugin/Makefile
cvs rdiff -u -r1.29 -r1.30 \
pkgsrc/sysutils/xfce4-diskperf-plugin/buildlink3.mk
cvs rdiff -u -r1.21 -r1.22 pkgsrc/sysutils/xfce4-fsguard-plugin/Makefile
cvs rdiff -u -r1.26 -r1.27 pkgsrc/sysutils/xfce4-fsguard-plugin/buildlink3.mk
cvs rdiff -u -r1.14 -r1.15 pkgsrc/sysutils/xfce4-genmon-plugin/Makefile
cvs rdiff -u -r1.16 -r1.17 pkgsrc/sysutils/xfce4-genmon-plugin/buildlink3.mk
cvs rdiff -u -r1.30 -r1.31 pkgsrc/sysutils/xfce4-netload-plugin/Makefile
cvs rdiff -u -r1.32 -r1.33 pkgsrc/sysutils/xfce4-netload-plugin/buildlink3.mk
cvs rdiff -u -r1.22 -r1.23 \
pkgsrc/sysutils/xfce4-quicklauncher-plugin/Makefile
cvs rdiff -u -r1.28 -r1.29 \
pkgsrc/sysutils/xfce4-quicklauncher-plugin/buildlink3.mk
cvs rdiff -u -r1.28 -r1.29 pkgsrc/sysutils/xfce4-systemload-plugin/Makefile
cvs rdiff -u -r1.30 -r1.31 \
pkgsrc/sysutils/xfce4-systemload-plugin/buildlink3.mk
cvs rdiff -u -r1.27 -r1.28 pkgsrc/sysutils/xfce4-thunar/Makefile
cvs rdiff -u -r1.23 -r1.24 pkgsrc/sysutils/xfce4-thunar/buildlink3.mk
cvs rdiff -u -r1.19 -r1.20 pkgsrc/sysutils/xfce4-volman/Makefile
cvs rdiff -u -r1.18 -r1.19 pkgsrc/sysutils/xfce4-xarchiver/Makefile
cvs rdiff -u -r1.17 -r1.18 pkgsrc/sysutils/xfce4-xarchiver/buildlink3.mk
cvs rdiff -u -r1.26 -r1.27 pkgsrc/sysutils/xfce4-xkb-plugin/Makefile
cvs rdiff -u -r1.29 -r1.30 pkgsrc/sysutils/xfce4-xkb-plugin/buildlink3.mk
cvs rdiff -u -r1.15 -r1.16 pkgsrc/textproc/FlightCrew/Makefile
cvs rdiff -u -r1.19 -r1.20 pkgsrc/textproc/OdfConverter/Makefile
cvs rdiff -u -r1.9 -r1.10 pkgsrc/textproc/dikt/Makefile
cvs rdiff -u -r1.16 -r1.17 pkgsrc/textproc/ebview/Makefile
cvs rdiff -u -r1.49 -r1.50 pkgsrc/textproc/gnome-spell/Makefile
cvs rdiff -u -r1.35 -r1.36 pkgsrc/textproc/gnome-spell/buildlink3.mk
cvs rdiff -u -r1.26 -r1.27 pkgsrc/textproc/gnome-subtitles/Makefile
cvs rdiff -u -r1.48 -r1.49 pkgsrc/textproc/gtkspell/Makefile
cvs rdiff -u -r1.25 -r1.26 pkgsrc/textproc/gtkspell/buildlink3.mk
cvs rdiff -u -r1.31 -r1.32 pkgsrc/textproc/py-gdick/Makefile
cvs rdiff -u -r1.28 -r1.29 pkgsrc/textproc/soprano/Makefile
cvs rdiff -u -r1.16 -r1.17 pkgsrc/textproc/soprano/buildlink3.mk
cvs rdiff -u -r1.14 -r1.15 pkgsrc/textproc/xfce4-dict-plugin/Makefile
cvs rdiff -u -r1.16 -r1.17 pkgsrc/textproc/xfce4-dict-plugin/buildlink3.mk
cvs rdiff -u -r1.26 -r1.27 pkgsrc/time/cairo-clock/Makefile
cvs rdiff -u -r1.58 -r1.59 pkgsrc/time/evolution-webcal/Makefile
cvs rdiff -u -r1.17 -r1.18 pkgsrc/time/gchore/Makefile
cvs rdiff -u -r1.43 -r1.44 pkgsrc/time/gdeskcal/Makefile
cvs rdiff -u -r1.54 -r1.55 pkgsrc/time/gnotime/Makefile
cvs rdiff -u -r1.42 -r1.43 pkgsrc/time/gtodo/Makefile
cvs rdiff -u -r1.46 -r1.47 pkgsrc/time/gtodo-applet/Makefile
cvs rdiff -u -r1.28 -r1.29 pkgsrc/time/hamster-applet/Makefile
cvs rdiff -u -r1.5 -r1.6 pkgsrc/time/ktimer/Makefile
cvs rdiff -u -r1.36 -r1.37 pkgsrc/time/planner/Makefile
cvs rdiff -u -r1.27 -r1.28 pkgsrc/time/rsibreak/Makefile
cvs rdiff -u -r1.28 -r1.29 pkgsrc/time/xfce4-datetime-plugin/Makefile \
pkgsrc/time/xfce4-datetime-plugin/buildlink3.mk
cvs rdiff -u -r1.18 -r1.19 pkgsrc/time/xfce4-orage/Makefile
cvs rdiff -u -r1.14 -r1.15 pkgsrc/time/xfce4-timer-plugin/Makefile
cvs rdiff -u -r1.16 -r1.17 pkgsrc/time/xfce4-timer-plugin/buildlink3.mk
cvs rdiff -u -r1.57 -r1.58 pkgsrc/wm/afterstep/Makefile
cvs rdiff -u -r1.30 -r1.31 pkgsrc/wm/awesome/Makefile
cvs rdiff -u -r1.9 -r1.10 pkgsrc/wm/bmpanel2/Makefile
cvs rdiff -u -r1.51 -r1.52 pkgsrc/wm/compiz/Makefile
cvs rdiff -u -r1.16 -r1.17 pkgsrc/wm/compiz/buildlink3.mk
cvs rdiff -u -r1.19 -r1.20 pkgsrc/wm/compiz-fusion-plugins-extra/Makefile
cvs rdiff -u -r1.21 -r1.22 pkgsrc/wm/compiz-fusion-plugins-main/Makefile
cvs rdiff -u -r1.16 -r1.17 pkgsrc/wm/compiz-fusion-plugins-main/buildlink3.mk
cvs rdiff -u -r1.34 -r1.35 pkgsrc/wm/e16menuedit2/Makefile
cvs rdiff -u -r1.15 -r1.16 pkgsrc/wm/fluxconf/Makefile
cvs rdiff -u -r1.102 -r1.103 pkgsrc/wm/metacity/Makefile
cvs rdiff -u -r1.32 -r1.33 pkgsrc/wm/metacity/buildlink3.mk
cvs rdiff -u -r1.26 -r1.27 pkgsrc/wm/metisse/Makefile
cvs rdiff -u -r1.77 -r1.78 pkgsrc/wm/openbox/Makefile
cvs rdiff -u -r1.33 -r1.34 pkgsrc/wm/oroborox/Makefile
cvs rdiff -u -r1.66 -r1.67 pkgsrc/wm/sawfish/Makefile
cvs rdiff -u -r1.20 -r1.21 pkgsrc/wm/selectwm/Makefile
cvs rdiff -u -r1.10 -r1.11 pkgsrc/wm/wbar/Makefile
cvs rdiff -u -r1.56 -r1.57 pkgsrc/wm/wmakerconf/Makefile
cvs rdiff -u -r1.42 -r1.43 pkgsrc/wm/xfce4-wm/Makefile
cvs rdiff -u -r1.30 -r1.31 pkgsrc/wm/xfce4-wm-themes/Makefile
cvs rdiff -u -r1.73 -r1.74 pkgsrc/www/amaya/Makefile
cvs rdiff -u -r1.17 -r1.18 pkgsrc/www/ap22-dnssd/Makefile
cvs rdiff -u -r1.100 -r1.101 pkgsrc/www/bluefish/Makefile
cvs rdiff -u -r1.32 -r1.33 pkgsrc/www/browser-bookmarks-menu/Makefile
cvs rdiff -u -r1.64 -r1.65 pkgsrc/www/drivel/Makefile
cvs rdiff -u -r1.130 -r1.131 pkgsrc/www/epiphany/Makefile
cvs rdiff -u -r1.49 -r1.50 pkgsrc/www/epiphany/buildlink3.mk
cvs rdiff -u -r1.75 -r1.76 pkgsrc/www/epiphany-extensions/Makefile
cvs rdiff -u -r1.111 -r1.112 pkgsrc/www/firefox/Makefile
cvs rdiff -u -r1.7 -r1.8 pkgsrc/www/firefox10/Makefile
cvs rdiff -u -r1.17 -r1.18 pkgsrc/www/firefox36/Makefile
cvs rdiff -u -r1.51 -r1.52 pkgsrc/www/gtkhtml314/Makefile
cvs rdiff -u -r1.13 -r1.14 pkgsrc/www/icedtea-web/Makefile
cvs rdiff -u -r1.49 -r1.50 pkgsrc/www/kazehakase/Makefile
cvs rdiff -u -r1.30 -r1.31 pkgsrc/www/kdewebdev4/Makefile
cvs rdiff -u -r1.61 -r1.62 pkgsrc/www/libgtkhtml/Makefile
cvs rdiff -u -r1.34 -r1.35 pkgsrc/www/libgtkhtml/buildlink3.mk
cvs rdiff -u -r1.4 -r1.5 pkgsrc/www/libmediawiki/Makefile \
pkgsrc/www/libmediawiki/buildlink3.mk
cvs rdiff -u -r1.107 -r1.108 pkgsrc/www/liferea/Makefile
cvs rdiff -u -r1.33 -r1.34 pkgsrc/www/liferea-current/Makefile
cvs rdiff -u -r1.47 -r1.48 pkgsrc/www/midori/Makefile
cvs rdiff -u -r1.20 -r1.21 pkgsrc/www/netsurf/Makefile
cvs rdiff -u -r1.31 -r1.32 pkgsrc/www/nspluginwrapper/Makefile
cvs rdiff -u -r1.77 -r1.78 pkgsrc/www/seamonkey/Makefile
cvs rdiff -u -r1.58 -r1.59 pkgsrc/www/webkit-gtk/Makefile
