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Revision 1.195 / (download) - annotate - [select for diffs], Wed Mar 13 15:42:41 2019 UTC (2 months, 1 week ago) by wen
Branch: MAIN
CVS Tags: pkgsrc-2019Q1-base, pkgsrc-2019Q1, HEAD
Changes since 1.194: +2 -2 lines
Diff to previous 1.194 (colored)

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.

Revision 1.194 / (download) - annotate - [select for diffs], Fri Dec 21 02:55:06 2018 UTC (4 months, 4 weeks ago) by wen
Branch: MAIN
CVS Tags: pkgsrc-2018Q4-base, pkgsrc-2018Q4
Changes since 1.193: +2 -3 lines
Diff to previous 1.193 (colored)

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.

Revision 1.193 / (download) - annotate - [select for diffs], Thu Dec 13 19:52:08 2018 UTC (5 months ago) by adam
Branch: MAIN
Changes since 1.192: +2 -2 lines
Diff to previous 1.192 (colored)

revbump for boost 1.69.0

Revision 1.192 / (download) - annotate - [select for diffs], Wed Nov 14 22:21:59 2018 UTC (6 months ago) by kleink
Branch: MAIN
Changes since 1.191: +2 -2 lines
Diff to previous 1.191 (colored)

Revbump after cairo 1.16.0 update.

Revision 1.191 / (download) - annotate - [select for diffs], Mon Nov 12 14:40:22 2018 UTC (6 months ago) by jperkin
Branch: MAIN
Changes since 1.190: +4 -1 lines
Diff to previous 1.190 (colored)

*: Add CTF_SUPPORTED/CTF_FILES_SKIP where necessary.

Revision 1.190 / (download) - annotate - [select for diffs], Mon Nov 12 03:52:30 2018 UTC (6 months, 1 week ago) by ryoon
Branch: MAIN
Changes since 1.189: +2 -2 lines
Diff to previous 1.189 (colored)

Recursive revbump from hardbuzz-2.1.1

Revision 1.189 / (download) - annotate - [select for diffs], Wed Aug 22 09:45:35 2018 UTC (8 months, 4 weeks ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2018Q3-base, pkgsrc-2018Q3
Changes since 1.188: +2 -2 lines
Diff to previous 1.188 (colored)

Recursive bump for perl5-5.28.0

Revision 1.188 / (download) - annotate - [select for diffs], Thu Aug 16 18:54:59 2018 UTC (9 months ago) by adam
Branch: MAIN
Changes since 1.187: +2 -1 lines
Diff to previous 1.187 (colored)

revbump after boost-libs update

Revision 1.187 / (download) - annotate - [select for diffs], Thu Jul 19 01:41:32 2018 UTC (10 months ago) by maya
Branch: MAIN
Changes since 1.186: +1 -9 lines
Diff to previous 1.186 (colored)

R: remove cases for ancient NetBSD versions.

Revision 1.186 / (download) - annotate - [select for diffs], Wed Jul 4 07:27:13 2018 UTC (10 months, 2 weeks ago) by wen
Branch: MAIN
Changes since 1.185: +2 -2 lines
Diff to previous 1.185 (colored)

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.

    Renvironon 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.

Revision 1.185 / (download) - annotate - [select for diffs], Thu May 31 10:23:02 2018 UTC (11 months, 2 weeks ago) by wen
Branch: MAIN
CVS Tags: pkgsrc-2018Q2-base, pkgsrc-2018Q2
Changes since 1.184: +2 -3 lines
Diff to previous 1.184 (colored)

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 tmpdirectory).

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 (imeout.

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 (mdand 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 efault("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 ϥESCRIPTIONfile, 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 umeric-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 orkaroundcompatible 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 ate-timeclasses "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 imeout(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 imeouts(elapsed-time limits) for most parts of R CMD check via environment variables documented in the ϳ Internalsmanual.

The ϣioC extrarepository which was dropped from Bioconductor 3.6 and later has been removed from setRepositories(). This changes the mapping for 6 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 ϳ 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
ϸriting R Extensionsdocuments 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.

ϸriting R Extensionsnow 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 iddenobjects .__H__.cbind and .__H__.rbind in package base are deprecated (in favour of cbind and rbind).

The declaration of pythag() in ϳmath.hhas 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 ematchesto 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 ul 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 bnormal(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 eplacement 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 Ϣlpine Linuxdoes 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 rc

Revision 1.184 / (download) - annotate - [select for diffs], Sun Apr 29 21:31:52 2018 UTC (12 months, 2 weeks ago) by adam
Branch: MAIN
Changes since 1.183: +2 -2 lines
Diff to previous 1.183 (colored)

revbump for boost-libs update

Revision 1.183 / (download) - annotate - [select for diffs], Mon Apr 16 14:34:51 2018 UTC (13 months ago) by wiz
Branch: MAIN
Changes since 1.182: +2 -2 lines
Diff to previous 1.182 (colored)

Recursive bump for new fribidi dependency in pango.

Revision 1.182 / (download) - annotate - [select for diffs], Mon Mar 12 11:17:01 2018 UTC (14 months, 1 week ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2018Q1-base, pkgsrc-2018Q1
Changes since 1.181: +2 -2 lines
Diff to previous 1.181 (colored)

Recursive bumps for fontconfig and libzip dependency changes.

Revision 1.181 / (download) - annotate - [select for diffs], Tue Mar 6 01:43:44 2018 UTC (14 months, 2 weeks ago) by minskim
Branch: MAIN
Changes since 1.180: +9 -3 lines
Diff to previous 1.180 (colored)

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.

Revision 1.180 / (download) - annotate - [select for diffs], Mon Jan 1 21:18:40 2018 UTC (16 months, 2 weeks ago) by adam
Branch: MAIN
Changes since 1.179: +2 -1 lines
Diff to previous 1.179 (colored)

Revbump after boost update

Revision 1.179 / (download) - annotate - [select for diffs], Fri Dec 1 03:19:30 2017 UTC (17 months, 2 weeks ago) by wen
Branch: MAIN
CVS Tags: pkgsrc-2017Q4-base, pkgsrc-2017Q4
Changes since 1.178: +3 -2 lines
Diff to previous 1.178 (colored)

- 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.

Revision 1.178 / (download) - annotate - [select for diffs], Sat Oct 21 02:40:56 2017 UTC (18 months, 4 weeks ago) by markd
Branch: MAIN
Changes since 1.177: +4 -3 lines
Diff to previous 1.177 (colored)

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.

Revision 1.177 / (download) - annotate - [select for diffs], Wed Oct 18 16:14:30 2017 UTC (19 months ago) by adam
Branch: MAIN
Changes since 1.176: +27 -16 lines
Diff to previous 1.176 (colored)

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)

Revision 1.176 / (download) - annotate - [select for diffs], Fri Oct 6 20:47:37 2017 UTC (19 months, 1 week ago) by rumko
Branch: MAIN
Changes since 1.175: +5 -5 lines
Diff to previous 1.175 (colored)

math/R: better fix for fbsd

Also move fixes from configure to configure.ac
m4/R.m4 fix by @joerg

Oked @joerg

Revision 1.175 / (download) - annotate - [select for diffs], Sun Sep 10 20:36:56 2017 UTC (20 months, 1 week ago) by rumko
Branch: MAIN
CVS Tags: pkgsrc-2017Q3-base, pkgsrc-2017Q3, pkgsrc-
Changes since 1.174: +5 -1 lines
Diff to previous 1.174 (colored)

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

Revision 1.174 / (download) - annotate - [select for diffs], Thu Aug 24 20:03:28 2017 UTC (20 months, 3 weeks ago) by adam
Branch: MAIN
Changes since 1.173: +2 -2 lines
Diff to previous 1.173 (colored)

Revbump for boost update

Revision 1.173 / (download) - annotate - [select for diffs], Sun Apr 30 01:21:49 2017 UTC (2 years ago) by ryoon
Branch: MAIN
CVS Tags: pkgsrc-2017Q2-base, pkgsrc-2017Q2
Changes since 1.172: +2 -1 lines
Diff to previous 1.172 (colored)

Recursive revbump from boost update

Revision 1.172 / (download) - annotate - [select for diffs], Sat Mar 11 09:50:34 2017 UTC (2 years, 2 months ago) by wen
Branch: MAIN
CVS Tags: pkgsrc-2017Q1-base, pkgsrc-2017Q1
Changes since 1.171: +2 -3 lines
Diff to previous 1.171 (colored)

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 ϳ Internalsmanual).

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 Rdfiles (usually the titles were omitted).

Revision 1.171 / (download) - annotate - [select for diffs], Sun Jan 1 16:06:26 2017 UTC (2 years, 4 months ago) by adam
Branch: MAIN
Changes since 1.170: +2 -1 lines
Diff to previous 1.170 (colored)

Revbump after boost update

Revision 1.170 / (download) - annotate - [select for diffs], Sun Nov 6 02:08:16 2016 UTC (2 years, 6 months ago) by wen
Branch: MAIN
CVS Tags: pkgsrc-2016Q4-base, pkgsrc-2016Q4
Changes since 1.169: +2 -3 lines
Diff to previous 1.169 (colored)

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.)

