[med-svn] samtools annotated tag 1.3-1_bpo8+1 created (now 1adda30)

Charles Plessy plessy at moszumanska.debian.org
Fri Feb 12 04:03:56 UTC 2016


This is an automated email from the git hooks/post-receive script.

plessy pushed a change to annotated tag 1.3-1_bpo8+1
in repository samtools.

        at  1adda30   (tag)
   tagging  7a28ed058f5add0214f721a11e36ad1fbc4ed7b6 (commit)
  replaces  1.3
 tagged by  Charles Plessy
        on  Fri Feb 12 13:03:31 2016 +0900

- Log -----------------------------------------------------------------
samtools (1.3-1~bpo8+1) jessie-backports; urgency=medium

  * Rebuild for jessie-backports.

 -- Charles Plessy <plessy at debian.org>  Fri, 12 Feb 2016 12:54:03 +0900
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Afif Elghraoui (10):
      Set up a new changelog entry
      Add patch to fix building on i386
      Remove source files not present in upstream tarball
      Allow all scripts to be called without language extensions
      Update changelog for 1.2-2 release
      Mark release and remove redundant changelog entry
      Revert "Allow all scripts to be called without language extensions"
      Revert "Remove source files not present in upstream tarball"
      Prepare for upload
      Prepare backport

Andreas Tille (9):
      debian/upstream: replace a perfectly valid BibTeX entry which happens to cause problems in the replacement algorith for the tasks pages written by Michael Banck
      Versioned Build-Depends libhts-dev >= 1.0
      Fix synopsis and vcs-browser
      Add lintian-override to document that the language extensions are used internally
      Fix spelling
      Mark as team upload since I do not intend to become Uploader for samtools
      Fix Mayhem issues caused by unlimited reads of gz input
      Provide some more manpages
      Upload to unstable

