[med-svn] r20154 - in trunk/packages/vsearch/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Tue Sep 29 07:09:41 UTC 2015
Author: tille
Date: 2015-09-29 07:09:40 +0000 (Tue, 29 Sep 2015)
New Revision: 20154
Removed:
trunk/packages/vsearch/trunk/debian/patches/fix_build_issue_on_hurd.patch
trunk/packages/vsearch/trunk/debian/patches/fix_optimisation_flags.patch
trunk/packages/vsearch/trunk/debian/patches/hardening.patch
trunk/packages/vsearch/trunk/debian/patches/x86_spezific_opts.patch
trunk/packages/vsearch/trunk/debian/vsearch-data.lintian-overrides
trunk/packages/vsearch/trunk/debian/vsearch.links
Modified:
trunk/packages/vsearch/trunk/debian/changelog
trunk/packages/vsearch/trunk/debian/control
trunk/packages/vsearch/trunk/debian/copyright
trunk/packages/vsearch/trunk/debian/patches/series
trunk/packages/vsearch/trunk/debian/patches/sysconf_memory_sizing.patch
trunk/packages/vsearch/trunk/debian/rules
trunk/packages/vsearch/trunk/debian/vsearch-data.install
trunk/packages/vsearch/trunk/debian/vsearch.docs
trunk/packages/vsearch/trunk/debian/vsearch.install
trunk/packages/vsearch/trunk/debian/vsearch.manpages
trunk/packages/vsearch/trunk/debian/watch
Log:
New upstream version with strong simplifications for packaging
Modified: trunk/packages/vsearch/trunk/debian/changelog
===================================================================
--- trunk/packages/vsearch/trunk/debian/changelog 2015-09-28 13:54:04 UTC (rev 20153)
+++ trunk/packages/vsearch/trunk/debian/changelog 2015-09-29 07:09:40 UTC (rev 20154)
@@ -1,3 +1,9 @@
+vsearch (1.4.0-1) UNRELEASED; urgency=medium
+
+ * New upstream version (no need to exclude files any more)
+
+ -- Andreas Tille <tille at debian.org> Mon, 28 Sep 2015 18:05:27 +0200
+
vsearch (1.1.3+dfsg-1) unstable; urgency=medium
* New upstream version
Modified: trunk/packages/vsearch/trunk/debian/control
===================================================================
--- trunk/packages/vsearch/trunk/debian/control 2015-09-28 13:54:04 UTC (rev 20153)
+++ trunk/packages/vsearch/trunk/debian/control 2015-09-29 07:09:40 UTC (rev 20154)
@@ -4,7 +4,14 @@
Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 9), zlib1g-dev, libbz2-dev, python-markdown, time
+Build-Depends: debhelper (>= 9),
+ dh-autoreconf,
+ zlib1g-dev,
+ libbz2-dev,
+ libssl-dev,
+ python-markdown,
+ ghostscript,
+ time
Standards-Version: 3.9.6
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/vsearch/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/vsearch/trunk/
@@ -49,4 +56,3 @@
- be as fast or faster than usearch
.
This package only contains data to run the vsearch test suite.
-
Modified: trunk/packages/vsearch/trunk/debian/copyright
===================================================================
--- trunk/packages/vsearch/trunk/debian/copyright 2015-09-28 13:54:04 UTC (rev 20153)
+++ trunk/packages/vsearch/trunk/debian/copyright 2015-09-29 07:09:40 UTC (rev 20154)
@@ -2,15 +2,6 @@
Upstream-Name: VSEARCH
Upstream-Contact: Torbjørn Rognes <torognes at ifi.uio.no>
Source: https://github.com/torognes/vsearch/
-Files-Excluded: bin/*
- data/BioMarKs.fsa.gz
- data/PR2-18S-rRNA-V4.fsa
-Comment: data/BioMarKs.fsa.gz has the very same content as
- data/BioMarKs.fsa.bz2 but just a different compression method.
- To save disk space the former is deleted from source tarball and
- recreated in the test target where it is needed.