Revision 1.169 / (download) - annotate - [select for diffs], Fri Oct 7 18:25:59 2016 UTC (2 years, 7 months ago) by adam
Branch: MAIN
Changes since 1.168: +2 -1 lines
Diff to previous 1.168 (colored)

Revbump post boost update

Revision 1.168 / (download) - annotate - [select for diffs], Thu Sep 8 20:41:25 2016 UTC (2 years, 8 months ago) by joerg
Branch: MAIN
CVS Tags: pkgsrc-2016Q3-base, pkgsrc-2016Q3
Changes since 1.167: +3 -2 lines
Diff to previous 1.167 (colored)

Override zlib 1.2.5 check in configure, it is not required. Unbreaks
NetBSD 7.0 and earlier.

Revision 1.167 / (download) - annotate - [select for diffs], Tue Jul 26 04:53:33 2016 UTC (2 years, 9 months ago) by wen
Branch: MAIN
Changes since 1.166: +5 -5 lines
Diff to previous 1.166 (colored)

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)

Revision 1.166 / (download) - annotate - [select for diffs], Sat Jul 9 06:38:32 2016 UTC (2 years, 10 months ago) by wiz
Branch: MAIN
Changes since 1.165: +2 -1 lines
Diff to previous 1.165 (colored)

Bump PKGREVISION for perl-5.24.0 for everything mentioning perl.

Revision 1.165 / (download) - annotate - [select for diffs], Wed Apr 13 21:04:04 2016 UTC (3 years, 1 month ago) by markd
Branch: MAIN
CVS Tags: pkgsrc-2016Q2-base, pkgsrc-2016Q2
Changes since 1.164: +2 -2 lines
Diff to previous 1.164 (colored)

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 ϳconfig.his 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
tc/Makeconfis deprecated and will be removed in R 3.3.0.

The C header file ϴ.his no longer documented: its use should be
replaced by ϳ.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 ϳgui.exe ϳterm.exeand ϳscript.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 mulationpart 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.

Revision 1.164 / (download) - annotate - [select for diffs], Thu Feb 25 15:26:55 2016 UTC (3 years, 2 months ago) by jperkin
Branch: MAIN
CVS Tags: pkgsrc-2016Q1-base, pkgsrc-2016Q1
Changes since 1.163: +2 -6 lines
Diff to previous 1.163 (colored)

Use OPSYSVARS.

Revision 1.163 / (download) - annotate - [select for diffs], Fri Feb 19 21:57:42 2016 UTC (3 years, 2 months ago) by jperkin
Branch: MAIN
Changes since 1.162: +2 -8 lines
Diff to previous 1.162 (colored)

Fix more library install names on Darwin.

Revision 1.162 / (download) - annotate - [select for diffs], Fri Sep 11 13:16:16 2015 UTC (3 years, 8 months ago) by jperkin
Branch: MAIN
CVS Tags: pkgsrc-2015Q4-base, pkgsrc-2015Q4, pkgsrc-2015Q3-base, pkgsrc-2015Q3
Changes since 1.161: +19 -1 lines
Diff to previous 1.161 (colored)

Use install_name_tool to fix up Darwin library names.  Fixes check-shlib.

Revision 1.161 / (download) - annotate - [select for diffs], Fri Aug 14 12:40:19 2015 UTC (3 years, 9 months ago) by wen
Branch: MAIN
Changes since 1.160: +2 -2 lines
Diff to previous 1.160 (colored)

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.

Revision 1.160 / (download) - annotate - [select for diffs], Tue Jun 30 02:38:52 2015 UTC (3 years, 10 months ago) by wen
Branch: MAIN
Changes since 1.159: +2 -3 lines
Diff to previous 1.159 (colored)

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 ϯEWS.Rdfiles.

    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.

Revision 1.159 / (download) - annotate - [select for diffs], Mon Jun 29 21:35:04 2015 UTC (3 years, 10 months ago) by markd
Branch: MAIN
Changes since 1.158: +2 -2 lines
Diff to previous 1.158 (colored)

Fix symbol visibility.

Revision 1.158 / (download) - annotate - [select for diffs], Mon Jun 22 13:21:59 2015 UTC (3 years, 10 months ago) by jperkin
Branch: MAIN
CVS Tags: pkgsrc-2015Q2-base, pkgsrc-2015Q2
Changes since 1.157: +2 -2 lines
Diff to previous 1.157 (colored)

Update the fixwrap substitution to work correctly after the recent
libtool changes.  Fixes CHECK_WRKREF builds.

Revision 1.157 / (download) - annotate - [select for diffs], Fri Jun 12 10:50:27 2015 UTC (3 years, 11 months ago) by wiz
Branch: MAIN
Changes since 1.156: +2 -2 lines
Diff to previous 1.156 (colored)

Recursive PKGREVISION bump for all packages mentioning 'perl',
having a PKGNAME of p5-*, or depending such a package,
for perl-5.22.0.

Revision 1.156 / (download) - annotate - [select for diffs], Sat May 30 12:31:01 2015 UTC (3 years, 11 months ago) by ryoon
Branch: MAIN
Changes since 1.155: +3 -2 lines
Diff to previous 1.155 (colored)

Bump PKGREVISION.

* Fix build under NetBSD 6.1.5.
  Newer texinfo is required. From wen@.

Revision 1.155 / (download) - annotate - [select for diffs], Wed May 13 12:48:05 2015 UTC (4 years ago) by ryoon
Branch: MAIN
Changes since 1.154: +2 -3 lines
Diff to previous 1.154 (colored)

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.

Revision 1.154 / (download) - annotate - [select for diffs], Sat Apr 25 14:23:29 2015 UTC (4 years ago) by tnn
Branch: MAIN
Changes since 1.153: +2 -1 lines
Diff to previous 1.153 (colored)

Recursive revbump following MesaLib update, categories g through n.

Revision 1.153 / (download) - annotate - [select for diffs], Thu Oct 9 14:06:41 2014 UTC (4 years, 7 months ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2015Q1-base, pkgsrc-2015Q1, pkgsrc-2014Q4-base, pkgsrc-2014Q4
Changes since 1.152: +1 -3 lines
Diff to previous 1.152 (colored)

Remove pkgviews: don't set PKG_INSTALLATION_TYPES in Makefiles.

Revision 1.152 / (download) - annotate - [select for diffs], Wed Sep 24 10:53:22 2014 UTC (4 years, 7 months ago) by jperkin
Branch: MAIN
CVS Tags: pkgsrc-2014Q3-base, pkgsrc-2014Q3
Changes since 1.151: +5 -1 lines
Diff to previous 1.151 (colored)

Replace WRAPPER_BINDIR reference with real path in generated file.

Revision 1.151 / (download) - annotate - [select for diffs], Thu Jul 24 21:33:03 2014 UTC (4 years, 9 months ago) by markd
Branch: MAIN
Changes since 1.150: +2 -3 lines
Diff to previous 1.150 (colored)

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).

Revision 1.150 / (download) - annotate - [select for diffs], Thu May 29 23:36:52 2014 UTC (4 years, 11 months ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2014Q2-base, pkgsrc-2014Q2
Changes since 1.149: +2 -2 lines
Diff to previous 1.149 (colored)

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.

Revision 1.149 / (download) - annotate - [select for diffs], Mon May 5 00:48:07 2014 UTC (5 years ago) by ryoon
Branch: MAIN
Changes since 1.148: +2 -1 lines
Diff to previous 1.148 (colored)

Recursive revbump from x11/pixman
Fix PR pkg/48777

Revision 1.148 / (download) - annotate - [select for diffs], Sat May 3 22:29:42 2014 UTC (5 years ago) by markd
Branch: MAIN
Changes since 1.147: +6 -3 lines
Diff to previous 1.147 (colored)

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().

Revision 1.147 / (download) - annotate - [select for diffs], Fri Mar 14 20:15:38 2014 UTC (5 years, 2 months ago) by markd
Branch: MAIN
CVS Tags: pkgsrc-2014Q1-base, pkgsrc-2014Q1
Changes since 1.146: +6 -1 lines
Diff to previous 1.146 (colored)

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).

Revision 1.146 / (download) - annotate - [select for diffs], Thu Mar 13 11:08:51 2014 UTC (5 years, 2 months ago) by jperkin
Branch: MAIN
Changes since 1.145: +3 -1 lines
Diff to previous 1.145 (colored)

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.

Revision 1.145 / (download) - annotate - [select for diffs], Mon Feb 17 17:11:07 2014 UTC (5 years, 3 months ago) by jperkin
Branch: MAIN
Changes since 1.144: +5 -1 lines
Diff to previous 1.144 (colored)

Pass --disable-openmp on Darwin.  With changes to g95 and tk, this package
finally builds.

Revision 1.144 / (download) - annotate - [select for diffs], Thu Feb 6 10:57:21 2014 UTC (5 years, 3 months ago) by markd
Branch: MAIN
Changes since 1.143: +23 -23 lines
Diff to previous 1.143 (colored)

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.