cvs rdiff -u -r1.26 -r1.27 pkgsrc/www/webkit-gtk/buildlink3.mk
cvs rdiff -u -r1.13 -r1.14 pkgsrc/www/webkit-gtk3/Makefile
cvs rdiff -u -r1.9 -r1.10 pkgsrc/www/webkit-gtk3/buildlink3.mk
cvs rdiff -u -r1.40 -r1.41 pkgsrc/x11/alacarte/Makefile
cvs rdiff -u -r1.20 -r1.21 pkgsrc/x11/antiright/Makefile
cvs rdiff -u -r1.10 -r1.11 pkgsrc/x11/avant-window-navigator/Makefile
cvs rdiff -u -r1.12 -r1.13 pkgsrc/x11/clisp-gtk2/Makefile
cvs rdiff -u -r1.14 -r1.15 pkgsrc/x11/deskmenu/Makefile
cvs rdiff -u -r1.51 -r1.52 pkgsrc/x11/devilspie/Makefile
cvs rdiff -u -r1.16 -r1.17 pkgsrc/x11/eekboard/Makefile
cvs rdiff -u -r1.14 -r1.15 pkgsrc/x11/eekboard/buildlink3.mk
cvs rdiff -u -r1.44 -r1.45 pkgsrc/x11/fast-user-switch-applet/Makefile
cvs rdiff -u -r1.3 -r1.4 pkgsrc/x11/fltk13/Makefile
cvs rdiff -u -r1.16 -r1.17 pkgsrc/x11/ftmenu/Makefile
cvs rdiff -u -r1.169 -r1.170 pkgsrc/x11/gdm/Makefile
cvs rdiff -u -r1.104 -r1.105 pkgsrc/x11/gnome-applets/Makefile
cvs rdiff -u -r1.54 -r1.55 pkgsrc/x11/gnome-control-center/Makefile
cvs rdiff -u -r1.27 -r1.28 pkgsrc/x11/gnome-control-center/buildlink3.mk
cvs rdiff -u -r1.116 -r1.117 pkgsrc/x11/gnome-desktop/Makefile
cvs rdiff -u -r1.42 -r1.43 pkgsrc/x11/gnome-desktop/buildlink3.mk
cvs rdiff -u -r1.37 -r1.38 pkgsrc/x11/gnome-desktop-sharp/Makefile
cvs rdiff -u -r1.30 -r1.31 pkgsrc/x11/gnome-desktop-sharp/buildlink3.mk
cvs rdiff -u -r1.3 -r1.4 pkgsrc/x11/gnome-desktop3/Makefile \
pkgsrc/x11/gnome-desktop3/buildlink3.mk
cvs rdiff -u -r1.72 -r1.73 pkgsrc/x11/gnome-mag/Makefile
cvs rdiff -u -r1.30 -r1.31 pkgsrc/x11/gnome-mag/buildlink3.mk
cvs rdiff -u -r1.147 -r1.148 pkgsrc/x11/gnome-panel/Makefile
cvs rdiff -u -r1.51 -r1.52 pkgsrc/x11/gnome-panel/buildlink3.mk
cvs rdiff -u -r1.57 -r1.58 pkgsrc/x11/gnome-screensaver/Makefile
cvs rdiff -u -r1.138 -r1.139 pkgsrc/x11/gnome-session/Makefile
cvs rdiff -u -r1.35 -r1.36 pkgsrc/x11/gnome-sharp/Makefile
cvs rdiff -u -r1.29 -r1.30 pkgsrc/x11/gnome-sharp/buildlink3.mk
cvs rdiff -u -r1.45 -r1.46 pkgsrc/x11/gnome-terminal/Makefile
cvs rdiff -u -r1.88 -r1.89 pkgsrc/x11/gnome-themes/Makefile
cvs rdiff -u -r1.57 -r1.58 pkgsrc/x11/gnome-themes-extras/Makefile
cvs rdiff -u -r1.77 -r1.78 pkgsrc/x11/gnopernicus/Makefile
cvs rdiff -u -r1.26 -r1.27 pkgsrc/x11/grandr_applet/Makefile
cvs rdiff -u -r1.23 -r1.24 pkgsrc/x11/gromit/Makefile
cvs rdiff -u -r1.11 -r1.12 pkgsrc/x11/gselt/Makefile
cvs rdiff -u -r1.29 -r1.30 pkgsrc/x11/gtk-sharp/Makefile
cvs rdiff -u -r1.235 -r1.236 pkgsrc/x11/gtk2/Makefile
cvs rdiff -u -r1.55 -r1.56 pkgsrc/x11/gtk2/buildlink3.mk
cvs rdiff -u -r1.19 -r1.20 pkgsrc/x11/gtk2+extra/Makefile
cvs rdiff -u -r1.22 -r1.23 pkgsrc/x11/gtk2+extra/buildlink3.mk
cvs rdiff -u -r1.23 -r1.24 pkgsrc/x11/gtk2-chtheme/Makefile
cvs rdiff -u -r1.76 -r1.77 pkgsrc/x11/gtk2-engines/Makefile
cvs rdiff -u -r1.25 -r1.26 pkgsrc/x11/gtk2-engines/buildlink3.mk
cvs rdiff -u -r1.30 -r1.31 pkgsrc/x11/gtk2-engines-bluecurve/Makefile
cvs rdiff -u -r1.16 -r1.17 pkgsrc/x11/gtk2-engines-murrine/Makefile
cvs rdiff -u -r1.31 -r1.32 pkgsrc/x11/gtk2-theme-switch/Makefile
cvs rdiff -u -r1.26 -r1.27 pkgsrc/x11/gtk3/Makefile
cvs rdiff -u -r1.7 -r1.8 pkgsrc/x11/gtk3/buildlink3.mk
cvs rdiff -u -r1.10 -r1.11 pkgsrc/x11/gtkada/Makefile
cvs rdiff -u -r1.9 -r1.10 pkgsrc/x11/gtkada/buildlink3.mk
cvs rdiff -u -r1.24 -r1.25 pkgsrc/x11/gtkglarea2/Makefile
cvs rdiff -u -r1.19 -r1.20 pkgsrc/x11/gtkglarea2/buildlink3.mk
cvs rdiff -u -r1.84 -r1.85 pkgsrc/x11/gtkmm/Makefile
cvs rdiff -u -r1.31 -r1.32 pkgsrc/x11/gtkmm/buildlink3.mk
cvs rdiff -u -r1.11 -r1.12 pkgsrc/x11/gtkmm-utils/Makefile
cvs rdiff -u -r1.13 -r1.14 pkgsrc/x11/gtkmm-utils/buildlink3.mk
cvs rdiff -u -r1.63 -r1.64 pkgsrc/x11/gtksourceview/Makefile
cvs rdiff -u -r1.31 -r1.32 pkgsrc/x11/gtksourceview/buildlink3.mk
cvs rdiff -u -r1.32 -r1.33 pkgsrc/x11/gtksourceview-sharp2/Makefile
cvs rdiff -u -r1.32 -r1.33 pkgsrc/x11/gtksourceview2/Makefile
cvs rdiff -u -r1.18 -r1.19 pkgsrc/x11/gtksourceview2/buildlink3.mk
cvs rdiff -u -r1.3 -r1.4 pkgsrc/x11/gtksourceview3/Makefile \
pkgsrc/x11/gtksourceview3/buildlink3.mk
cvs rdiff -u -r1.26 -r1.27 pkgsrc/x11/gtkterm2/Makefile
cvs rdiff -u -r1.32 -r1.33 pkgsrc/x11/hot-babe/Makefile
cvs rdiff -u -r1.5 -r1.6 pkgsrc/x11/kactivities/Makefile \
pkgsrc/x11/kactivities/buildlink3.mk
cvs rdiff -u -r1.7 -r1.8 pkgsrc/x11/kde-baseapps4/Makefile
cvs rdiff -u -r1.11 -r1.12 pkgsrc/x11/kde-runtime4/Makefile
cvs rdiff -u -r1.5 -r1.6 pkgsrc/x11/kde-runtime4/buildlink3.mk
cvs rdiff -u -r1.10 -r1.11 pkgsrc/x11/kde-workspace4/Makefile
cvs rdiff -u -r1.5 -r1.6 pkgsrc/x11/kde-workspace4/buildlink3.mk
cvs rdiff -u -r1.46 -r1.47 pkgsrc/x11/kdelibs4/Makefile
cvs rdiff -u -r1.21 -r1.22 pkgsrc/x11/kdelibs4/buildlink3.mk
cvs rdiff -u -r1.5 -r1.6 pkgsrc/x11/konsole/Makefile
cvs rdiff -u -r1.67 -r1.68 pkgsrc/x11/lablgtk/Makefile
cvs rdiff -u -r1.21 -r1.22 pkgsrc/x11/lablgtk/buildlink3.mk
cvs rdiff -u -r1.9 -r1.10 pkgsrc/x11/libdesktop-agnostic/Makefile
cvs rdiff -u -r1.6 -r1.7 pkgsrc/x11/libdesktop-agnostic/buildlink3.mk
cvs rdiff -u -r1.36 -r1.37 pkgsrc/x11/libgnomekbd/Makefile
cvs rdiff -u -r1.20 -r1.21 pkgsrc/x11/libunique/Makefile
cvs rdiff -u -r1.14 -r1.15 pkgsrc/x11/libunique/buildlink3.mk
cvs rdiff -u -r1.8 -r1.9 pkgsrc/x11/libunique3/Makefile
cvs rdiff -u -r1.40 -r1.41 pkgsrc/x11/libxfce4gui/Makefile
cvs rdiff -u -r1.39 -r1.40 pkgsrc/x11/libxfce4gui/buildlink3.mk
cvs rdiff -u -r1.10 -r1.11 pkgsrc/x11/libxfce4menu/Makefile
cvs rdiff -u -r1.12 -r1.13 pkgsrc/x11/libxfce4menu/buildlink3.mk
cvs rdiff -u -r1.26 -r1.27 pkgsrc/x11/libxfce4util/Makefile
cvs rdiff -u -r1.23 -r1.24 pkgsrc/x11/matchbox-panel-manager/Makefile
cvs rdiff -u -r1.71 -r1.72 pkgsrc/x11/mlterm/Makefile
cvs rdiff -u -r1.28 -r1.29 pkgsrc/x11/nucleo/Makefile
cvs rdiff -u -r1.23 -r1.24 pkgsrc/x11/nucleo/buildlink3.mk
cvs rdiff -u -r1.19 -r1.20 pkgsrc/x11/p5-Alien-wxWidgets/Makefile
cvs rdiff -u -r1.23 -r1.24 pkgsrc/x11/p5-Wx/Makefile
cvs rdiff -u -r1.14 -r1.15 pkgsrc/x11/p5-Wx/buildlink3.mk
