[Debian-med-packaging] Bug#1073355: ghmm: FTBFS: xmlwriter.c:1105:5: error: implicit declaration of function ‘xmlSubstituteEntitiesDefault’ [-Werror=implicit-function-declaration]

Lucas Nussbaum lucas at debian.org
Sun Jun 16 13:51:56 BST 2024 

Source: ghmm
Version: 0.9~rc3-6
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lucas at 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=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20240615&fusertaguser=lucas@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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