[med-svn] r13848 - in trunk/packages/mira/trunk/debian: . patches
Thorsten Alteholz
alteholz at alioth.debian.org
Wed Jun 5 18:10:34 UTC 2013
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 <debian at 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-packaging at lists.alioth.debian.org>
-DM-Upload-Allowed: yes
-Uploaders: Charles Plessy <plessy at debian.org>, Steffen Moeller <moeller at debian.org>,
- Tim Booth <tbooth at ceh.ac.uk>, Andreas Tille <tille at 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 <plessy at debian.org>,
+ Steffen Moeller <moeller at debian.org>,
+ Tim Booth <tbooth at ceh.ac.uk>,
+ Andreas Tille <tille at debian.org>,
+ Thorsten Alteholz <debian at 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
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