[med-svn] [Git][med-team/vienna-rna][master] 10 commits: link-against-lapack.patch: explicitly link bin/ components against lapack
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Thu Feb 9 21:50:41 GMT 2023
Étienne Mollier pushed to branch master at Debian Med / vienna-rna
Commits:
3ec0119d by Étienne Mollier at 2023-02-09T21:15:59+01:00
link-against-lapack.patch: explicitly link bin/ components against lapack
- - - - -
5311852d by Étienne Mollier at 2023-02-09T21:21:01+01:00
use_debian_packaged_dlib.patch: link also Perl modules.
- - - - -
652a56b8 by Étienne Mollier at 2023-02-09T21:47:25+01:00
d/rules: ventilate dh_auto_configure target.
- - - - -
340c5626 by Étienne Mollier at 2023-02-09T21:48:04+01:00
d/rules: upstream assumes --with-python is --with-python3.
- - - - -
230e5d73 by Étienne Mollier at 2023-02-09T21:54:19+01:00
python3.11.patch: remove FIXME item.
- - - - -
81ba45c6 by Étienne Mollier at 2023-02-09T21:54:41+01:00
python3.11.patch: restore in the d/t/series.
- - - - -
39b0fc1e by Étienne Mollier at 2023-02-09T21:58:34+01:00
d/control: build depends on liblapack-dev.
- - - - -
cb534611 by Étienne Mollier at 2023-02-09T22:35:48+01:00
python3.11.patch: hardcode .so extension.
The mechanism for identifying which extension to use doesn't work
anymore.
- - - - -
466c345a by Étienne Mollier at 2023-02-09T22:38:56+01:00
use_debian_packaged_dlib.patch: link python3 module too.
- - - - -
5ad1c155 by Étienne Mollier at 2023-02-09T22:50:10+01:00
update changelog.
- - - - -
6 changed files:
- debian/changelog
- debian/control
- debian/patches/python3.11.patch
- debian/patches/series
- debian/patches/use_debian_packaged_dlib.patch
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,5 +1,6 @@
vienna-rna (2.5.1+dfsg-1) UNRELEASED; urgency=medium
+ [ Andreas Tille ]
* Team upload.
* New upstream version
* Point watch file to github
@@ -8,8 +9,19 @@ vienna-rna (2.5.1+dfsg-1) UNRELEASED; urgency=medium
line 5-7.
* DEP3
* Build-Depends: libdlib-dev
-
- -- Andreas Tille <tille at debian.org> Wed, 08 Feb 2023 15:31:33 +0100
+ * Use Debian packaged dlib
+
+ [ Étienne Mollier ]
+ * d/control: build depends on liblapack-dev.
+ * use_debian_packaged_dlib.patch: link bin/ components against lapack.
+ * use_debian_packaged_dlib.patch: link also Perl modules.
+ * use_debian_packaged_dlib.patch: link also Python 3 module.
+ * d/rules: ventilate dh_auto_configure target.
+ * d/rules: upstream assumes --with-python is for python3 now.
+ * python3.11.patch: restore in the d/t/series.
+ * python3.11.patch: hardcode .so extension.
