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Revision 1.20 / (download) - annotate - [select for diffs], Tue Jun 28 11:34:36 2022 UTC (15 months, 1 week ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2023Q3-base,
pkgsrc-2023Q3,
pkgsrc-2023Q2-base,
pkgsrc-2023Q2,
pkgsrc-2023Q1-base,
pkgsrc-2023Q1,
pkgsrc-2022Q4-base,
pkgsrc-2022Q4,
pkgsrc-2022Q3-base,
pkgsrc-2022Q3,
HEAD
Changes since 1.19: +2 -1
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Diff to previous 1.19 (colored)
*: recursive bump for perl 5.36
Revision 1.19 / (download) - annotate - [select for diffs], Sat Sep 11 14:28:04 2021 UTC (2 years ago) by mef
Branch: MAIN
CVS Tags: pkgsrc-2022Q2-base,
pkgsrc-2022Q2,
pkgsrc-2022Q1-base,
pkgsrc-2022Q1,
pkgsrc-2021Q4-base,
pkgsrc-2021Q4,
pkgsrc-2021Q3-base,
pkgsrc-2021Q3
Changes since 1.18: +2 -4
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Diff to previous 1.18 (colored)
(math/R-genetics) Updated to 1.3.8.1.3, ChangeLog unknown
Revision 1.18 / (download) - annotate - [select for diffs], Mon May 24 19:52:55 2021 UTC (2 years, 4 months ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2021Q2-base,
pkgsrc-2021Q2
Changes since 1.17: +2 -2
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Diff to previous 1.17 (colored)
*: recursive bump for perl 5.34
Revision 1.17 / (download) - annotate - [select for diffs], Mon Aug 31 18:10:10 2020 UTC (3 years, 1 month ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2021Q1-base,
pkgsrc-2021Q1,
pkgsrc-2020Q4-base,
pkgsrc-2020Q4,
pkgsrc-2020Q3-base,
pkgsrc-2020Q3
Changes since 1.16: +2 -2
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Diff to previous 1.16 (colored)
*: bump PKGREVISION for perl-5.32.
Revision 1.16 / (download) - annotate - [select for diffs], Sun Aug 11 13:21:43 2019 UTC (4 years, 1 month ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2020Q2-base,
pkgsrc-2020Q2,
pkgsrc-2020Q1-base,
pkgsrc-2020Q1,
pkgsrc-2019Q4-base,
pkgsrc-2019Q4,
pkgsrc-2019Q3-base,
pkgsrc-2019Q3
Changes since 1.15: +2 -1
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Diff to previous 1.15 (colored)
Bump PKGREVISIONs for perl 5.30.0
Revision 1.15 / (download) - annotate - [select for diffs], Thu Aug 8 19:53:49 2019 UTC (4 years, 1 month ago) by brook
Branch: MAIN
Changes since 1.14: +4 -6
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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 (4 years, 2 months ago) by brook
Branch: MAIN
Changes since 1.13: +9 -9
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Diff to previous 1.13 (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 (5 years, 1 month 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
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Diff to previous 1.12 (colored)
Recursive bump for perl5-5.28.0
Revision 1.12 / (download) - annotate - [select for diffs], Sat Jul 28 14:40:48 2018 UTC (5 years, 2 months ago) by brook
Branch: MAIN
Changes since 1.11: +1 -2
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Diff to previous 1.11 (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 (7 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
Changes since 1.10: +2 -1
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Diff to previous 1.10 (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 (7 years, 5 months ago) by wen
Branch: MAIN
CVS Tags: pkgsrc-2016Q2-base,
pkgsrc-2016Q2
Changes since 1.9: +2 -3
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Diff to previous 1.9 (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 (8 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
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Diff to previous 1.8 (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 (9 years, 4 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
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Diff to previous 1.7 (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 (10 years, 4 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
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Diff to previous 1.6 (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 (10 years, 8 months ago) by wen
Branch: MAIN
CVS Tags: pkgsrc-2013Q1-base,
pkgsrc-2013Q1
Changes since 1.5: +5 -3
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Diff to previous 1.5 (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 (11 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
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Diff to previous 1.4 (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 (14 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
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Diff to previous 1.3 (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 (17 years, 3 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
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Diff to previous 1.2 (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 (17 years, 8 months ago) by joerg
Branch: MAIN
CVS Tags: pkgsrc-2006Q2-base,
pkgsrc-2006Q2,
pkgsrc-2006Q1-base,
pkgsrc-2006Q1
Changes since 1.1: +2 -1
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Diff to previous 1.1 (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 (17 years, 11 months ago) by rillig
Branch: TNF
CVS Tags: pkgsrc-base,
pkgsrc-2005Q4-base,
pkgsrc-2005Q4
Changes since 1.1: +0 -0
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Diff to previous 1.1 (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 (17 years, 11 months ago) by rillig
Branch: MAIN
Initial revision