[med-svn] [Git][med-team/prime-phylo][master] 3 commits: openmpi5.patch: new: fix build failure with openmpi 5.

[Étienne Mollier (@emollier)]

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 <emollier at debian.org>  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 <emollier at debian.org>
+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
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