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CVS log for pkgsrc/math/R-genetics/Makefile

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Default branch: MAIN


Revision 1.16 / (download) - annotate - [select for diffs], Sun Aug 11 13:21:43 2019 UTC (5 weeks, 5 days ago) by wiz
Branch: MAIN
CVS Tags: HEAD
Changes since 1.15: +2 -1 lines
Diff to previous 1.15 (colored)

Bump PKGREVISIONs for perl 5.30.0

Revision 1.15 / (download) - annotate - [selected], Thu Aug 8 19:53:49 2019 UTC (6 weeks ago) by brook
Branch: MAIN
Changes since 1.14: +4 -6 lines
Diff to previous 1.14 (colored)

Update all R packages to canonical form.

The canonical form [1] of an R package Makefile includes the
following:

- The first stanza includes R_PKGNAME, R_PKGVER, PKGREVISION (as
  needed), and CATEGORIES.

- HOMEPAGE is not present but defined in math/R/Makefile.extension to
  refer to the CRAN web page describing the package.  Other relevant
  web pages are often linked from there via the URL field.

This updates all current R packages to this form, which will make
regular updates _much_ easier, especially using pkgtools/R2pkg.

[1] http://mail-index.netbsd.org/tech-pkg/2019/08/02/msg021711.html

Revision 1.14 / (download) - annotate - [select for diffs], Wed Jul 31 19:31:13 2019 UTC (7 weeks, 1 day ago) by brook
Branch: MAIN
Changes since 1.13: +9 -9 lines
Diff to previous 1.13 (colored) to selected 1.15 (colored)

R-genetics: update to version 1.3.8.1.2.

Update to the canonical form of an R package and fix the LICENSE
field.

Revision 1.13 / (download) - annotate - [select for diffs], Wed Aug 22 09:45:35 2018 UTC (12 months, 4 weeks ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2019Q2-base, pkgsrc-2019Q2, pkgsrc-2019Q1-base, pkgsrc-2019Q1, pkgsrc-2018Q4-base, pkgsrc-2018Q4, pkgsrc-2018Q3-base, pkgsrc-2018Q3
Changes since 1.12: +2 -2 lines
Diff to previous 1.12 (colored) to selected 1.15 (colored)

Recursive bump for perl5-5.28.0

Revision 1.12 / (download) - annotate - [select for diffs], Sat Jul 28 14:40:48 2018 UTC (13 months, 3 weeks ago) by brook
Branch: MAIN
Changes since 1.11: +1 -2 lines
Diff to previous 1.11 (colored) to selected 1.15 (colored)

Remove MASTER_SITES= from individual R package Makefiles.

Each R package should include ../../math/R/Makefile.extension, which also
defines MASTER_SITES.  Consequently, it is redundant for the individual
packages to do the same.  Package-specific definitions also prevent
redefining MASTER_SITES in a single common place.

Revision 1.11 / (download) - annotate - [select for diffs], Sat Jul 9 06:38:32 2016 UTC (3 years, 2 months ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2018Q2-base, pkgsrc-2018Q2, pkgsrc-2018Q1-base, pkgsrc-2018Q1, pkgsrc-2017Q4-base, pkgsrc-2017Q4, pkgsrc-2017Q3-base, pkgsrc-2017Q3, pkgsrc-2017Q2-base, pkgsrc-2017Q2, pkgsrc-2017Q1-base, pkgsrc-2017Q1, pkgsrc-2016Q4-base, pkgsrc-2016Q4, pkgsrc-2016Q3-base, pkgsrc-2016Q3, pkgsrc-
Changes since 1.10: +2 -1 lines
Diff to previous 1.10 (colored) to selected 1.15 (colored)

Bump PKGREVISION for perl-5.24.0 for everything mentioning perl.

Revision 1.10 / (download) - annotate - [select for diffs], Sat Apr 9 13:34:16 2016 UTC (3 years, 5 months ago) by wen
Branch: MAIN
CVS Tags: pkgsrc-2016Q2-base, pkgsrc-2016Q2
Changes since 1.9: +2 -3 lines
Diff to previous 1.9 (colored) to selected 1.15 (colored)

Update to 1.3.8.1

No upstream changelog.