- The same is true for data/PR2-18S-rRNA-V4.fsa which is just
- an uncompressed copy of data/PR2-18S-rRNA-V4.fsa.bz2
Files: *
Copyright: © 2014-2015 Torbjorn Rognes <torognes at ifi.uio.no>,
Deleted: trunk/packages/vsearch/trunk/debian/patches/fix_build_issue_on_hurd.patch
===================================================================
--- trunk/packages/vsearch/trunk/debian/patches/fix_build_issue_on_hurd.patch 2015-09-28 13:54:04 UTC (rev 20153)
+++ trunk/packages/vsearch/trunk/debian/patches/fix_build_issue_on_hurd.patch 2015-09-29 07:09:40 UTC (rev 20154)
@@ -1,18 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Changed: Mon, 02 Feb 2015 07:40:07 +0100
-Bugs-Debian: http://bugs.debian.org/776815
-Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2015-February/031414.html
-Description: Fix build issue on Hurd which does not harm anywhere else
-
---- a/src/vsearch.h
-+++ b/src/vsearch.h
-@@ -20,7 +20,9 @@
- */
-
- #include <sys/types.h>
-+#ifdef __APPLE__
- #include <sys/sysctl.h>
-+#endif
- #include <sys/stat.h>
- #include <sys/time.h>
- #include <sys/resource.h>
Deleted: trunk/packages/vsearch/trunk/debian/patches/fix_optimisation_flags.patch
===================================================================
--- trunk/packages/vsearch/trunk/debian/patches/fix_optimisation_flags.patch 2015-09-28 13:54:04 UTC (rev 20153)
+++ trunk/packages/vsearch/trunk/debian/patches/fix_optimisation_flags.patch 2015-09-29 07:09:40 UTC (rev 20154)
@@ -1,39 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Changed: Mon, 02 Feb 2015 07:40:07 +0100
-Bugs-Debian: http://bugs.debian.org/776812
-Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2015-February/031414.html
-Description: Drop -msse2 flag
-
---- a/src/Makefile.BZLIB
-+++ b/src/Makefile.BZLIB
-@@ -27,7 +27,7 @@ WARN=-Wall -Wsign-compare
- #WARN=-Weverything
-
- CXX=g++
--CXXFLAGS=-O3 -DHAVE_BZLIB -msse2 -mtune=core2 -Icityhash $(WARN) $(PROFILING)
-+CXXFLAGS=-O3 -DHAVE_BZLIB -mtune=core2 -Icityhash $(WARN) $(PROFILING)
- LINKFLAGS=$(PROFILING)
- LIBS=-lpthread -lbz2
-
---- a/src/Makefile.ZLIB
-+++ b/src/Makefile.ZLIB
-@@ -27,7 +27,7 @@ WARN=-Wall -Wsign-compare
- #WARN=-Weverything
-
- CXX=g++
--CXXFLAGS=-O3 -DHAVE_ZLIB -msse2 -mtune=core2 -Icityhash $(WARN) $(PROFILING)
-+CXXFLAGS=-O3 -DHAVE_ZLIB -mtune=core2 -Icityhash $(WARN) $(PROFILING)
- LINKFLAGS=$(PROFILING)
- LIBS=-lpthread -lz
-
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -27,7 +27,7 @@ WARN=-Wall -Wsign-compare
- #WARN=-Weverything
-
- CXX=g++
--CXXFLAGS=-O3 -msse2 -mtune=core2 -Icityhash $(WARN) $(PROFILING)
-+CXXFLAGS=-O3 -mtune=core2 -Icityhash $(WARN) $(PROFILING)
- LINKFLAGS=$(PROFILING)
- LIBS=-lpthread
-
Deleted: trunk/packages/vsearch/trunk/debian/patches/hardening.patch
===================================================================
--- trunk/packages/vsearch/trunk/debian/patches/hardening.patch 2015-09-28 13:54:04 UTC (rev 20153)
+++ trunk/packages/vsearch/trunk/debian/patches/hardening.patch 2015-09-29 07:09:40 UTC (rev 20154)
@@ -1,38 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Changed: Wed, 14 Jan 2015 10:40:22 +0000
-Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2015-February/031414.html
-Description: Propagate hardening options
-
---- a/src/Makefile.BZLIB
-+++ b/src/Makefile.BZLIB
-@@ -34,7 +34,7 @@ endif
-
- CXX=g++
- CXXFLAGS=-O3 -DHAVE_BZLIB $(MTUNE) -Icityhash $(WARN) $(PROFILING)
--LINKFLAGS=$(PROFILING)
-+LINKFLAGS=$(PROFILING) $(LDFLAGS)
- LIBS=-lpthread -lbz2
-
- PROG=vsearch-bz
---- a/src/Makefile.ZLIB
-+++ b/src/Makefile.ZLIB
-@@ -34,7 +34,7 @@ endif
-
- CXX=g++
- CXXFLAGS=-O3 -DHAVE_ZLIB $(MTUNE) -Icityhash $(WARN) $(PROFILING)
--LINKFLAGS=$(PROFILING)
-+LINKFLAGS=$(PROFILING) $(LDFLAGS)
- LIBS=-lpthread -lz
-
- PROG=vsearch-gz
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -34,7 +34,7 @@ endif
-
- CXX=g++
- CXXFLAGS=-O3 $(MTUNE) -Icityhash $(WARN) $(PROFILING)
--LINKFLAGS=$(PROFILING)
-+LINKFLAGS=$(PROFILING) $(LDFLAGS)
- LIBS=-lpthread
-
- PROG=vsearch
Modified: trunk/packages/vsearch/trunk/debian/patches/series
===================================================================
--- trunk/packages/vsearch/trunk/debian/patches/series 2015-09-28 13:54:04 UTC (rev 20153)
+++ trunk/packages/vsearch/trunk/debian/patches/series 2015-09-29 07:09:40 UTC (rev 20154)
@@ -1,4 +1 @@
-fix_optimisation_flags.patch
-x86_spezific_opts.patch
-hardening.patch
sysconf_memory_sizing.patch
Modified: trunk/packages/vsearch/trunk/debian/patches/sysconf_memory_sizing.patch
===================================================================
--- trunk/packages/vsearch/trunk/debian/patches/sysconf_memory_sizing.patch 2015-09-28 13:54:04 UTC (rev 20153)
+++ trunk/packages/vsearch/trunk/debian/patches/sysconf_memory_sizing.patch 2015-09-29 07:09:40 UTC (rev 20154)
@@ -9,7 +9,7 @@
--- a/src/arch.cc
+++ b/src/arch.cc
-@@ -21,6 +21,8 @@
+@@ -60,6 +60,8 @@
#include "vsearch.h"
@@ -18,8 +18,8 @@
unsigned long arch_get_memused()
{
struct rusage r_usage;
-@@ -63,7 +65,15 @@ unsigned long arch_get_memtotal()
- if(-1 == sysctl(mib, 2, &ram, &length, NULL, 0))
+@@ -92,7 +94,15 @@ unsigned long arch_get_memtotal()
+ if(sysctl(mib, 2, &ram, &length, NULL, 0) == -1)
fatal("Cannot determine amount of RAM");
return ram;
-
Deleted: trunk/packages/vsearch/trunk/debian/patches/x86_spezific_opts.patch
===================================================================
--- trunk/packages/vsearch/trunk/debian/patches/x86_spezific_opts.patch 2015-09-28 13:54:04 UTC (rev 20153)
+++ trunk/packages/vsearch/trunk/debian/patches/x86_spezific_opts.patch 2015-09-29 07:09:40 UTC (rev 20154)
@@ -1,60 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Changed: Mon, 02 Feb 2015 07:40:07 +0100
-Bugs-Debian: http://bugs.debian.org/776812
-Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2015-February/031414.html
-Description: Conditional use of -mtune flag
-
---- a/src/Makefile.BZLIB
-+++ b/src/Makefile.BZLIB
-@@ -26,8 +26,14 @@ PROFILING=-g
- WARN=-Wall -Wsign-compare
- #WARN=-Weverything
-
-+ifeq ($(USEOPT),no)
-+ MTUNE:=
-+else
-+ MTUNE:=-mtune=core2
-+endif
-+
- CXX=g++
--CXXFLAGS=-O3 -DHAVE_BZLIB -mtune=core2 -Icityhash $(WARN) $(PROFILING)
