[med-svn] [Git][med-team/abyss][master] 4 commits: mpi-libs.patch: new: fix a link error against openmpi.

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / abyss


Commits:
6c7988b1 by Étienne Mollier at 2026-10-17T17:39:23+02:00
mpi-libs.patch: new: fix a link error against openmpi.

Closes: #1150081

- - - - -
679644db by Étienne Mollier at 2026-10-17T17:41:50+02:00
d/control: declare compliance to standards version 4.7.4.

- - - - -
dcbfcfe3 by Étienne Mollier at 2026-10-17T17:42:42+02:00
d/control: bump to debhelper 14 in single-binary mode.

- - - - -
c19cca6f by Étienne Mollier at 2026-10-17T17:51:19+02:00
d/changelog: ready for upload to unstable.

- - - - -


4 changed files:

- debian/changelog
- debian/control
- + debian/patches/mpi-libs.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+abyss (2.3.10-3) unstable; urgency=medium
+
+  * mpi-libs.patch: new: fix a link error against openmpi. (Closes: #1150081)
+  * d/control: declare compliance to standards version 4.7.4.
+  * d/control: bump to debhelper 14 in single-binary mode.
+
+ -- Étienne Mollier <emollier at debian.org>  Sat, 17 Oct 2026 17:43:32 +0200
+
 abyss (2.3.10-2) unstable; urgency=medium
 
   [ Michael R. Crusoe ]


=====================================
debian/control
=====================================
@@ -4,7 +4,8 @@ Uploaders: Andreas Tille <tille at debian.org>,
            Michael R. Crusoe <crusoe at debian.org>,
            Étienne Mollier <emollier at debian.org>
 Section: science
-Build-Depends: debhelper-compat (= 13),
+Build-Depends: debhelper-compat (= 14),
+               dh-sequence-single-binary,
                architecture-is-64-bit,
                libboost-graph-dev,
                libbtllib-dev,
@@ -15,7 +16,7 @@ Build-Depends: debhelper-compat (= 13),
                pkgconf,
                help2man,
                debhelper
-Standards-Version: 4.7.3
+Standards-Version: 4.7.4
 Vcs-Browser: https://salsa.debian.org/med-team/abyss
 Vcs-Git: https://salsa.debian.org/med-team/abyss.git
 Homepage: https://github.com/bcgsc/abyss


=====================================
debian/patches/mpi-libs.patch
=====================================
@@ -0,0 +1,35 @@
+Description: fix link failure due to missing libraries.
+ This change works around the failure to link ABYSS-P, having following
+ symptoms by injecting a `pkgconf --libs mpi` strategically:
+ .
+        x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/x86_64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o ABYSS-P ABYSS_P-parallelAbyss.o ABYSS_P-CommLayer.o ABYSS_P-NetworkSequenceCollection.o ABYSS_P-MessageBuffer.o ABYSS_P-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm  -lmpi  -ldl -lm
+        /usr/bin/x86_64-linux-gnu-ld.bfd: ABYSS_P-CommLayer.o: undefined reference to symbol 'ompi_mpi_unsigned_long_long'
+        /usr/bin/x86_64-linux-gnu-ld.bfd: /usr/lib/x86_64-linux-gnu/libopen_mpi.so.40: error adding symbols: DSO missing from command line
+        collect2: error: ld returned 1 exit status
+ .
+ There are probably more appropriate approaches than hijacking the file
+ Parallel/Makefile.am for this, but it does the job.
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/1150081
+Forwarded: no
+Last-Update: 2026-10-17
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- abyss.orig/Parallel/Makefile.am
++++ abyss/Parallel/Makefile.am
+@@ -4,6 +4,7 @@
+ endif
+ 
+ libdb = $(top_builddir)/DataBase/libdb.a $(SQLITE_LIBS)
++pkgconf_libs != pkgconf --libs mpi
+ 
+ ABYSS_P_CPPFLAGS = -I$(top_srcdir)
+ 
+@@ -12,6 +13,7 @@
+ 	$(top_builddir)/Common/libcommon.a \
+ 	$(top_builddir)/DataLayer/libdatalayer.a \
+ 	$(libdb) \
++	$(pkgconf_libs) \
+ 	$(MPI_LIBS)
+ 
+ ABYSS_P_SOURCES = \


=====================================
debian/patches/series
=====================================
@@ -3,3 +3,4 @@ abyss-pe.patch
 #abyss-32-bit.patch
 fix-privacy-breach.patch
 gcc-16.patch
+mpi-libs.patch



View it on GitLab: https://salsa.debian.org/med-team/abyss/-/compare/0ea0298e405d2e016a8026f84deb63e53a6679f2...c19cca6fa8002f8132c5e8496b958f2774946669

-- 
View it on GitLab: https://salsa.debian.org/med-team/abyss/-/compare/0ea0298e405d2e016a8026f84deb63e53a6679f2...c19cca6fa8002f8132c5e8496b958f2774946669
You're receiving this email because of your account on salsa.debian.org. Manage all notifications: https://salsa.debian.org/-/profile/notifications | Help: https://salsa.debian.org/help


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20261017/cca8e0b8/attachment-0001.htm>