[med-svn] r13851 - in trunk/packages/mira/trunk/debian: . patches
Author: xnox
Date: 2013-06-06 09:43:45 + (Thu, 06 Jun 2013)
New Revision: 13851
Added:
trunk/packages/mira/trunk/debian/patches/boost1.53
Modified:
trunk/packages/mira/trunk/debian/changelog
trunk/packages/mira/trunk/debian/control
trunk/packages/mira/trunk/debian/patches/series
trunk/packages/mira/trunk/debian/rules
Log:
* TODO: lintian stuff: manpages
* Use dh-autoreconf
* Build depend on libboost-system-dev.
* Add boost 1.53 patch, link against boost_system, fixing FTBFS (Closes:
#701322)
* Enable parallel builds, to speed up compilation.
* TODO:
figure out why above doesn't work in sbuild
convert remaining patches to patch Makefile.ams, instead of ins
Modified: trunk/packages/mira/trunk/debian/changelog
===
--- trunk/packages/mira/trunk/debian/changelog 2013-06-05 21:05:26 UTC (rev
13850)
+++ trunk/packages/mira/trunk/debian/changelog 2013-06-06 09:43:45 UTC (rev
13851)
@@ -1,5 +1,6 @@
mira (3.9.17-1) UNRELEASED; urgency=low
+ [ Thorsten Alteholz ]
* new upstream version
* debian/control: Standards-Version set to 3.9.4 (no changes)
* debian/control: DM-Upload-Allowed: removed
@@ -7,15 +8,23 @@
* 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
+ * TODO: 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.
+ [ Dmitrijs Ledkovs ]
+ * Use dh-autoreconf
+ * Build depend on libboost-system-dev.
+ * Add boost 1.53 patch, link against boost_system, fixing FTBFS (Closes:
+#701322)
+ * Enable parallel builds, to speed up compilation.
+ * TODO:
+ figure out why above doesn't work in sbuild
+ convert remaining patches to patch Makefile.ams, instead of ins
+
-- Thorsten Alteholz deb...@alteholz.de Wed, 05 Jun 2013 18:00:01 +0200
mira (3.4.0.1-3) unstable; urgency=low
Modified: trunk/packages/mira/trunk/debian/control
===
--- trunk/packages/mira/trunk/debian/control2013-06-05 21:05:26 UTC (rev
13850)
+++ trunk/packages/mira/trunk/debian/control2013-06-06 09:43:45 UTC (rev
13851)
@@ -8,10 +8,12 @@
Andreas Tille ti...@debian.org,
Thorsten Alteholz deb...@alteholz.de
Build-Depends: debhelper (= 9),
- autotools-dev,
- dblatex,
+ dblatex,
+ dh-autoreconf,
+ autoconf-archive,
docbook-xsl,
- libboost-thread-dev,
+ libboost-thread-dev,
+ libboost-system-dev,
libboost-regex-dev,
libboost-iostreams-dev,
libexpat1-dev,
Added: trunk/packages/mira/trunk/debian/patches/boost1.53
===
--- trunk/packages/mira/trunk/debian/patches/boost1.53
(rev 0)
+++ trunk/packages/mira/trunk/debian/patches/boost1.53 2013-06-06 09:43:45 UTC
(rev 13851)
@@ -0,0 +1,72 @@
+Description: link against boost_system, fixing FTBFS
+Author: Dmitrijs Ledkovs x...@debian.org
+Bug-Debian: http://bugs.debian.org/701322
+
+--- a/configure.in
b/configure.in
+@@ -715,16 +715,6 @@
+ fi
+
+
+-# some of the BOOST checks below break on older systems with newer BOOSTs
+-# e.g., boost_thread implicitly needs boost_clock and boost_system,
