[med-svn] [Git][med-team/libmems][master] 6 commits: Fix ftbfs with boost 1.90. Closes: #1127076.
Santiago Vila (@sanvila)
gitlab at salsa.debian.org
Mon Feb 16 18:51:54 GMT 2026
Santiago Vila pushed to branch master at Debian Med / libmems
Commits:
edcfccd5 by Santiago Vila at 2026-02-16T19:40:00+01:00
Fix ftbfs with boost 1.90. Closes: #1127076.
- - - - -
4d554e3f by Santiago Vila at 2026-02-16T19:41:00+01:00
libMems.pc.in: Drop @BOOST_SYSTEM_LDFLAGS@ (lintian error).
- - - - -
e86f9e77 by Santiago Vila at 2026-02-16T19:42:00+01:00
d/control: Drop "Priority: optional" (default).
- - - - -
eec5a7df by Santiago Vila at 2026-02-16T19:43:00+01:00
d/control: Update standards-version.
- - - - -
6ac5945e by Santiago Vila at 2026-02-16T19:44:00+01:00
d/salsa-ci.yml: Use the simplified version.
- - - - -
a23a8cfd by Santiago Vila at 2026-02-16T19:45:00+01:00
Upload for unstable as 1.6.0+4725-13
- - - - -
6 changed files:
- debian/changelog
- debian/control
- + debian/patches/boost1.90.patch
- + debian/patches/drop-boost-system-ldflags.patch
- debian/patches/series
- debian/salsa-ci.yml
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+libmems (1.6.0+4725-13) unstable; urgency=medium
+
+ * Team upload.
+ * Fix ftbfs with boost 1.90. Closes: #1127076.
+ * libMems.pc.in: Drop @BOOST_SYSTEM_LDFLAGS@ (lintian error).
+ * Drop "Priority: optional" (default).
+ * Update standards-version.
+ * Simplify salsa-ci.yml.
+
+ -- Santiago Vila <sanvila at debian.org> Mon, 16 Feb 2026 19:45:00 +0100
+
libmems (1.6.0+4725-12) unstable; urgency=medium
* boost1.88.patch: new: fix ftbfs with boost1.88. (Closes: #1110623)
=====================================
debian/control
=====================================
@@ -3,7 +3,6 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Andreas Tille <tille at debian.org>,
Étienne Mollier <emollier at debian.org>
Section: science
-Priority: optional
Build-Depends: dpkg-dev (>= 1.22.5),
debhelper-compat (= 13),
d-shlibs (>= 0.106~),
@@ -13,7 +12,7 @@ Build-Depends: dpkg-dev (>= 1.22.5),
libboost-iostreams-dev,
libboost-program-options-dev,
libmuscle-dev
-Standards-Version: 4.7.2
+Standards-Version: 4.7.3
Vcs-Browser: https://salsa.debian.org/med-team/libmems
Vcs-Git: https://salsa.debian.org/med-team/libmems.git
Homepage: http://sourceforge.net/p/mauve/code/HEAD/tree/libMems/trunk/
=====================================
debian/patches/boost1.90.patch
=====================================
@@ -0,0 +1,54 @@
+From: Matthias Klose <doko at debian.org>
+Subject: Fix FTBFS with boost 1.90
+Bug-Debian: https://bugs.debian.org/1127076
+
+--- a/m4/boost.m4
++++ b/m4/boost.m4
+@@ -563,7 +563,7 @@
+ # added as of 1.35.0. If we have a version <1.35, we must not attempt to
+ # find Boost.System as it didn't exist by then.
+ if test $boost_major_version -ge 135; then
+- BOOST_SYSTEM([$1])
++ :
+ fi # end of the Boost.System check.
+ boost_filesystem_save_LIBS=$LIBS
+ boost_filesystem_save_LDFLAGS=$LDFLAGS
+@@ -630,7 +630,7 @@
+ BOOST_CONTEXT([$1])
+ # Starting from Boost 1.55 a dependency on Boost.System is added
+ if test $boost_major_version -ge 155; then
+- BOOST_SYSTEM([$1])
++ :
+ fi
+ m4_pattern_allow([^BOOST_(CONTEXT|SYSTEM)_(LIBS|LDFLAGS)])
+ LIBS="$LIBS $BOOST_CONTEXT_LIBS $BOOST_SYSTEM_LIBS"
+@@ -685,7 +685,7 @@
+ # added as of 1.35.0. If we have a version <1.35, we must not attempt to
+ # find Boost.System as it didn't exist by then.