cvs rdiff -u -r1.18 -r1.19 pkgsrc/x11/p5-Wx-Perl-ProcessStream/Makefile
cvs rdiff -u -r1.48 -r1.49 pkgsrc/x11/p5-gtk2/Makefile
cvs rdiff -u -r1.15 -r1.16 pkgsrc/x11/p5-gtk2/buildlink3.mk
cvs rdiff -u -r1.85 -r1.86 pkgsrc/x11/py-gnome2/Makefile
cvs rdiff -u -r1.40 -r1.41 pkgsrc/x11/py-gnome2/buildlink3.mk
cvs rdiff -u -r1.66 -r1.67 pkgsrc/x11/py-gnome2-desktop/Makefile
cvs rdiff -u -r1.20 -r1.21 pkgsrc/x11/py-gnome2-desktop/buildlink3.mk
cvs rdiff -u -r1.56 -r1.57 pkgsrc/x11/py-gnome2-extras/Makefile
cvs rdiff -u -r1.31 -r1.32 pkgsrc/x11/py-gnome2-extras/buildlink3.mk
cvs rdiff -u -r1.86 -r1.87 pkgsrc/x11/py-gtk2/Makefile
cvs rdiff -u -r1.39 -r1.40 pkgsrc/x11/py-gtk2/buildlink3.mk
cvs rdiff -u -r1.23 -r1.24 pkgsrc/x11/py-gtksourceview/Makefile
cvs rdiff -u -r1.13 -r1.14 pkgsrc/x11/py-kde4/Makefile
cvs rdiff -u -r1.21 -r1.22 pkgsrc/x11/py-kiwi/Makefile
cvs rdiff -u -r1.53 -r1.54 pkgsrc/x11/py-qt4/Makefile
cvs rdiff -u -r1.21 -r1.22 pkgsrc/x11/py-qt4-qscintilla/Makefile
cvs rdiff -u -r1.15 -r1.16 pkgsrc/x11/py-qt4-qscintilla/buildlink3.mk
cvs rdiff -u -r1.10 -r1.11 pkgsrc/x11/py-vte/Makefile \
pkgsrc/x11/py-vte/buildlink3.mk
cvs rdiff -u -r1.38 -r1.39 pkgsrc/x11/py-wxWidgets/Makefile
cvs rdiff -u -r1.32 -r1.33 pkgsrc/x11/py-wxWidgets/buildlink3.mk
cvs rdiff -u -r1.14 -r1.15 pkgsrc/x11/qt4-creator/Makefile
cvs rdiff -u -r1.22 -r1.23 pkgsrc/x11/qt4-docs/Makefile
cvs rdiff -u -r1.77 -r1.78 pkgsrc/x11/qt4-libs/Makefile
cvs rdiff -u -r1.33 -r1.34 pkgsrc/x11/qt4-libs/buildlink3.mk
cvs rdiff -u -r1.16 -r1.17 pkgsrc/x11/qt4-mng/Makefile
cvs rdiff -u -r1.25 -r1.26 pkgsrc/x11/qt4-mysql/Makefile
cvs rdiff -u -r1.33 -r1.34 pkgsrc/x11/qt4-pgsql/Makefile
cvs rdiff -u -r1.27 -r1.28 pkgsrc/x11/qt4-qdbus/Makefile
cvs rdiff -u -r1.16 -r1.17 pkgsrc/x11/qt4-qdbus/buildlink3.mk
cvs rdiff -u -r1.20 -r1.21 pkgsrc/x11/qt4-qscintilla/Makefile
cvs rdiff -u -r1.14 -r1.15 pkgsrc/x11/qt4-qscintilla/buildlink3.mk
cvs rdiff -u -r1.28 -r1.29 pkgsrc/x11/qt4-sqlite3/Makefile
cvs rdiff -u -r1.25 -r1.26 pkgsrc/x11/qt4-tiff/Makefile
cvs rdiff -u -r1.53 -r1.54 pkgsrc/x11/qt4-tools/Makefile
cvs rdiff -u -r1.23 -r1.24 pkgsrc/x11/qt4-tools/buildlink3.mk
cvs rdiff -u -r1.19 -r1.20 pkgsrc/x11/qwt-qt4/Makefile
cvs rdiff -u -r1.16 -r1.17 pkgsrc/x11/qwt-qt4/buildlink3.mk
cvs rdiff -u -r1.4 -r1.5 pkgsrc/x11/qwt6-qt4/Makefile
cvs rdiff -u -r1.3 -r1.4 pkgsrc/x11/qwt6-qt4/buildlink3.mk
cvs rdiff -u -r1.14 -r1.15 pkgsrc/x11/qwtplot3d-qt4/Makefile \
pkgsrc/x11/qwtplot3d-qt4/buildlink3.mk
cvs rdiff -u -r1.21 -r1.22 pkgsrc/x11/rep-gtk2/Makefile
cvs rdiff -u -r1.30 -r1.31 pkgsrc/x11/rox-session/Makefile
cvs rdiff -u -r1.35 -r1.36 pkgsrc/x11/ruby-gnome2-gtk/Makefile
cvs rdiff -u -r1.20 -r1.21 pkgsrc/x11/ruby-gnome2-gtk/buildlink3.mk
cvs rdiff -u -r1.24 -r1.25 pkgsrc/x11/ruby-gnome2-gtksourceview2/Makefile
cvs rdiff -u -r1.27 -r1.28 pkgsrc/x11/ruby-gnome2-vte/Makefile
cvs rdiff -u -r1.7 -r1.8 pkgsrc/x11/ruby-wxruby/Makefile
cvs rdiff -u -r1.9 -r1.10 pkgsrc/x11/sakura/Makefile
cvs rdiff -u -r1.18 -r1.19 pkgsrc/x11/tint2/Makefile
cvs rdiff -u -r1.91 -r1.92 pkgsrc/x11/vte/Makefile
cvs rdiff -u -r1.32 -r1.33 pkgsrc/x11/vte/buildlink3.mk
cvs rdiff -u -r1.3 -r1.4 pkgsrc/x11/vte029/Makefile \
pkgsrc/x11/vte029/buildlink3.mk
cvs rdiff -u -r1.21 -r1.22 pkgsrc/x11/wxGTK24/Makefile
cvs rdiff -u -r1.24 -r1.25 pkgsrc/x11/wxGTK24/buildlink3.mk
cvs rdiff -u -r1.17 -r1.18 pkgsrc/x11/wxGTK26/Makefile
cvs rdiff -u -r1.16 -r1.17 pkgsrc/x11/wxGTK26/buildlink3.mk
cvs rdiff -u -r1.14 -r1.15 pkgsrc/x11/wxGTK26-contrib/Makefile
cvs rdiff -u -r1.17 -r1.18 pkgsrc/x11/wxGTK26-contrib/buildlink3.mk
cvs rdiff -u -r1.25 -r1.26 pkgsrc/x11/wxGTK28/Makefile
cvs rdiff -u -r1.18 -r1.19 pkgsrc/x11/wxGTK28/buildlink3.mk
cvs rdiff -u -r1.17 -r1.18 pkgsrc/x11/wxGTK28-contrib/Makefile \
pkgsrc/x11/wxGTK28-contrib/buildlink3.mk
cvs rdiff -u -r1.37 -r1.38 pkgsrc/x11/wxhaskell/Makefile
cvs rdiff -u -r1.42 -r1.43 pkgsrc/x11/x11vnc/Makefile
cvs rdiff -u -r1.33 -r1.34 pkgsrc/x11/xdialog/Makefile
cvs rdiff -u -r1.26 -r1.27 pkgsrc/x11/xfce4-clipman-plugin/Makefile
cvs rdiff -u -r1.30 -r1.31 pkgsrc/x11/xfce4-clipman-plugin/buildlink3.mk
cvs rdiff -u -r1.47 -r1.48 pkgsrc/x11/xfce4-desktop/Makefile
cvs rdiff -u -r1.22 -r1.23 pkgsrc/x11/xfce4-exo/Makefile
cvs rdiff -u -r1.17 -r1.18 pkgsrc/x11/xfce4-exo/buildlink3.mk
cvs rdiff -u -r1.14 -r1.15 pkgsrc/x11/xfce4-eyes-plugin/Makefile
cvs rdiff -u -r1.16 -r1.17 pkgsrc/x11/xfce4-eyes-plugin/buildlink3.mk
cvs rdiff -u -r1.23 -r1.24 pkgsrc/x11/xfce4-gtk2-engine/Makefile
cvs rdiff -u -r1.28 -r1.29 pkgsrc/x11/xfce4-notes-plugin/Makefile
cvs rdiff -u -r1.32 -r1.33 pkgsrc/x11/xfce4-notes-plugin/buildlink3.mk
cvs rdiff -u -r1.50 -r1.51 pkgsrc/x11/xfce4-panel/Makefile
cvs rdiff -u -r1.37 -r1.38 pkgsrc/x11/xfce4-panel/buildlink3.mk
cvs rdiff -u -r1.17 -r1.18 pkgsrc/x11/xfce4-places-plugin/Makefile
cvs rdiff -u -r1.19 -r1.20 pkgsrc/x11/xfce4-places-plugin/buildlink3.mk
cvs rdiff -u -r1.14 -r1.15 pkgsrc/x11/xfce4-screenshooter-plugin/Makefile
cvs rdiff -u -r1.16 -r1.17 \
pkgsrc/x11/xfce4-screenshooter-plugin/buildlink3.mk
cvs rdiff -u -r1.38 -r1.39 pkgsrc/x11/xfce4-session/Makefile
cvs rdiff -u -r1.33 -r1.34 pkgsrc/x11/xfce4-session/buildlink3.mk
cvs rdiff -u -r1.17 -r1.18 pkgsrc/x11/xfce4-settings/Makefile
cvs rdiff -u -r1.24 -r1.25 pkgsrc/x11/xfce4-terminal/Makefile
cvs rdiff -u -r1.45 -r1.46 pkgsrc/x11/xfce4-utils/Makefile
cvs rdiff -u -r1.97 -r1.98 pkgsrc/x11/xlockmore/Makefile
cvs rdiff -u -r1.40 -r1.41 pkgsrc/x11/xpad/Makefile
cvs rdiff -u -r1.58 -r1.59 pkgsrc/x11/xplanet/Makefile
cvs rdiff -u -r1.46 -r1.47 pkgsrc/x11/xscreensaver-demo/Makefile
cvs rdiff -u -r1.22 -r1.23 pkgsrc/x11/xvidcap-gtk2/Makefile
cvs rdiff -u -r1.70 -r1.71 pkgsrc/x11/zenity/Makefile
-------------------------------------------------------------------
Module Name: pkgsrc
Committed By: tron
Date: Tue Oct 2 17:18:28 UTC 2012
Modified Files:
pkgsrc/graphics/cairo: Makefile buildlink3.mk
Log Message:
Revert unintentional revision bump.
