Your message dated Thu, 27 Jun 2024 09:57:43 +0000
with message-id <e1smlst-00g4r2...@fasolo.debian.org>
and subject line Bug#1073355: fixed in ghmm 0.9~rc3-7
has caused the Debian Bug report #1073355,
regarding ghmm: FTBFS: xmlwriter.c:1105:5: error: implicit declaration of
function ‘xmlSubstituteEntitiesDefault’ [-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
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immediately.)
--
1073355: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1073355
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: ghmm
Version: 0.9~rc3-6
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lu...@debian.org
Usertags: ftbfs-20240615 ftbfs-trixie
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I..
> -I.. -Wdate-time -D_FORTIFY_SOURCE=2
> -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2
> -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
> -fstack-protector-strong -fstack-clash-protection -Wformat
> -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu
> -I/usr/include/libxml2 -c -o foba.lo foba.c
> xmlwriter.c: In function ‘ghmm_xmlfile_write’:
> xmlwriter.c:1105:5: error: implicit declaration of function
> ‘xmlSubstituteEntitiesDefault’ [-Werror=implicit-function-declaration]
> 1105 | xmlSubstituteEntitiesDefault(1);
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
> xmlwriter.c:1166:3: error: implicit declaration of function
> ‘xmlCleanupParser’ [-Werror=implicit-function-declaration]
> 1166 | xmlCleanupParser();
> | ^~~~~~~~~~~~~~~~
> /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I..
> -I.. -Wdate-time -D_FORTIFY_SOURCE=2
> -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2
> -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
> -fstack-protector-strong -fstack-clash-protection -Wformat
> -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu
> -I/usr/include/libxml2 -c -o viterbi.lo viterbi.c
> model.c: In function ‘ghmm_dmodel_free’:
> model.c:632:33: warning: macro "__DATE__" might prevent reproducible builds
> [-Wdate-time]
> 632 | mes_check_ptr (mo, return (-1));
> | ^
> model.c:634:32: warning: macro "__DATE__" might prevent reproducible builds
> [-Wdate-time]
> 634 | mes_check_ptr (m, return (-1));
> | ^
> model.c: In function ‘ghmm_dstate_clean’:
> model.c:1758:35: warning: macro "__DATE__" might prevent reproducible builds
> [-Wdate-time]
> 1758 | mes_check_ptr (my_state, return;);
> | ^
> /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I..
> -I.. -Wdate-time -D_FORTIFY_SOURCE=2
> -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2
> -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
> -fstack-protector-strong -fstack-clash-protection -Wformat
> -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu
> -I/usr/include/libxml2 -c -o reestimate.lo reestimate.c
> libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time
> -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2
> -Werror=implicit-function-declaration "-ffile-prefix-map=/<<PKGBUILDDIR>>=."
> -fstack-protector-strong -fstack-clash-protection -Wformat
> -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu
> -I/usr/include/libxml2 -c foba.c -fPIC -DPIC -o .libs/foba.o
> libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time
> -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2
> -Werror=implicit-function-declaration "-ffile-prefix-map=/<<PKGBUILDDIR>>=."
> -fstack-protector-strong -fstack-clash-protection -Wformat
> -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu
> -I/usr/include/libxml2 -c viterbi.c -fPIC -DPIC -o .libs/viterbi.o
> foba.c: In function ‘ghmm_dmodel_backward’:
> foba.c:286:37: warning: macro "__DATE__" might prevent reproducible builds
> [-Wdate-time]
> 286 | mes_check_0 (scale[t], goto STOP);
> | ^
> libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time
> -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2
> -Werror=implicit-function-declaration "-ffile-prefix-map=/<<PKGBUILDDIR>>=."
