Author: plessy Date: 2012-05-28 02:07:14 +0000 (Mon, 28 May 2012) New Revision: 11031
Added: trunk/packages/mira/tags/3.4.0.1-3/ trunk/packages/mira/tags/3.4.0.1-3/debian/README.source trunk/packages/mira/tags/3.4.0.1-3/debian/changelog trunk/packages/mira/tags/3.4.0.1-3/debian/control trunk/packages/mira/tags/3.4.0.1-3/debian/rules Removed: trunk/packages/mira/tags/3.4.0.1-3/debian/README.source trunk/packages/mira/tags/3.4.0.1-3/debian/TODO trunk/packages/mira/tags/3.4.0.1-3/debian/changelog trunk/packages/mira/tags/3.4.0.1-3/debian/control trunk/packages/mira/tags/3.4.0.1-3/debian/rules Log: [svn-buildpackage] Tagging mira 3.4.0.1-3 Deleted: trunk/packages/mira/tags/3.4.0.1-3/debian/README.source =================================================================== --- trunk/packages/mira/trunk/debian/README.source 2012-05-27 15:34:20 UTC (rev 11022) +++ trunk/packages/mira/tags/3.4.0.1-3/debian/README.source 2012-05-28 02:07:14 UTC (rev 11031) @@ -1,27 +0,0 @@ -mira for Debian ---------------- - -debian/patches/read_default_constructor.patch: - - adding default constructor to class to circumvent error - read.C:45:28: error: uninitialized const ‘Read::REA_bposhashstat_default’ [-fpermissive] - ../../src/mira/read.H:159:10: note: ‘const struct Read::bposhashstat_t’ has no user-provided default constructor - -mira-3.4.0/doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf -was removed by a request from upstream. - - -- Steffen Moeller <[email protected]> Tue, 23 Aug 2011 22:56:50 +0200 - -Basic packaging seems fine. There are issues with the location of -Google's tcmalloc library. - - -- Charles Plessy <[email protected]> Sun, 5 Aug 2007 14:01:14 +0900 - Steffen Moeller <[email protected]> Fri, 04 Mar 2011 17:39:07 +0100 - -Further to the above, on Sid right now it looks like this should build fine with a -build dependency on libgoogle-perftools-dev and a runtime dependency on -libtcmalloc-minimal0. However, backporting this package to Lucid is a non-starter -so instead I've made it build against the runtime. - - -- Tim Booth <[email protected]> Thu, 18 Aug 2011 11:34:11 +0100 - Copied: trunk/packages/mira/tags/3.4.0.1-3/debian/README.source (from rev 11025, trunk/packages/mira/trunk/debian/README.source) =================================================================== --- trunk/packages/mira/tags/3.4.0.1-3/debian/README.source (rev 0) +++ trunk/packages/mira/tags/3.4.0.1-3/debian/README.source 2012-05-28 02:07:14 UTC (rev 11031) @@ -0,0 +1,19 @@ +mira for Debian +--------------- + +debian/patches/read_default_constructor.patch: + + adding default constructor to class to circumvent error + read.C:45:28: error: uninitialized const ‘Read::REA_bposhashstat_default’ [-fpermissive] + ../../src/mira/read.H:159:10: note: ‘const struct Read::bposhashstat_t’ has no user-provided default constructor + +mira-3.4.0/doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf +was removed by a request from upstream. + + -- Steffen Moeller <[email protected]> Tue, 23 Aug 2011 22:56:50 +0200 + +Basic packaging seems fine. There are issues with the location of +Google's tcmalloc library. + + -- Charles Plessy <[email protected]> Sun, 5 Aug 2007 14:01:14 +0900 + -- Steffen Moeller <[email protected]> Fri, 04 Mar 2011 17:39:07 +0100 Deleted: trunk/packages/mira/tags/3.4.0.1-3/debian/TODO =================================================================== --- trunk/packages/mira/trunk/debian/TODO 2012-05-27 15:34:20 UTC (rev 11022) +++ trunk/packages/mira/tags/3.4.0.1-3/debian/TODO 2012-05-28 02:07:14 UTC (rev 11031) @@ -1,3 +0,0 @@ -Maybe the mira package should be renamed mira-assembler, as there are other -software