Your message dated Sat, 06 Dec 2025 22:34:36 +0000
with message-id <[email protected]>
and subject line Bug#1106652: fixed in phyml 3:3.3.20250515-1
has caused the Debian Bug report #1106652,
regarding phyml FTCBFS: cross compilation support reverted
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1106652: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1106652
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: phyml
Version: 3:3.3.20220408-4
Tags: patch upstream
User: [email protected]
Usertags: ftcbfs
Hi,
I'm sorry for my earlier patch having broken phyml on 32bit
architectures. Reverting it was the right thing to do. Thanks for taking
that action.
Now of course we're back to phyml failing to cross build. I'm asking for
a compromise now. Rather than switch from mpicc to pkgconf, how about
trying pkgconf and falling back to mpicc?
* When compiling for 64bit case, openmpi will provide mpi-c.pc, so
that'll be used.
* When compiling natively on 32bit, mpi-c.pc will be missing and mpicc
will be used.
* Cross compiling for 32bit will be broken.
I see two advantages here. One is that we can then generally test cross
building phyml and will see other possible regressions (on 64bit
architectures). The other is that I can use phyml as a test case for
sending patches to mpich.
The patch likely is not appropriate for trixie. How about adding it
early in forky?
Helmut
Author: Helmut Grohne <[email protected]>
Last-Update: 2025-05-27
Bug-Debian: https://bugs.debian.org/902433
Description: Use MPI_C to enable cross building
--- phyml-3.3.20220408.orig/configure.ac
+++ phyml-3.3.20220408/configure.ac
@@ -105,7 +105,8 @@
AC_ARG_ENABLE([phyml-mpi],
[AS_HELP_STRING([--enable-phyml-mpi],
[Compile with mpicc instead of gcc.])])
-AS_IF([test "x$enable_phyml_mpi" = "xyes"],[CC="mpicc"])
+AS_IF([test "x$enable_phyml_mpi" = "xyes"],
+ [PKG_CHECK_MODULES([MPI_C],[mpi-c],,[CC="mpicc"])])
AS_IF([test "x$enable_phyml_mpi" = "xyes"],AC_DEFINE([MPI],[1],[MPI tag on]))
AM_CONDITIONAL([WANT_MPI], [test "$enable_phyml_mpi" = yes])
--- phyml-3.3.20220408.orig/src/Makefile.am
+++ phyml-3.3.20220408/src/Makefile.am
@@ -187,7 +187,8 @@
avx.c avx.h\
ancestral.c ancestral.h\
mpi_boot.c mpi_boot.h
-phyml_mpi_LDADD = -lm
+phyml_mpi_CFLAGS = $(MPI_C_CFLAGS)
+phyml_mpi_LDADD = -lm $(MPI_C_LIBS)
else
if WANT_WIN
phyml_windows_SOURCES = main.c \
--- End Message ---
--- Begin Message ---
Source: phyml
Source-Version: 3:3.3.20250515-1
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
phyml, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated phyml package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sat, 06 Dec 2025 23:08:00 +0100
Source: phyml
Architecture: source
Version: 3:3.3.20250515-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 1106652
Changes:
phyml (3:3.3.20250515-1) unstable; urgency=medium
.
* Restrict to 64 bit architectures only by Build-Depending
architecture-is-64-bit
Closes: #1106652
* d/watch: version=5
* New upstream version
* Standards-Version: 4.7.2 (routine-update)
* Work around broken clean target
Checksums-Sha1:
298b616b985f68e5b78d6ba11324ad10a06f7a24 2156 phyml_3.3.20250515-1.dsc
3ea58074cbeabbf598f1ca5604e19857fc3b7d2a 2002728 phyml_3.3.20250515.orig.tar.gz
10f6c5c6d7129c0adf831a6f1f6ad9abc744feee 27628
phyml_3.3.20250515-1.debian.tar.xz
e7ca8ea568c88e4e475a58b7d227c6be1f325cb9 8321
phyml_3.3.20250515-1_amd64.buildinfo
Checksums-Sha256:
61310535274458e75b5aeed087be3860db1c2e0b849b280a696188c07c3fdb72 2156
phyml_3.3.20250515-1.dsc
ae8dae7182169d40ac9cdfd7a07a1236fcf3dd526ead593103fe9768dc6b6d10 2002728
phyml_3.3.20250515.orig.tar.gz
bfab6830dd0d17806551da1451067f4cf4bed26536c7eec89f2ee1afc6068a1e 27628
phyml_3.3.20250515-1.debian.tar.xz
796e70d041547c402e561b896208e6b0bd5b8a293bc53c33bd144c1daa034c07 8321
phyml_3.3.20250515-1_amd64.buildinfo
Files:
07c392d6bad8908ae5756d83bbad65a6 2156 science optional phyml_3.3.20250515-1.dsc
beb8c207a66818b1bd2b7e130aaa80cc 2002728 science optional
phyml_3.3.20250515.orig.tar.gz
07d0758a8b2f5815e6fcd2a285fc91e5 27628 science optional
phyml_3.3.20250515-1.debian.tar.xz
0fbe5ac73cdc4794282c9ccc8f266008 8321 science optional
phyml_3.3.20250515-1_amd64.buildinfo
-----BEGIN PGP SIGNATURE-----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=DwQE
-----END PGP SIGNATURE-----
pgpYZ7Kc9hTKR.pgp
Description: PGP signature
--- End Message ---