+
+ -- Étienne Mollier <emollier at debian.org> Thu, 09 Feb 2023 22:37:35 +0100
vienna-rna (2.4.17+dfsg-2) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -17,6 +17,7 @@ Build-Depends: debhelper-compat (= 13),
graphviz,
libdlib-dev,
libgsl-dev,
+ liblapack-dev,
libmpfr-dev,
libsvm-dev,
xxd,
=====================================
debian/patches/python3.11.patch
=====================================
@@ -1,16 +1,10 @@
Author: Andreas Tille <tille at debian.org>
Last-Update: Wed, 08 Feb 2023 15:31:33 +0100
Description: Attempt to get Python3 beeing detected in configure step
-FIXME: Log says:
-Scripting Language Interfaces
------------------------------
- * Perl 5 : yes
- * Python 3.x : no
- * Python 2.x : no
---- a/m4/ax_python3_devel.m4
-+++ b/m4/ax_python3_devel.m4
-@@ -3,7 +3,7 @@ AC_DEFUN([AX_PYTHON3_DEVEL],[
+--- vienna-rna.orig/m4/ax_python3_devel.m4
++++ vienna-rna/m4/ax_python3_devel.m4
+@@ -3,7 +3,7 @@
# (AM_PATH_PYTHON) cannot be used for multiple Python version at once
if test -z "$PYTHON3" ; then
@@ -19,3 +13,13 @@ Scripting Language Interfaces
fi
AC_ARG_VAR(PYTHON3, [Path to Python3 interpreter (e.g.: /usr/bin/python3)])
+@@ -63,8 +63,7 @@
+
+ AC_MSG_CHECKING([for Python3 module extension])
+ dnl Usually ".so", but for example, Mac OS X uses ".dylib".
+- PYTHON3_SO=`$PYTHON3 -c "import distutils.sysconfig; \
+- print(distutils.sysconfig.get_config_vars('SO')[[0]])"`
++ PYTHON3_SO=".so"
+ AC_SUBST(PYTHON3_SO)
+ AC_MSG_RESULT([$PYTHON3_SO])
+
=====================================
debian/patches/series
=====================================
@@ -1,4 +1,4 @@
g2.patch
tutorial.patch
use_debian_packaged_dlib.patch
-# python3.11.patch
+python3.11.patch
=====================================
debian/patches/use_debian_packaged_dlib.patch
=====================================
@@ -1,10 +1,10 @@
Author: Andreas Tille <tille at debian.org>
Last-Update: Wed, 08 Feb 2023 15:31:33 +0100
Description: Use Debian packaged dlib
-
---- a/m4/ac_rna_build_requirements.m4
-+++ b/m4/ac_rna_build_requirements.m4
-@@ -229,27 +229,28 @@ static const unsigned char parameter_set
+Reviewed-By: Étienne Mollier <emollier at debian.org>
+--- vienna-rna.orig/m4/ac_rna_build_requirements.m4
++++ vienna-rna/m4/ac_rna_build_requirements.m4
+@@ -229,27 +229,28 @@
AC_DEFUN([RNA_CHECK_DLIB], [
AX_CXX_COMPILE_STDCXX(11, noext, mandatory)
@@ -54,9 +54,9 @@ Description: Use Debian packaged dlib
])
---- a/src/ViennaRNA/Makefile.am
-+++ b/src/ViennaRNA/Makefile.am
-@@ -342,7 +342,6 @@ libRNA_eval_la_SOURCES = \
+--- vienna-rna.orig/src/ViennaRNA/Makefile.am
++++ vienna-rna/src/ViennaRNA/Makefile.am
+@@ -342,7 +342,6 @@
libRNA_concentrations_la_SOURCES = \
concentrations.c \
@@ -64,9 +64,9 @@ Description: Use Debian packaged dlib
wrap_dlib.cpp
---- a/src/Cluster/Makefile.am
-+++ b/src/Cluster/Makefile.am
-@@ -6,7 +6,7 @@ man_MANS = AnalyseDists.1 AnalyseSeqs.1
+--- vienna-rna.orig/src/Cluster/Makefile.am