called Mira around, such as http://www.mirametrics.com/ (proprietary, -but...) Deleted: trunk/packages/mira/tags/3.4.0.1-3/debian/changelog =================================================================== --- trunk/packages/mira/trunk/debian/changelog 2012-05-27 15:34:20 UTC (rev 11022) +++ trunk/packages/mira/tags/3.4.0.1-3/debian/changelog 2012-05-28 02:07:14 UTC (rev 11031) @@ -1,96 +0,0 @@ -mira (3.4.0.1-3) UNRELEASED; urgency=low - - * debian/upstream: very small fix to prevent bibcheck warning - - -- Andreas Tille <[email protected]> Wed, 09 May 2012 09:38:21 +0200 - -mira (3.4.0.1-2) unstable; urgency=low - - [ Andreas Tille ] - * Remove two patches: - - read_default_constructor.patch which introduces a duplicate - bposhashstat_t() definition - - fix_duplicate_bposhashstat_t_definition.patch which removes - this duplicate afterwards - - [ Charles Plessy ] - * Removed unconditional dependency on libtcmalloc-minimal0 (debian/control). - Closes: #654884 - * Machine-readable debian/copyright file. - - -- Charles Plessy <[email protected]> Sat, 07 Jan 2012 13:24:48 +0900 - -mira (3.4.0.1-1) unstable; urgency=low - - * New upstream version - Closes: #648762 (at least if I'm not mislead - feel free to reopen) - * debian/control: - - Added myself to Uploaders - - Depends: libtcmalloc-minimal0 [i386 amd64] - Thanks for the patch to Michael Terry <[email protected]> - however I left out powerpc where libtcmalloc-minimal0 is not - available - Closes: #649093 - - Fixed Vcs fields - * debian/patches/fix_duplicate_bposhashstat_t_definition.patch - Remove duplicate definition of bposhashstat_t() - - -- Andreas Tille <[email protected]> Thu, 08 Dec 2011 08:50:19 +0100 - -mira (3.4.0-3ubuntu1) lucid; urgency=low - - * Small fix to dependencies - there is no "mira" binary package - - -- Tim Booth <[email protected]> Fri, 02 Dec 2011 15:00:35 +0000 - -mira (3.4.0-3) unstable; urgency=low - - * Rendering Tim's additions available for Debian - - -- Steffen Moeller <[email protected]> Sat, 03 Sep 2011 01:02:10 +0200 - -mira (3.4.0-2ubuntu5) lucid; urgency=low - - * Small fix to clean target and suppress warnings - on Lucid backport. - * Fixed missing dependency which caused misleading configure - failure. - * Yet another missing build dep - flex and xxd - - -- Tim Booth <[email protected]> Tue, 30 Aug 2011 17:17:11 +0100 - -mira (3.4.0-2) unstable; urgency=low - - * Fixing source tree (removed PDF with no source) - - -- Steffen Moeller <[email protected]> Mon, 29 Aug 2011 22:54:53 +0200 - -mira (3.4.0-1) UNRELEASED; urgency=low - - * New upstream version. - - added default constructor to avoid FTBFS - * Sponsoring Tim's work for Debian - * Using 3.0 (quilt) source format for bz2 upstream - - -- Steffen Moeller <[email protected]> Tue, 23 Aug 2011 20:46:32 +0200 - -mira (3.4rc3-2) lucid; urgency=low - - * Version 3.2.1.8 has been removed from SF.net. Packaging the - latest RC instead. - * Fixed linking against tcmalloc (see README) - * Fixed build of docs - HTML is installed in mira-doc - - -- Tim Booth <[email protected]> Fri, 19 Aug 2011 12:35:12 +0100 - -mira (3.2.1.8-1) UNRELEASED; urgency=low - - * Initial release (Closes: #435915) - - -- Steffen Moeller <[email protected]> Fri, 04 Mar 2011 11:55:25 +0100 - -mira (3~rc2-1) UNRELEASED; urgency=low - - * Initial packaging. - - -- Charles Plessy <[email protected]> Tue, 08 Sep 2009 13:35:31 +0900 Copied: trunk/packages/mira/tags/3.4.0.1-3/debian/changelog (from rev 11030, trunk/packages/mira/trunk/debian/changelog) =================================================================== --- trunk/packages/mira/tags/3.4.0.1-3/debian/changelog (rev 0) +++ trunk/packages/mira/tags/3.4.0.1-3/debian/changelog 2012-05-28 02:07:14 UTC (rev 11031) @@ -0,0 +1,106 @@ +mira (3.4.0.1-3) unstable; urgency=low + + [ Charles Plessy ] + * Build-depend on libgoogle-perftools-dev instead of libtcmalloc-minimal0 + (debian/control, debian/README.source, debian/rules). + Closes: #673527, #674822 + * Conforms to Policy 3.9.3 (debian/control, no other changes needed). + * Rely on dpkg source format 3.0 (quilt) for the patches, and remove + build dependance on quilt (debian/control, debian/rules). + * Verbose Debhelper (debian/rules). + + [ Andreas Tille ] + * debian/upstream: very small fix to prevent bibcheck warning + + -- Charles Plessy <[email protected]> Mon, 28 May 2012 10:51:01 +0900 + +mira (3.4.0.1-2) unstable; urgency=low + + [ Andreas Tille ] + * Remove two patches: + - read_default_constructor.patch which introduces a duplicate + bposhashstat_t() definition + - fix_duplicate_bposhashstat_t_definition.patch which removes + this duplicate afterwards + + [ Charles Plessy ] + * Removed unconditional dependency on libtcmalloc-minimal0 (debian/control). + Closes: #654884 + * Machine-readable debian/copyright file. + + -- Charles Plessy <[email protected]> Sat, 07 Jan 2012 13:24:48 +0900 + +mira (3.4.0.1-1) unstable; urgency=low + + * New upstream version + Closes: #648762 (at least if I'm not mislead - feel free to reopen) + * debian/control: + - Added myself to Uploaders + - Depends: libtcmalloc-minimal0 [i386 amd64] + Thanks for the patch to Michael Terry <[email protected]> + however I left out powerpc where libtcmalloc-minimal0 is not + available + Closes: #649093 + - Fixed Vcs fields + * debian/patches/fix_duplicate_bposhashstat_t_definition.patch + Remove duplicate definition of bposhashstat_t() + + -- Andreas Tille <[email protected]> Thu, 08 Dec 2011 08:50:19 +0100 + +mira (3.4.0-3ubuntu1) lucid; urgency=low + + * Small fix to dependencies - there is no "mira" binary package + + -- Tim Booth <[email protected]> Fri, 02 Dec 2011 15:00:35 +0000 + +mira (3.4.0-3) unstable; urgency=low + + * Rendering Tim's additions available for Debian + + -- Steffen Moeller <[email protected]> Sat, 03 Sep 2011 01:02:10 +0200 + +mira (3.4.0-2ubuntu5) lucid; urgency=low + + * Small fix to clean target and suppress warnings + on Lucid backport. + * Fixed missing dependency which caused misleading configure + failure. + * Yet another missing build dep - flex and xxd + + -- Tim Booth <[email protected]> Tue, 30 Aug 2011 17:17:11 +0100 + +mira (3.4.0-2) unstable; urgency=low + + * Fixing source tree (removed PDF with no source) + + -- Steffen Moeller <[email protected]> Mon, 29 Aug 2011 22:54:53 +0200 + +mira (3.4.0-1) UNRELEASED; urgency=low + + * New upstream version. + - added default constructor to avoid FTBFS + * Sponsoring Tim's work for Debian + * Using 3.0 (quilt) source format for bz2 upstream + + -- Steffen Moeller <[email protected]> Tue, 23 Aug 2011 20:46:32 +0200 + +mira (3.4rc3-2) lucid; urgency=low + + * Version 3.2.1.8 has been removed from SF.net. Packaging the + latest RC instead. + * Fixed linking against tcmalloc (see README) + * Fixed build of docs - HTML is installed in mira-doc + + -- Tim Booth <[email protected]> Fri, 19 Aug 2011 12:35:12 +0100 + +mira (3.2.1.8-1) UNRELEASED; urgency=low + + * Initial release (Closes: #435915) + + -- Steffen Moeller <[email protected]> Fri, 04 Mar 2011 11:55:25 +0100 + +mira (3~rc2-1) UNRELEASED; urgency=low + + * Initial packaging. + + -- Charles Plessy <[email protected]> Tue, 08 Sep 2009 13:35:31 +0900 Deleted: trunk/packages/mira/tags/3.4.0.1-3/debian/control =================================================================== --- trunk/packages/mira/trunk/debian/control 