[Debian-med-packaging] Bug#1074994: ghmm: ftbfs with GCC-14

Matthias Klose doko at debian.org
Wed Jul 3 13:27:40 BST 2024


Package: src:ghmm
Version: 0.9~rc3-7
Severity: important
Tags: sid trixie
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-14

[This bug is targeted to the upcoming trixie release]

Please keep this issue open in the bug tracker for the package it
was filed for.  If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.

The package fails to build in a test rebuild on at least amd64 with
gcc-14/g++-14, but succeeds to build with gcc-13/g++-13. The
severity of this report will be raised before the trixie release.

The full build log can be found at:
http://qa-logs.debian.net/2024/07/01/ghmm_0.9~rc3-7_unstable_gccexp.log
The last lines of the build log are at the end of this report.

To build with GCC 14, either set CC=gcc-14 CXX=g++-14 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

  apt-get -t=experimental install g++ 

Common build failures are new warnings resulting in build failures with
-Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-14/porting_to.html

[...]
gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2  -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 scluster.o scluster.c
gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2  -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 smix_hmm.o smix_hmm.c
/bin/bash ../libtool  --tag=CC   --mode=link gcc  -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   -Wl,-z,relro -Wl,-z,now -o smix_hmm smix_hmm.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread  -llapacke  -lxml2 
/bin/bash ../libtool  --tag=CC   --mode=link gcc  -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   -Wl,-z,relro -Wl,-z,now -o scluster scluster.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread  -llapacke  -lxml2 
/bin/bash ../libtool  --tag=CC   --mode=link gcc  -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   -Wl,-z,relro -Wl,-z,now -o cluster cluster.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread  -llapacke  -lxml2 
/bin/bash ../libtool  --tag=CC   --mode=link gcc  -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   -Wl,-z,relro -Wl,-z,now -o probdist probdist.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread  -llapacke  -lxml2 
libtool: link: gcc -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 -Wl,-z -Wl,relro -Wl,-z -Wl,now -o scluster scluster.o  ../ghmm/.libs/libghmm.a -lm -lpthread -llapacke -lxml2
libtool: link: gcc -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 -Wl,-z -Wl,relro -Wl,-z -Wl,now -o smix_hmm smix_hmm.o  ../ghmm/.libs/libghmm.a -lm -lpthread -llapacke -lxml2
libtool: link: gcc -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 -Wl,-z -Wl,relro -Wl,-z -Wl,now -o cluster cluster.o  ../ghmm/.libs/libghmm.a -lm -lpthread -llapacke -lxml2
libtool: link: gcc -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 -Wl,-z -Wl,relro -Wl,-z -Wl,now -o probdist probdist.o  ../ghmm/.libs/libghmm.a -lm -lpthread -llapacke -lxml2
make[6]: Leaving directory '/<<PKGBUILDDIR>>/tools'
make[5]: Leaving directory '/<<PKGBUILDDIR>>/tools'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/tools'
Making all in tests
make[4]: Entering directory '/<<PKGBUILDDIR>>/tests'
Making all in data
make[5]: Entering directory '/<<PKGBUILDDIR>>/tests/data'
Making all in .
make[6]: Entering directory '/<<PKGBUILDDIR>>/tests/data'
make[6]: Nothing to be done for 'all-am'.
make[6]: Leaving directory '/<<PKGBUILDDIR>>/tests/data'
make[5]: Leaving directory '/<<PKGBUILDDIR>>/tests/data'
make[5]: Entering directory '/<<PKGBUILDDIR>>/tests'
gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2  -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 randvar_test.o randvar_test.c
gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2  -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 root_finder_test.o root_finder_test.c
gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2  -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 coin_toss_test.o coin_toss_test.c
gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2  -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 two_states_three_symbols.o two_states_three_symbols.c
gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2  -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 libxml-test.o libxml-test.c
gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2  -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 chmm.o chmm.c
gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2  -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 chmm_test.o chmm_test.c
gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2  -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 shmm_viterbi_test.o shmm_viterbi_test.c
gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2  -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 test_gsl_ran_gaussian_tail.o test_gsl_ran_gaussian_tail.c
gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2  -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 sequences_test.o sequences_test.c
gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2  -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 sequences_old_format.o sequences_old_format.c
gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2  -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 label_higher_order_test.o label_higher_order_test.c
gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2  -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 read_fa.o read_fa.c
gcc -DHAVE_CONFIG_H -I. -I.. -I..  -Wdate-time -D_FORTIFY_SOURCE=2  -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 mcmc.o mcmc.c
/bin/bash ../libtool  --tag=CC   --mode=link gcc  -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   -Wl,-z,relro -Wl,-z,now -o randvar_test randvar_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread  -llapacke  -lxml2 
/bin/bash ../libtool  --tag=CC   --mode=link gcc  -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   -Wl,-z,relro -Wl,-z,now -o root_finder_test root_finder_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread  -llapacke  -lxml2 
mcmc.c: In function ‘main’:
mcmc.c:148:15: error: initialization of ‘int *’ from incompatible pointer type ‘int **’ [-Wincompatible-pointer-types]
  148 |   int * Q =   ghmm_dmodel_cfbgibbs(mo, my_output,
      |               ^~~~~~~~~~~~~~~~~~~~
mcmc.c:150:108: error: passing argument 4 of ‘ghmm_dmodel_viterbi_logp’ makes pointer from integer without a cast [-Wint-conversion]
  150 |   printf("viterbi prob mcmc%f \n", ghmm_dmodel_viterbi_logp(mo, my_output->seq[0], my_output->seq_len[0], Q[0]));
      |                                                                                                           ~^~~
      |                                                                                                            |
      |                                                                                                            int
In file included from mcmc.c:13:
../ghmm/viterbi.h:75:76: note: expected ‘int *’ but argument is of type ‘int’
   75 |   double ghmm_dmodel_viterbi_logp (ghmm_dmodel * mo, int *o, int len, int *state_seq);
      |                                                                       ~~~~~^~~~~~~~~
/bin/bash ../libtool  --tag=CC   --mode=link gcc  -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   -Wl,-z,relro -Wl,-z,now -o two_states_three_symbols two_states_three_symbols.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread  -llapacke  -lxml2 
make[5]: *** [Makefile:823: mcmc.o] Error 1
make[5]: *** Waiting for unfinished jobs....
libtool: link: gcc -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 -Wl,-z -Wl,relro -Wl,-z -Wl,now -o randvar_test randvar_test.o  ../ghmm/.libs/libghmm.a -lm -lpthread -llapacke -lxml2
libtool: link: gcc -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 -Wl,-z -Wl,relro -Wl,-z -Wl,now -o root_finder_test root_finder_test.o  ../ghmm/.libs/libghmm.a -lm -lpthread -llapacke -lxml2
libtool: link: gcc -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 -Wl,-z -Wl,relro -Wl,-z -Wl,now -o two_states_three_symbols two_states_three_symbols.o  ../ghmm/.libs/libghmm.a -lm -lpthread -llapacke -lxml2
make[5]: Leaving directory '/<<PKGBUILDDIR>>/tests'
make[4]: *** [Makefile:852: all-recursive] Error 1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/tests'
make[3]: *** [Makefile:536: all-recursive] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: *** [Makefile:446: all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j8 returned exit code 2
make[1]: *** [debian/rules:17: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:10: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2



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