Charles Plessy (185):
      Imported Upstream version 0.1.5c
      Imported Debian patch 0.1.5c-1
      Imported Debian patch 0.1.5c-2
      Merge branch 'upstream'
      Imported Upstream version 0.1.6~dfsg
      Imported Debian patch 0.1.6~dfsg-1
      Merge commit 'upstream/0.1.7.dfsg'
      Imported Upstream version 0.1.7~dfsg
      Update in preparation for new upstream release.
      Converted to the source format ‘3.0 (quilt)’.
      Imported Upstream version 0.1.7a~dfsg
      Merge commit 'upstream/0.1.7a.dfsg'
      Minor upstream update correcting a build failure.
      Simple manpage created with help2man.
      Tidied the minimalistic razip.1 manual page.
      Uploaded package after misc. improvements.
      In version 1.8, there are no binary files to remove from the upstream tarball.
      Imported Upstream version 0.1.8
      Merge commit 'upstream/0.1.8'
      The 1.8 tarball does not contain Windows binaries anymore.
      Copyright notice bureaucracy.
      This source package is managed with Git since upstream version 1.7~dfsg.
      Copied from SVN revision 4710 and adapted to Git.
      New upstream release, with among many changes a new python script.
      Added notes on how the package is tested.
      Merge commit 'upstream/0.1.9'
      Imported Upstream version 0.1.9
      # New files in the new upstream release.
      # Updated and reformatted debian/copyright according to latest DEP-5 draft.
      # Incremented Standards-Version to reflect conformance with Policy 3.9.1.
      # Install bcftools, its manpage, bcf-fix.pl, vcfutils.pl, and new examples.
      # New upstream release, and new program: bcftools.
      Imported Upstream version 0.1.10
      Merge commit 'upstream/0.1.10'
      # New upstream release.
      Imported Upstream version 0.1.11
      Merge commit 'upstream/0.1.11'
      Imported Upstream version 0.1.12a
      Merge commit 'upstream/0.1.12a'
      # New usptream release; no change for licenses or copyrights.
      # Use bzip2 compression for the binary packages and raised DH compat level.
      # Uploaded 0.1.12a-1 to Debian.
      # Install the manual page of bcftools.
      Merge commit 'upstream/0.1.13'
      Imported Upstream version 0.1.13
      # Copyright review of the diff between 0.1.12 and 0.1.13.
      # bcftools/bcf-fix.pl removed upstream.
      # Uploaded 0.1.13 to Sid.
      Merge commit 'upstream/0.1.14'
      Imported Upstream version 0.1.14
      # New upstream release (new copyright notices and licenses proofchecked).
      # Uploaded samtools version 0.1.14-1.
      Merge commit 'upstream/0.1.15'
      Imported Upstream version 0.1.15
      New upstream release (no new copyright notices).
      Uploaded 0.1.15-1 to Sid.
      Imported Upstream version 0.1.16
      Merge commit 'upstream/0.1.16'
      New upstream release, introducing two files with new copyright statements.
      Added a configuration file to make it obvious git-buildpackage is used.
      Distribute transiently sam.h in /usr/include.
      Move the headers to /usr/include/samtools.
      Uploaded samtools_0.1.16-1_amd64.changes.
      Imported Upstream version 0.1.17
      Merge commit 'upstream/0.1.17'
      New upstream release (no new copyright holder nor license statement).
      bcftools.1 and samtools.1 were merged in upstream release 0.1.17.
      Patched the example makefile to not use samtools pileup, deprecated.
      Uploading samtools_0.1.17-1_amd64.changes.
      Imported Upstream version 0.1.18
      Merge commit 'upstream/0.1.18'
      New upstream release.
      Compress binary packages with xz.
      Added a DEP 3 header to debian/patches/no-pileup-tests.patch.
      Uploading 0.1.18-1 to unstable.
      Starting the work on next package update.
      Mention ‘SAMtools’ in libbam-dev's description, to make it easier to find with apt-cache.
      Do not compress the example binary alignment file.
      Renamed debian/upstream-metadata.yaml to debian/upstream.
      Moved DOI and PubMed to the Reference namespace.
      Pass build flaggs set by dpkg-buildflags via Debhelper.
      Build-depend on	Debhelper 9 (see e6882df5b3e4a66100acf69c8f0f213208d16c92).
      Bash completion, see https://github.com/arq5x/bash_completion.
      Normalised with config-model.
      Include 7 digits of the commit id in the changelog entry.
      Imported Upstream version 0.1.19
      Merge tag 'upstream/0.1.19'
      New upstream release, no new license nor copyright statements.
      Binary files (re-)introduced by the update.
      Collapsed copyright notices from main holders.
      Normalised with cme (from the libconfig-model-perl package).
      Deleted DM-Upload-Allowed field.
      Conforms to Policy version 3.9.4.
      Removed fix_float_tag.patch, corrected upstream.
      Refreshed patches.
      Rename no-pileup-tests.patch fix_example_makefile.patch.
      Pass -lpthread when compiling calDepth.
      Harden by concatenating Debian's LDFLAGS and CPPFLAGS in CFLAGS.
      Moved to GitHub.
      New tools ace2sam, bamcheck, plot-bamcheck, r2plot.lua and vcfutils.lua.