+-# but the linker on KUbuntu 9.10 somehow does not find them automatically
+-# Way out: for the boost checks, set the linker rpath to include boost lib
path
+-# (only valid for gcc)
+-oldCFLAGS=${CFLAGS}
+-if test x$GCC = xyes; then
+- CFLAGS=${CFLAGS} -Wl,-rpath,${ac_boost_lib_path}
+-fi
+-
+ echo
+ echo +
+ echo BOOST_CPPFLAGS:${BOOST_CPPFLAGS}
+--- a/src/progs/Makefile.am
b/src/progs/Makefile.am
+@@ -46,7 +46,8 @@
+ MEMORC= -lmemorc
+ endif
+
+-MIRALIBS=-lmiradebuggersupport $(MEMORC) -lmira -lmiraestass -lmiracaf
-lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport
$(LINKEDITLIB)
++BOOST_LIBS=$(BOOST_FILESYSTEM_LIB) $(BOOST_IOSTREAMS_LIB) $(BOOST_REGEX_LIB)
$(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB)
++MIRALIBS=-lmiradebuggersupport $(MEMORC) -lmira -lmiraestass -lmiracaf
-lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport
$(LINKEDITLIB) $(BOOST_LIBS)
+
+ install-exec-hook:
+ cd $(DESTDIR)$(bindir) \
+--- a/config/m4/ax_boost_thread.m4
b/config/m4/ax_boost_thread.m4
+@@ -60,7 +60,7 @@
+ export CPPFLAGS
+
+ LDFLAGS_SAVED=$LDFLAGS
+- LDFLAGS=$LDFLAGS $BOOST_LDFLAGS
++ LDFLAGS=$LDFLAGS $BOOST_LDFLAGS -lboost_system
+ export LDFLAGS
+
+ AC_CACHE_CHECK(whether the Boost::Thread library is available,
+@@ -107,14 +107,14 @@
+
[med-svn] r13852 - in trunk/packages/profit/trunk/debian: . bin
Author: moeller Date: 2013-06-06 10:51:48 + (Thu, 06 Jun 2013) New Revision: 13852 Added: trunk/packages/profit/trunk/debian/bin/ trunk/packages/profit/trunk/debian/bin/profit Removed: trunk/packages/profit/trunk/debian/profit.sh Modified: trunk/packages/profit/trunk/debian/profit.dirs trunk/packages/profit/trunk/debian/profit.install Log: Fine tuning. Copied: trunk/packages/profit/trunk/debian/bin/profit (from rev 13845, trunk/packages/profit/trunk/debian/profit.sh) === --- trunk/packages/profit/trunk/debian/bin/profit (rev 0) +++ trunk/packages/profit/trunk/debian/bin/profit 2013-06-06 10:51:48 UTC (rev 13852) @@ -0,0 +1,5 @@ +#!/bin/sh + +export HELPDIR=/usr/share/profit/ +export DATADIR=/usr/share/profit/ +/usr/lib/profit/profit $* Modified: trunk/packages/profit/trunk/debian/profit.dirs === --- trunk/packages/profit/trunk/debian/profit.dirs 2013-06-06 09:43:45 UTC (rev 13851) +++ trunk/packages/profit/trunk/debian/profit.dirs 2013-06-06 10:51:48 UTC (rev 13852) @@ -1 +1,2 @@ usr/lib/profit +usr/bin Modified: trunk/packages/profit/trunk/debian/profit.install === --- trunk/packages/profit/trunk/debian/profit.install 2013-06-06 09:43:45 UTC (rev 13851) +++ trunk/packages/profit/trunk/debian/profit.install 2013-06-06 10:51:48 UTC (rev 13852) @@ -1,2 +1,2 @@ src/profit usr/lib/profit/ -debian/profit.sh usr/bin/profit +debian/bin/profit usr/bin/ Deleted: trunk/packages/profit/trunk/debian/profit.sh === --- trunk/packages/profit/trunk/debian/profit.sh2013-06-06 09:43:45 UTC (rev 13851) +++ trunk/packages/profit/trunk/debian/profit.sh2013-06-06 10:51:48 UTC (rev 13852) @@ -1,5 +0,0 @@ -#!/bin/sh - -export HELPDIR=/usr/share/profit/ -export DATADIR=/usr/share/profit/ -/usr/lib/profit/profit $* ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13854 - trunk/packages/gdcm/trunk/debian
