Author: alteholz Date: 2013-06-05 18:10:33 +0000 (Wed, 05 Jun 2013) New Revision: 13848
Added: trunk/packages/mira/trunk/debian/obsolete.mira-assembler.install trunk/packages/mira/trunk/debian/patches/hardening-flags.patch Removed: trunk/packages/mira/trunk/debian/mira-assembler.install Modified: trunk/packages/mira/trunk/debian/changelog trunk/packages/mira/trunk/debian/compat trunk/packages/mira/trunk/debian/control trunk/packages/mira/trunk/debian/patches/series trunk/packages/mira/trunk/debian/patches/xsltproc_nonet_for_doc_build trunk/packages/mira/trunk/debian/rules trunk/packages/mira/trunk/debian/watch Log: some progress Modified: trunk/packages/mira/trunk/debian/changelog =================================================================== --- trunk/packages/mira/trunk/debian/changelog 2013-06-05 16:22:11 UTC (rev 13847) +++ trunk/packages/mira/trunk/debian/changelog 2013-06-05 18:10:33 UTC (rev 13848) @@ -1,3 +1,23 @@ +mira (3.9.17-1) UNRELEASED; urgency=low + + * new upstream version + * debian/control: Standards-Version set to 3.9.4 (no changes) + * debian/control: DM-Upload-Allowed: removed + * debian/control: use dh 9 + * debian/control: add dependency to libboost-iostreams-dev + * debian/rules: get-orig-source added + * debian/watch: do not look at dev-versions + * TODO: RC bug (gcc4.8) + boost 1.53 + lintian stuff: manpages + spelling errors + hardening flags for fastatool + extended description + docbase + Up to now the new version builds with old gcc and old boost. + + -- Thorsten Alteholz <deb...@alteholz.de> Wed, 05 Jun 2013 18:00:01 +0200 + mira (3.4.0.1-3) unstable; urgency=low [ Charles Plessy ] Modified: trunk/packages/mira/trunk/debian/compat =================================================================== --- trunk/packages/mira/trunk/debian/compat 2013-06-05 16:22:11 UTC (rev 13847) +++ trunk/packages/mira/trunk/debian/compat 2013-06-05 18:10:33 UTC (rev 13848) @@ -1 +1 @@ -7 +9 Modified: trunk/packages/mira/trunk/debian/control =================================================================== --- trunk/packages/mira/trunk/debian/control 2013-06-05 16:22:11 UTC (rev 13847) +++ trunk/packages/mira/trunk/debian/control 2013-06-05 18:10:33 UTC (rev 13848) @@ -2,14 +2,25 @@ Section: science Priority: optional Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> -DM-Upload-Allowed: yes -Uploaders: Charles Plessy <ple...@debian.org>, Steffen Moeller <moel...@debian.org>, - Tim Booth <tbo...@ceh.ac.uk>, Andreas Tille <ti...@debian.org> -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 +Uploaders: Charles Plessy <ple...@debian.org>, + Steffen Moeller <moel...@debian.org>, + Tim Booth <tbo...@ceh.ac.uk>, + Andreas Tille <ti...@debian.org>, + Thorsten Alteholz <deb...@alteholz.de> +Build-Depends: debhelper (>= 9), + autotools-dev, + dblatex, + docbook-xsl, + libboost-thread-dev, + libboost-regex-dev, + libboost-iostreams-dev, + libexpat1-dev, + libgoogle-perftools-dev [i386 amd64], + perl, + flex, + vim-common, + zlib1g-dev +Standards-Version: 3.9.4 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/ Deleted: trunk/packages/mira/trunk/debian/mira-assembler.install =================================================================== --- trunk/packages/mira/trunk/debian/mira-assembler.install 2013-06-05 16:22:11 UTC (rev 13847) +++ trunk/packages/mira/trunk/debian/mira-assembler.install 2013-06-05 18:10:33 UTC (rev 13848) @@ -1,8 +0,0 @@ -src/progs/fastatool usr/bin/ -src/progs/mira usr/bin/ -src/progs/scftool usr/bin/ -src/progs/sw usr/bin/ -src/progs/convert_project usr/bin/ -src/scripts/fasta2frag.tcl usr/bin/ -src/scripts/fastaselect.tcl usr/bin/ -src/scripts/fastqselect.tcl usr/bin/ Copied: trunk/packages/mira/trunk/debian/obsolete.mira-assembler.install (from rev 13765, trunk/packages/mira/trunk/debian/mira-assembler.install) =================================================================== --- trunk/packages/mira/trunk/debian/obsolete.mira-assembler.install (rev 0) +++ trunk/packages/mira/trunk/debian/obsolete.mira-assembler.install 2013-06-05 18:10:33 UTC (rev 13848) @@ -0,0 +1,8 @@ +#src/progs/fastatool usr/bin/ +#src/progs/mira usr/bin/ +#src/progs/scftool usr/bin/ +#src/progs/sw usr/bin/ +#src/progs/convert_project usr/bin/ +#src/scripts/fasta2frag.tcl usr/bin/ +#src/scripts/fastaselect.tcl usr/bin/ +#src/scripts/fastqselect.tcl usr/bin/ Added: trunk/packages/mira/trunk/debian/patches/hardening-flags.patch =================================================================== --- trunk/packages/mira/trunk/debian/patches/hardening-flags.patch (rev 0) +++ trunk/packages/mira/trunk/debian/patches/hardening-flags.patch 2013-06-05 18:10:33 UTC (rev 13848) @@ -0,0 +1,41 @@ +Index: mira-3.9.17/src/progs/Makefile.in +=================================================================== +--- mira-3.9.17.orig/src/progs/Makefile.in 2013-05-21 20:17:52.000000000 +0200 ++++ mira-3.9.17/src/progs/Makefile.in 2013-06-05 15:58:01.000000000 +0200 +@@ -378,25 +378,29 @@ + rm -f $$list + convert_project$(EXEEXT): $(convert_project_OBJECTS) $(convert_project_DEPENDENCIES) $(EXTRA_convert_project_DEPENDENCIES) + @rm -f convert_project$(EXEEXT) +- $(CXXLINK) $(convert_project_OBJECTS) $(convert_project_LDADD) $(LIBS) ++ echo "XXX blubber $(LDFLAGS)" ++ echo "XXX blubber $(CXXFLAGS)" ++ echo "XXX blubber $(CPPFLAGS)" ++ $(CXXLINK) $(LDFLAGS) $(convert_project_OBJECTS) $(convert_project_LDADD) $(LIBS) ++ echo "XXX blubber ende" + dbgreplay$(EXEEXT): $(dbgreplay_OBJECTS) $(dbgreplay_DEPENDENCIES) $(EXTRA_dbgreplay_DEPENDENCIES) + @rm -f dbgreplay$(EXEEXT) +- $(CXXLINK) $(dbgreplay_OBJECTS) $(dbgreplay_LDADD) $(LIBS) ++ $(CXXLINK) $(LDFLAGS) $(dbgreplay_OBJECTS) $(dbgreplay_LDADD) $(LIBS) + fastatool$(EXEEXT): $(fastatool_OBJECTS) $(fastatool_DEPENDENCIES) $(EXTRA_fastatool_DEPENDENCIES) + @rm -f fastatool$(EXEEXT) +- $(CXXLINK) $(fastatool_OBJECTS) $(fastatool_LDADD) $(LIBS) ++ $(CXXLINK) $(LDFLAGS) $(fastatool_OBJECTS) $(fastatool_LDADD) $(LIBS) + mira$(EXEEXT): $(mira_OBJECTS) $(mira_DEPENDENCIES) $(EXTRA_mira_DEPENDENCIES) + @rm -f mira$(EXEEXT) +- $(CXXLINK) $(mira_OBJECTS) $(mira_LDADD) $(LIBS) ++ $(CXXLINK) $(LDFLAGS) $(mira_OBJECTS) $(mira_LDADD) $(LIBS) + miramer$(EXEEXT): $(miramer_OBJECTS) $(miramer_DEPENDENCIES) $(EXTRA_miramer_DEPENDENCIES) + @rm -f miramer$(EXEEXT) +- $(CXXLINK) $(miramer_OBJECTS) $(miramer_LDADD) $(LIBS) ++ $(CXXLINK) $(LDFLAGS) $(miramer_OBJECTS) $(miramer_LDADD) $(LIBS) + miratest$(EXEEXT): $(miratest_OBJECTS) $(miratest_DEPENDENCIES) $(EXTRA_miratest_DEPENDENCIES) + @rm -f miratest$(EXEEXT) +- $(CXXLINK) $(miratest_OBJECTS) $(miratest_LDADD) $(LIBS) ++ $(CXXLINK) $(LDFLAGS) $(miratest_OBJECTS) $(miratest_LDADD) $(LIBS) + scftool$(EXEEXT): $(scftool_OBJECTS) $(scftool_DEPENDENCIES) $(EXTRA_scftool_DEPENDENCIES) + @rm -f scftool$(EXEEXT) +- $(CXXLINK) $(scftool_OBJECTS) $(scftool_LDADD) $(LIBS) ++ $(CXXLINK) $(LDFLAGS) $(scftool_OBJECTS) $(scftool_LDADD) $(LIBS) + + mostlyclean-compile: + -rm -f *.$(OBJEXT) Modified: trunk/packages/mira/trunk/debian/patches/series =================================================================== --- trunk/packages/mira/trunk/debian/patches/series 2013-06-05 16:22:11 UTC (rev 13847) +++ trunk/packages/mira/trunk/debian/patches/series 2013-06-05 18:10:33 UTC (rev 13848) @@ -1,2 +1,3 @@ +xsltproc_nonet_for_doc_build +hardening-flags.patch add_shebang_lines -xsltproc_nonet_for_doc_build Modified: trunk/packages/mira/trunk/debian/patches/xsltproc_nonet_for_doc_build =================================================================== --- trunk/packages/mira/trunk/debian/patches/xsltproc_nonet_for_doc_build 2013-06-05 16:22:11 UTC (rev 13847) +++ trunk/packages/mira/trunk/debian/patches/xsltproc_nonet_for_doc_build 2013-06-05 18:10:33 UTC (rev 13848) @@ -1,21 +1,30 @@ -# Makes sure the