[med-svn] samtools annotated tag debian/1.0-1_experimental created (now 94e72dd)
Charles Plessy
plessy at moszumanska.debian.org
Sat Aug 23 07:20:40 UTC 2014
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to annotated tag debian/1.0-1_experimental
in repository samtools.
at 94e72dd (tag)
tagging 9be38118d45c2819cc672043f9b9be8ed771a9bd (commit)
replaces 1.0
tagged by Charles Plessy
on Sat Aug 23 16:20:06 2014 +0900
- Log -----------------------------------------------------------------
samtools (1.0-1~experimental) experimental; urgency=low
54ca0c1 Merge with upstream's develop branch.
241a731 razip was removed from samtools.
dc25b81 debian/watch: also track release candidates.
07aaf71 Indicate repository layout in git-buildpackage conf. file.
* debian/control
8bc0fb7 Stop depending on CDBS and quilt.
e613142 Drop static libbam, replaced by the dynamic libhts (Closes: #544976).
b5f284c Build-depend on tabix for the regression tests, that use bgzip.
9febad6 Recommend python since samtools installs a python script in /usr/bin.
e6ad97f Conforms to Policy 3.9.5.
* New package samtools-test
7293cca Create a test package for the test data.
6bd7b89 Adjust install file for two-package build.
caff5f5 Clean before installing test files (this removes compiled files).
* debian/rules
c930cbb Use Debhelper instead of CDBS and rely on the new upstream Makefile.
845581d Adjust for dynamic linking.
d859052 Indicate path to packaged bgzip.
cb23517 Mimick Makefile's CPPFLAGS.
aee1c6c Allow parallel building.
* debian/patches
f73d764 d062687 Refreshed patches.
2c52f6a 61ac2c5 Forwarded patches on GitHub.
b8eb378 Dropped fix_example_makefile.patch, obsolete.
66079b9 Correct path to python interpreter.
218c1c1 Modify Makefile to facilitate dynamic linking.
-- Charles Plessy <plessy at debian.org> Sat, 23 Aug 2014 16:02:12 +0900
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Andreas Tille (1):
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
Charles Plessy (146):
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
Dominique Belhachemi (1):
added 3 bug fixes
James McCoy (1):
Move debian/upstream to debian/upstream/metadata
-----------------------------------------------------------------------
This annotated tag includes the following new commits:
new 14ef470 Re-enable fix_segfault_with_small_ref.patch after refreshing it.
new 218c1c1 Temporary patch to build dynamically samtools.
new aee1c6c Allow parallel building.
new caff5f5 Clean before installing test files (this removes compiled files).
new 9febad6 Recommend python since samtools installs a python script in /usr/bin.
new 66079b9 One more small patch that I hope removing at the next upstream release.
new 66e256b Current changelog.
new 5e83465 Branch to build packages for Experimental.
new 9be3811 samtools (1.0-1~experimental) experimental; urgency=low
The 9 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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