Author: malat Date: 2013-06-06 15:33:16 + (Thu, 06 Jun 2013) New Revision: 13854 Modified: trunk/packages/gdcm/trunk/debian/changelog trunk/packages/gdcm/trunk/debian/rules Log: Prepare new upload Modified: trunk/packages/gdcm/trunk/debian/changelog === --- trunk/packages/gdcm/trunk/debian/changelog 2013-06-06 14:28:34 UTC (rev 13853) +++ trunk/packages/gdcm/trunk/debian/changelog 2013-06-06 15:33:16 UTC (rev 13854) @@ -1,3 +1,10 @@ +gdcm (2.2.3-2) unstable; urgency=low + + * Fix compilation with multi-arch python + * Fix GDCM import (new CMake generated files breaks compat). Closes: #711214 + + -- Mathieu Malaterre ma...@debian.org Thu, 06 Jun 2013 17:32:30 +0200 + gdcm (2.2.3-1) unstable; urgency=low * New upstream Modified: trunk/packages/gdcm/trunk/debian/rules === --- trunk/packages/gdcm/trunk/debian/rules 2013-06-06 14:28:34 UTC (rev 13853) +++ trunk/packages/gdcm/trunk/debian/rules 2013-06-06 15:33:16 UTC (rev 13854) @@ -38,6 +38,14 @@ PYMODDIR := /usr/lib/$(shell pyversions -r) VTKVERS=$(shell apt-cache policy libvtk5-dev | grep Installed: | cut -d: -f2 | cut -d' ' -f2 | cut -d- -f1 | cut -d. -f1-2) +PYTHON_INCLUDE_DIRS=$(shell python-config --includes | cut -f1 -d' '|cut -c3-) +PYTHON_INCLUDE_DIR=$(PYTHON_INCLUDE_DIRS) +# See bug #709181 +PYTHON_INCLUDE_DIRS2=$(shell python-config --includes | cut -f2 -d' '|cut -c3-) +PYTHON_INCLUDE_DIR2=$(PYTHON_INCLUDE_DIRS2) +PYTHON_CONFIG_DIR=$(shell python-config --configdir) +PYTHON_LIBRARY=$(PYTHON_CONFIG_DIR)/libpython2.7.so + # GDCM_DOCUMENTATION:BOOL=ON is required to build man page (build target) # Need to make sure to build using the same vtk/python version: CMAKE_EXTRA_FLAGS += -DCMAKE_SKIP_RPATH=ON \ @@ -66,8 +74,9 @@ -DGDCM_USE_SYSTEM_POPPLER:BOOL=ON \ -DGDCM_USE_PARAVIEW:BOOL=OFF \ -DGDCM_USE_ACTIVIZ:BOOL=ON \ - -DPYTHON_INCLUDE_DIR:PATH=/usr/include/python2.7 \ - -DPYTHON_LIBRARY:FILEPATH=/usr/lib/python2.7/config/libpython2.7.so \ + -DPYTHON_INCLUDE_DIR=$(PYTHON_INCLUDE_DIR) \ + -DPYTHON_INCLUDE_DIR2=$(PYTHON_INCLUDE_DIR2) \ + -DPYTHON_LIBRARY=$(PYTHON_LIBRARY) \ -DGDCM_INSTALL_DOC_DIR:STRING=share/doc/gdcm-doc \ -DTAGFILES:STRING=/usr/share/doc/vtk-doc/html/vtk$(VTKVERS).tag=/usr/share/doc/vtk-doc/html/ \ -DGDCM_USE_VTK:BOOL=ON @@ -81,6 +90,8 @@ override_dh_auto_install: # See #664188 sed -i -e s/FATAL_ERROR/STATUS/g obj-*/CMake/ExportConfiguration/CMakeFiles/Export/lib/gdcm-2.2/GDCMTargets-relwithdebinfo.cmake + # See #711214 + sed -i -e s/FATAL_ERROR/STATUS/g obj-*/CMake/ExportConfiguration/CMakeFiles/Export/lib/gdcm-2.2/GDCMTargets.cmake dh_auto_install # PHP mkdir -p debian/tmp/$(PHP_EX) ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r13855 - in trunk/packages/mira/trunk/debian: . patches