Revision 1.143 / (download) - annotate - [select for diffs], Sat Jan 11 14:42:04 2014 UTC (5 years, 4 months ago) by adam
Branch: MAIN
Changes since 1.142: +2 -1 lines
Diff to previous 1.142 (colored)

Revbump after updating tcl/tk.

Revision 1.142 / (download) - annotate - [select for diffs], Tue Aug 13 19:53:30 2013 UTC (5 years, 9 months ago) by markd
Branch: MAIN
CVS Tags: pkgsrc-2013Q4-base, pkgsrc-2013Q4, pkgsrc-2013Q3-base, pkgsrc-2013Q3
Changes since 1.141: +3 -4 lines
Diff to previous 1.141 (colored)

Update to R 3.0.1

Changes: many new features and bug fixes.  See NEWS file for details.

Revision 1.141 / (download) - annotate - [select for diffs], Mon Jul 15 02:02:25 2013 UTC (5 years, 10 months ago) by ryoon
Branch: MAIN
Changes since 1.140: +2 -2 lines
Diff to previous 1.140 (colored)

* .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".

Revision 1.140 / (download) - annotate - [select for diffs], Thu Jun 6 12:54:42 2013 UTC (5 years, 11 months ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2013Q2-base, pkgsrc-2013Q2
Changes since 1.139: +2 -2 lines
Diff to previous 1.139 (colored)

Bump PKGREVISION for libXft changes for NetBSD native X support on
NetBSD 6, requested by tron.

Revision 1.139 / (download) - annotate - [select for diffs], Tue Jun 4 22:16:37 2013 UTC (5 years, 11 months ago) by tron
Branch: MAIN
Changes since 1.138: +2 -2 lines
Diff to previous 1.138 (colored)

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.

Revision 1.138 / (download) - annotate - [select for diffs], Mon Jun 3 10:05:31 2013 UTC (5 years, 11 months ago) by wiz
Branch: MAIN
Changes since 1.137: +2 -2 lines
Diff to previous 1.137 (colored)

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

Revision 1.137 / (download) - annotate - [select for diffs], Fri May 31 12:41:21 2013 UTC (5 years, 11 months ago) by wiz
Branch: MAIN
Changes since 1.136: +2 -2 lines
Diff to previous 1.136 (colored)

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.

Revision 1.136 / (download) - annotate - [select for diffs], Sat Apr 6 03:16:50 2013 UTC (6 years, 1 month ago) by markd
Branch: MAIN
Changes since 1.135: +5 -2 lines
Diff to previous 1.135 (colored)

Install info files.  Bump PKGREVISION.
Fixes PR pkg/47391

Revision 1.135 / (download) - annotate - [select for diffs], Sat Feb 16 11:23:02 2013 UTC (6 years, 3 months ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2013Q1-base, pkgsrc-2013Q1
Changes since 1.134: +2 -2 lines
Diff to previous 1.134 (colored)

Recursive bump for png-1.6.

Revision 1.134 / (download) - annotate - [select for diffs], Sat Jan 26 21:38:09 2013 UTC (6 years, 3 months ago) by adam
Branch: MAIN
Changes since 1.133: +2 -1 lines
Diff to previous 1.133 (colored)

Revbump after graphics/jpeg and textproc/icu

Revision 1.133 / (download) - annotate - [select for diffs], Mon Dec 17 09:08:46 2012 UTC (6 years, 5 months ago) by wen
Branch: MAIN
CVS Tags: pkgsrc-2012Q4-base, pkgsrc-2012Q4
Changes since 1.132: +2 -3 lines
Diff to previous 1.132 (colored)

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).

Revision 1.132 / (download) - annotate - [select for diffs], Sat Dec 15 21:35:54 2012 UTC (6 years, 5 months ago) by markd
Branch: MAIN
Changes since 1.131: +2 -2 lines
Diff to previous 1.131 (colored)

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.

Revision 1.131 / (download) - annotate - [select for diffs], Wed Oct 3 21:56:35 2012 UTC (6 years, 7 months ago) by wiz
Branch: MAIN
Changes since 1.130: +2 -2 lines
Diff to previous 1.130 (colored)

Bump all packages that use perl, or depend on a p5-* package, or
are called p5-*.

I hope that's all of them.

Revision 1.129.2.1 / (download) - annotate - [select for diffs], Wed Oct 3 12:08:36 2012 UTC (6 years, 7 months ago) by spz
Branch: pkgsrc-2012Q3
Changes since 1.129: +2 -2 lines
Diff to previous 1.129 (colored) next main 1.130 (colored)

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
- devel/at-spi/Makefile                                         1.67
- devel/at-spi/buildlink3.mk                                    1.31
- devel/automoc4/Makefile                                       1.20
- devel/blib/Makefile                                           1.27
- devel/blib/buildlink3.mk                                      1.22
- devel/boa-constructor/Makefile                                1.18
- devel/coconut/Makefile                                        1.49
- devel/compizconfig-backend-gconf/Makefile                     1.17
- devel/cppcheck/Makefile                                       1.17
- devel/cutter/Makefile                                         1.20
- devel/dconf-editor/Makefile                                   1.12
- devel/devhelp/Makefile                                        1.78
- devel/devhelp/buildlink3.mk                                   1.24
- devel/distccmon-gnome/Makefile                                1.36
- devel/distccmon-gtk/Makefile                                  1.21
- devel/eric4/Makefile                                          1.28
- devel/ethos/Makefile                                          1.13
- devel/ethos/buildlink3.mk                                     1.12
- devel/frama-c/Makefile                                        1.27
- devel/gconfmm/Makefile                                        1.50
- devel/gconfmm/buildlink3.mk                                   1.26
- devel/gdl/Makefile                                            1.33
- devel/gdl/buildlink3.mk                                       1.22
- devel/geany/Makefile                                          1.25
- devel/glade/Makefile                                          1.74
- devel/glade3/Makefile                                         1.26
- devel/glade3/buildlink3.mk                                    1.16
- devel/gmtk/Makefile                                           1.9
- devel/gmtk/buildlink3.mk                                      1.9
- devel/gnome-build/Makefile                                    1.32
- devel/gnome-build/buildlink3.mk                               1.24
- devel/gobject-introspection/Makefile                          1.24
- devel/gps/Makefile                                            1.16
- devel/gst-plugins0.10-pango/Makefile                          1.17
- devel/guile-gnome/Makefile                                    1.33
- devel/kdesdk4/Makefile                                        1.44
- devel/kdevelop4/Makefile                                      1.22
- devel/kdevplatform/Makefile                                   1.23
- devel/kdiff3/Makefile                                         1.24
- devel/libbonoboui/Makefile                                    1.93
- devel/libbonoboui/buildlink3.mk                               1.37
- devel/libcompizconfig/Makefile                                1.20
- devel/libdbusmenu-qt/Makefile                                 1.12
- devel/libdbusmenu-qt/buildlink3.mk                            1.9
- devel/libextractor/Makefile                                   1.54
- devel/libgail-gnome/Makefile                                  1.49
- devel/libgail-gnome/buildlink3.mk                             1.40
- devel/libglade/Makefile                                       1.82
- devel/libglade/buildlink3.mk                                  1.28
- devel/libglademm/Makefile                                     1.28
- devel/libglademm/buildlink3.mk                                1.24
- devel/libgnome/Makefile                                       1.95
- devel/libgnome/buildlink3.mk                                  1.37
- devel/libgnomemm/Makefile                                     1.42
- devel/libgnomemm/buildlink3.mk                                1.31
- devel/libgnomeui/Makefile                                     1.109
- devel/libgnomeui/buildlink3.mk                                1.44
- devel/libgnomeuimm/Makefile                                   1.41
- devel/libgnomeuimm/buildlink3.mk                              1.32
- devel/libgweather/Makefile                                    1.35
- devel/libgweather/buildlink3.mk                               1.20
- devel/libpeas/Makefile                                        1.5
- devel/libpeas/buildlink3.mk                                   1.4
- devel/libsexy/Makefile                                        1.19
- devel/libsexy/buildlink3.mk                                   1.20
- devel/libsexymm/Makefile                                      1.17
- devel/libsexymm/buildlink3.mk                                 1.16
- devel/libview/Makefile                                        1.12
- devel/libview/buildlink3.mk                                   1.13
- devel/libwnck/Makefile                                        1.86
- devel/libwnck/buildlink3.mk                                   1.32
- devel/mono-tools/Makefile                                     1.44
- devel/monodevelop-database/Makefile                           1.16
- devel/monodevelop/Makefile                                    1.51
- devel/monodevelop/buildlink3.mk                               1.16
- devel/monotone-viz/Makefile                                   1.43
- devel/p5-Gnome2/Makefile                                      1.16
- devel/p5-Gtk2-GladeXML/Makefile                               1.19
- devel/p5-Wx-Perl-DataWalker/Makefile                          1.16
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- x11/gtkada/Makefile                                           1.11
- x11/gtkada/buildlink3.mk                                      1.10
- x11/gtkglarea2/Makefile                                       1.25
- x11/gtkglarea2/buildlink3.mk                                  1.20
- x11/gtkmm-utils/Makefile                                      1.12
- x11/gtkmm-utils/buildlink3.mk                                 1.14
- x11/gtkmm/Makefile                                            1.85
- x11/gtkmm/buildlink3.mk                                       1.32
- x11/gtksourceview-sharp2/Makefile                             1.33
- x11/gtksourceview/Makefile                                    1.64
- x11/gtksourceview/buildlink3.mk                               1.32
- x11/gtksourceview2/Makefile                                   1.33
- x11/gtksourceview2/buildlink3.mk                              1.19
- x11/gtksourceview3/Makefile                                   1.4
- x11/gtksourceview3/buildlink3.mk                              1.4
- x11/gtkterm2/Makefile                                         1.27
- x11/hot-babe/Makefile                                         1.33
- x11/kactivities/Makefile                                      1.6
- x11/kactivities/buildlink3.mk                                 1.6
- x11/kde-baseapps4/Makefile                                    1.8
- x11/kde-runtime4/Makefile                                     1.12
- x11/kde-runtime4/buildlink3.mk                                1.6
- x11/kde-workspace4/Makefile                                   1.11
- x11/kde-workspace4/buildlink3.mk                              1.6
- x11/kdelibs4/Makefile                                         1.47
- x11/kdelibs4/buildlink3.mk                                    1.22
- x11/konsole/Makefile                                          1.6
- x11/lablgtk/Makefile                                          1.68
- 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
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   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