To generate a diff of this commit:
cvs rdiff -u -r1.106 -r1.107 pkgsrc/graphics/cairo/Makefile
cvs rdiff -u -r1.45 -r1.46 pkgsrc/graphics/cairo/buildlink3.mk
Mass recursive bump after the dependence fix of the "cairo" package requested by Thomas Klausner.
"user-destdir" is default these days
Revbump after updating graphics/cairo
Recursive PKGREVISION bump for tcl and tk upgrade to 8.5.12
Update to 2.14.2
CHANGES IN R VERSION 2.14.2:
NEW FEATURES:
o The internal untar() (as used by default by R CMD INSTALL) now
knows about some pax headers which bsdtar (e.g., the default tar
for Mac OS >= 10.6) can incorrectly include in tar files, and
will skip them with a warning.
o Function compactPDF() in package tools now takes the default for
argument gs_quality from environment variable GS_QUALITY: there
is a new value "none", the ultimate default, which prevents
GhostScript being used in preference to qpdf just because
environment variable R_GSCMD is set. If R_GSCMD is unset or set
to "", the function will try to find a suitable GhostScript
executable.
o For consistency with the logLik() method, nobs() for "nls" files
now excludes observations with zero weight. (Reported by Berwin
Turlach.)
UTILITIES:
o R CMD check now reports by default on licenses not according to
the description in 'Writing R Extensions'.
o R CMD check has a new option --as-cran to turn on most of the
customizations that CRAN uses for its incoming checks.
PACKAGE INSTALLATION:
o R CMD INSTALL will now no longer install certain file types from
inst/doc: these are almost certainly mistakes and for some
packages are wasting a lot of space.
+ BUG FIXES
CHANGES IN R VERSION 2.14.1:
NEW FEATURES:
o parallel::detectCores() is now able to find the number of
physical cores (rather than CPUs) on Sparc Solaris.
It can also do so on most versions of Windows; however the
default remains detectCores(logical = TRUE) on that platform.
o Reference classes now keep a record of which fields are locked.
$lock() with no arguments returns the names of the locked fields.
o HoltWinters() reports a warning rather than an error for some
optimization failures (where the answer might be a reasonable
one).
o tools::dependsOnPkg() now accepts the shorthand dependencies =
"all".
o parallel::clusterExport() now allows specification of an
environment from which to export.
o The quartz() device now does tilde expansion on its file
argument.
o Option print in Sweave's RweaveLatex() driver now emulates
auto-printing rather than printing (which can differ for an S4
object by calling show() rather than print()).
o filled.contour() now accepts infinite values: previously it might
have generated invalid graphics files (e.g. containing NaN
values).
+ BUG FIXES
Recursive bump for pcre-8.30* (shlib major change)
Revbump for a) tiff update to 4.0 (shlib major change) b) glib2 update 2.30.2 (adds libffi dependency to buildlink3.mk) Enjoy.
This needs a pile more tex packages to build successfully in a clean environment. Note: some of the ones I'm adding may not be absolutely required; I made this list by checking atimes after building R with all tex stuff available, and confirmed that with (only) these packages available it does build. It doesn't help that the R makefile, apparently intentionally, doesn't stop if running tex fails.
fix pasto
Add BUILD_DEPENDS on some TeX components so that NEWS.pdf is successfully built. Fix PLIST. Bump PKGREVISION.
Cairo support needs pkg-config
s/fortran77/fortran/ as uses some features that f2c can't handle.
Update R to 2.14.0 changes to many to list - see NEWS file in distribution for details.
Recursive bump for graphics/freetype2 buildlink addition.
Add LIBnn=lib to ./configure environment. This fixes a build failure on 64bit linux. Briefly discussed with wiz@
recursive bump from gettext-lib shlib bump.
As suggested by joerg@, set PTHREAD_AUTO_VARS="yes". This fixes the issues discussed in: http://mail-index.netbsd.org/pkgsrc-users/2011/01/24/msg013585.html
png shlib name changed for png>=1.5.0, so bump PKGREVISIONs.
Mechanically replace references to graphics/jpeg with the suitable
alternative from mk/jpeg.buildlink3.mk
This allows selection of an alternative jpeg library (namely the x86 MMX,
SSE, SSE2 accelerated libjpeg-turbo) via JPEG_DEFAULT=libjpeg-turbo, and
follows the current standard model for alternatives (fam, motif, fuse etc).
The mechanical edits were applied via the following script:
#!/bin/sh
for d in */*; do
[ -d "$d" ] || continue
for i in "$d/"Makefile* "$d/"*.mk; do
case "$i" in *.orig|*"*"*) continue;; esac
out="$d/x"
sed -e 's;graphics/jpeg/buildlink3\.mk;mk/jpeg.buildlink3.mk;g' \
-e 's;BUILDLINK_PREFIX\.jpeg;JPEGBASE;g' \
< "$i" > "$out"
if cmp -s "$i" "$out"; then
rm -f "$out"
else
echo "Edited $i"
mv -f "$i" "$i.orig" && mv "$out" "$i"
fi
done
done
Bump dependency on pixman to 0.18.4 because cairo-1.10 needs that version, and bump all depends. Per discussion on pkgsrc-changes.
"fortran" -> "fortran77" except where it is clear that it isn't F77. "fortran" is alias of "fortran77" for now, but it will change later.
Changes 2.11.1: * R CMD INSTALL checks if dependent packages are available early on * in the installation of source packages, thereby giving clearer error messages. * R CMD INSTALL --build now names the file in the format used for Mac OS X binary files on that platform. * BIC() in package stats4 now also works with multiple fitted models, analogously to AIC(). * Use of file extension .C for C++ code in packages is now deprecated: it has caused problems for some 'make's on case-insensitive file systems (although it currently works with the recommended toolkits). * The C function mkCharLenCE now no longer reads past 'len' bytes (unlikely to be a problem except in user code). * On systems without any default LD_LIBRARY_PATH (not even /usr/local/lib), [DY]LIB_LIBRARY_PATH is now set without a trailing colon. * More efficient utf8ToInt() on long multi-byte strings with many multi-byte characters. * aggregate.ts() gave platform-depedent results due to rounding error for ndeltat != 1. * package.skeleton() sometimes failed to fix filenames for .R or .Rd files to start with an alphanumeric.
Bump PKGREVISION for libpng shlib name change. Also add some patches to remove use of deprecated symbols and fix other problems when looking for or compiling against libpng-1.4.x.
Changes 2.11.0: * Packages must have been installed under R >= 2.10.0, as the current help system is the only one now supported. * A port to 64-bit Windows is now available as well as binary package repositiories: see the 'R Administration and Installation Manual'. * Argument matching for primitive functions is now done in the same way as for interpreted functions except for the deliberate exceptions call switch .C .Fortran .Call .External all of which use positional matching for their first argument, and also some internal-use-only primitives. * The default device for command-line R at the console on Mac OS X is now quartz() and not X11(). New features * The 'open' modes for connections are now interpreted more consistently. * R CMD INSTALL now uses the internal untar() in package utils. * help(try.all.packages = TRUE) is much faster. * R CMD check has a new option '--timings' to record per-example timings in file <pkg>.Rcheck/<pkg>-Ex.timings. * The TRE library has been updated to version 0.8.0 (minor bugfixes). More...