2012-05-27 15:34:20 UTC (rev 11022) +++ trunk/packages/mira/tags/3.4.0.1-3/debian/control 2012-05-28 02:07:14 UTC (rev 11031) @@ -1,72 +0,0 @@ -Source: mira -Section: science -Priority: optional -Maintainer: Debian Med Packaging Team <[email protected]> -DM-Upload-Allowed: yes -Uploaders: Charles Plessy <[email protected]>, Steffen Moeller <[email protected]>, - Tim Booth <[email protected]>, Andreas Tille <[email protected]> -Build-Depends: debhelper (>= 7.0.50~), autotools-dev, dblatex, docbook-xsl, - libboost-thread-dev, libboost-regex-dev, libexpat1-dev, - libtcmalloc-minimal0 [i386 amd64], perl, quilt (>= 0.46-7~), flex, - vim-common, zlib1g-dev -Standards-Version: 3.9.2 -Homepage: http://chevreux.org/projects_mira.html -Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mira/trunk/ -Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mira/trunk/ - -Package: mira-assembler -Architecture: any -Depends: ${shlibs:Depends}, ${misc:Depends} -Suggests: mira-examples, mira-doc -Description: Whole Genome Shotgun and EST Sequence Assembler - The mira genome fragment assembler is a specialised assembler for - sequencing projects classified as 'hard' due to high number of similar - repeats. For expressed sequence tags (ESTs) transcripts, miraEST is - specialised on reconstructing pristine mRNA transcripts while - detecting and classifying single nucleotide polymorphisms (SNP) - occuring in different variations thereof. - . - The assembler is routinely used for such various tasks as mutation - detection in different cell types, similarity analysis of transcripts - between organisms, and pristine assembly of sequences from various - sources for oligo design in clinical microarray experiments. - . - The package provides the following executables: - Binaries provided: - * mira: for assembly of genome sequences - * miramem: estimating memory needed to assemble projects. Realised through - link to mira. - * convert_project: for converting project file types into other types - * caf2fasta, caf2gbf, caf2text, caf2html, gbf2caf and gbf2fasta are some - frequently used file converters (realised through links to convert_project) - * scftool: set of tools useful when working with SCF trace files - * fastatool: set of tools useful when working with FASTA trace files - . - Scripts provided: - * fasta2frag.tcl: fragmenting sequences into smaller, overlapping - subsequences. Useful for simulating shotgun sequences. Can create - subsequences in both directions (/default) and also paired-end sequences. - * fastaselect.tcl: given a FASTA file (and possibly a FASTA quality file) and - a file with names of reads, select the sequences from the input FASTA (and - quality file) and writes them to an output FASTA - * fastqselect.tcl: like fastaselect.tcl, only for FASTQ - * fixACE4consed.tcl: Consed has a bug which incapacitates it from reading - consensus tags in ACE files written by the MIRA assembler (and possibly - other programs). This script massages an ACE file so that consed can read - the consensus tags. - - -Package: mira-examples -Architecture: all -Depends: ${misc:Depends} -Suggests: mira-assembler, mira-doc -Description: files to experiment with the mira assembler - A series of files to exploit the functionality of mira. - -Package: mira-doc -Section: doc -Architecture: all -Depends: ${misc:Depends} -Suggests: mira-assembler -Description: documentation for the mira assembler - An HTML book introducing to mira. Copied: trunk/packages/mira/tags/3.4.0.1-3/debian/control (from rev 11027, trunk/packages/mira/trunk/debian/control) =================================================================== --- trunk/packages/mira/tags/3.4.0.1-3/debian/control (rev 0) +++ trunk/packages/mira/tags/3.4.0.1-3/debian/control 2012-05-28 02:07:14 UTC (rev 11031) @@ -0,0 +1,72 @@ +Source: mira +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +DM-Upload-Allowed: yes +Uploaders: Charles Plessy <[email protected]>, Steffen Moeller <[email protected]>, + Tim Booth <[email protected]>, Andreas Tille <[email protected]> +Build-Depends: debhelper (>= 7.0.50~), autotools-dev, dblatex, docbook-xsl, + libboost-thread-dev, libboost-regex-dev, libexpat1-dev, + libgoogle-perftools-dev [i386 amd64], perl, flex, + vim-common, zlib1g-dev +Standards-Version: 3.9.3 +Homepage: http://chevreux.org/projects_mira.html +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mira/trunk/ +Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mira/trunk/ + +Package: mira-assembler +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Suggests: mira-examples, mira-doc +Description: Whole Genome Shotgun and EST Sequence Assembler + The mira genome fragment assembler is a specialised assembler for + sequencing projects classified as 'hard' due to high number of similar + repeats. For expressed sequence tags (ESTs) transcripts, miraEST is + specialised on reconstructing pristine mRNA transcripts while + detecting and classifying single nucleotide polymorphisms (SNP) + occuring in different variations thereof. + . + The assembler is routinely used for such various tasks as mutation + detection in different cell types, similarity analysis of transcripts + between organisms, and pristine assembly of sequences from various + sources for oligo design in clinical microarray experiments. + . + The package provides the following executables: + Binaries provided: + * mira: for assembly of genome sequences + * miramem: estimating memory needed to assemble projects. Realised through + link to mira. + * convert_project: for converting project file types into other types + * caf2fasta, caf2gbf, caf2text, caf2html, gbf2caf and gbf2fasta are some + frequently used file converters (realised through links to convert_project) + * scftool: set of tools useful when working with SCF trace files + * fastatool: set of tools useful when working with FASTA trace files + . + Scripts provided: + * fasta2frag.tcl: fragmenting sequences into smaller, overlapping + subsequences. Useful for simulating shotgun sequences. Can create + subsequences in both directions (/default) and also paired-end sequences. + * fastaselect.tcl: given a FASTA file (and possibly a FASTA quality file) and + a file with names of reads, select the sequences from the input FASTA (and + quality file) and writes them to an output FASTA + * fastqselect.tcl: like fastaselect.tcl, only for FASTQ + * fixACE4consed.tcl: Consed has a bug which incapacitates it from reading + consensus tags in ACE files written by the MIRA assembler (and possibly + other programs). This script massages an ACE file so that consed can read + the consensus tags. + + +Package: mira-examples +Architecture: all +Depends: ${misc:Depends} +Suggests: mira-assembler, mira-doc +Description: files to experiment with the mira assembler + A series of files to exploit the functionality of mira. + +Package: mira-doc +Section: doc +Architecture: all +Depends: ${misc:Depends} +Suggests: mira-assembler +Description: documentation for the mira assembler + An HTML book introducing to mira. Deleted: trunk/packages/mira/tags/3.4.0.1-3/debian/rules =================================================================== --- trunk/packages/mira/trunk/debian/rules 2012-05-27 15:34:20 UTC (rev 11022) +++ trunk/packages/mira/tags/3.4.0.1-3/debian/rules 2012-05-28 02:07:14 UTC (rev 11031) @@ -1,55 +0,0 @@ -#!