Revision 1.130 / (download) - annotate - [select for diffs], Tue Oct 2 17:11:30 2012 UTC (6 years, 7 months ago) by tron
Branch: MAIN
Changes since 1.129: +2 -2 lines
Diff to previous 1.129 (colored)

Mass recursive bump after the dependence fix of the "cairo" package
requested by Thomas Klausner.

Revision 1.129 / (download) - annotate - [select for diffs], Tue Sep 11 23:04:15 2012 UTC (6 years, 8 months ago) by asau
Branch: MAIN
CVS Tags: pkgsrc-2012Q3-base
Branch point for: pkgsrc-2012Q3
Changes since 1.128: +1 -2 lines
Diff to previous 1.128 (colored)

"user-destdir" is default these days

Revision 1.128 / (download) - annotate - [select for diffs], Fri Sep 7 19:17:04 2012 UTC (6 years, 8 months ago) by adam
Branch: MAIN
Changes since 1.127: +2 -2 lines
Diff to previous 1.127 (colored)

Revbump after updating graphics/cairo

Revision 1.127 / (download) - annotate - [select for diffs], Tue Aug 21 23:49:23 2012 UTC (6 years, 8 months ago) by marino
Branch: MAIN
Changes since 1.126: +2 -1 lines
Diff to previous 1.126 (colored)

Recursive PKGREVISION bump for tcl and tk upgrade to 8.5.12

Revision 1.126 / (download) - annotate - [select for diffs], Sun Apr 15 03:29:47 2012 UTC (7 years, 1 month ago) by markd
Branch: MAIN
CVS Tags: pkgsrc-2012Q2-base, pkgsrc-2012Q2
Changes since 1.125: +2 -3 lines
Diff to previous 1.125 (colored)

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

Revision 1.125 / (download) - annotate - [select for diffs], Sat Mar 3 00:13:32 2012 UTC (7 years, 2 months ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2012Q1-base, pkgsrc-2012Q1
Changes since 1.124: +2 -2 lines
Diff to previous 1.124 (colored)

Recursive bump for pcre-8.30* (shlib major change)

Revision 1.124 / (download) - annotate - [select for diffs], Mon Feb 6 12:40:51 2012 UTC (7 years, 3 months ago) by wiz
Branch: MAIN
Changes since 1.123: +2 -2 lines
Diff to previous 1.123 (colored)

Revbump for
a) tiff update to 4.0 (shlib major change)
b) glib2 update 2.30.2 (adds libffi dependency to buildlink3.mk)

Enjoy.

Revision 1.123 / (download) - annotate - [select for diffs], Mon Dec 12 06:49:26 2011 UTC (7 years, 5 months ago) by dholland
Branch: MAIN
CVS Tags: pkgsrc-2011Q4-base, pkgsrc-2011Q4
Changes since 1.122: +18 -1 lines
Diff to previous 1.122 (colored)

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.

Revision 1.122 / (download) - annotate - [select for diffs], Sun Dec 11 21:10:05 2011 UTC (7 years, 5 months ago) by dholland
Branch: MAIN
Changes since 1.121: +2 -2 lines
Diff to previous 1.121 (colored)

fix pasto

Revision 1.121 / (download) - annotate - [select for diffs], Sun Dec 11 18:41:47 2011 UTC (7 years, 5 months ago) by markd
Branch: MAIN
Changes since 1.120: +7 -1 lines
Diff to previous 1.120 (colored)

Add BUILD_DEPENDS on some TeX components so that NEWS.pdf is successfully
built.  Fix PLIST.  Bump PKGREVISION.

Revision 1.120 / (download) - annotate - [select for diffs], Wed Dec 7 10:18:23 2011 UTC (7 years, 5 months ago) by joerg
Branch: MAIN
Changes since 1.119: +2 -1 lines
Diff to previous 1.119 (colored)

Cairo support needs pkg-config

Revision 1.119 / (download) - annotate - [select for diffs], Sun Dec 4 18:42:02 2011 UTC (7 years, 5 months ago) by markd
Branch: MAIN
Changes since 1.118: +2 -2 lines
Diff to previous 1.118 (colored)

s/fortran77/fortran/  as uses some features that f2c can't handle.

Revision 1.118 / (download) - annotate - [select for diffs], Sun Nov 20 04:57:02 2011 UTC (7 years, 6 months ago) by markd
Branch: MAIN
Changes since 1.117: +2 -3 lines
Diff to previous 1.117 (colored)

Update R to 2.14.0

changes to many to list - see NEWS file in distribution for details.

Revision 1.117 / (download) - annotate - [select for diffs], Tue Nov 1 06:02:01 2011 UTC (7 years, 6 months ago) by sbd
Branch: MAIN
Changes since 1.116: +2 -2 lines
Diff to previous 1.116 (colored)

Recursive bump for graphics/freetype2 buildlink addition.

Revision 1.116 / (download) - annotate - [select for diffs], Fri May 6 19:42:48 2011 UTC (8 years ago) by alnsn
Branch: MAIN
CVS Tags: pkgsrc-2011Q3-base, pkgsrc-2011Q3, pkgsrc-2011Q2-base, pkgsrc-2011Q2
Changes since 1.115: +4 -1 lines
Diff to previous 1.115 (colored)

Add LIBnn=lib to ./configure environment. This fixes a build failure on 64bit linux.

Briefly discussed with wiz@

Revision 1.115 / (download) - annotate - [select for diffs], Fri Apr 22 13:44:07 2011 UTC (8 years ago) by obache
Branch: MAIN
Changes since 1.114: +2 -2 lines
Diff to previous 1.114 (colored)

recursive bump from gettext-lib shlib bump.

Revision 1.114 / (download) - annotate - [select for diffs], Tue Mar 29 18:07:50 2011 UTC (8 years, 1 month ago) by jruoho
Branch: MAIN
CVS Tags: pkgsrc-2011Q1-base, pkgsrc-2011Q1
Changes since 1.113: +3 -1 lines
Diff to previous 1.113 (colored)

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

Revision 1.113 / (download) - annotate - [select for diffs], Thu Jan 13 13:38:42 2011 UTC (8 years, 4 months ago) by wiz
Branch: MAIN
Changes since 1.112: +2 -2 lines
Diff to previous 1.112 (colored)

png shlib name changed for png>=1.5.0, so bump PKGREVISIONs.

Revision 1.112 / (download) - annotate - [select for diffs], Thu Dec 23 11:44:48 2010 UTC (8 years, 4 months ago) by dsainty
Branch: MAIN
CVS Tags: pkgsrc-2010Q4-base, pkgsrc-2010Q4
Changes since 1.111: +2 -2 lines
Diff to previous 1.111 (colored)

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

Revision 1.111 / (download) - annotate - [select for diffs], Tue Sep 14 11:02:21 2010 UTC (8 years, 8 months ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2010Q3-base, pkgsrc-2010Q3
Changes since 1.110: +2 -1 lines
Diff to previous 1.110 (colored)

Bump dependency on pixman to 0.18.4 because cairo-1.10 needs that
version, and bump all depends.

Per discussion on pkgsrc-changes.

Revision 1.110 / (download) - annotate - [select for diffs], Fri Jul 30 10:36:25 2010 UTC (8 years, 9 months ago) by asau
Branch: MAIN
Changes since 1.109: +2 -2 lines
Diff to previous 1.109 (colored)

"fortran" -> "fortran77" except where it is clear that it isn't F77.
"fortran" is alias of "fortran77" for now, but it will change later.

Revision 1.109 / (download) - annotate - [select for diffs], Sat Jul 3 07:25:57 2010 UTC (8 years, 10 months ago) by adam
Branch: MAIN
Changes since 1.108: +2 -3 lines
Diff to previous 1.108 (colored)

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.