-+CXXFLAGS=-O3 -DHAVE_BZLIB $(MTUNE) -Icityhash $(WARN) $(PROFILING)
- LINKFLAGS=$(PROFILING)
- LIBS=-lpthread -lbz2
-
---- a/src/Makefile.ZLIB
-+++ b/src/Makefile.ZLIB
-@@ -26,8 +26,14 @@ PROFILING=-g
- WARN=-Wall -Wsign-compare
- #WARN=-Weverything
-
-+ifeq ($(USEOPT),no)
-+ MTUNE:=
-+else
-+ MTUNE:=-mtune=core2
-+endif
-+
- CXX=g++
--CXXFLAGS=-O3 -DHAVE_ZLIB -mtune=core2 -Icityhash $(WARN) $(PROFILING)
-+CXXFLAGS=-O3 -DHAVE_ZLIB $(MTUNE) -Icityhash $(WARN) $(PROFILING)
- LINKFLAGS=$(PROFILING)
- LIBS=-lpthread -lz
-
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -26,8 +26,14 @@ PROFILING=-g
- WARN=-Wall -Wsign-compare
- #WARN=-Weverything
-
-+ifeq ($(USEOPT),no)
-+ MTUNE:=
-+else
-+ MTUNE:=-mtune=core2
-+endif
-+
- CXX=g++
--CXXFLAGS=-O3 -mtune=core2 -Icityhash $(WARN) $(PROFILING)
-+CXXFLAGS=-O3 $(MTUNE) -Icityhash $(WARN) $(PROFILING)
- LINKFLAGS=$(PROFILING)
- LIBS=-lpthread
-
Modified: trunk/packages/vsearch/trunk/debian/rules
===================================================================
--- trunk/packages/vsearch/trunk/debian/rules 2015-09-28 13:54:04 UTC (rev 20153)
+++ trunk/packages/vsearch/trunk/debian/rules 2015-09-29 07:09:40 UTC (rev 20154)
@@ -19,33 +19,17 @@
endif
%:
- dh $@ --sourcedirectory=src
+ dh $@ --with autoreconf
override_dh_auto_build:
- # See notes in README.source
- dh_auto_build -- -f Makefile.BZLIB USEOPT="$(USEOPT)"
- dh_auto_clean
- dh_auto_build -- -f Makefile.ZLIB USEOPT="$(USEOPT)"
- dh_auto_clean
dh_auto_build
markdown_py -f README.html README.md
- markdown_py -f data/README.html data/README.md
-override_dh_auto_clean:
- dh_auto_clean
- rm -f src/vsearch-gz src/vsearch-bz
-
override_dh_auto_test:
- # restore data files from original tarball as well as those files needed for the full testsuite
- cd data && bunzip2 --keep BioMarKs.fsa.bz2 && gzip --keep --rsyncable BioMarKs.fsa
- cd data && bunzip2 --keep PR2-18S-rRNA-V4.fsa.bz2 && gzip --keep --rsyncable PR2-18S-rRNA-V4.fsa
- cd data && tar -xvzf simm.tar.gz
cd test && \
for t in *.sh ; do \
bash $$t v ; \
done
- rm -f data/BioMarKs.fsa data/BioMarKs.fsa.gz \
- data/PR2-18S-rRNA-V4.fsa data/PR2-18S-rRNA-V4.fsa.gz
override_dh_clean:
dh_clean
@@ -63,9 +47,3 @@
mkdir -p $(testdir)/test
for tst in test/*.sh ; do sed 's?\.\./src/vsearch?/usr/bin/vsearch?' $${tst} > $(testdir)/$${tst} ; done
-override_dh_compress:
- for f in $(exampledir)/*.fsa $(exampledir)/*.fasta ; do xz --best $$f ; done
- dh_compress --exclude=.xz
-
-get-orig-source:
- uscan --verbose --force-download --repack --compression xz
Modified: trunk/packages/vsearch/trunk/debian/vsearch-data.install
===================================================================
--- trunk/packages/vsearch/trunk/debian/vsearch-data.install 2015-09-28 13:54:04 UTC (rev 20153)
+++ trunk/packages/vsearch/trunk/debian/vsearch-data.install 2015-09-29 07:09:40 UTC (rev 20154)
@@ -1,9 +1,2 @@
-data/simm.tar.gz usr/share/doc/vsearch/examples
-data/BioMarKs50k.fsa usr/share/doc/vsearch/examples
-data/BioMarKs.fsa.* usr/share/doc/vsearch/examples