Author: alteholz
Date: 2013-06-06 18:08:34 + (Thu, 06 Jun 2013)
New Revision: 13855
Added:
trunk/packages/mira/trunk/debian/convert_project.1
trunk/packages/mira/trunk/debian/fasta2frag.1
trunk/packages/mira/trunk/debian/fastaselect.1
trunk/packages/mira/trunk/debian/fastatool.1
trunk/packages/mira/trunk/debian/fastqselect.1
trunk/packages/mira/trunk/debian/mira-assembler.lintian-overrides
trunk/packages/mira/trunk/debian/mira-assembler.manpages
trunk/packages/mira/trunk/debian/mira-doc.doc-base
trunk/packages/mira/trunk/debian/miradiff.1
trunk/packages/mira/trunk/debian/miramer.1
trunk/packages/mira/trunk/debian/patches/spelling.patch
trunk/packages/mira/trunk/debian/scftool.1
Removed:
trunk/packages/mira/trunk/debian/patches/hardening-flags.patch
Modified:
trunk/packages/mira/trunk/debian/changelog
trunk/packages/mira/trunk/debian/control
trunk/packages/mira/trunk/debian/mira-doc.README.Debian
trunk/packages/mira/trunk/debian/patches/series
Log:
some progress on lintian complaints
Modified: trunk/packages/mira/trunk/debian/changelog
===
--- trunk/packages/mira/trunk/debian/changelog 2013-06-06 15:33:16 UTC (rev
13854)
+++ trunk/packages/mira/trunk/debian/changelog 2013-06-06 18:08:34 UTC (rev
13855)
@@ -6,14 +6,13 @@
* debian/control: DM-Upload-Allowed: removed
* debian/control: use dh 9
* debian/control: add dependency to libboost-iostreams-dev
+ * debian/control: improve extended descriptions
+ * debian/control: change VCS-tags according to new lintian
* debian/rules: get-orig-source added
* debian/watch: do not look at dev-versions
+ * debian/mira-doc.README.Debian: correct path to documentation
* TODO: 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.
+Up to now the new version builds with old gcc and old/new boost.
[ Dmitrijs Ledkovs ]
* Use dh-autoreconf
Modified: trunk/packages/mira/trunk/debian/control
===
--- trunk/packages/mira/trunk/debian/control2013-06-06 15:33:16 UTC (rev
13854)
+++ trunk/packages/mira/trunk/debian/control2013-06-06 18:08:34 UTC (rev
13855)
@@ -24,8 +24,8 @@
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/
+Vcs-Browser:
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/mira/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/mira/trunk/
Package: mira-assembler
Architecture: any
@@ -74,7 +74,12 @@
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.
+ The mira genome fragment assembler is a specialised assembler for
+ sequencing projects classified as 'hard' due to high number of similar
+ repeats.
+ .
+ This package contains a series of files to exploit the functionality
+ of mira.
Package: mira-doc
Section: doc
@@ -82,4 +87,8 @@
Depends: ${misc:Depends}
Suggests: mira-assembler
Description: documentation for the mira assembler
- An HTML book introducing to mira.
+ The mira genome fragment assembler is a specialised assembler for
+ sequencing projects classified as 'hard' due to high number of similar
+ repeats.