Revision 1.108 / (download) - annotate - [select for diffs], Sun Jun 13 22:44:55 2010 UTC (8 years, 11 months ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2010Q2-base, pkgsrc-2010Q2
Changes since 1.107: +2 -1 lines
Diff to previous 1.107 (colored)

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.

Revision 1.107 / (download) - annotate - [select for diffs], Thu May 6 07:33:40 2010 UTC (9 years ago) by adam
Branch: MAIN
Changes since 1.106: +3 -2 lines
Diff to previous 1.106 (colored)

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...

Revision 1.106 / (download) - annotate - [select for diffs], Tue Feb 9 07:02:53 2010 UTC (9 years, 3 months ago) by adam
Branch: MAIN
CVS Tags: pkgsrc-2010Q1-base, pkgsrc-2010Q1
Changes since 1.105: +2 -3 lines
Diff to previous 1.105 (colored)

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

Revision 1.105 / (download) - annotate - [select for diffs], Mon Jan 18 09:59:12 2010 UTC (9 years, 4 months ago) by wiz
Branch: MAIN
Changes since 1.104: +2 -1 lines
Diff to previous 1.104 (colored)

Second try at jpeg-8 recursive PKGREVISION bump.

Revision 1.104 / (download) - annotate - [select for diffs], Fri Dec 11 18:53:40 2009 UTC (9 years, 5 months ago) by adam
Branch: MAIN
CVS Tags: pkgsrc-2009Q4-base, pkgsrc-2009Q4
Changes since 1.103: +10 -10 lines
Diff to previous 1.103 (colored)

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...

Revision 1.103 / (download) - annotate - [select for diffs], Thu Dec 3 13:06:53 2009 UTC (9 years, 5 months ago) by asau
Branch: MAIN
Changes since 1.102: +2 -2 lines
Diff to previous 1.102 (colored)

Follow f2c/libf2c split: bump revision of all packages
that list Fortran in used languages.

Revision 1.102 / (download) - annotate - [select for diffs], Wed Aug 26 19:57:59 2009 UTC (9 years, 8 months ago) by sno
Branch: MAIN
CVS Tags: pkgsrc-2009Q3-base, pkgsrc-2009Q3
Changes since 1.101: +2 -2 lines
Diff to previous 1.101 (colored)

bump revision because of graphics/jpeg update

Revision 1.101 / (download) - annotate - [select for diffs], Wed May 20 00:58:21 2009 UTC (10 years ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2009Q2-base, pkgsrc-2009Q2
Changes since 1.100: +2 -1 lines
Diff to previous 1.100 (colored)

Recursive ABI depends update and PKGREVISION bump for readline-6.0 shlib
major change.

Reported by Robert Elz in PR 41345.

Revision 1.97.4.1 / (download) - annotate - [select for diffs], Tue Sep 2 19:39:45 2008 UTC (10 years, 8 months ago) by tron
Branch: pkgsrc-2008Q2
Changes since 1.97: +2 -1 lines
Diff to previous 1.97 (colored) next main 1.98 (colored)

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.

Revision 1.100 / (download) - annotate - [select for diffs], Sun Aug 31 12:37:27 2008 UTC (10 years, 8 months ago) by markd
Branch: MAIN
CVS Tags: pkgsrc-2009Q1-base, pkgsrc-2009Q1, pkgsrc-2008Q4-base, pkgsrc-2008Q4, pkgsrc-2008Q3-base, pkgsrc-2008Q3, cube-native-xorg-base, cube-native-xorg
Changes since 1.99: +3 -2 lines
Diff to previous 1.99 (colored)

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

Revision 1.99 / (download) - annotate - [select for diffs], Sun Aug 31 12:33:53 2008 UTC (10 years, 8 months ago) by markd
Branch: MAIN
Changes since 1.98: +2 -1 lines
Diff to previous 1.98 (colored)

Fix for http://secunia.com/advisories/31647/ from R svn.

Revision 1.98 / (download) - annotate - [select for diffs], Sun Jul 20 23:18:28 2008 UTC (10 years, 10 months ago) by dbj
Branch: MAIN
Changes since 1.97: +5 -1 lines
Diff to previous 1.97 (colored)

set --disable-R-framework and --without-aqua
these options are only used by R.app on Mac OS X

Revision 1.97 / (download) - annotate - [select for diffs], Sat Apr 26 02:39:27 2008 UTC (11 years ago) by markd
Branch: MAIN
CVS Tags: pkgsrc-2008Q2-base, cwrapper
Branch point for: pkgsrc-2008Q2
Changes since 1.96: +9 -3 lines
Diff to previous 1.96 (colored)

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.

Revision 1.96 / (download) - annotate - [select for diffs], Sat Mar 15 22:16:41 2008 UTC (11 years, 2 months ago) by markd
Branch: MAIN
CVS Tags: pkgsrc-2008Q1-base, pkgsrc-2008Q1
Changes since 1.95: +2 -3 lines
Diff to previous 1.95 (colored)

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.

Revision 1.95 / (download) - annotate - [select for diffs], Fri Mar 7 16:11:39 2008 UTC (11 years, 2 months ago) by jlam
Branch: MAIN
Changes since 1.94: +3 -5 lines
Diff to previous 1.94 (colored)

+ 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.

Revision 1.94 / (download) - annotate - [select for diffs], Thu Nov 8 19:39:43 2007 UTC (11 years, 6 months ago) by joerg
Branch: MAIN
CVS Tags: pkgsrc-2007Q4-base, pkgsrc-2007Q4
Changes since 1.93: +2 -1 lines
Diff to previous 1.93 (colored)

Bump version or revision of all packages that have a runtime dependency
on gzip.

Revision 1.93 / (download) - annotate - [select for diffs], Sat Nov 3 20:14:39 2007 UTC (11 years, 6 months ago) by markd
Branch: MAIN
Changes since 1.92: +3 -3 lines
Diff to previous 1.92 (colored)

Update R to version 2.6.0

Many new features, changes and bug fixes. See lib/R/doc/NEWS for details.

Revision 1.92 / (download) - annotate - [select for diffs], Sat Sep 8 13:44:48 2007 UTC (11 years, 8 months ago) by rillig
Branch: MAIN
CVS Tags: pkgsrc-2007Q3-base, pkgsrc-2007Q3
Changes since 1.91: +4 -3 lines
Diff to previous 1.91 (colored)

Fixed the path to unzip. PKGREVISION++

Revision 1.91 / (download) - annotate - [select for diffs], Wed Mar 28 11:06:29 2007 UTC (12 years, 1 month ago) by dmcmahill
Branch: MAIN
CVS Tags: pkgsrc-2007Q2-base, pkgsrc-2007Q2, pkgsrc-2007Q1-base, pkgsrc-2007Q1
Changes since 1.90: +3 -3 lines
Diff to previous 1.90 (colored)

Wants at least version 4.7 of makeinfo to build the docs.  Bump pkgrev.

Revision 1.90 / (download) - annotate - [select for diffs], Tue Mar 20 11:00:58 2007 UTC (12 years, 2 months ago) by markd
Branch: MAIN
Changes since 1.89: +2 -7 lines
Diff to previous 1.89 (colored)

Fix configure's handling of libblas when compiling with f2c and therefore
remove conditional PLIST entry no longer required. Bump PKGREVISION.

Revision 1.89 / (download) - annotate - [select for diffs], Sun Mar 18 13:13:02 2007 UTC (12 years, 2 months ago) by markd
Branch: MAIN
Changes since 1.88: +7 -1 lines
Diff to previous 1.88 (colored)

Building with f2c effects what libs get installed. Adjust PLIST.

Revision 1.88 / (download) - annotate - [select for diffs], Wed Mar 14 11:50:17 2007 UTC (12 years, 2 months ago) by markd
Branch: MAIN
Changes since 1.87: +8 -29 lines
Diff to previous 1.87 (colored)

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.

Revision 1.87 / (download) - annotate - [select for diffs], Mon Jan 8 15:00:36 2007 UTC (12 years, 4 months ago) by joerg
Branch: MAIN
Changes since 1.86: +2 -1 lines
Diff to previous 1.86 (colored)

Needs libXt explicitly.

Revision 1.85.4.1 / (download) - annotate - [select for diffs], Tue Oct 17 15:32:08 2006 UTC (12 years, 7 months ago) by salo
Branch: pkgsrc-2006Q3
Changes since 1.85: +5 -5 lines
Diff to previous 1.85 (colored) next main 1.86 (colored)

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.

Revision 1.86 / (download) - annotate - [select for diffs], Sun Oct 8 23:12:48 2006 UTC (12 years, 7 months ago) by dmcmahill
Branch: MAIN
CVS Tags: pkgsrc-2006Q4-base, pkgsrc-2006Q4
Changes since 1.85: +5 -5 lines
Diff to previous 1.85 (colored)

The variable modifier $${dir#${PREFIX}/} is not portable so eliminate its
use.  Fixes R packaging on solaris.

Revision 1.85 / (download) - annotate - [select for diffs], Tue Jun 13 12:28:09 2006 UTC (12 years, 11 months ago) by markd
Branch: MAIN
CVS Tags: pkgsrc-2006Q3-base, pkgsrc-2006Q2-base, pkgsrc-2006Q2
Branch point for: pkgsrc-2006Q3
Changes since 1.84: +2 -3 lines
Diff to previous 1.84 (colored)

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.