Changes 2.10.1: * The PCRE library has been updated to version 8.00. * R CMD INSTALL has new options --no-R, --no-libs, --no-data, --no-help, --no-demo, --no-exec, and --no-inst to suppress installation of the specified part of the package. * The documented line-length limit of 4095 bytes when reading from the console now also applies also to parse(file="") (which previously had a limit of around 1024 bytes). * A Bioconductor mirror can be set for use by setRepositories() via the option "BioC_mirror". * Double-clicking in a tk_select.list() list box now selects the item and closes the list box (as happens on the Windows select.list() widget). * configure will be able to find a usable libtiff in some rare circumstances where it did not previously (where libtiff needed to be linked explicitly against -ljpeg). * Making refman.pdf works around a problem with the indexing with hyperref 6.79d and later. * The 'extended' argument is deprecated in strsplit(), grep(), grepl(), sub(), gsub(), regexpr() and gregexpr() (not just the value extended = FALSE) and will be removed in R 2.11.0. * bug fixes
Second try at jpeg-8 recursive PKGREVISION bump.
Changes 2.10.0:
* Package help is now converted from Rd by the R-based converters
that were first introduced in 2.9.0.
* HTML help is now generated dynamically using an HTTP server
running in the R process and listening on the loopback interface.
* polygon(), pdf() and postscript() now have a parameter
'fillOddEven' (default FALSE), which controls the mode used for
polygon fills of self-intersecting shapes.
* New debugonce() function; further,
getOption("deparse.max.lines") is now observed when debugging.
* plot() methods for "stepfun" and hence "ecdf" no longer plot
points by default for n >= 1000.
* [g]sub(*, perl=TRUE) now also supports '\E' in order to *end*
\U and \L case changes, thanks to a patch from Bill Dunlap.
* factor(), `levels<-`(), etc, now ensure that the resulting factor
levels are unique (as was always the implied intention). Factors
with duplicated levels are still constructible by low-level means,
but are now declared illegal.
* New print() (S3) method for class "function", also used for
auto-printing. Further, .Primitive functions now print and
auto-print identically.
* The print() and toLatex() methods for class "sessionInfo" now
show the locale in a nicer format and have arguments to
suppress locale information.
* In addition to previously only round(), there are other 'Math'
group (S3) methods for 'difftime', such as floor(), signif(), abs(), etc.
* For completeness, old.packages() and available.packages() allow
'type' to be specified (you could always specify 'available'
or 'contriburl').
* More...
Follow f2c/libf2c split: bump revision of all packages that list Fortran in used languages.
bump revision because of graphics/jpeg update
Recursive ABI depends update and PKGREVISION bump for readline-6.0 shlib major change. Reported by Robert Elz in PR 41345.
Pullup ticket #2513 - requested by markd R: security patch Revisions pulled up: - math/R/Makefile 1.99 - math/R/distinfo 1.39 - math/R/patches/patch-ae 1.15 --- Module Name: pkgsrc Committed By: markd Date: Sun Aug 31 12:33:53 UTC 2008 Modified Files: pkgsrc/math/R: Makefile distinfo Added Files: pkgsrc/math/R/patches: patch-ae Log Message: Fix for http://secunia.com/advisories/31647/ from R svn.
Update to R 2.7.2
NEW FEATURES
o sprintf() returns elements of the result in UTF-8 when the
format or any character input has a corresponding element
declared as UTF-8. Similarly for paste(), elements of the
result are in UTF-8 when any input to that element is declared
as UTF-8.
o axis() has new arguments 'col.ticks' and 'lwd.ticks' to allow
the colour and line width of ticks to be set separately from
that of the line (e.g. to set one or the other to transparent
or zero width).
o legend() has a new argument 'box.col' to set the colour of the
enclosing box.
o legend() gains a 'xpd' argument to make it easier to place a
legend in the margins or outer margins.
o stripchart() now passes '...' to title() (as well as to
plot.default() and axis()). (Wish of PR#12202)
o help.search() has new argument 'searchEngine' to go
directly to the search form: this is needed by users of
Firefox 3 to workaround a bug in interpreting the search
results pages.
+ BUG FIXES
2.7.1 NEW FEATURES
o tools::texi2dvi() has a new argument 'texinputs' to allow the
TeX and bibtex input paths to be specified (even on MiKTeX).
o dev.copy2pdf() gains an 'out.type' argument to allow it to be
used with cairo_pdf() or quartz(type = "pdf").
o poly() has additional checks against user error (as in PR#11243).
o The Mac OS quartz() device draws contiguous lines much faster.
o A field containing just a sign is no longer regarded as numeric
(it was on all platforms in 2.7.0, but not on most in earlier
versions of R). Similarly, '.' is now always non-numeric.
o CITATION files are now read in Latin-1: quite a few were
failing if used in a multibyte locale such as UTF-8.
o The DESCRIPTION file of a package can specify an 'OS_type' field
as either 'unix' or 'windows' to confine installation to that
OS type.
o HoltWinters() now uses optimize() rather than optim for
one-parameter problems which should be more reliable (PR#11469).
o axis() now respects the setting of par("xpd") when clipping.
o The 'factor' method of format() now preserves names, dims and
dimnames in the same way as for character and numeric inputs.
(PR#11512)
o read.DIF(*, transpose=TRUE) now allows to correctly read DIF files
produced by some versions of Excel.
DEPRECATED & DEFUNCT
o The use of unserialize() on character strings is deprecated:
that was a format used in R < 2.4.0.
o The use of embedded nuls in character strings is deprecated:
They will no longer be allowed in R 2.8.0.
UTILITIES
o R CMD check checks for possible check directories in the
sources -- in mid-2008 there were about 20 examples on CRAN.
o R CMD build tries harder to clean up the inst/doc directory
from the remnants of earlier builds.
It also removes any directories with extension .Rcheck, and
files .DS_Store and ._* (created by tar on Mac OS X under some
circumstances: it now sets environment variables to ask for
such files not to be created by that tar.)
+ BUG FIXES
Fix for http://secunia.com/advisories/31647/ from R svn.
set --disable-R-framework and --without-aqua these options are only used by R.app on Mac OS X
Update to 2.7.0
SIGNIFICANT USER-VISIBLE CHANGES
o The default graphics device in non-interactive use is now
pdf() rather than postscript(). [PDF viewers are now
more widely available than PostScript viewers.]
The default width and height for pdf() and bitmap() have been
changed to 7 (inches) to match the screen devices.
o Most users of the X11() device will see a new device that has
different fonts, anti-aliasing of lines and fonts and
supports semi-transparent colours.
o Considerable efforts have been made to make the default output
from graphics devices as similar as possible (and in
particular close to that from postscript/pdf). Many devices
were misinterpreting 'pointsize' in some way, for example as
being in device units (pixels) rather than in points.
o Packages which include graphics devices need to be re-installed
for this version of R, with recently updated versions.
+ New features and bug fixes.
Update to R 2.6.2. Changes are basically bugfixes. pkgsrc changes: Don't bother patching configure.ac - it was only part of the changes being made to configure so don't pretend you could use it to regerate configure. Use -fPIC rather than -fpic for NetBSD powerpc. Should fix PR 38032.
+ Remove modifications to configure.in and configure in patch-aa and
patch-ac that altered the order in which the terminal library for
readline was detected. The termcap.buildlink3.mk file (included
indirectly by readline/buildlink3.mk) will do the right thing by
itself.
+ Modify the pkg-index.tmpl INSTALL script fragment: we can just use
${PKG_PREFIX} instead of substituting for @PREFIX@ everywhere. Also
refactor the commands to rebuild the package index into a shell
function and give some indication to the user what is happening.
+ Remove chown operation in post-install that was basically
cargo-culted from the very first version of R imported into pkgsrc.
It's not necessary.
+ Support user-destdir installation.
Bump the PKGREVISION to 2.
Bump version or revision of all packages that have a runtime dependency on gzip.
Update R to version 2.6.0 Many new features, changes and bug fixes. See lib/R/doc/NEWS for details.
Fixed the path to unzip. PKGREVISION++
Wants at least version 4.7 of makeinfo to build the docs. Bump pkgrev.
Fix configure's handling of libblas when compiling with f2c and therefore remove conditional PLIST entry no longer required. Bump PKGREVISION.
Building with f2c effects what libs get installed. Adjust PLIST.
Update R to version 2.4.1.
pkgsrc changes: no longer automatically generate the PLIST.
use (de)install templates for handling updating the index files
when adding/removing R packages.
Changes 2.4.1
This is a maintenance release and fixes a number of mostly minor bugs.
Changes 2.4.0
This release has many new features. One important aspect is that S4
classes now have their own internal type, and S4 method dispatch has
been completely revised to using cached generic functions, giving
substantial performance improvements. As a consequence, all packages
depending on "methods" need to be reinstalled.
Needs libXt explicitly.
Pullup ticket 1853 - requested by dmcmahill
portability fixes for R
Revisions pulled up:
- pkgsrc/math/R/Makefile 1.86
Module Name: pkgsrc
Committed By: dmcmahill
Date: Sun Oct 8 23:12:48 UTC 2006
Modified Files:
pkgsrc/math/R: Makefile
Log Message:
The variable modifier $${dir#${PREFIX}/} is not portable so eliminate its
use. Fixes R packaging on solaris.
The variable modifier $${dir#${PREFIX}/} is not portable so eliminate its
use. Fixes R packaging on solaris.
Update to R 2.3.1 This version contains several minor fixups and removes a couple of bad bugs such as NA-handling of mean() for integer vectors. Changes 2.3.0 This version contains several changes and additions, mostly incremental.
Fixed pkglint warnings.
Bump BUILDLINK_ABI_DEPENDS.png and PKGREVISION for png-1.2.9nb2 update.
Over 1200 files touched but no revisions bumped :) RECOMMENDED is removed. It becomes ABI_DEPENDS. BUILDLINK_RECOMMENDED.foo becomes BUILDLINK_ABI_DEPENDS.foo. BUILDLINK_DEPENDS.foo becomes BUILDLINK_API_DEPENDS.foo. BUILDLINK_DEPENDS does not change. IGNORE_RECOMMENDED (which defaulted to "no") becomes USE_ABI_DEPENDS which defaults to "yes". Added to obsolete.mk checking for IGNORE_RECOMMENDED. I did not manually go through and fix any aesthetic tab/spacing issues. I have tested the above patch on DragonFly building and packaging subversion and pkglint and their many dependencies. I have also tested USE_ABI_DEPENDS=no on my NetBSD workstation (where I have used IGNORE_RECOMMENDED for a long time). I have been an active user of IGNORE_RECOMMENDED since it was available. As suggested, I removed the documentation sentences suggesting bumping for "security" issues. As discussed on tech-pkg. I will commit to revbump, pkglint, pkg_install, createbuildlink separately. Note that if you use wip, it will fail! I will commit to pkgsrc-wip later (within day).
