Étienne Mollier pushed to branch master at Debian Med / prime-phylo
Commits: df7afa8c by Étienne Mollier at 2024-11-03T13:41:29+01:00 openmpi5.patch: new: fix build failure with openmpi 5. Closes: #1086370 - - - - - 7615f79a by Étienne Mollier at 2024-11-03T13:42:07+01:00 d/lintian-overrides: flag rpath, needed for openmpi. - - - - - 6fcac14e by Étienne Mollier at 2024-11-03T13:42:53+01:00 d/changelog: ready for upload to unstable. - - - - - 4 changed files: - debian/changelog - debian/lintian-overrides - + debian/patches/openmpi5.patch - debian/patches/series Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,10 @@ +prime-phylo (1.0.11-13) unstable; urgency=medium + + * openmpi5.patch: new: fix build failure with openmpi 5. (Closes: #1086370) + * d/lintian-overrides: flag rpath, needed for openmpi. + + -- Étienne Mollier <[email protected]> Sun, 03 Nov 2024 13:42:41 +0100 + prime-phylo (1.0.11-12) unstable; urgency=medium * gcc-14.patch: fix improper use of close(2) by using fclose(3). ===================================== debian/lintian-overrides ===================================== @@ -4,3 +4,8 @@ spelling-error-in-binary WIh With [usr/lib/prime-phylo/libprime-phylo.so] spelling-error-in-binary defaul default [usr/bin/primeDTLSR] spelling-error-in-binary ofthe of the [usr/bin/chainsaw] + +# DT_RUNPATH needs to be set so these binaries are able to locate their +# openmpi resources, otherwise executables fail to run properly. +custom-library-search-path RUNPATH /usr/lib/x86_64-linux-gnu/openmpi/lib [usr/bin/*] +custom-library-search-path RUNPATH /usr/lib/x86_64-linux-gnu/openmpi/lib [usr/lib/prime-phylo/libprime-phylo.so] ===================================== debian/patches/openmpi5.patch ===================================== @@ -0,0 +1,46 @@ +Description: remove inclusion of mpicxx.h. + The header is not provided by openmpi 5 anymore, resulting in several + instances of: + . + /<<PKGBUILDDIR>>/src/cxx/libraries/prime/MpiMCMC.cc:11:10: fatal error: mpicxx.h: No such file or directory + 11 | #include "mpicxx.h" + | ^~~~~~~~~~ + . + It seems that plain drop of the header file is sufficient to put the + build back on tracks. +Author: Étienne Mollier <[email protected]> +Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1086370 +Forwarded: no +Last-Update: 2024-11-03 +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- prime-phylo.orig/src/cxx/libraries/prime/MpiMCMC.cc ++++ prime-phylo/src/cxx/libraries/prime/MpiMCMC.cc +@@ -8,7 +8,6 @@ + #include "MpiMCMC.hh" + #include "MCMCModel.hh" + #include "MCMCObject.hh" +-#include "mpicxx.h" + #include "PRNG.hh" + + +--- prime-phylo.orig/src/cxx/libraries/prime/MpiMultiGSR.cc ++++ prime-phylo/src/cxx/libraries/prime/MpiMultiGSR.cc +@@ -9,7 +9,6 @@ + #include "Probability.hh" + #include "TreeIO.hh" + #include "TreeIOTraits.hh" +-#include "mpicxx.h" + #include "TreePerturbationEvent.hh" + #include <iostream> + #include <sstream> +--- prime-phylo.orig/src/cxx/libraries/prime/MultiGSR.cc ++++ prime-phylo/src/cxx/libraries/prime/MultiGSR.cc +@@ -9,7 +9,6 @@ + #include "Probability.hh" + #include "TreeIO.hh" + #include "TreeIOTraits.hh" +-#include "mpicxx.h" + #include "TreePerturbationEvent.hh" + #include <iostream> + #include <sstream> ===================================== debian/patches/series ===================================== @@ -6,3 +6,4 @@ fix-gcc-8.patch fix-ftbfs-with-gcc13.patch gcc-14.patch typos.patch +openmpi5.patch View it on GitLab: https://salsa.debian.org/med-team/prime-phylo/-/compare/659d3d7e97b0897aa8d9d8a487b0271dbc244512...6fcac14e1e5e6bf0e1700c742ea1f0c8b8aaf3b0 -- View it on GitLab: https://salsa.debian.org/med-team/prime-phylo/-/compare/659d3d7e97b0897aa8d9d8a487b0271dbc244512...6fcac14e1e5e6bf0e1700c742ea1f0c8b8aaf3b0 You're receiving this email because of your account on salsa.debian.org.
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