Revision 1.9 / (download) - annotate - [select for diffs], Fri Jun 12 10:50:27 2015 UTC (4 years, 3 months ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2016Q1-base, pkgsrc-2016Q1, pkgsrc-2015Q4-base, pkgsrc-2015Q4, pkgsrc-2015Q3-base, pkgsrc-2015Q3, pkgsrc-2015Q2-base, pkgsrc-2015Q2
Changes since 1.8: +2 -2 lines
Diff to previous 1.8 (colored) to selected 1.15 (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 1.8 / (download) - annotate - [select for diffs], Thu May 29 23:36:52 2014 UTC (5 years, 3 months ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2015Q1-base, pkgsrc-2015Q1, pkgsrc-2014Q4-base, pkgsrc-2014Q4, pkgsrc-2014Q3-base, pkgsrc-2014Q3, pkgsrc-2014Q2-base, pkgsrc-2014Q2
Changes since 1.7: +2 -2 lines
Diff to previous 1.7 (colored) to selected 1.15 (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 1.7 / (download) - annotate - [select for diffs], Fri May 31 12:41:21 2013 UTC (6 years, 3 months ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2014Q1-base, pkgsrc-2014Q1, pkgsrc-2013Q4-base, pkgsrc-2013Q4, pkgsrc-2013Q3-base, pkgsrc-2013Q3, pkgsrc-2013Q2-base, pkgsrc-2013Q2
Changes since 1.6: +2 -1 lines
Diff to previous 1.6 (colored) to selected 1.15 (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 1.6 / (download) - annotate - [select for diffs], Thu Jan 24 02:24:15 2013 UTC (6 years, 7 months ago) by wen
Branch: MAIN
CVS Tags: pkgsrc-2013Q1-base, pkgsrc-2013Q1
Changes since 1.5: +5 -3 lines
Diff to previous 1.5 (colored) to selected 1.15 (colored)

Update to 1.3.8
Update LICENSE

Upstream changes:
genetics 1.3.8 - 2012-12-14
---------------------------

Bug fixes:

- Regenerate broken PDF files in inst/doc.


genetics 1.3.7 - 2012-09-14
---------------------------

Enhancements:

- Improve descripiton of last examples in manual page for HWE.test().

Other Changes:

- Correct warnings issued by recent versions of R CMD CHECK.

Revision 1.5 / (download) - annotate - [select for diffs], Sun Apr 15 16:54:17 2012 UTC (7 years, 5 months ago) by brook
Branch: MAIN
CVS Tags: pkgsrc-2012Q4-base, pkgsrc-2012Q4, pkgsrc-2012Q3-base, pkgsrc-2012Q3, pkgsrc-2012Q2-base, pkgsrc-2012Q2
Changes since 1.4: +8 -6 lines
Diff to previous 1.4 (colored) to selected 1.15 (colored)

Updated to genetics v1.3.6, added LICENSE (commented) and updated MAINTAINER.

Revision 1.4 / (download) - annotate - [select for diffs], Tue Oct 14 07:38:26 2008 UTC (10 years, 11 months ago) by markd
Branch: MAIN
CVS Tags: pkgsrc-2012Q1-base, pkgsrc-2012Q1, pkgsrc-2011Q4-base, pkgsrc-2011Q4, pkgsrc-2011Q3-base, pkgsrc-2011Q3, pkgsrc-2011Q2-base, pkgsrc-2011Q2, pkgsrc-2011Q1-base, pkgsrc-2011Q1, pkgsrc-2010Q4-base, pkgsrc-2010Q4, pkgsrc-2010Q3-base, pkgsrc-2010Q3, pkgsrc-2010Q2-base, pkgsrc-2010Q2, pkgsrc-2010Q1-base, pkgsrc-2010Q1, pkgsrc-2009Q4-base, pkgsrc-2009Q4, pkgsrc-2009Q3-base, pkgsrc-2009Q3, pkgsrc-2009Q2-base, pkgsrc-2009Q2, pkgsrc-2009Q1-base, pkgsrc-2009Q1, pkgsrc-2008Q4-base, pkgsrc-2008Q4
Changes since 1.3: +3 -3 lines
Diff to previous 1.3 (colored) to selected 1.15 (colored)

Update R-genetics to 1.3.4

genetics 1.3.4 - 2008-08-20
---------------------------

- Fix bug in makeGenotypes that caused it to ignore the 'sep' argument
  when determining which columns contain genotypes & add a corresponing
  regression test


genetics 1.3.3 - 2007-04-29
---------------------------

- Correct 'obsolete' use of '$'.  R no longer permits '$' to be used
  to extract named elements from vectors (just lists).