-data/PR2-18S-rRNA-V4* usr/share/doc/vsearch/examples
-data/Rfam_11_0.* usr/share/doc/vsearch/examples
-data/Rfam_9_1.fasta usr/share/doc/vsearch/examples
-data/README.html usr/share/doc/vsearch/examples
eval/*.pl usr/share/doc/vsearch/tests/eval
eval/*.txt usr/share/doc/vsearch/tests/eval
Deleted: trunk/packages/vsearch/trunk/debian/vsearch-data.lintian-overrides
===================================================================
--- trunk/packages/vsearch/trunk/debian/vsearch-data.lintian-overrides 2015-09-28 13:54:04 UTC (rev 20153)
+++ trunk/packages/vsearch/trunk/debian/vsearch-data.lintian-overrides 2015-09-29 07:09:40 UTC (rev 20154)
@@ -1,2 +0,0 @@
-# This is just a copy from upstream gzipped file which will not change in packaging process
-vsearch-data: package-contains-timestamped-gzip usr/share/doc/vsearch/examples/simm.tar.gz
Modified: trunk/packages/vsearch/trunk/debian/vsearch.docs
===================================================================
--- trunk/packages/vsearch/trunk/debian/vsearch.docs 2015-09-28 13:54:04 UTC (rev 20153)
+++ trunk/packages/vsearch/trunk/debian/vsearch.docs 2015-09-29 07:09:40 UTC (rev 20154)
@@ -1,3 +1,3 @@
*.html
-doc/*.pdf
+man/*.pdf
debian/tests/run-unit-test
Modified: trunk/packages/vsearch/trunk/debian/vsearch.install
===================================================================
--- trunk/packages/vsearch/trunk/debian/vsearch.install 2015-09-28 13:54:04 UTC (rev 20153)
+++ trunk/packages/vsearch/trunk/debian/vsearch.install 2015-09-29 07:09:40 UTC (rev 20154)
@@ -1,3 +1 @@
-src/vsearch /usr/bin
-src/vsearch-gz /usr/bin
-src/vsearch-bz /usr/bin
+bin/vsearch
Deleted: trunk/packages/vsearch/trunk/debian/vsearch.links
===================================================================
--- trunk/packages/vsearch/trunk/debian/vsearch.links 2015-09-28 13:54:04 UTC (rev 20153)
+++ trunk/packages/vsearch/trunk/debian/vsearch.links 2015-09-29 07:09:40 UTC (rev 20154)
@@ -1,2 +0,0 @@
-usr/share/man/man1/vsearch.1.gz usr/share/man/man1/vsearch-bz.1.gz
-usr/share/man/man1/vsearch.1.gz usr/share/man/man1/vsearch-gz.1.gz
Modified: trunk/packages/vsearch/trunk/debian/vsearch.manpages
===================================================================
--- trunk/packages/vsearch/trunk/debian/vsearch.manpages 2015-09-28 13:54:04 UTC (rev 20153)
+++ trunk/packages/vsearch/trunk/debian/vsearch.manpages 2015-09-29 07:09:40 UTC (rev 20154)
@@ -1 +1 @@
-doc/*.1
+man/*.1
Modified: trunk/packages/vsearch/trunk/debian/watch
===================================================================
--- trunk/packages/vsearch/trunk/debian/watch 2015-09-28 13:54:04 UTC (rev 20153)
+++ trunk/packages/vsearch/trunk/debian/watch 2015-09-29 07:09:40 UTC (rev 20154)
@@ -1,4 +1,4 @@
version=3
-opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,downloadurlmangle=s/\/tree\/(.*)/\/archive\/$1.tar.gz/" \
+opts="downloadurlmangle=s/\/tree\/(.*)/\/archive\/$1.tar.gz/" \
https://github.com/torognes/vsearch/releases .*/archive/v([0-9.rc-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
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