+ .
+ This package contains an HTML book introducing to mira.
Added: trunk/packages/mira/trunk/debian/convert_project.1
===
--- trunk/packages/mira/trunk/debian/convert_project.1
(rev 0)
+++ trunk/packages/mira/trunk/debian/convert_project.1 2013-06-06 18:08:34 UTC
(rev 13855)
@@ -0,0 +1,554 @@
+.\ DO NOT MODIFY THIS FILE! It was generated by help2man 1.42.1.
+.TH CONVERT_PROJECT 1 June 2013 convert_project (MIRALIB version 3.9.17
()) User Commands
+.SH NAME
+convert_project \- convert assembly and sequencing file types
+.SH DESCRIPTION
+.PP
+convert_project (MIRALIB version 3.9.17 ())
+.PP
+Author: Bastien Chevreux (b...@chevreux.org)
+.PP
+Usage:
+convert_project [\-f fromtype] [\-t totype [\-t totype ...]]
+.IP
+[\-aChimMsuZ]
+[\-AcflnNoqrtvxXyz {...}]
+{infile} {outfile} [totype totype ...]
+.SH OPTIONS
+.TP
+\fB\-f\fR fromtype
+load this type of project files, where fromtype is:
+.TP
+caf
+a complete assembly or single sequences from CAF
+.TP
+maf
+a complete assembly or single sequences from CAF
+.TP
+fasta
+sequences from a FASTA file
+.TP
+fastq
+sequences from a FASTQ file
+.TP
+gbf
+sequences from a GBF file
+.TP
+phd
+sequences from a PHD file
+.TP
+fofnexp
+sequences in
[med-svn] r13856 - in trunk/packages/mira/trunk/debian: . patches
Author: xnox
Date: 2013-06-07 00:24:29 + (Fri, 07 Jun 2013)
New Revision: 13856
Added:
trunk/packages/mira/trunk/debian/patches/boost-minimal
Removed:
trunk/packages/mira/trunk/debian/patches/boost1.53
Modified:
trunk/packages/mira/trunk/debian/changelog
trunk/packages/mira/trunk/debian/control
trunk/packages/mira/trunk/debian/patches/series
trunk/packages/mira/trunk/debian/rules
Log:
* Build depend on libboost-all-dev and libbz2-dev.
* Add boost-minimal patch, to add boost-libraries in final linking,
fixing FTBFS (Closes: #701322)
Modified: trunk/packages/mira/trunk/debian/changelog
===
--- trunk/packages/mira/trunk/debian/changelog 2013-06-06 18:08:34 UTC (rev
13855)
+++ trunk/packages/mira/trunk/debian/changelog 2013-06-07 00:24:29 UTC (rev
13856)
@@ -12,17 +12,12 @@
* debian/watch: do not look at dev-versions
* debian/mira-doc.README.Debian: correct path to documentation
* TODO: lintian stuff: manpages
-Up to now the new version builds with old gcc and old/new boost.
[ Dmitrijs Ledkovs ]
- * Use dh-autoreconf
- * Build depend on libboost-system-dev.
- * Add boost 1.53 patch, link against boost_system, fixing FTBFS (Closes:
-#701322)
+ * Build depend on libboost-all-dev and libbz2-dev.
+ * Add boost-minimal patch, to add boost-libraries in final linking,
+fixing FTBFS (Closes: #701322)
* Enable parallel builds, to speed up compilation.