documentation builds without needing network access. -# This magically works if docbook-xsl is installed, otherwise it fails -# complaining that it needs to access http://docbook.sourceforge.net/release/xsl/current/html/docbook.xsl +Author: Tim Booth +Description: Do not use the Internet to fetch DTDs, entities or documents. + Makes sure the documentation builds without needing network access. + This magically works if docbook-xsl is installed, otherwise it fails + complaining that it needs to access http://docbook.sourceforge.net/release/xsl/current/html/docbook.xsl ---- mira-3.4.0.1.orig/doc/docbook/Makefile.in -+++ mira-3.4.0.1/doc/docbook/Makefile.in -@@ -387,12 +387,12 @@ +Index: mira-3.9.17/doc/docbook/Makefile.in +=================================================================== +--- mira-3.9.17.orig/doc/docbook/Makefile.in 2013-05-21 20:17:52.000000000 +0200 ++++ mira-3.9.17/doc/docbook/Makefile.in 2013-06-05 09:57:40.000000000 +0200 +@@ -405,16 +405,16 @@ %_part.html: %_part.xml @echo "Making .html out of _part.xml" $@ - @$(SHELL) -ec 'xsltproc --xinclude --output $@ $(top_srcdir)/doc/docbook/mira.xsl $<' -+ $(SHELL) -ec 'xsltproc --nonet --xinclude --output $@ $(top_srcdir)/doc/docbook/mira.xsl $<' ++ @$(SHELL) -ec 'xsltproc --nonet --xinclude --output $@ $(top_srcdir)/doc/docbook/mira.xsl $<' - chapters: ${CHAP_HTML} + chapters: ${CHAP_HTML} versionfile - books: ${CHAP_XML} book_definitiveguide.xml + book_3rdparty: versionfile ${CHAP_XML} book_3rdparty.xml +- xsltproc --xinclude --output 3rdparty_MIRA.html $(top_srcdir)/doc/docbook/book.xsl $(top_srcdir)/doc/docbook/book_3rdparty.xml ++ xsltproc --nonet --xinclude --output 3rdparty_MIRA.html $(top_srcdir)/doc/docbook/book.xsl $(top_srcdir)/doc/docbook/book_3rdparty.xml + dblatex --xslt-opts=--nonet --output=3rdparty_MIRA.pdf $(top_srcdir)/doc/docbook/book_3rdparty.xml + + book_definitive: versionfile ${CHAP_XML} book_definitiveguide.xml - xsltproc --xinclude --output DefinitiveGuideToMIRA.html $(top_srcdir)/doc/docbook/book.xsl $(top_srcdir)/doc/docbook/book_definitiveguide.xml -+ xsltproc --xinclude --nonet --output DefinitiveGuideToMIRA.html $(top_srcdir)/doc/docbook/book.xsl $(top_srcdir)/doc/docbook/book_definitiveguide.xml ++ xsltproc --nonet --xinclude --output DefinitiveGuideToMIRA.html $(top_srcdir)/doc/docbook/book.xsl $(top_srcdir)/doc/docbook/book_definitiveguide.xml dblatex --xslt-opts=--nonet --output=DefinitiveGuideToMIRA.pdf $(top_srcdir)/doc/docbook/book_definitiveguide.xml - all: chapters books + books: versionfile book_definitive book_3rdparty Modified: trunk/packages/mira/trunk/debian/rules =================================================================== --- trunk/packages/mira/trunk/debian/rules 2013-06-05 16:22:11 UTC (rev 13847) +++ trunk/packages/mira/trunk/debian/rules 2013-06-05 18:10:33 UTC (rev 13848) @@ -2,6 +2,9 @@ # Uncomment this to turn on verbose mode. export DH_VERBOSE=1 +#Hacky thing to allow building against tcmalloc without installing +#troublesome libbgoogle-perftools-dev, see README.Debian +export DEB_CFLAGS_MAINT_APPEND=-L$(CURDIR)/lib %: dh $@ @@ -30,10 +33,6 @@ 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: @@ -53,3 +52,7 @@ ln -s /usr/lib/libtcmalloc_minimal.so.4 lib/libtcmalloc_minimal.so dh_auto_configure +get-orig-source: + mkdir -p ../tarballs + uscan --verbose --force-download --destdir=../tarballs + Modified: trunk/packages/mira/trunk/debian/watch =================================================================== --- trunk/packages/mira/trunk/debian/watch 2013-06-05 16:22:11 UTC (rev 13847) +++ trunk/packages/mira/trunk/debian/watch 2013-06-05 18:10:33 UTC (rev 13848) @@ -1,2 +1,2 @@ version=3 -opts="uversionmangle=s/rc/~rc/" http://sf.net/mira-assembler/mira-(.*).tar.bz2 +opts="uversionmangle=s/rc/~rc/" http://sf.net/mira-assembler/mira-(\d.*).tar.bz2 _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
