Bug 205525 - biology/samtools: Update to 1.3
Summary: biology/samtools: Update to 1.3
Status: Closed FIXED
Alias: None
Product: Ports & Packages
Classification: Unclassified
Component: Individual Port(s) (show other bugs)
Version: Latest
Hardware: Any Any
: --- Affects Some People
Assignee: Jason Unovitch
URL:
Keywords: easy, patch, patch-ready
Depends on: 205524
Blocks:
  Show dependency tree / graph
 
Reported: 2015-12-22 23:23 UTC by cartwright
Modified: 2015-12-25 01:33 UTC (History)
1 user (show)

See Also:
cartwright: maintainer-feedback+

Attachments
patch to upgrade biology/samtools to 1.3 (41.45 KB, text/plain)
2015-12-22 23:23 UTC, cartwright 		vlad-fbsd: maintainer-approval+
Details
poudriere testport output for releng_10_2 (31.37 KB, text/plain)
2015-12-22 23:24 UTC, cartwright 		no flags Details
poudriere testport output for releng_9_3 (29.53 KB, text/plain)
2015-12-22 23:24 UTC, cartwright 		no flags Details
View All Add an attachment (proposed patch, testcase, etc.)

Note You need to log in before you can comment on or make changes to this bug.
Description cartwright 2015-12-22 23:23:55 UTC 
Created attachment 164514 [details]
patch to upgrade biology/samtools to 1.3

Update biology/samtools to version 1.3.

Requires biology/htslib v1.3 (https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=205524)
Comment 1 cartwright 2015-12-22 23:24:20 UTC 
Created attachment 164515 [details]
poudriere testport output for releng_10_2
Comment 2 cartwright 2015-12-22 23:24:41 UTC 
Created attachment 164517 [details]
poudriere testport output for releng_9_3
Comment 3 commit-hook freebsd_committer freebsd_triage 2015-12-25 01:32:06 UTC 
A commit references this bug:

Author: junovitch
Date: Fri Dec 25 01:31:11 UTC 2015
New revision: 404398
URL: https://svnweb.freebsd.org/changeset/ports/404398

Log:
  biology/{bcftools,htslib,samtools}: update 1.2.x -> 1.3

  - Update ports to 1.3 and set BUILD_DEPENDS of dependent ports to require
    version 1.3 of htslib.
  - Add CURL option to htslib
  - Add TEST_TARGET with perl and bash dependencies for testing
  - Tidy up spacing and pkg-message's

  PR:		205524
  PR:		205525
  PR:		205526
  Submitted by:	cartwright@asu.edu (maintainer)

Changes:
  head/biology/bcftools/Makefile
  head/biology/bcftools/distinfo
  head/biology/bcftools/files/patch-Makefile
  head/biology/bcftools/files/patch-plugins_fixploidy.mk
  head/biology/bcftools/files/patch-plugins_vcf2sex.mk
  head/biology/bcftools/files/patch-prob1.c
  head/biology/bcftools/files/patch-test_test.pl
  head/biology/bcftools/files/pkg-message.in
  head/biology/bcftools/pkg-plist
  head/biology/htslib/Makefile
  head/biology/htslib/distinfo
  head/biology/htslib/files/patch-Makefile
  head/biology/htslib/files/patch-configure.ac
  head/biology/htslib/files/patch-cram_cram__io.c
  head/biology/htslib/files/patch-hfile__libcurl.c
  head/biology/htslib/pkg-plist
  head/biology/samtools/Makefile
  head/biology/samtools/distinfo
  head/biology/samtools/files/ax_with_curses.m4
  head/biology/samtools/files/ax_with_htslib.m4
  head/biology/samtools/files/patch-Makefile
  head/biology/samtools/files/patch-configure.ac
  head/biology/samtools/files/patch-dict.c
  head/biology/samtools/files/patch-errmod.c
  head/biology/samtools/files/patch-test_test.pl
  head/biology/samtools/files/pkg-message.in
  head/biology/samtools/pkg-plist
Comment 4 Jason Unovitch freebsd_committer freebsd_triage 2015-12-25 01:33:54 UTC 
Committed. Thanks!