/usr/bin/make -f - -# Uncomment this to turn on verbose mode. -#export DH_VERBOSE=1 - -%: - dh $@ --with quilt - -override_dh_auto_install : - make install DESTDIR=$(CURDIR)/debian/mira-assembler - #There is no installation target for the docs - mkdir -p $(CURDIR)/debian/tmp/usr/share/doc/mira-assembler - cp -r -t $(CURDIR)/debian/tmp/usr/share/doc/mira-assembler doc/docbook/bookfigures doc/docbook/images \ - doc/docbook/doccss doc/docbook/DefinitiveGuideToMIRA.html || true - -override_dh_auto_test: - make check - -#Make the docs -override_dh_auto_build: - dh_auto_build -ifneq (,$(findstring mira-doc, $(shell dh_listpackages))) - dh_auto_build --sourcedir=doc -endif - -#Remove unneeded .tcl extensions from scripts -override_dh_install: - dh_install - if [ -d debian/mira-assembler ] ; then \ - for f in $$(ls debian/mira-assembler/usr/bin/*.tcl) ; do mv "$$f" "$${f%.tcl}"; done \ - fi - -#Hacky thing to allow building against tcmalloc without installing -#troublesome libbgoogle-perftools-dev, see README.Debian -export LDFLAGS=-L$(CURDIR)/lib - -#Must clean up the docs before cleaning out config.status -#Then scrub some junk not picked up by 'make clean' -override_dh_auto_clean: - ( cd doc ; make clean ) || true - dh_auto_clean - find * -name Makefile -exec rm '{}' ';' - find * -name '*.xxd.H' -exec rm '{}' ';' - find * -name '*.par.H' -exec rm '{}' ';' - find * -name 'compileinfo.*' -exec rm '{}' ';' - -override_dh_clean: - dh_clean - rm -rf lib - -override_dh_auto_configure : - mkdir lib - ln -s /usr/lib/libtcmalloc_minimal.so.0 lib/libtcmalloc_minimal.so - dh_auto_configure - Copied: trunk/packages/mira/tags/3.4.0.1-3/debian/rules (from rev 11029, trunk/packages/mira/trunk/debian/rules) =================================================================== --- trunk/packages/mira/tags/3.4.0.1-3/debian/rules (rev 0) +++ trunk/packages/mira/tags/3.4.0.1-3/debian/rules 2012-05-28 02:07:14 UTC (rev 11031) @@ -0,0 +1,55 @@ +#!/usr/bin/make -f + +# Uncomment this to turn on verbose mode. +export DH_VERBOSE=1 + +%: + dh $@ + +override_dh_auto_install : + make install DESTDIR=$(CURDIR)/debian/mira-assembler + #There is no installation target for the docs + mkdir -p $(CURDIR)/debian/tmp/usr/share/doc/mira-assembler + cp -r -t $(CURDIR)/debian/tmp/usr/share/doc/mira-assembler doc/docbook/bookfigures doc/docbook/images \ + doc/docbook/doccss doc/docbook/DefinitiveGuideToMIRA.html || true + +override_dh_auto_test: + make check + +#Make the docs +override_dh_auto_build: + dh_auto_build +ifneq (,$(findstring mira-doc, $(shell dh_listpackages))) + dh_auto_build --sourcedir=doc +endif + +#Remove unneeded .tcl extensions from scripts +override_dh_install: + dh_install + if [ -d debian/mira-assembler ] ; then \ + for f in $$(ls debian/mira-assembler/usr/bin/*.tcl) ; do mv "$$f" "$${f%.tcl}"; done \ + fi + +#Hacky thing to allow building against tcmalloc without installing +#troublesome libbgoogle-perftools-dev, see README.Debian +export LDFLAGS=-L$(CURDIR)/lib + +#Must clean up the docs before cleaning out config.status +#Then scrub some junk not picked up by 'make clean' +override_dh_auto_clean: + ( cd doc ; make clean ) || true + dh_auto_clean + find * -name Makefile -exec rm '{}' ';' + find * -name '*.xxd.H' -exec rm '{}' ';' + find * -name '*.par.H' -exec rm '{}' ';' + find * -name 'compileinfo.*' -exec rm '{}' ';' + +override_dh_clean: + dh_clean + rm -rf lib + +override_dh_auto_configure : + mkdir lib + ln -s /usr/lib/libtcmalloc_minimal.so.4 lib/libtcmalloc_minimal.so + dh_auto_configure + _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