Revision 1.84 / (download) - annotate - [select for diffs], Fri Jun 9 11:15:32 2006 UTC (12 years, 11 months ago) by rillig
Branch: MAIN
Changes since 1.83: +7 -7 lines
Diff to previous 1.83 (colored)

Fixed pkglint warnings.

Revision 1.83 / (download) - annotate - [select for diffs], Mon Apr 17 13:46:39 2006 UTC (13 years, 1 month ago) by wiz
Branch: MAIN
Changes since 1.82: +2 -2 lines
Diff to previous 1.82 (colored)

Bump BUILDLINK_ABI_DEPENDS.png and PKGREVISION for png-1.2.9nb2 update.

Revision 1.82 / (download) - annotate - [select for diffs], Thu Apr 6 06:22:19 2006 UTC (13 years, 1 month ago) by reed
Branch: MAIN
Changes since 1.81: +2 -2 lines
Diff to previous 1.81 (colored)

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).

Revision 1.81 / (download) - annotate - [select for diffs], Sun Mar 5 16:27:27 2006 UTC (13 years, 2 months ago) by jlam
Branch: MAIN
CVS Tags: pkgsrc-2006Q1-base, pkgsrc-2006Q1
Changes since 1.80: +2 -3 lines
Diff to previous 1.80 (colored)

* 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.

Revision 1.80 / (download) - annotate - [select for diffs], Sun Feb 5 23:09:59 2006 UTC (13 years, 3 months ago) by joerg
Branch: MAIN
Changes since 1.79: +2 -2 lines
Diff to previous 1.79 (colored)

Recursive revision bump / recommended bump for gettext ABI change.

Revision 1.79 / (download) - annotate - [select for diffs], Thu Jan 12 01:41:48 2006 UTC (13 years, 4 months ago) by markd
Branch: MAIN
Changes since 1.78: +4 -2 lines
Diff to previous 1.78 (colored)

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.

Revision 1.78 / (download) - annotate - [select for diffs], Thu Dec 29 23:23:53 2005 UTC (13 years, 4 months ago) by markd
Branch: MAIN
Changes since 1.77: +2 -2 lines
Diff to previous 1.77 (colored)

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

Revision 1.77 / (download) - annotate - [select for diffs], Sun Dec 11 14:37:12 2005 UTC (13 years, 5 months ago) by markd
Branch: MAIN
CVS Tags: pkgsrc-2005Q4-base, pkgsrc-2005Q4
Changes since 1.76: +5 -6 lines
Diff to previous 1.76 (colored)

Update R to 2.2.0

Changes:
 This version contains several changes and additions, mostly incremental.

Revision 1.76 / (download) - annotate - [select for diffs], Mon Dec 5 20:50:36 2005 UTC (13 years, 5 months ago) by rillig
Branch: MAIN
Changes since 1.75: +3 -3 lines
Diff to previous 1.75 (colored)

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

Revision 1.75 / (download) - annotate - [select for diffs], Thu Dec 1 23:11:26 2005 UTC (13 years, 5 months ago) by joerg
Branch: MAIN
Changes since 1.74: +4 -1 lines
Diff to previous 1.74 (colored)

- 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

Revision 1.74 / (download) - annotate - [select for diffs], Wed Sep 28 20:52:24 2005 UTC (13 years, 7 months ago) by rillig
Branch: MAIN
Changes since 1.73: +3 -3 lines
Diff to previous 1.73 (colored)

Replaced "# defined" with "yes" in Makefile variables like GNU_CONFIGURE,
NO_BUILD, USE_LIBTOOL.

Revision 1.73 / (download) - annotate - [select for diffs], Tue Sep 20 12:47:14 2005 UTC (13 years, 8 months ago) by dmcmahill
Branch: MAIN
CVS Tags: pkgsrc-2005Q3-base, pkgsrc-2005Q3
Changes since 1.72: +2 -1 lines
Diff to previous 1.72 (colored)

add missing libiconv buildlink3.mk

Revision 1.72 / (download) - annotate - [select for diffs], Sat Jul 16 01:19:13 2005 UTC (13 years, 10 months ago) by jlam
Branch: MAIN
Changes since 1.71: +2 -3 lines
Diff to previous 1.71 (colored)

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.

Revision 1.71 / (download) - annotate - [select for diffs], Fri Jun 24 12:28:31 2005 UTC (13 years, 10 months ago) by markd
Branch: MAIN
Changes since 1.70: +3 -5 lines
Diff to previous 1.70 (colored)

Update R to version 2.1.1.

minor bug fixes.

Revision 1.70 / (download) - annotate - [select for diffs], Sun Jun 19 00:45:45 2005 UTC (13 years, 11 months ago) by kristerw
Branch: MAIN
CVS Tags: pkgsrc-2005Q2-base, pkgsrc-2005Q2
Changes since 1.69: +4 -3 lines
Diff to previous 1.69 (colored)

Prevent paths to the build directories from being included in the package.
Bump PKGREVISION.

Revision 1.69 / (download) - annotate - [select for diffs], Sat Jun 11 02:37:00 2005 UTC (13 years, 11 months ago) by markd
Branch: MAIN
Changes since 1.68: +5 -17 lines
Diff to previous 1.68 (colored)

Cleanup of tools paths appearing in installed files for the new tools
framework.  Bump PKGREVISION.

Revision 1.68 / (download) - annotate - [select for diffs], Wed Jun 1 18:03:00 2005 UTC (13 years, 11 months ago) by jlam
Branch: MAIN
Changes since 1.67: +1 -2 lines
Diff to previous 1.67 (colored)

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.

Revision 1.67 / (download) - annotate - [select for diffs], Sun May 22 20:08:13 2005 UTC (14 years ago) by jlam
Branch: MAIN
Changes since 1.66: +2 -3 lines
Diff to previous 1.66 (colored)

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

Revision 1.66 / (download) - annotate - [select for diffs], Sun May 22 05:35:33 2005 UTC (14 years ago) by jlam
Branch: MAIN
Changes since 1.65: +2 -2 lines
Diff to previous 1.65 (colored)

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.

Revision 1.65 / (download) - annotate - [select for diffs], Thu May 19 13:12:52 2005 UTC (14 years ago) by markd
Branch: MAIN
Changes since 1.64: +5 -1 lines
Diff to previous 1.64 (colored)

Don't try and use wide chars on NetBSD 1.6 as the support isn't complete
enough.  Fixes PR pkg/30274

Revision 1.64 / (download) - annotate - [select for diffs], Mon May 2 16:57:19 2005 UTC (14 years ago) by drochner
Branch: MAIN
Changes since 1.63: +2 -2 lines
Diff to previous 1.63 (colored)

update to 2.1.0
too many changes to list here
...still doesn't work within TEXmacs

Revision 1.63 / (download) - annotate - [select for diffs], Mon Apr 11 21:46:28 2005 UTC (14 years, 1 month ago) by tv
Branch: MAIN
Changes since 1.62: +1 -2 lines
Diff to previous 1.62 (colored)

Remove USE_BUILDLINK3 and NO_BUILDLINK; these are no longer used.

Revision 1.62 / (download) - annotate - [select for diffs], Wed Jan 12 22:50:20 2005 UTC (14 years, 4 months ago) by jlam
Branch: MAIN
CVS Tags: pkgsrc-2005Q1-base, pkgsrc-2005Q1
Changes since 1.61: +12 -11 lines
Diff to previous 1.61 (colored)

Move buildlink3.mk files ahead of targets as per example Makefile.

Revision 1.61 / (download) - annotate - [select for diffs], Wed Jan 12 22:49:35 2005 UTC (14 years, 4 months ago) by jlam
Branch: MAIN
Changes since 1.60: +13 -14 lines
Diff to previous 1.60 (colored)

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.

Revision 1.60 / (download) - annotate - [select for diffs], Wed Jan 12 15:32:00 2005 UTC (14 years, 4 months ago) by jlam
Branch: MAIN
Changes since 1.59: +1 -2 lines
Diff to previous 1.59 (colored)

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.

Revision 1.59 / (download) - annotate - [select for diffs], Thu Nov 18 12:31:29 2004 UTC (14 years, 6 months ago) by markd
Branch: MAIN
CVS Tags: pkgsrc-2004Q4-base, pkgsrc-2004Q4
Changes since 1.58: +4 -6 lines
Diff to previous 1.58 (colored)

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.

Revision 1.58 / (download) - annotate - [select for diffs], Sat Nov 13 21:28:28 2004 UTC (14 years, 6 months ago) by jlam
Branch: MAIN
Changes since 1.57: +2 -2 lines
Diff to previous 1.57 (colored)

USE_BUILDLINK3 is a yes/no variable.

Revision 1.57 / (download) - annotate - [select for diffs], Sun Oct 3 00:12:55 2004 UTC (14 years, 7 months ago) by tv
Branch: MAIN
Changes since 1.56: +2 -1 lines
Diff to previous 1.56 (colored)

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.