- * TODO:
- figure out why above doesn't work in sbuild
- convert remaining patches to patch Makefile.ams, instead of ins
-- Thorsten Alteholz deb...@alteholz.de Wed, 05 Jun 2013 18:00:01 +0200
Modified: trunk/packages/mira/trunk/debian/control
===
--- trunk/packages/mira/trunk/debian/control2013-06-06 18:08:34 UTC (rev
13855)
+++ trunk/packages/mira/trunk/debian/control2013-06-07 00:24:29 UTC (rev
13856)
@@ -12,10 +12,8 @@
dh-autoreconf,
autoconf-archive,
docbook-xsl,
- libboost-thread-dev,
- libboost-system-dev,
- libboost-regex-dev,
- libboost-iostreams-dev,
+ libboost-all-dev,
+ libbz2-dev,
libexpat1-dev,
libgoogle-perftools-dev [i386 amd64],
perl,
Added: trunk/packages/mira/trunk/debian/patches/boost-minimal
===
--- trunk/packages/mira/trunk/debian/patches/boost-minimal
(rev 0)
+++ trunk/packages/mira/trunk/debian/patches/boost-minimal 2013-06-07
00:24:29 UTC (rev 13856)
@@ -0,0 +1,13 @@
+Description: boost minimal
+
+--- mira-3.9.17.orig/src/progs/Makefile.in
mira-3.9.17/src/progs/Makefile.in
+@@ -265,7 +265,7 @@ noinst_HEADERS = quirks.H
+ # EdIt_abi373 EdIt_alf skimmer
+ @BUILDMIRASTATIC_TRUE@AM_LDFLAGS = $(BLOODYDARWINSTATLIBDIRHACK)
-L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/
-L../mira -L../caf $(LINKEDITDIR) $(BOOST_LDFLAGS) -all-static
+ @BUILDMIRAMEMORC_TRUE@MEMORC = -lmemorc
+-MIRALIBS = -lmiradebuggersupport $(MEMORC) -lmira -lmiraestass -lmiracaf
-lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport
$(LINKEDITLIB)
++MIRALIBS = -lmiradebuggersupport $(MEMORC) -lmira -lmiraestass -lmiracaf
-lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport
-lboost_filesystem -lboost_iostreams -lboost_regex -lboost_thread
-lboost_system $(LINKEDITLIB)
+ sw_SOURCES = sw.C
+ sw_LDADD = $(MIRALIBS)
+ mira_SOURCES = mira.C
Deleted: trunk/packages/mira/trunk/debian/patches/boost1.53
===
--- trunk/packages/mira/trunk/debian/patches/boost1.53 2013-06-06 18:08:34 UTC
(rev 13855)
+++ trunk/packages/mira/trunk/debian/patches/boost1.53 2013-06-07 00:24:29 UTC
(rev 13856)
@@ -1,72 +0,0 @@
-Description: link against boost_system, fixing FTBFS
-Author: Dmitrijs Ledkovs x...@debian.org
-Bug-Debian: http://bugs.debian.org/701322
-
a/configure.in
-+++ b/configure.in
-@@ -715,16 +715,6 @@
- fi
-
-
--# some of the BOOST checks below break on older systems with newer BOOSTs
--# e.g., boost_thread implicitly needs boost_clock and boost_system,
--# but the linker on KUbuntu 9.10 somehow does not find them automatically
--# Way out: for the boost checks, set the linker rpath to include boost lib
path
--# (only valid for gcc)
--oldCFLAGS=${CFLAGS}
--if test x$GCC = xyes; then
-- CFLAGS=${CFLAGS} -Wl,-rpath,${ac_boost_lib_path}
--fi
--
- echo
- echo +
- echo BOOST_CPPFLAGS:${BOOST_CPPFLAGS}
a/src/progs/Makefile.am
-+++ b/src/progs/Makefile.am
-@@ -46,7 +46,8 @@
- MEMORC= -lmemorc
- endif
-
--MIRALIBS=-lmiradebuggersupport $(MEMORC) -lmira -lmiraestass -lmiracaf
-lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport
$(LINKEDITLIB)
-+BOOST_LIBS=$(BOOST_FILESYSTEM_LIB) $(BOOST_IOSTREAMS_LIB) $(BOOST_REGEX_LIB)
$(BOOST_THREAD_LIB)