* Teach the tools framework how to supply the pkgsrc version of
makeinfo if no native makeinfo executable exists. Honor TEXINFO_REQD
when determining whether the native makeinfo can be used.
* Remove USE_MAKEINFO and replace it with USE_TOOLS+=makeinfo.
* Get rid of all the "split" argument deduction for makeinfo since
the PLIST module already handles varying numbers of split info files
correctly.
NOTE: Platforms that have "makeinfo" in the base system should check
that the makeinfo entries of pkgsrc/mk/tools.${OPSYS}.mk are
correct.
Recursive revision bump / recommended bump for gettext ABI change.
If MANZ=yes was set then the subsequent USE_TOOLS+=gzip caused a gzip link to appear in the tools directory and be picked up and embedded in one of the installed scripts. Since this package clearly uses gzip at runtime add an explicit USE_TOOLS+=gzip:run and fixup the gzip path that gets embedded. Fixes PR pkg/32218. Bump PKGREVISION.
Update R to 2.2.1
USER-VISIBLE CHANGES
o options("expressions") has been reduced to 1000: the limit
of 5000 introduced in 2.1.0 was liable to give crashes from C
stack overflow.
NEW FEATURES
o Use of 'pch' (e.g. in points) in the symbol font 5 is now
interpreted in the single-byte encoding used by that font.
Similarly, strwidth now recognizes that font 5 has a different
encoding from that of the locale. (These are likely to affect
the answer only in MBCS locales such as UTF-8.)
o The URW font metrics have been updated to versions from late
2002 which cover more glyphs, including Cyrillic.
o New postscript encodings for CP1250 (Windows East European),
ISO Latin-7 (8859-13, Latvian, Lithuanian and Maori), Cyrillic
(8859-5), KOI8-R, KOI8-U and CP1251.
o configure has more support for the Intel and Portland Group
compilers on ix86 and x86_64 Linux.
o R CMD INSTALL will clean up if interrupted (e.g. by ctrl-C from
the keyboard).
o There is now a comprehensive French translation of the messages,
thanks to Philippe Grosjean.
DEPRECATED & DEFUNCT
o The undocumented use of atan() with two arguments is deprecated:
instead use atan2() (as documented).
o The 'vfont' argument of axis() and mtext() is deprecated
(it currently warns and does nothing).
o The function mauchley.test() is deprecated (was a misspelling)
and replaced by mauchly.test()
Many BUG FIXES
Update R to 2.2.0 Changes: This version contains several changes and additions, mostly incremental.
Fixed pkglint warnings. The warnings are mostly quoting issues, for
example MAKE_ENV+=FOO=${BAR} is changed to MAKE_ENV+=FOO=${BAR:Q}. Some
other changes are outlined in
http://mail-index.netbsd.org/tech-pkg/2005/12/02/0034.html
- correctly depend on devel/gettext-lib, bump revision for this - this uses libtool, tell the framework so - don't declare alloca on DragonFly, it conflicts with system headers - patch libtool.m4 fragment for DrgaonFly
Replaced "# defined" with "yes" in Makefile variables like GNU_CONFIGURE, NO_BUILD, USE_LIBTOOL.
add missing libiconv buildlink3.mk
Get rid of USE_PERL5. The new way to express needing the Perl executable around at either build-time or at run-time is: USE_TOOLS+= perl # build-time USE_TOOLS+= perl:run # run-time Also remove some places where perl5/buildlink3.mk was being included by a package Makefile, but all that the package wanted was the Perl executable.
Update R to version 2.1.1. minor bug fixes.
Prevent paths to the build directories from being included in the package. Bump PKGREVISION.
Cleanup of tools paths appearing in installed files for the new tools framework. Bump PKGREVISION.
Massive cleanup of buildlink3.mk and builtin.mk files in pkgsrc.
Several changes are involved since they are all interrelated. These
changes affect about 1000 files.
The first major change is rewriting bsd.builtin.mk as well as all of
the builtin.mk files to follow the new example in bsd.builtin.mk.
The loop to include all of the builtin.mk files needed by the package
is moved from bsd.builtin.mk and into bsd.buildlink3.mk. bsd.builtin.mk
is now included by each of the individual builtin.mk files and provides
some common logic for all of the builtin.mk files. Currently, this
includes the computation for whether the native or pkgsrc version of
the package is preferred. This causes USE_BUILTIN.* to be correctly
set when one builtin.mk file includes another.
The second major change is teach the builtin.mk files to consider
files under ${LOCALBASE} to be from pkgsrc-controlled packages. Most
of the builtin.mk files test for the presence of built-in software by
checking for the existence of certain files, e.g. <pthread.h>, and we
now assume that if that file is under ${LOCALBASE}, then it must be
from pkgsrc. This modification is a nod toward LOCALBASE=/usr. The
exceptions to this new check are the X11 distribution packages, which
are handled specially as noted below.
The third major change is providing builtin.mk and version.mk files
for each of the X11 distribution packages in pkgsrc. The builtin.mk
file can detect whether the native X11 distribution is the same as
the one provided by pkgsrc, and the version.mk file computes the
version of the X11 distribution package, whether it's built-in or not.
The fourth major change is that the buildlink3.mk files for X11 packages
that install parts which are part of X11 distribution packages, e.g.
Xpm, Xcursor, etc., now use imake to query the X11 distribution for
whether the software is already provided by the X11 distribution.
This is more accurate than grepping for a symbol name in the imake
config files. Using imake required sprinkling various builtin-imake.mk
helper files into pkgsrc directories. These files are used as input
to imake since imake can't use stdin for that purpose.
The fifth major change is in how packages note that they use X11.
Instead of setting USE_X11, package Makefiles should now include
x11.buildlink3.mk instead. This causes the X11 package buildlink3
and builtin logic to be executed at the correct place for buildlink3.mk
and builtin.mk files that previously set USE_X11, and fixes packages
that relied on buildlink3.mk files to implicitly note that X11 is
needed. Package buildlink3.mk should also include x11.buildlink3.mk
when linking against the package libraries requires also linking
against the X11 libraries. Where it was obvious, redundant inclusions
of x11.buildlink3.mk have been removed.
Remove USE_GNU_TOOLS and replace with the correct USE_TOOLS definitions: USE_GNU_TOOLS -> USE_TOOLS awk -> gawk m4 -> gm4 make -> gmake sed -> gsed yacc -> bison
For packages that use GNU configure, don't bother adding "TOOL" variables into CONFIGURE_ENV if the new tools framework already takes care of adding them automatically.
Don't try and use wide chars on NetBSD 1.6 as the support isn't complete enough. Fixes PR pkg/30274
update to 2.1.0 too many changes to list here ...still doesn't work within TEXmacs
Remove USE_BUILDLINK3 and NO_BUILDLINK; these are no longer used.
Move buildlink3.mk files ahead of targets as per example Makefile.
Fix up the comment to note that we still need to unwrap some files at post-configure time, even after the switch from buildlink2 to buildlink3. Also, use SUBST_CLASSES instead of the custom post-configure target, and take advantage of the fact that the "unwrap" SUBST_CLASS already does mostly the right thing.
Nuke USE_FORTRAN and bring the f2c handling within the mk/compiler
framework. The list of changes include:
* Modify compiler.mk so that "c" is always prepended to USE_LANGUAGES,
so we no longer need to say it in package Makefiles. Packages
should now append to USE_LANGUAGES instead of setting it.
* Create mk/compiler/f2c.mk which implements another pseudo-compiler
"f2c" that may be used with any C compiler backend, e.g.
PKGSRC_COMPILER= f2c ccache gcc
* Teach the various "real" compiler files, e.g., sunpro.mk, mipspro.mk,
etc., to use f2c if the native Fortran compiler isn't present.
Packages that use Fortran should now simply include the line:
USE_LANGUAGES+= fortran
in the package Makefile.
Update R to 2.0.1 Changes 2.0.1: This is a maintenance version mainly to fix a number of minor bugs and issues. Some rather nasty bugs were Windows-specific. Changes 2.0.0: Many things have changed since 1.0. The R language has acquired namespaces, exception handling constructs, formal methods and classes, much improved garbage collection, generalized I/O via connection objects, and considerable improvements in the graphics area. The user workspace has been reorganized, and so has the set of packages that ship with R. Several "recommended packages" deemed indispensable in a statistical system are bundled. In addition, there has been a large number of more specific new functions, tweaks, and bugfixes.
USE_BUILDLINK3 is a yes/no variable.
Libtool fix for PR pkg/26633, and other issues. Update libtool to 1.5.10 in the process. (More information on tech-pkg.) Bump PKGREVISION and BUILDLINK_DEPENDS of all packages using libtool and installing .la files. Bump PKGREVISION (only) of all packages depending directly on the above via a buildlink3 include.
Annotate a comment: # XXX: following comment still true for buildlink3? # R does ugly things in the configure to get the default list of arguments # for linking Fortran, which exposes the buildlink2 tricks so clean up # afterwards
Update R to 1.9.1
CHANGES IN R VERSION 1.9.1
NEW FEATURES
o as.Date() now has a method for "POSIXlt" objects.
o mean() has a method for "difftime" objects and so summary()
works for such objects.
o legend() has a new argument 'pt.cex'.
o plot.ts() has more arguments, particularly 'yax.flip'.
o heatmap() has a new 'keep.dendro' argument.
o The default barplot method now handles vectors and 1-d arrays
(e.g., obtained by table()) the same, and uses grey instead of
heat color palettes in these cases. (Also fixes PR#6776.)
o nls() now looks for variables and functions in its formula in
the environment of the formula before the search path, in the
same way lm() etc look for variables in their formulae.
