Bug 223094 - biology/htslib biology/samtools biology/bcftools: update to 1.6
Summary: biology/htslib biology/samtools biology/bcftools: update to 1.6
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: Luca Pizzamiglio
URL:
Keywords:
Depends on:
Blocks:
 
Reported: 2017-10-18 14:03 UTC by Motomichi Matsuzaki
Modified: 2017-10-25 10:21 UTC (History)
3 users (show)

See Also:
cartwright: maintainer-feedback+

Attachments
svn diff for biology/htslib (6.14 KB, patch)
2017-10-18 14:04 UTC, Motomichi Matsuzaki 		no flags Details | Diff
svn diff for biology/samtools (38.20 KB, patch)
2017-10-18 14:04 UTC, Motomichi Matsuzaki 		no flags Details | Diff
svn diff for biology/bcftools (11.61 KB, patch)
2017-10-18 14:05 UTC, Motomichi Matsuzaki 		no flags Details | Diff
View All Add an attachment (proposed patch, testcase, etc.)

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Description Motomichi Matsuzaki 2017-10-18 14:03:42 UTC 
Update the following ports to 1.6

biology/htslib
biology/samtools
biology/bcftools

common changes:
* using predefined BSD_INSTALL_* macros in ${WRKSRC}/Makefile rather than providing INSTALL_* macros via MAKE_ENV in Makefile
* @PORTVERSION@ substitution is no longer required for htslib&samtools
* to adjust shebangs in python scripts (for samtools&bcftools)

changes to htslib:
* to respect ${PREFIX} in ${WRKSRC}/Makefile

changes to bcftools:
* @PORTVERSION@ substitution is now required

All ports passed make test & poudriere testport in my environment (10.3 amd64).
Comment 1 Motomichi Matsuzaki 2017-10-18 14:04:24 UTC 
Created attachment 187279 [details]
svn diff for biology/htslib
Comment 2 Motomichi Matsuzaki 2017-10-18 14:04:52 UTC 
Created attachment 187280 [details]
svn diff for biology/samtools
Comment 3 Motomichi Matsuzaki 2017-10-18 14:05:16 UTC 
Created attachment 187281 [details]
svn diff for biology/bcftools
Comment 4 cartwright 2017-10-18 19:15:33 UTC 
Patch looks good. I haven't run poudriere on my Freebsd-11 machine, but will try to do that soon.
Comment 5 commit-hook freebsd_committer freebsd_triage 2017-10-25 10:20:25 UTC 
A commit references this bug:

Author: pizzamig
Date: Wed Oct 25 10:19:52 UTC 2017
New revision: 452840
URL: https://svnweb.freebsd.org/changeset/ports/452840

Log:
  biology/htslib biology/bcftools biology/samtools: Update to 1.6

  PR:		223094
  Submitted by:	mzaki@niid.go.jp
  Approved by:	cartwright@asu.edu (maintainer)
  Approved by:	olivier (mentor)
  Differential Revision:	https://reviews.freebsd.org/D12768

Changes:
  head/biology/bcftools/Makefile
  head/biology/bcftools/distinfo
  head/biology/bcftools/files/patch-Makefile
  head/biology/bcftools/files/patch-configure.ac
  head/biology/bcftools/files/patch-misc_run-roh.pl
  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-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
Comment 6 Luca Pizzamiglio freebsd_committer freebsd_triage 2017-10-25 10:21:36 UTC 
Thanks!