> -fstack-protector-strong -fstack-clash-protection -Wformat
> -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu
> -I/usr/include/libxml2 -c reestimate.c -fPIC -DPIC -o .libs/reestimate.o
> foba.c: In function ‘ghmm_dmodel_label_backward’:
> foba.c:848:37: warning: macro "__DATE__" might prevent reproducible builds
> [-Wdate-time]
> 848 | mes_check_0 (scale[t], goto STOP);
> | ^
> viterbi.c: In function ‘viterbi_free’:
> viterbi.c:71:31: warning: macro "__DATE__" might prevent reproducible builds
> [-Wdate-time]
> 71 | mes_check_ptr(v, return -1);
> | ^
> reestimate.c: In function ‘reestimate_free’:
> reestimate.c:79:32: warning: macro "__DATE__" might prevent reproducible
> builds [-Wdate-time]
> 79 | mes_check_ptr (r, return (-1));
> | ^
> reestimate.c: In function ‘reestimate_setlambda’:
> reestimate.c:306:38: warning: macro "__DATE__" might prevent reproducible
> builds [-Wdate-time]
> 306 | mes_check_0 (r->pi_denom, goto STOP);
> | ^
> /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I..
> -I.. -Wdate-time -D_FORTIFY_SOURCE=2
> -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2
> -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
> -fstack-protector-strong -fstack-clash-protection -Wformat
> -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu
> -I/usr/include/libxml2 -c -o gradescent.lo gradescent.c
> libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time
> -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2
> -Werror=implicit-function-declaration "-ffile-prefix-map=/<<PKGBUILDDIR>>=."
> -fstack-protector-strong -fstack-clash-protection -Wformat
> -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu
> -I/usr/include/libxml2 -c gradescent.c -fPIC -DPIC -o .libs/gradescent.o
> libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time
> -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2
> -Werror=implicit-function-declaration "-ffile-prefix-map=/<<PKGBUILDDIR>>=."
> -fstack-protector-strong -fstack-clash-protection -Wformat
> -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu
> -I/usr/include/libxml2 -c viterbi.c -o viterbi.o >/dev/null 2>&1
> libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time
> -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2
> -Werror=implicit-function-declaration "-ffile-prefix-map=/<<PKGBUILDDIR>>=."
> -fstack-protector-strong -fstack-clash-protection -Wformat
> -Werror=format-security -fcf-protection -I/usr/include/x86_64-linux-gnu
> -I/usr/include/libxml2 -c sequence.c -o sequence.o >/dev/null 2>&1
> cc1: some warnings being treated as errors
> make[5]: *** [Makefile:713: xmlwriter.lo] Error 1
The full build log is available from:
http://qa-logs.debian.net/2024/06/15/ghmm_0.9~rc3-6_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20240615;users=lu...@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20240615&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: ghmm
Source-Version: 0.9~rc3-7
Done: Bo YU <tsu.y...@gmail.com>
We believe that the bug you reported is fixed in the latest version of
ghmm, 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 1073...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Bo YU <tsu.y...@gmail.com> (supplier of updated ghmm 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: SHA256
Format: 1.8
Date: Thu, 27 Jun 2024 10:56:57 +0800
Source: ghmm
Architecture: source
Version: 0.9~rc3-7
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Bo YU <tsu.y...@gmail.com>
Closes: 1073355
Changes:
ghmm (0.9~rc3-7) unstable; urgency=medium
.
* Team upload.
* Add fix_imp_func_issue.patch to fix ftbfs issue.(Closes: #1073355)
* Modify override_dh_install to match more python version in mv cmd
Checksums-Sha1:
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9cd74b10aaae528681dd7575419877fc800128a6 23024 ghmm_0.9~rc3-7.debian.tar.xz
9a119c0dad45fe300c0addffdb23dc3e9cf4fdaa 8768 ghmm_0.9~rc3-7_amd64.buildinfo
Checksums-Sha256:
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ghmm_0.9~rc3-7.dsc
0a746c43d4be035ab98737e6ad8cb8f3ac83c251b42ba4fa2c82740b90934226 23024
ghmm_0.9~rc3-7.debian.tar.xz
ecd9b8308471dc43850ee5098afce691ce383e4e0dfc06dc928698ed14ba1899 8768
ghmm_0.9~rc3-7_amd64.buildinfo
Files:
11aee2b492a23aaaea9e34d2a69b6af5 2251 science optional ghmm_0.9~rc3-7.dsc
9a62344c031b902c0e350a2d611038e0 23024 science optional
ghmm_0.9~rc3-7.debian.tar.xz
4a3fd425e6c5cee19381008a320760b7 8768 science optional
ghmm_0.9~rc3-7_amd64.buildinfo
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