DEPRECATED & DEFUNCT
o Support for non-IEEE-754 arithmetic (which has been untested
for some time) will be removed in the next full release.
o Direct use of R INSTALL|REMOVE|BATCH|COMPILE|SHLIB is
deprecated: use R CMD instead.
o The gnome/GNOME graphics device is deprecated and will be
removed in the next full release.
Plus Bug Fixes.
Enable pkgviews installation.
R assumes it can append to the DESCRIPTION files of each R package while building even though it uses INSTALL_DATA on them so set SHAREMODE=644 rather than have to patch an ever increasing number of files. Idea from Julio M. Merino Vidal.
Update R to 1.9.0 and buildlink3ify
USER-VISIBLE CHANGES
o Underscore '_' is now allowed in syntactically valid names, and
make.names() no longer changes underscores. Very old code
that makes use of underscore for assignment may now give
confusing error messages.
o Package 'base' has been split into packages 'base', 'graphics',
'stats' and 'utils'. All four are loaded in a default
installation, but the separation allows a 'lean and mean'
version of R to be used for tasks such as building indices.
Packages ctest, eda, modreg, mva, nls, stepfun and ts have been
merged into stats, and lqs has been returned to MASS. In all
cases a stub has been left that will issue a warning and ensure
that the appropriate new home is loaded. All the time series
datasets have been moved to package stats. Sweave has been
moved to utils.
Package mle has been moved to stats4 which will become the
central place for statistical S4 classes and methods
distributed with base R. Package mle remains as a stub.
Users may notice that code in .Rprofile is run with only the
new base loaded and so functions may now not be found. For
example, ps.options(horizontal = TRUE) should be preceded by
library(graphics) or called as graphics::ps.options or,
better, set as a hook -- see ?setHook.
o There has been a concerted effort to speed up the startup of
an R session: it now takes about 2/3rds of the time of 1.8.1.
o A warning is issued at startup in a UTF-8 locale, as currently R
only supports single-byte encodings.
plus many new features and bug fixes.
Switch to using tk8.4 bump PKGREVISION
Enable tk84 and replace x11/tk with x11/tk83. Packages compatible with 8.4 will be updated to depend on x11/tk after Tk update.
USE_LANGUAGES= c fortran
replace deprecated USE_GMAKE with USE_GNU_TOOLS+=make.
Reintroduce reordering tests for termcap vs termlib vs ncurses and make dependency on libbz2 explicit Fixes build on Solaris 8.
Now uses shared blas library from math/blas
Update R to 1.8.1. Changes since 1.6.2 Many new features. Language changes. Additional standard package 'mle'. Some old features deprecated or defunct. Many many bug fixes. Update to 1.8.0 from Ray Brownrigg in private communication, cleaned up and updated to 1.8.1 by me.
s/netbsd.org/NetBSD.org/
Make this relay on blas 1.0nb1 and use libblas_pic.a instead of libblas.a so proper PIC objects get pulled into the .so's
Update to R-1.6.2
CHANGES IN R VERSION 1.6.2
BUG FIXES
o plot.stepfun() now obeys a `ylim=.' specification.
o removeClass() does a better job of removing inheritance
information.
o setIs() will not allow mismatched representations between two
classes (without an explicit coerce method).
o The code underlying polygon drawing contained a memory leak.
This showed up in persp, but did not affect other graphics
functions. It is now possible to draw big DEMs.
o logLik.nls() gave wrong df.
o rbind() with a mixture of data frames and matrices treated the
matrices as vectors.
o stripchart(method="stack") was not handling missing values.
o Arithmetic functions such as log() lost the object bit from
classed objects if coercion was needed.
o exp_rand would go into an infinite loop if unif_rand returned 0.
o formatC(x, format="fg") could return exponential format if
rounding pushed x over a positive power of 10.
o attr(x, foo) used partial matching for `foo' (even though not
documented to do so), and failed to find `foo' if there were
two or more partial matches before the exact match in the list
of attributes.
o Rdconv now creates direct HTML hyperlinks when linking to
documentation in the same package. The code now ensures that
links which can be resolved within the package are so resolved,
even when there are possible resolutions in other packages.
o If readBin(what=character()) is used incorrectly on a file which
does not contain C-style character strings, warnings (usually
many) are now given.
o Building libR.so with the zlib in the R sources was not
finding the local zlib headers.
o system(intern=TRUE) has an undocumented line length limit of
119 chars both on Unix and Windows. The limit is now 8096 and
documented. On Unix (only) every 120th character used to be
discarded.
o plot.POSIX[cl]t were not passing graphics parameters on to
axis.POSIXct.
o On some HP-UX systems, installed scripts were not executable
when using the BSD-compatible install system program found by
configure. We now always use install-sh on HP-UX.
o c() was converting NA names to "NA": now proper NA strings are
used wherever possible.
o A typo was causing segfaults when using data.entry under SuSE.
Update R to version 1.6.1.
Pkgsrc changes:
Now builds the libR.so and provides a buildlink2.mk for packages that want
to use it. From suggestions from Kent Polk.
Recommended library set is now included in the base package.
Changes:
CHANGES IN R VERSION 1.6.1
NEW FEATURES
o Added a few "trivial and obviously missing" functions to tcltk:
tkchooseDirectory, tkpopup, tkdialog, tkread
o barplot() has a new argument `axis.lty', which if set to 1
allows the pre-1.6.0 behaviour of plotting the axis and tick
marks for the categorical axis. (This was apparently not
intentional, but axis() used to ignore lty=0.)
The argument `border' is no longer ".NotYetUsed".
CHANGES IN R VERSION 1.6.0
USER-VISIBLE CHANGES
o The default colour palette now has "grey" instead of "white"
in location 8. See palette().
o grid(nx) behaves differently (but the same as in R versions <= 0.64).
NEW FEATURES
o Preparations for name space support:
o The objects created in the methods package to represent
classes, generic functions, method definitions, and
inheritance relations now themselves belong to true classes. In
particular, the "classRepresentation" objects follow the description
in "Programming with Data" (section 7.6).
o Other additions and changes to the methods package:
o New methods ([[, print, str) and extended plot() method
(incl. logical `horiz') for "dendrogram" class.
o sprintf() now checks the agreement between formats and object
types, and handles special values (NA, Inf, ...) correctly.
o chol() now uses a tolerance for non-positive-definiteness and
so should give more consistent results across platforms.
o New function agrep() for approximate (fuzzy) string matching.
o help.search() can now use both approximate (fuzzy) and regular
expression matching. By default, if the pattern to be matched
consists of only alphanumeric characters, whitespace or a dash,
approximate matching is used.
o axis() has three new optional arguments `col', `lty', and `lwd'
all for drawing the axis line and tick marks.
o Function vcov() (formerly in MASS), a generic function to
return the variance-covariance matrix of the parameter
estimates of a fitted model.
o duplicated() and unique() have methods for matrices and arrays
(based on ideas from Jens Oehlschl<E4>gel).
o Internally memory sizes and counts of cons cells are now stored
in unsigned longs. This allows memory limits to be set and
objects created in the range 2-4Gb on 32-bit platforms, and
allows 64-bit platforms to use much larger amounts of memory.
o Command-line flags to set memory can now use the suffix `G'
for gigabytes. The setting of maximum vsize is now only
limited by the platform's address space.
o All warning and error messages are truncated to a length set
by options(warning.length=), defaulting to 1000. (Previously
most (but not quite all) were truncated at 8192 characters.)
o [dpqr]gamma() check for shape parameter > 0.
o as.POSIX[cl]t can now convert logical NAs.
o All installed packages (even those shipped with R) are
given a `Built' field in the DESCRIPTION file.
o as.data.frame() now coerces logical matrices into logical
columns (rather than factors).
o [[<-.data.frame no longer coerces character replacement values
to factor. This is consistent with using $ to replace and
with S4.
o library() attempts to detect improperly installed packages, so
as from this version an installed package must have a
DESCRIPTION file and that file must have been stamped with a
`Built:' line (which was introduced in 1.2.0). Under
Unix-alikes, the platform is checked against that used for
installation.
o print.factor() has new arguments `max.levels' (with a smart default)
and `width'. print.ordered() is no longer needed.
o RNGkind() has an additional option for normal random generators:
"Inversion".
o data.frame() recycles factors and "AsIs" objects as well as
atomic vectors.
o rect() accepts additional graphics parameters through a ...
argument (in the same way as polygon).
o strwidth/strheight() now coerce their first argument in exactly
the same way text() does, so a wider range of inputs is allowed.
o prompt()'s default and data.frame methods have a new 3rd argument
`name' allowing them to used more easily in scripts and loops.
o rgb() has a new `maxColorValue' argument, allowing r,g,b in [0,M],
particularly in {0:255}, efficiently and non-error-prone.
o summaryRprof() provides the functionality of R CMD Rprof in R
code, though more slowly.
o pdf() now uses PDF not R code for clipping, which ensures that
partially visible text strings are (partially) shown.
o Each R session uses a per-session temporary directory which
is removed at normal termination. The directory name is given
by the tempdir() function, and filenames returned by
tempfile() will be within that directory.
o help.start() on Unix now uses a .R subdirectory of the
per-session temporary directory and not ~/.R. A side effect
is that ~/.R is now never deleted by R.
o cbind/rbind() used to ignore all zero-length vectors, an
undocumented quirk for S-compatibility. This caused problems
when combining zero-extent matrices and zero-length vectors, and
now zero-length vectors are ignored unless the result would
have zero rows/columns.
o plot.spec(x) now also works for other x than AR and Pgram results.
o New functions La.chol() and La.chol2inv() for Cholesky
decomposition and inverse of positive definite matrices using
Lapack.
o Changes to the tcltk package
o New function axTicks() returning tick mark locations like axis().
o grid() has a more sensible default behavior. Tick axis alignment
only happens when no numbers of grid cells are specified. New
arguments lwd and equilogs; nx/ny = NA for not drawing, see ?grid.
o installed.packages() has a new argument `priority'.
o termplot() uses factor levels rather than 1,2,3... for x-axis.
o The trace() function has been robustified and a new function
tracingState() added to turn tracing temporarily on and off.
o New cophenetic() in "mva" as utility for hierarchical clustering.
o p.adjust() has two new methods, 'Hommel' and 'FDR', contributed
by Gordon Smyth <smyth@wehi.edu.au>.
o stars() now has add and plot arguments.
and lots of bug fixes.