++++ vienna-rna/src/Cluster/Makefile.am
+@@ -6,7 +6,7 @@
AM_CFLAGS = $(RNA_CFLAGS) $(PTHREAD_CFLAGS)
AM_CXXFLAGS = $(RNA_CXXFLAGS) $(PTHREAD_CFLAGS)
AM_CPPFLAGS = $(RNA_CPPFLAGS) -I$(top_srcdir)/src -I$(top_srcdir) -I$(top_builddir)
@@ -75,9 +75,9 @@ Description: Use Debian packaged dlib
if VRNA_AM_SWITCH_STATIC_EXECUTABLES
AM_LDFLAGS += -all-static
---- a/src/RNAforester/src/Makefile.am
-+++ b/src/RNAforester/src/Makefile.am
-@@ -15,6 +15,7 @@ AM_CPPFLAGS = -I${includedir}\
+--- vienna-rna.orig/src/RNAforester/src/Makefile.am
++++ vienna-rna/src/RNAforester/src/Makefile.am
+@@ -15,6 +15,7 @@
AM_CXXFLAGS = -Wall -std=c++98 #-fmudflap -funwind-tables
# C++ linker flags
#AM_LDFLAGS = -lmudflap
@@ -85,14 +85,34 @@ Description: Use Debian packaged dlib
BUILT_SOURCES = anchors/shape.hpp anchors/shape.cpp
---- a/src/bin/Makefile.am
-+++ b/src/bin/Makefile.am
-@@ -60,7 +60,7 @@ LDADD += $(SVM_LIBS)
+--- vienna-rna.orig/src/bin/Makefile.am
++++ vienna-rna/src/bin/Makefile.am
+@@ -60,7 +60,7 @@
endif
RNAmultifold_LDADD = $(LDADD)
-RNAmultifold_LDADD += -lstdc++
-+RNAmultifold_LDADD += -lstdc++ -ldlib
++RNAmultifold_LDADD += -lstdc++ -ldlib -llapack
GENGETOPT_CMDL = \
RNAfold_cmdl.c RNAfold_cmdl.h \
+--- vienna-rna.orig/interfaces/Perl/Makefile.am
++++ vienna-rna/interfaces/Perl/Makefile.am
+@@ -41,6 +41,7 @@
+
+ RNA_la_LIBADD = \
+ $(LDADD) \
++ -ldlib \
+ $(top_builddir)/src/ViennaRNA/libRNA_conv.la
+
+ if VRNA_AM_SWITCH_SVM
+--- vienna-rna.orig/interfaces/Python/Makefile.am
++++ vienna-rna/interfaces/Python/Makefile.am
+@@ -39,6 +39,7 @@
+
+ _RNA_la_LIBADD = \
+ $(LDADD) \
++ -ldlib \
+ $(top_builddir)/src/ViennaRNA/libRNA_conv.la
+
+ if VRNA_AM_SWITCH_SVM
=====================================
debian/rules
=====================================
@@ -6,8 +6,18 @@
override_dh_auto_configure:
- CFLAGS="-I/usr/include/json-c/ -I/usr/include/libsvm/" CXXFLAGS="-I/usr/include/json-c/ -I/usr/include/libsvm/" dh_auto_configure -- --with-cluster --without-python --with-python3 --without-forester --without-doc --without-tutorial
- if [ -r man/help2manWrapper.sh ]; then chmod +x man/help2manWrapper.sh; fi
+ CFLAGS="-I/usr/include/json-c/ -I/usr/include/libsvm/" \
+ CXXFLAGS="-I/usr/include/json-c/ -I/usr/include/libsvm/" \
+ dh_auto_configure -- \
+ --with-cluster \
+ --without-python2 \
+ --with-python \
+ --without-forester \
+ --without-doc \
+ --without-tutorial
+ if [ -r man/help2manWrapper.sh ] \
+ ; then chmod +x man/help2manWrapper.sh \
+ ; fi
override_dh_auto_build:
if [ ! -d src/cthreadpool ]; then \
View it on GitLab: https://salsa.debian.org/med-team/vienna-rna/-/compare/ef19559f915d44e0ddcb9ab83f84318da9df76ef...5ad1c155961e30a2d70abdfbb96628deb1a59622
--
View it on GitLab: https://salsa.debian.org/med-team/vienna-rna/-/compare/ef19559f915d44e0ddcb9ab83f84318da9df76ef...5ad1c155961e30a2d70abdfbb96628deb1a59622
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