Your message dated Sat, 12 Aug 2023 22:33:51 +0000 with message-id <e1quxb9-00fdui...@fasolo.debian.org> and subject line Bug#1037817: fixed in phyx 1.3.1+ds-1 has caused the Debian Bug report #1037817, regarding phyx: FTBFS: E: Build killed with signal TERM after 150 minutes of inactivity 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 ow...@bugs.debian.org immediately.) -- 1037817: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1037817 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: phyx Version: 1.3+ds-2 Severity: serious Justification: FTBFS Tags: trixie sid ftbfs User: lu...@debian.org Usertags: ftbfs-20230724 ftbfs-trixie Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part (hopefully): > cat man/pxbdfit.1.in > man/pxbdfit.1 > cat man/pxseqgen.1.in > man/pxseqgen.1 > building pxcontrates > g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong > -Wformat -Werror=format-security -o "pxcontrates" -O3 -std=c++14 -fopenmp > -Wall -DOMP -ftree-vectorize -ffast-math main_contrates.o > optimize_cont_models_nlopt.o ./rate_model.o ./state_reconstructor.o > ./optimize_state_reconstructor_nlopt.o > ./optimize_state_reconstructor_periods_nlopt.o ./branch_segment.o > ./cont_models.o ./seq_gen.o ./utils.o ./citations.o ./log.o ./superdouble.o > ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o > ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o > -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -llapack -lblas > -lpthread -lm -lnlopt -larmadillo > cat man/pxcontrates.1.in > man/pxcontrates.1 > building pxstrec > g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong > -Wformat -Werror=format-security -o "pxstrec" -O3 -std=c++14 -fopenmp -Wall > -DOMP -ftree-vectorize -ffast-math main_strec.o ./utils.o ./citations.o > ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o > ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o > ./tree_utils.o ./rate_model.o ./state_reconstructor.o > ./optimize_state_reconstructor_nlopt.o > ./optimize_state_reconstructor_periods_nlopt.o ./branch_segment.o > ./cont_models.o ./seq_gen.o -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro > -Wl,-z,now -llapack -lblas -lpthread -lm -lnlopt -larmadillo # -lgfortran > cat man/pxstrec.1.in > man/pxstrec.1 > make[1]: Leaving directory '/<<PKGBUILDDIR>>/src' > debian/rules override_dh_auto_test > make[1]: Entering directory '/<<PKGBUILDDIR>>' > cd src && python3 run_tests.py > character: 0 > character: 1 > character: 2 > E: Build killed with signal TERM after 150 minutes of inactivity The full build log is available from: http://qa-logs.debian.net/2023/07/24/phyx_1.3+ds-2_unstable.log All bugs filed during this archive rebuild are listed at: https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20230724;users=lu...@debian.org or: https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20230724&fusertaguser=lu...@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results A list of current common problems and possible solutions is available at http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute! If you reassign this bug to another package, please mark it as 'affects'-ing this package. See https://www.debian.org/Bugs/server-control#affects If you fail to reproduce this, please provide a build log and diff it with mine so that we can identify if something relevant changed in the meantime.
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--- Begin Message ---Source: phyx Source-Version: 1.3.1+ds-1 Done: Étienne Mollier <emoll...@debian.org> We believe that the bug you reported is fixed in the latest version of phyx, 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 1037...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Étienne Mollier <emoll...@debian.org> (supplier of updated phyx 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 ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Sun, 13 Aug 2023 00:01:53 +0200 Source: phyx Architecture: source Version: 1.3.1+ds-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Étienne Mollier <emoll...@debian.org> Closes: 1037817 Changes: phyx (1.3.1+ds-1) unstable; urgency=medium . * Team upload. * New upstream version * Standards-Version: 4.6.2 (routine-update) * hardening.patch: delete: applied upstream. * build-more-programs.patch: refresh. * deoptimize.patch: new: fix ftbfs with gcc-13. This disables building phyx with -ffast-math. (Closes: #1037817) * d/rules: remove -ffloat-store for i386. Upstream included this change in their build routines. Checksums-Sha1: 6f11a4412fb4761d3c123fffedd2a4c841366c25 2130 phyx_1.3.1+ds-1.dsc b91fef57e035c34bf92fedc8d7dbc8cad0fbed0c 1191388 phyx_1.3.1+ds.orig.tar.xz fc2f153f87b665ca3854acd99edd44ac24f6cdd2 6256 phyx_1.3.1+ds-1.debian.tar.xz Checksums-Sha256: a5d3e9a5837f9f27162efff5c28dd7a6251fa5aa51f4e2bea6250cd8790a64c9 2130 phyx_1.3.1+ds-1.dsc ab788a470997954c3cec6a4b60d2d131ca3f129a3f8946f4b63041abeba35b53 1191388 phyx_1.3.1+ds.orig.tar.xz 36803c2bee221eed70235dd3d3ab7f614406fe8716f3950b02f64222737c5393 6256 phyx_1.3.1+ds-1.debian.tar.xz Files: ea49077b73de9b8f0f6156b6a645f43b 2130 science optional phyx_1.3.1+ds-1.dsc 874ffc6583f2de805514029b216d75a6 1191388 science optional phyx_1.3.1+ds.orig.tar.xz abc46987ebf1c3a965f87140aed8667a 6256 science optional phyx_1.3.1+ds-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmTYBLUUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdpzDhAAtteJKZcaeAPwlibjc4TDeeh1q3BP RETkTY+GzT15OZfbD6ncwsOploPLMJFCXeJPcrro/mT7NmklpDx+4lYahKPFWbmc IPdfmBY9TDzl5iuyEGjF3bMYnFlQ2+pn4VcBGZvosHonOPgIFNOUrqqqRUrHNFvp 3hmgVuxIFANMrqf2RsNKLj3YIW/qDW0NyH5bNzz5AJxGz8VKxsiqP/aKLCg+QF0d 81zGvwHW6eXtyXM+UTDLKOFo+5aV3Wl7wFvch8dudW2OMWawrBjwi41z6sCany52 NdlQQuHGlFgY+84Louto/N4Q4YZcWo6PUWGibFAvcfeCvVyl857Hu27QDPxWwHfM 7OOEzcmOCzXgFW2UjTmkpWyBB9mZrmjyRzCHZljKoH8oC48dMkIcfVI98Cn7gfOy dl9paDM1iz+BAR8n01kLSAhvlsMXJcFgWTqLa2G3Y9r6a35dLqYBCeq4KwC+Sq6a JbH/QF8sy3/K6a1OMaK7nxWHszAVnRSvXVwKNPdXwLM5p7ZPyN/PfaQbfaxz4Mt7 6HPH3v/IW1OHtJzUaGWgalswijzqTM8K+VKgFDe3ZemAvyHDxOnjaPGyiZgDEWdO hrrqyR+T4YA155m6eLHurN2mJtFFfskgSd0O5ON1aHGshBt3RbiMMGGQSaPlrP4U xpUiXtObNjX/3OE= =gWGP -----END PGP SIGNATURE-----
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