- Remove the power.casectl() function, which was based on invalid
  assumpations.  It has been marked depreciated.  Please use the
  functions in the Bioconductor package 'GeneticsDesign' instead.

genetics 1.3.2 - 2007-11-20
---------------------------

- Fix bug in handling of assignment of NA value(s) to elements of an
  existing genotype object.

- Fix warning messages from R CMD CHECK

- Correct documentation error by swapping definitions of kp and alpha
  arguments of power.casectl().

genetics 1.3.1
--------------

- fixes in genotypeOrder to ensure all genotype/haplotype combinations
  are used.

- genotypeOrder<- is now exported

genetics 1.3.0
--------------

- A note is now displayed on startup:

  The R-Genetics project has developed an set of enhanced genetics
  packages that will shortly replace 'genetics'. Please visit the
  project homepage at http://rgenetics.org for more information.

- binsearch() has been moved to the gtools package

- New function groupGenotype to create groups/levels based on genotype
  names

- Added some internal utility functions
  (.genotype2Haplotype, .genotype2Allele, and .matchGenotype)

- Genotype class gets additional slot genotypeOrder (and genotype()
  function gets additional argument with the same name) in order to enable
  predefined order of genotypes in other functions e.g. summary

- Added order, sort and %in% methods for genotype and haplotype classes.

- Fixed genotype() with allow.partial.missing=FALSE when 'alleles' argument
  is passed

- There is no more warning in genotype() if 'a1' or 'a2' have NA value(s)
  and 'alleles'' argument is specified, since NA is NA anyway

- Fixed documentation of power.casectrl()

- added gtools to Depends as needed by expectedGenotypes(); the latter now
  gives sorted genotypes according to order of given alleles

- print.HWE.test() wasn't displaying the observed vs expected genotype
  frequency table.  Fixed.

genetics 1.2.1
--------------

- Update Greg's email address

- Fixed a bug in function allele.number, as pointed out by Chris
  Wallace

Revision 1.3 / (download) - annotate - [select for diffs], Sun Jul 2 13:19:53 2006 UTC (13 years, 2 months ago) by markd
Branch: MAIN
CVS Tags: pkgsrc-2008Q3-base, pkgsrc-2008Q3, pkgsrc-2008Q2-base, pkgsrc-2008Q2, pkgsrc-2008Q1-base, pkgsrc-2008Q1, pkgsrc-2007Q4-base, pkgsrc-2007Q4, pkgsrc-2007Q3-base, pkgsrc-2007Q3, pkgsrc-2007Q2-base, pkgsrc-2007Q2, pkgsrc-2007Q1-base, pkgsrc-2007Q1, pkgsrc-2006Q4-base, pkgsrc-2006Q4, pkgsrc-2006Q3-base, pkgsrc-2006Q3, cwrapper, cube-native-xorg-base, cube-native-xorg
Changes since 1.2: +12 -9 lines
Diff to previous 1.2 (colored) to selected 1.15 (colored)

Update to version 1.2.0, add correct dependencies.
Fixes build problem seen in bulk builds.

Revision 1.2 / (download) - annotate - [select for diffs], Sun Feb 5 23:10:00 2006 UTC (13 years, 7 months ago) by joerg
Branch: MAIN
CVS Tags: pkgsrc-2006Q2-base, pkgsrc-2006Q2, pkgsrc-2006Q1-base, pkgsrc-2006Q1
Changes since 1.1: +2 -1 lines
Diff to previous 1.1 (colored) to selected 1.15 (colored)

Recursive revision bump / recommended bump for gettext ABI change.

Revision 1.1.1.1 / (download) - annotate - [select for diffs] (vendor branch), Fri Nov 4 08:13:15 2005 UTC (13 years, 10 months ago) by rillig
Branch: TNF
CVS Tags: pkgsrc-base, pkgsrc-2005Q4-base, pkgsrc-2005Q4
Changes since 1.1: +0 -0 lines
Diff to previous 1.1 (colored) to selected 1.15 (colored)

Imported R-genetics from pkgsrc-wip.

Classes and methods for handling genetic data. Includes classes to
represent genotypes and haplotypes at single markers up to multiple
markers on multiple chromosomes. Function include allele frequencies,
flagging homo/heterozygotes, flagging carriers of certain alleles,
estimating and testing for Hardy-Weinberg disequilibrium, estimating
and testing for linkage disequilibrium, ...

Revision 1.1 / (download) - annotate - [select for diffs], Fri Nov 4 08:13:15 2005 UTC (13 years, 10 months ago) by rillig
Branch: MAIN
Diff to selected 1.15 (colored)

Initial revision

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