      URL to the latest upstream changelog.
      Normalised VCS URLs.
      Use NEWS as upstream changelog.
      samtools (0.1.19-1) unstable; urgency=low
      Also track release candidates.
      This package uses pristine-tar, and does not follow the canonical layout of git-buildpackage.
      Merge branch 'develop' into debian/unstable
      New upstream release candidate.
      Disable patches for the moment.
      Stop depending on CDBS and quilt.
      Use the single-debian-patch option.
      Stop providing the static libbam, replaced by the dynamic libhts.
      razip was removed from samtools.
      Breaks and replace tabix for the bgzip program.
      Rely on the new upstream Makefile.
      Merge branch 'develop' into debian/unstable
      Updated changelog.
      Merge branch 'master' into debian/unstable
      Merge branch 'debian/unstable' of git+ssh://git.debian.org/git/debian-med/samtools into debian/unstable
      Build-depend on tabix for the regression tests, that use bgzip.
      Adjust for dynamic linking.
      Indicate path to packaged bgzip.
      Mimick Makefile's CPPFLAGS.
      Create a test package for the test data.
      Current changelog.
      Close #544976, about libbam being built with -fPIC, since libbam is dropped.
      Move back Homepage field where it belongs.
      Adjust install file for two-package build.
      No new copyright nor license notice.
      Conforms to Policy 3.9.5.
      Opened https://github.com/samtools/samtools/issues/284
      Refreshed for upstream version 1.0.
      Re-enable fix_coverage_cap.patch.
      Drop patch for file that was dropped.
      Refreshed to for upstream version 1.0.
      Sent pull request.
      New homepage.
      Re-enable fix_segfault_with_small_ref.patch after refreshing it.
      Temporary patch to build dynamically samtools.
      Allow parallel building.
      Clean before installing test files (this removes compiled files).
      Recommend python since samtools installs a python script in /usr/bin.
      One more small patch that I hope removing at the next upstream release.
      Current changelog.
      Branch to build packages for Experimental.
      samtools (1.0-1~experimental) experimental; urgency=low
      Merge branch 'debian/experimental' into debian/unstable
      Prevent Makefile from including local copy of the HTSlib.
      Build for Unstable.
      Build-depend on libhts-dev...
      Current changelog.
      Conforms with Policy 3.5.6.
      samtools (1.0-1) unstable; urgency=low
      Add autopkg tests.
      Current changelog.
      Merge tag '1.1' into debian/unstable
      Merge branch 'develop' into debian/unstable
      Removed python-wrong-path-for-interpreter.patch, solved upstream.
      Removed sed command redundant with patch dynamic-build.patch.
      samtools (1.1-1) unstable; urgency=medium
      Build-depend and recommend libio-pty-perl for the regression tests.
      Current changelog.
      Make autopkg test depend on tabix.
      Merge tag '1.2' into debian/unstable
      New upstream release ; no new copyright notice nor license term.
      Corrected syntax.
      Removed fix_coverage_cap.patch, obsoleted by -d option.
      Refreshed fuzzy patches.
      Build-depend on libhts-dev 1.2.
      Current changelog.
      Revert last commit, that included patched files by mistake.
      Current changelog.
      samtools (1.2-1) unstable; urgency=medium
      Revert "Remove source files not present in upstream tarball"
      Note that this source package is managed like htslib.
      samtools (1.2-2) unstable; urgency=medium
      Update GBP configuration for jessie-backport branch.
      Merge branch 'debian/unstable' of git+ssh://git.debian.org/git/debian-med/samtools into debian/unstable
      Merge tag '1.3' into debian/unstable
      New upstream release; no new copyright nor license notice.
      Replace LDLIBS by LIBS, following upstream changelog.
      Removed patch; issue solved upstream.
      Removed patch; issue solved upstream.
      Merge branch 'debian/unstable' into debian/jessie-backports
      samtools (1.3-1~bpo8+1) jessie-backports; urgency=medium

Dominique Belhachemi (1):
      added 3 bug fixes

James McCoy (1):
      Move debian/upstream to debian/upstream/metadata

Sascha Steinbiss (10):
      adapt to new build system
      use secure Vcs-Git
      patch configure.in to not call make in m4_esyscmd_s()
      add Build-Dep to automake
      cleanup copyright
      add patch header
      patch spelling
      update d/changelog
      add NEWS for 1.3 commandline API changes
      dch -r

-----------------------------------------------------------------------

This annotated tag includes the following new commits:

       new  24274e5   Merge branch 'debian/unstable' into debian/jessie-backports
       new  7a28ed0   samtools (1.3-1~bpo8+1) jessie-backports; urgency=medium

The 2 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


-- 
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