Revision 1.56 / (download) - annotate - [select for diffs], Tue Jul 6 22:56:32 2004 UTC (14 years, 10 months ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2004Q3-base, pkgsrc-2004Q3
Changes since 1.55: +2 -1 lines
Diff to previous 1.55 (colored)

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

Revision 1.55 / (download) - annotate - [select for diffs], Thu Jun 24 11:09:05 2004 UTC (14 years, 10 months ago) by markd
Branch: MAIN
Changes since 1.54: +2 -2 lines
Diff to previous 1.54 (colored)

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.

Revision 1.54 / (download) - annotate - [select for diffs], Tue May 18 11:27:29 2004 UTC (15 years ago) by uebayasi
Branch: MAIN
CVS Tags: pkgsrc-2004Q2-base, pkgsrc-2004Q2
Changes since 1.53: +3 -1 lines
Diff to previous 1.53 (colored)

Enable pkgviews installation.

Revision 1.53 / (download) - annotate - [select for diffs], Fri May 7 22:47:26 2004 UTC (15 years ago) by markd
Branch: MAIN
Changes since 1.52: +5 -1 lines
Diff to previous 1.52 (colored)

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.

Revision 1.52 / (download) - annotate - [select for diffs], Tue Apr 27 11:24:31 2004 UTC (15 years ago) by markd
Branch: MAIN
Changes since 1.51: +16 -12 lines
Diff to previous 1.51 (colored)

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.

Revision 1.51 / (download) - annotate - [select for diffs], Thu Mar 11 21:04:47 2004 UTC (15 years, 2 months ago) by markd
Branch: MAIN
CVS Tags: pkgsrc-2004Q1-base, pkgsrc-2004Q1
Changes since 1.50: +3 -3 lines
Diff to previous 1.50 (colored)

Switch to using tk8.4
bump PKGREVISION

Revision 1.50 / (download) - annotate - [select for diffs], Mon Mar 8 20:27:14 2004 UTC (15 years, 2 months ago) by minskim
Branch: MAIN
Changes since 1.49: +2 -2 lines
Diff to previous 1.49 (colored)

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.

Revision 1.49 / (download) - annotate - [select for diffs], Mon Mar 1 11:42:13 2004 UTC (15 years, 2 months ago) by markd
Branch: MAIN
Changes since 1.48: +2 -1 lines
Diff to previous 1.48 (colored)

USE_LANGUAGES= c fortran

Revision 1.48 / (download) - annotate - [select for diffs], Sat Jan 24 13:58:23 2004 UTC (15 years, 3 months ago) by grant
Branch: MAIN
Changes since 1.47: +2 -2 lines
Diff to previous 1.47 (colored)

replace deprecated USE_GMAKE with USE_GNU_TOOLS+=make.

Revision 1.47 / (download) - annotate - [select for diffs], Mon Jan 5 12:20:57 2004 UTC (15 years, 4 months ago) by markd
Branch: MAIN
Changes since 1.46: +2 -1 lines
Diff to previous 1.46 (colored)

Reintroduce reordering tests for termcap vs termlib vs ncurses and
make dependency on libbz2 explicit

Fixes build on Solaris 8.

Revision 1.46 / (download) - annotate - [select for diffs], Thu Dec 4 13:42:37 2003 UTC (15 years, 5 months ago) by adam
Branch: MAIN
Changes since 1.45: +3 -5 lines
Diff to previous 1.45 (colored)

Now uses shared blas library from math/blas

Revision 1.45 / (download) - annotate - [select for diffs], Wed Dec 3 12:05:18 2003 UTC (15 years, 5 months ago) by markd
Branch: MAIN
Changes since 1.44: +6 -2 lines
Diff to previous 1.44 (colored)

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.

Revision 1.44 / (download) - annotate - [select for diffs], Thu Jul 17 21:47:15 2003 UTC (15 years, 10 months ago) by grant
Branch: MAIN
CVS Tags: pkgsrc-2003Q4-base, pkgsrc-2003Q4
Changes since 1.43: +2 -2 lines
Diff to previous 1.43 (colored)

s/netbsd.org/NetBSD.org/

Revision 1.43 / (download) - annotate - [select for diffs], Tue Mar 11 02:30:24 2003 UTC (16 years, 2 months ago) by jmc
Branch: MAIN
Changes since 1.42: +5 -2 lines
Diff to previous 1.42 (colored)

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

Revision 1.42 / (download) - annotate - [select for diffs], Thu Jan 23 21:24:58 2003 UTC (16 years, 3 months ago) by markd
Branch: MAIN
CVS Tags: netbsd-1-6-1-base, netbsd-1-6-1
Changes since 1.41: +2 -2 lines
Diff to previous 1.41 (colored)

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.

Revision 1.41 / (download) - annotate - [select for diffs], Tue Dec 10 11:58:10 2002 UTC (16 years, 5 months ago) by markd
Branch: MAIN
Changes since 1.40: +3 -2 lines
Diff to previous 1.40 (colored)

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.

Revision 1.40 / (download) - annotate - [select for diffs], Thu Oct 31 23:30:36 2002 UTC (16 years, 6 months ago) by jlam
Branch: MAIN
Changes since 1.39: +1 -2 lines
Diff to previous 1.39 (colored)

BUILDLINK_X11PKG_DIR is no more.

Revision 1.39 / (download) - annotate - [select for diffs], Thu Sep 26 05:36:48 2002 UTC (16 years, 7 months ago) by markd
Branch: MAIN
Changes since 1.38: +4 -4 lines
Diff to previous 1.38 (colored)

INSTALL_DIRS -> R_INSTALL_DIRS to not conflict with the variable introduced
in bsd.pkg.mk revision 1.1045.  Fixes pkg/18332

Revision 1.38 / (download) - annotate - [select for diffs], Mon Sep 23 13:41:15 2002 UTC (16 years, 7 months ago) by markd
Branch: MAIN
Changes since 1.37: +2 -2 lines
Diff to previous 1.37 (colored)

find ... -or ... -> find ... -o ... for more portability.

Revision 1.37 / (download) - annotate - [select for diffs], Mon Sep 9 00:59:00 2002 UTC (16 years, 8 months ago) by markd
Branch: MAIN
Changes since 1.36: +26 -18 lines
Diff to previous 1.36 (colored)

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.

Revision 1.36 / (download) - annotate - [select for diffs], Wed Jul 17 13:12:54 2002 UTC (16 years, 10 months ago) by markd
Branch: MAIN
CVS Tags: pkgviews-base, pkgviews, netbsd-1-6-RELEASE-base, netbsd-1-6
Changes since 1.35: +2 -2 lines
Diff to previous 1.35 (colored)

Give path for -lblas so modules such as R-KernSmooth can find it when
they try to link it.

Revision 1.33.2.1 / (download) - annotate - [select for diffs], Sun Jun 23 18:52:29 2002 UTC (16 years, 11 months ago) by jlam
Branch: buildlink2
Changes since 1.33: +7 -3 lines
Diff to previous 1.33 (colored) next main 1.34 (colored)

Merge from pkgsrc-current to buildlink2 branch.

Revision 1.35 / (download) - annotate - [select for diffs], Sun Jun 16 02:56:50 2002 UTC (16 years, 11 months ago) by dmcmahill
Branch: MAIN
CVS Tags: buildlink2-base
Changes since 1.34: +5 -1 lines
Diff to previous 1.34 (colored)

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!).

Revision 1.34 / (download) - annotate - [select for diffs], Fri May 24 13:24:36 2002 UTC (17 years ago) by markd
Branch: MAIN
Changes since 1.33: +3 -3 lines
Diff to previous 1.33 (colored)

Reorder PLIST so pkg_delete works cleanly

Revision 1.33 / (download) - annotate - [select for diffs], Fri May 3 12:34:39 2002 UTC (17 years ago) by markd
Branch: MAIN
Branch point for: buildlink2
Changes since 1.32: +2 -2 lines
Diff to previous 1.32 (colored)

Add etc/Makeconf to REPLACE_BUILDLINK.  Fixes pkg/16620

Revision 1.32 / (download) - annotate - [select for diffs], Tue Apr 23 01:14:49 2002 UTC (17 years, 1 month ago) by markd
Branch: MAIN
Changes since 1.31: +10 -14 lines
Diff to previous 1.31 (colored)

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.

Revision 1.31 / (download) - annotate - [select for diffs], Wed Mar 13 17:37:23 2002 UTC (17 years, 2 months ago) by fredb
Branch: MAIN
CVS Tags: netbsd-1-5-PATCH003
Changes since 1.30: +2 -1 lines
Diff to previous 1.30 (colored)

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".]

Revision 1.30 / (download) - annotate - [select for diffs], Fri Mar 1 10:46:53 2002 UTC (17 years, 2 months ago) by markd
Branch: MAIN
Changes since 1.29: +1 -1 lines
Diff to previous 1.29 (colored)

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.

Revision 1.29 / (download) - annotate - [select for diffs], Tue Dec 11 22:35:07 2001 UTC (17 years, 5 months ago) by jlam
Branch: MAIN
Changes since 1.28: +1 -6 lines
Diff to previous 1.28 (colored)

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>.