BUILDLINK_X11PKG_DIR is no more.
INSTALL_DIRS -> R_INSTALL_DIRS to not conflict with the variable introduced in bsd.pkg.mk revision 1.1045. Fixes pkg/18332
find ... -or ... -> find ... -o ... for more portability.
Update R to 1.5.1, switch to buildlink2, change maintainer.
User-Visible Changes
o XDR support is now guaranteed to be available, so the default
save format will always be XDR binary files, and it is safe to
distribute data in that format. (We are unaware of any
platform that did not support XDR in recent versions of R.)
gzfile() is guaranteed to be available, so the preferred
method to distribute sizeable data objects is now via
save(compress = TRUE).
o pie() replaces piechart() and defaults to using pastel colours.
o formatC has new arguments (see below) and formatC(*, d = <dig>)
is no longer valid and must be written as formatC(*, digits = <dig>).
o Missingness of character strings is treated much more
consistently, and the character string "NA" can be used as a
non-missing value.
o summary.factor() now uses a stable sort, so the output will
change where there are ties in the frequencies.
Plus lots of new features and many bug fixes.
Give path for -lblas so modules such as R-KernSmooth can find it when they try to link it.
Merge from pkgsrc-current to buildlink2 branch.
don't key off of `alpha' to decide to do OSF specific things (-fpe3 flag to the fortran compiler). Also mark as not for older netbsd-alpha systems as this is an IEEE-754 infected program (hi ross!).
Reorder PLIST so pkg_delete works cleanly
Add etc/Makeconf to REPLACE_BUILDLINK. Fixes pkg/16620
Change MASTER_SITES to use the CRAN list. Add support for building R extension packages as pkgsrc packages. Bump PKGREVISION so extension packages can depend on a version of R with this support. Discussed with Johnny Lam.
Give all packages which depend on "png" a version bump, and update all dependencies on packages depending on "png" which contain shared libraries, all for the (imminent) update to the "png" package. [List courtesy of John Darrow, courtesy of "bulk-build".]
Update to version 1.4.1 from PR pkg/15757 by Ray Brownrigg with minor mods by me. Changes and bug fixes from 1.3.1 are numerous. See the NEWS file in the distribution for details.
Include a patch for the generated configure script so that we don't have to depend on auto* tools at build-time. This fixes pkg/14916 by Brook Milligan <brook@biology.nmsu.edu>.
I am a triple idiot. The only relevant variable that x11.buildlink.mk
redefines about which buildlink.mk files would care is BUILDLINK_X11_DIR,
which points to the location of the X11R6 hierarchy used during building.
If x11.buildlink.mk isn't included, then BUILDLINK_X11_DIR defaults to
${X11BASE} (set in bsd.pkg.mk), so its value is always safe to use. Remove
the ifdefs surrounding the use of BUILDLINK_X11_DIR in tk/buildlink.mk and
revert changes to move x11.buildlink.mk before the other buildlink.mk files.
Use wildcard dependence on "autoconf" package.
Add back COMMENT definition which got lost.
Update R to 1.3.0. This is a two-generation upgrade from the previous 1.1.1 version in pkgsrc. There are many, many bugfixes, better compliance with S3/S4, and many additional statistical analysis functions added to the base library. There is also an improved (faster) garbage collector and support for dynamically sizing the memory used by R. The full summary of changes may be found on the R Project website.
LIBS is automatically added to CONFIGURE_ENV by bsd.pkg.mk if GNU_CONFIGURE is defined, so simply set LIBS to the appropriate value.
CPPFLAGS is now passed to MAKE_ENV and CONFIGURE_ENV by bsd.pkg.mk, so adapt by moving CPPFLAGS settings to top-level, and removing explicit inclusion of CPPFLAGS into MAKE_ENV and CONFIGURE_ENV.
Update dependency on png to >=1.0.11 because of the shlib major bump. Noted by Frederick Bruckman.
Change BUILD_DEPENDS semantics: first component is now a package name+version/pattern, no more executable/patchname/whatnot. While there, introduce BUILD_USES_MSGFMT as shorthand to pull in devel/gettext unless /usr/bin/msgfmt exists (i.e. on post-1.5 -current). Patch by Alistair Crooks <agc@netbsd.org>
Because the minor number of the PNG library was increased packages compiled using the newest PNG library won't work on system with an older one. To prevent such problems with precompiled binary packages require at least "png-1.0.9nb1" in all dependences.
Add NOT_FOR_PLATFORMS=*-*-alpha as R requires IEEE math. Information gleaned from port-alpha mailing list posting by Paul Mather <paul@gromit.dlib.vt.edu> in: http://mail-index.netbsd.org/port-alpha/2001/02/14/0004.html
Update to new COMMENT style: COMMENT var in Makefile instead of pkg/COMMENT.
Make that "autoreconf" -- there is no "autoremake".
Use full pathname "${LOCALBASE}/bin/auto..." in dependences and make
targets. This includes a fix for PR pkg/12125 by Tomasz Luchowski.
Homepage has moved.
Update R to 1.1.1. This is primarily a bugfix release from version 1.1.0,
particularly fixing the table editor, but also contains a few additions:
o data(), example() and help() now search the loaded packages, then
in their .lib.loc argument, the latter as pre-0.99.0. See
their help pages for the precise details.
o help() has a new argument `try.all.packages' set by the option
"help.try.all.packages". If help is not found in the normal
path and this is TRUE then a search is made of all packages
for possible matches.
o prop.trend.test() - test for trend in proportions.
o write.table() has new argument `dec' for setting the decimal
separator (SPSS/Windows and probably others want commas in
continental European locales).
o Advance warning: save(, oldstyle=TRUE) will no longer be
available after this release.
o Symbols can now be coerced to expressions, making
as.expression(quote(a)) work
Update R to 1.1.0. Many additions and bug-fixes from 1.1.0 make this a more usable replacement for S/S-PLUS.
Update to R-1.0.1. Move R library tree to ${PREFIX}/lib (a la perl5)
since it contains loadable shared object files that are platform-specific.
Lots of bug-fixes and additions ... it's getting closer to a usable
replacement for S-PLUS.
Update R to 0.90.1. Changes are tons of changes and bugfixes, too numerous to list here (see http://cran.r-project.org/src/base/NEWS for more information).
add USE_FORTRAN
Update R to 0.64.2. Changes from 0.64.1:
NEW FEATURES
o new target for R installation testing : make strict-tests.
o symnum(x) now nicely codes logical x.
o convolve() has a new type = c("circular", "open", "filter")
argument allowing more than the only circular convolution.
o par(xpd) now has three settings: FALSE (clip to plot region),
TRUE (clip to figure region), or NA (clip to device region).
o zapsmall(x) works for complex x.
o new global variable R.version.string (for plots & reports).
Deprecated version & Version for new R.version & R.Version.
o R CMD Rd2dvi has builtin "Usage" help and works for multiple files.
Useful for automatic reference manual of a package.
(doc/manual/lib2tex is more efficient for installed packages, however).
BUG FIXES
o power() is now fully implemented and documented.
o A couple of problems with group generic operations.
o A bug which meant that it was not possible to add elements
to zero length lists in the obvious way has been fixed.
x <- list(); x[[1]] <- 10
x <- list(); x[["a"]] <- 11
both now work.
o save.image() ignored dot-names. (esp. .First())
o lab= argument to plot() misinterpreted by axis() via ... passing
o NULL labels in text() caused segfault
o matrix(f,...) with f a factor now coerces to character
o documentation errors for substitute and is.vector, minor fixups for
trig and nlm
o Background colours are set properly on X11 devices with
colortype="pseudo": sometimes they were not allocated separately.
o C() works (again?) for a single argument.
o is.na() didn't work properly for "list" arguments.
o symnum() sometimes failed with arrays of rank >= 3.
o in some cases one could get nonblack color instead of
black on 2nd x11() window.
o influence.measures(.) $ is.influential was wrong on the
cooks.distance.
o printing of complex NaN/Inf was wrong as well.
o printing of complex named vectors had a wrong initial space.
o allow trailing space in character->numeric coercion
o library() gave wrong "masked" warnings in some cases.
o par(xpd) semantics were not compatible with S.
o rect() output was not clipped in PostScript.
o par(pin=c(width, height)) was behaving as par(pin=c(width, width)).
o Non-blank separated data files didn't have their 1st field
handled properly.
o "aux" directory moved to "tools" to avoid difficulties on
Windows.
o structure() clobbered factors with missing levels.
o pmatch() misbehaved on duplicate matches.
o R CMD Rd2dvi <file.Rd> works again.
o logical binops tried to set time series parameters before dimensions.
o upped the BUFSIZE in model.c (NOT proper long-term solution).
o dput(), dump() and deparse() now always use DBL_DIG (=15) digits
for numeric formatting.
o chull() now works for vertical borders, such as in chull(c(1,1,2),3:1).
Update readline dependency.
default R_PAPERSIZE to A4 if PAPERSIZE is not set.
Updated R to 0.64.1. Too many changes from 0.62.1 to enumerate. See NEWS file in distribution.
add USE_X11=yes
Fix CONFLICTS (remove redundancy, mostly)
Reflect update of f2c.
Update R to 0.63.1, provided in pr 6618 by Johnny C. Lam. Changes since 0.63.0 are mostly bigfixes and patches that make it actually work properly with NetBSD.
Initial addition of R-0.63.0, a language for data analysis and graphics. Provided in pr 6493 by Johnny C. Lam.
Initial revision