Your message dated Thu, 11 Apr 2024 14:49:02 +0000
with message-id <e1ruvja-00abfn...@fasolo.debian.org>
and subject line Bug#1066386: fixed in examl 3.0.22-5
has caused the Debian Bug report #1066386,
regarding examl: FTBFS: quartets.c:393:31: error: implicit declaration of
function ‘basename’; did you mean ‘rename’?
[-Werror=implicit-function-declaration]
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.)
--
1066386: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1066386
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: examl
Version: 3.0.22-4
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lu...@debian.org
Usertags: ftbfs-20240313 ftbfs-trixie ftbfs-impfuncdef
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
This is most likely caused by a change in dpkg 1.22.6, that enabled
-Werror=implicit-function-declaration. For more information, see
https://wiki.debian.org/qa.debian.org/FTBFS#A2024-03-13_-Werror.3Dimplicit-function-declaration
Relevant part (hopefully):
> make[2]: Entering directory '/<<PKGBUILDDIR>>/examl'
> rm -f *.o examl-avx2
> mpicc -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
> -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -mavx2 -Wdate-time
> -D_FORTIFY_SOURCE=2 -c -o axml.o axml.c
> In function ‘initializePartitions’,
> inlined from ‘initializeTree’ at axml.c:2217:3,
> inlined from ‘main’ at axml.c:2631:5:
> axml.c:2121:40: warning: argument 1 range [18446744071562067968,
> 18446744073709551615] exceeds maximum object size 9223372036854775807
> [-Walloc-size-larger-than=]
> 2121 | *modelWeights = (unsigned long*) calloc(tr->NumberOfModels,
> sizeof(unsigned long));
> |
> ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> In file included from axml.c:44:
> /usr/include/stdlib.h: In function ‘main’:
> /usr/include/stdlib.h:556:14: note: in a call to allocation function ‘calloc’
> declared here
> 556 | extern void *calloc (size_t __nmemb, size_t __size)
> | ^~~~~~
> mpicc -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
> -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -mavx2 -Wdate-time
> -D_FORTIFY_SOURCE=2 -c -o optimizeModel.o optimizeModel.c
> mpicc -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
> -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -mavx2 -Wdate-time
> -D_FORTIFY_SOURCE=2 -c -o trash.o trash.c
> mpicc -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
> -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -mavx2 -Wdate-time
> -D_FORTIFY_SOURCE=2 -c -o searchAlgo.o searchAlgo.c
> mpicc -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
> -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -mavx2 -Wdate-time
> -D_FORTIFY_SOURCE=2 -c -o topologies.o topologies.c
> mpicc -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
> -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -mavx2 -Wdate-time
> -D_FORTIFY_SOURCE=2 -c -o treeIO.o treeIO.c
> mpicc -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
> -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -mavx2 -D_OPTIMIZED_FUNCTIONS
> -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D_USE_ALLREDUCE -O1
> -Wdate-time -D_FORTIFY_SOURCE=2 -c -o models.o models.c
> mpicc -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
> -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -mavx2 -Wdate-time
> -D_FORTIFY_SOURCE=2 -c -o evaluatePartialGenericSpecial.o
> evaluatePartialGenericSpecial.c
> mpicc -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
> -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -mavx2 -Wdate-time
> -D_FORTIFY_SOURCE=2 -c -o evaluateGenericSpecial.o evaluateGenericSpecial.c
> mpicc -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
> -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -mavx2 -Wdate-time
> -D_FORTIFY_SOURCE=2 -c -o newviewGenericSpecial.o newviewGenericSpecial.c
> mpicc -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
> -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -mavx2 -Wdate-time
> -D_FORTIFY_SOURCE=2 -c -o makenewzGenericSpecial.o makenewzGenericSpecial.c
> mpicc -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
> -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -mavx2 -Wdate-time
> -D_FORTIFY_SOURCE=2 -c -o bipartitionList.o bipartitionList.c
> mpicc -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