Revision 1.28 / (download) - annotate - [select for diffs], Wed Oct 24 22:11:04 2001 UTC (17 years, 6 months ago) by jlam
Branch: MAIN
Changes since 1.27: +2 -1 lines
Diff to previous 1.27 (colored)

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.

Revision 1.27 / (download) - annotate - [select for diffs], Mon Aug 27 14:35:10 2001 UTC (17 years, 8 months ago) by tron
Branch: MAIN
Changes since 1.26: +2 -2 lines
Diff to previous 1.26 (colored)

Use wildcard dependence on "autoconf" package.

Revision 1.26 / (download) - annotate - [select for diffs], Mon Aug 13 10:25:03 2001 UTC (17 years, 9 months ago) by agc
Branch: MAIN
Changes since 1.25: +2 -1 lines
Diff to previous 1.25 (colored)

Add back COMMENT definition which got lost.

Revision 1.25 / (download) - annotate - [select for diffs], Mon Jul 23 13:14:44 2001 UTC (17 years, 10 months ago) by jlam
Branch: MAIN
Changes since 1.24: +43 -30 lines
Diff to previous 1.24 (colored)

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.

Revision 1.24 / (download) - annotate - [select for diffs], Tue Jun 12 20:33:05 2001 UTC (17 years, 11 months ago) by jlam
Branch: MAIN
Changes since 1.23: +1 -2 lines
Diff to previous 1.23 (colored)

LIBS is automatically added to CONFIGURE_ENV by bsd.pkg.mk if
GNU_CONFIGURE is defined, so simply set LIBS to the appropriate value.

Revision 1.23 / (download) - annotate - [select for diffs], Mon Jun 11 06:34:41 2001 UTC (17 years, 11 months ago) by jlam
Branch: MAIN
Changes since 1.22: +1 -2 lines
Diff to previous 1.22 (colored)

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.

Revision 1.22 / (download) - annotate - [select for diffs], Tue May 22 09:32:24 2001 UTC (18 years ago) by wiz
Branch: MAIN
Changes since 1.21: +2 -2 lines
Diff to previous 1.21 (colored)

Update dependency on png to >=1.0.11 because of the shlib major bump.
Noted by Frederick Bruckman.

Revision 1.21 / (download) - annotate - [select for diffs], Tue Mar 27 03:20:05 2001 UTC (18 years, 1 month ago) by hubertf
Branch: MAIN
CVS Tags: netbsd-1-5-PATCH001
Changes since 1.20: +2 -2 lines
Diff to previous 1.20 (colored)

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>

Revision 1.20 / (download) - annotate - [select for diffs], Sun Mar 4 09:06:16 2001 UTC (18 years, 2 months ago) by tron
Branch: MAIN
Changes since 1.19: +2 -2 lines
Diff to previous 1.19 (colored)

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.

Revision 1.19 / (download) - annotate - [select for diffs], Mon Feb 26 15:01:43 2001 UTC (18 years, 2 months ago) by jlam
Branch: MAIN
Changes since 1.18: +4 -1 lines
Diff to previous 1.18 (colored)

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

Revision 1.18 / (download) - annotate - [select for diffs], Sat Feb 17 18:22:10 2001 UTC (18 years, 3 months ago) by wiz
Branch: MAIN
Changes since 1.17: +2 -1 lines
Diff to previous 1.17 (colored)

Update to new COMMENT style: COMMENT var in Makefile instead of pkg/COMMENT.

Revision 1.17 / (download) - annotate - [select for diffs], Tue Feb 6 03:16:58 2001 UTC (18 years, 3 months ago) by fredb
Branch: MAIN
Changes since 1.16: +3 -3 lines
Diff to previous 1.16 (colored)

Make that "autoreconf" -- there is no "autoremake".

Revision 1.16 / (download) - annotate - [select for diffs], Mon Feb 5 09:00:59 2001 UTC (18 years, 3 months ago) by tron
Branch: MAIN
Changes since 1.15: +3 -3 lines
Diff to previous 1.15 (colored)

Use full pathname "${LOCALBASE}/bin/auto..." in dependences and make
targets. This includes a fix for PR pkg/12125 by Tomasz Luchowski.

Revision 1.15 / (download) - annotate - [select for diffs], Fri Nov 3 01:14:51 2000 UTC (18 years, 6 months ago) by jlam
Branch: MAIN
Changes since 1.14: +2 -2 lines
Diff to previous 1.14 (colored)

Homepage has moved.

Revision 1.14 / (download) - annotate - [select for diffs], Wed Aug 16 19:04:42 2000 UTC (18 years, 9 months ago) by jlam
Branch: MAIN
CVS Tags: netbsd-1-5-RELEASE, netbsd-1-4-PATCH003
Changes since 1.13: +23 -3 lines
Diff to previous 1.13 (colored)

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

Revision 1.13 / (download) - annotate - [select for diffs], Fri Aug 11 23:02:37 2000 UTC (18 years, 9 months ago) by jlam
Branch: MAIN
Changes since 1.12: +24 -15 lines
Diff to previous 1.12 (colored)

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.

Revision 1.12 / (download) - annotate - [select for diffs], Wed Apr 19 15:30:05 2000 UTC (19 years, 1 month ago) by jlam
Branch: MAIN
Changes since 1.11: +40 -36 lines
Diff to previous 1.11 (colored)

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.

Revision 1.11 / (download) - annotate - [select for diffs], Wed Jan 12 22:05:30 2000 UTC (19 years, 4 months ago) by rh
Branch: MAIN
CVS Tags: netbsd-1-4-PATCH002
Changes since 1.10: +9 -5 lines
Diff to previous 1.10 (colored)

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).

Revision 1.10 / (download) - annotate - [select for diffs], Tue Nov 23 17:37:28 1999 UTC (19 years, 6 months ago) by dmcmahill
Branch: MAIN
Changes since 1.9: +2 -4 lines
Diff to previous 1.9 (colored)

add USE_FORTRAN

Revision 1.9 / (download) - annotate - [select for diffs], Thu Aug 26 23:52:21 1999 UTC (19 years, 8 months ago) by jlam
Branch: MAIN
CVS Tags: comdex-fall-1999
Changes since 1.8: +2 -2 lines
Diff to previous 1.8 (colored)

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).

Revision 1.8 / (download) - annotate - [select for diffs], Tue Jul 13 01:20:12 1999 UTC (19 years, 10 months ago) by jlam
Branch: MAIN
CVS Tags: netbsd-1-4-PATCH001
Changes since 1.7: +2 -2 lines
Diff to previous 1.7 (colored)

Update readline dependency.

Revision 1.7 / (download) - annotate - [select for diffs], Wed Jun 9 00:45:08 1999 UTC (19 years, 11 months ago) by hubertf
Branch: MAIN
Changes since 1.6: +3 -1 lines
Diff to previous 1.6 (colored)

default R_PAPERSIZE to A4 if PAPERSIZE is not set.

Revision 1.6 / (download) - annotate - [select for diffs], Tue May 25 23:45:05 1999 UTC (19 years, 11 months ago) by jlam
Branch: MAIN
Changes since 1.5: +20 -10 lines
Diff to previous 1.5 (colored)

Updated R to 0.64.1.  Too many changes from 0.62.1 to enumerate.
See NEWS file in distribution.

Revision 1.5 / (download) - annotate - [select for diffs], Mon Apr 26 18:56:15 1999 UTC (20 years ago) by garbled
Branch: MAIN
CVS Tags: netbsd-1-4-RELEASE
Changes since 1.4: +2 -1 lines
Diff to previous 1.4 (colored)

add USE_X11=yes

Revision 1.4 / (download) - annotate - [select for diffs], Sat Feb 20 22:48:35 1999 UTC (20 years, 3 months ago) by hubertf
Branch: MAIN
Changes since 1.3: +1 -3 lines
Diff to previous 1.3 (colored)

Fix CONFLICTS (remove redundancy, mostly)

Revision 1.3 / (download) - annotate - [select for diffs], Thu Jan 14 13:57:04 1999 UTC (20 years, 4 months ago) by frueauf
Branch: MAIN
Changes since 1.2: +2 -2 lines
Diff to previous 1.2 (colored)

Reflect update of f2c.

Revision 1.2 / (download) - annotate - [select for diffs], Mon Dec 21 10:29:39 1998 UTC (20 years, 5 months ago) by frueauf
Branch: MAIN
Changes since 1.1: +9 -12 lines
Diff to previous 1.1 (colored)

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.

Revision 1.1.1.1 / (download) - annotate - [select for diffs] (vendor branch), Fri Dec 4 11:36:03 1998 UTC (20 years, 5 months ago) by frueauf
Branch: TNF
CVS Tags: pkgsrc-base
Changes since 1.1: +0 -0 lines
Diff to previous 1.1 (colored)

Initial addition of R-0.63.0, a language for data analysis and graphics.
Provided in pr 6493 by Johnny C. Lam.

Revision 1.1 / (download) - annotate - [select for diffs], Fri Dec 4 11:36:03 1998 UTC (20 years, 5 months ago) by frueauf
Branch: MAIN

Initial revision

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