+ if test $boost_major_version -ge 135; then
+- BOOST_SYSTEM([$1])
++ :
+ fi # end of the Boost.System check.
+ boost_filesystem_save_LIBS=$LIBS
+ boost_filesystem_save_LDFLAGS=$LDFLAGS
+--- a/libMems.pc.in
++++ b/libMems.pc.in
+@@ -7,6 +7,6 @@
+ Description: c++ library supporting DNA sequence and genome alignment
+ Version: @VERSION@
+ Requires: libGenome libMUSCLE
+-Libs: -L${libdir} @OPENMP_CXXFLAGS@ -lMems @BOOST_SYSTEM_LDFLAGS@ @BOOST_SYSTEM_LIBS@ @BOOST_FILESYSTEM_LIBS@ @BOOST_PROGRAM_OPTIONS_LIBS@ @BOOST_IOSTREAMS_LIBS@ @LIBS@
++Libs: -L${libdir} @OPENMP_CXXFLAGS@ -lMems @BOOST_SYSTEM_LDFLAGS@ @BOOST_FILESYSTEM_LIBS@ @BOOST_PROGRAM_OPTIONS_LIBS@ @BOOST_IOSTREAMS_LIBS@ @LIBS@
+ Cflags: -I${includedir}/@GENERIC_LIBRARY_NAME@ @BOOST_CPPFLAGS@ @OPENMP_CXXFLAGS@ @EXTRA_CXX_FLAGS@
+
+--- a/libMems/Makefile.am
++++ b/libMems/Makefile.am
+@@ -61,7 +61,7 @@
+ # build libraries with gcc (no suffix)
+ lib_LTLIBRARIES = libMems.la
+ libMems_la_SOURCES = $(LIBMEMS_SRC) $(HOMOLOGYHMM_SRC) $(DMSML_SRC)
+-libMems_la_LIBADD = @DEPS_LIBS@ @BOOST_FILESYSTEM_LIBS@ @BOOST_IOSTREAMS_LIBS@ @BOOST_SYSTEM_LIBS@
++libMems_la_LIBADD = @DEPS_LIBS@ @BOOST_FILESYSTEM_LIBS@ @BOOST_IOSTREAMS_LIBS@
+ libMems_la_LDFLAGS= -version-info $(GENERIC_LIBRARY_VERSION)
+
+ homologyhmm_includedir=$(includedir)/$(GENERIC_LIBRARY_NAME)/HomologyHMM
=====================================
debian/patches/drop-boost-system-ldflags.patch
=====================================
@@ -0,0 +1,13 @@
+From: Santiago Vila <sanvila at debian.org>
+Subject: Drop @BOOST_SYSTEM_LDFLAGS@
+
+--- a/libMems.pc.in
++++ b/libMems.pc.in
+@@ -7,6 +7,6 @@
+ Description: c++ library supporting DNA sequence and genome alignment
+ Version: @VERSION@
+ Requires: libGenome libMUSCLE
+-Libs: -L${libdir} @OPENMP_CXXFLAGS@ -lMems @BOOST_SYSTEM_LDFLAGS@ @BOOST_FILESYSTEM_LIBS@ @BOOST_PROGRAM_OPTIONS_LIBS@ @BOOST_IOSTREAMS_LIBS@ @LIBS@
++Libs: -L${libdir} @OPENMP_CXXFLAGS@ -lMems @BOOST_FILESYSTEM_LIBS@ @BOOST_PROGRAM_OPTIONS_LIBS@ @BOOST_IOSTREAMS_LIBS@ @LIBS@
+ Cflags: -I${includedir}/@GENERIC_LIBRARY_NAME@ @BOOST_CPPFLAGS@ @OPENMP_CXXFLAGS@ @EXTRA_CXX_FLAGS@
+
=====================================
debian/patches/series
=====================================
@@ -10,3 +10,5 @@ drop-version-number.patch
fix-system.patch
gcc-14.patch
boost1.88.patch
+boost1.90.patch
+drop-boost-system-ldflags.patch
=====================================
debian/salsa-ci.yml
=====================================
@@ -1,4 +1,3 @@
---
include:
- - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
- - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/recipes/debian.yml
View it on GitLab: https://salsa.debian.org/med-team/libmems/-/compare/b68c1b3b94fba1e0240afd7016676125991fcdb4...a23a8cfdf3f8993c2f46533a46662010deded2db
--
View it on GitLab: https://salsa.debian.org/med-team/libmems/-/compare/b68c1b3b94fba1e0240afd7016676125991fcdb4...a23a8cfdf3f8993c2f46533a46662010deded2db
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