> -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -mavx2 -Wdate-time
> -D_FORTIFY_SOURCE=2 -c -o restartHashTable.o restartHashTable.c
> mpicc -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
> -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -mavx2 -Wdate-time
> -D_FORTIFY_SOURCE=2 -c -o avxLikelihood.o avxLikelihood.c
> mpicc -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
> -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -mavx2 -Wdate-time
> -D_FORTIFY_SOURCE=2 -c -o byteFile.o byteFile.c
> mpicc -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
> -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -mavx2 -Wdate-time
> -D_FORTIFY_SOURCE=2 -c -o partitionAssignment.o partitionAssignment.c
> mpicc -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
> -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -mavx2 -Wdate-time
> -D_FORTIFY_SOURCE=2 -c -o communication.o communication.c
> mpicc -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
> -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
> -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -mavx2 -Wdate-time
> -D_FORTIFY_SOURCE=2 -c -o quartets.o quartets.c
> quartets.c: In function ‘computeQuartets’:
> quartets.c:393:31: error: implicit declaration of function ‘basename’; did
> you mean ‘rename’? [-Werror=implicit-function-declaration]
> 393 | strcat(quartetFileName, basename(ckp.quartetFileName));
> | ^~~~~~~~
> | rename
> quartets.c:393:31: warning: passing argument 2 of ‘strcat’ makes pointer from
> integer without a cast [-Wint-conversion]
> 393 | strcat(quartetFileName, basename(ckp.quartetFileName));
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> | |
> | int
> In file included from /usr/include/features.h:490,
> from
> /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33,
> from /usr/include/limits.h:26,
> from /usr/lib/gcc/x86_64-linux-gnu/13/include/limits.h:205,
> from /usr/lib/gcc/x86_64-linux-gnu/13/include/syslimits.h:7,
> from /usr/lib/gcc/x86_64-linux-gnu/13/include/limits.h:34,
> from quartets.c:36:
> /usr/include/x86_64-linux-gnu/bits/string_fortified.h:128:1: note: expected
> ‘const char * restrict’ but argument is of type ‘int’
> 128 | __NTH (strcat (char *__restrict __dest, const char *__restrict __src))
> | ^~~~~
> cc1: some warnings being treated as errors
> make[2]: *** [<builtin>: quartets.o] Error 1
The full build log is available from:
http://qa-logs.debian.net/2024/03/13/examl_3.0.22-4_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20240313;users=lu...@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20240313&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.
--- End Message ---
--- Begin Message ---
Source: examl
Source-Version: 3.0.22-5
Done: Andreas Tille <ti...@debian.org>
We believe that the bug you reported is fixed in the latest version of
examl, 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 1066...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated examl 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: Thu, 11 Apr 2024 16:21:07 +0200
Source: examl
Architecture: source
Version: 3.0.22-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Closes: 1066386
Changes:
examl (3.0.22-5) unstable; urgency=medium
.
* Add missing include
Closes: #1066386
* Standards-Version: 4.7.0 (routine-update)
Checksums-Sha1:
2e04fe4346031435340fe9758a67ea6d10965a0b 2012 examl_3.0.22-5.dsc
ad34d9f9446dcf8a73841a353838ad601bca9c3d 27288 examl_3.0.22-5.debian.tar.xz
f6f42837b660cfb8fa5956377520a201a695e7c5 8455 examl_3.0.22-5_amd64.buildinfo
Checksums-Sha256:
08771df81cacae49f9928d1c811cfa92003542ffce94785936e959c79c119609 2012
examl_3.0.22-5.dsc
6e8e414b0dc7b91dc2a7a3eb3088ce87c16e166b458eafb4a8eae8bc69cb1748 27288
examl_3.0.22-5.debian.tar.xz
6d4e8d5f298cb94535f16ee22f4b677c040de6aeee31a515721278e3f0029870 8455
examl_3.0.22-5_amd64.buildinfo
Files:
2084d0152c05868a0a5c8d7e5ac767b8 2012 science optional examl_3.0.22-5.dsc
0c5840ca661a83ac09967b38fe7fcc32 27288 science optional
examl_3.0.22-5.debian.tar.xz
1c340dcf4ff707299b35d5cd4ac44b4e 8455 science optional
examl_3.0.22-5_amd64.buildinfo
-----BEGIN PGP SIGNATURE-----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=/uQj
-----END PGP SIGNATURE-----
pgpUJYekeiSqw.pgp
Description: PGP signature
--- End Message ---
