[Debian-med-packaging] Bug#1075383: phast: ftbfs with GCC-14

[Matthias Klose]

Package: src:phast
Version: 1.6+dfsg-5
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/phast_1.6+dfsg-5_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

[...]
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/prequel'
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/util'
../munge-help.sh base_evolve.help_src > base_evolve.help
../munge-help.sh clean_genes.help_src > clean_genes.help
../munge-help.sh consEntropy.help_src > consEntropy.help
../munge-help.sh indelFit.help_src > indelFit.help
../munge-help.sh indelHistory.help_src > indelHistory.help
../munge-help.sh makeHKY.help_src > makeHKY.help
../munge-help.sh modFreqs.help_src > modFreqs.help
../munge-help.sh msa_diff.help_src > msa_diff.help
../munge-help.sh phast.help_src > phast.help
../munge-help.sh phastBias.help_src > phastBias.help
../munge-help.sh treeGen.help_src > treeGen.help
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/util/../..\" -fno-strict-aliasing -c all_dists.c -o all_dists.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<PKGBUILDDIR>>/src/util/../../lib   -o /<<PKGBUILDDIR>>/src/util/../../bin/all_dists all_dists.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
/usr/bin/ld: all_dists.o: in function `main':
./src/util/./src/util/all_dists.c:75:(.text.startup+0x13b): undefined reference to `die'
/usr/bin/ld: ./src/util/./src/util/all_dists.c:70:(.text.startup+0x159): undefined reference to `phast_fopen'
/usr/bin/ld: ./src/util/./src/util/all_dists.c:70:(.text.startup+0x161): undefined reference to `tr_new_from_file'
/usr/bin/ld: ./src/util/./src/util/all_dists.c:68:(.text.startup+0x189): undefined reference to `tr_new_from_string'
/usr/bin/ld: ./src/util/./src/util/all_dists.c:82:(.text.startup+0x1a9): undefined reference to `set_seed'
/usr/bin/ld: ./src/util/./src/util/all_dists.c:86:(.text.startup+0x1b3): undefined reference to `str_new'
/usr/bin/ld: ./src/util/./src/util/all_dists.c:88:(.text.startup+0x1e1): undefined reference to `str_append_charstr'
/usr/bin/ld: ./src/util/./src/util/all_dists.c:91:(.text.startup+0x1f0): undefined reference to `get_arg_list'
/usr/bin/ld: ./src/util/./src/util/all_dists.c:94:(.text.startup+0x215): undefined reference to `smalloc'
/usr/bin/ld: ./src/util/./src/util/all_dists.c:106:(.text.startup+0x25c): undefined reference to `phast_fopen'
/usr/bin/ld: ./src/util/./src/util/all_dists.c:106:(.text.startup+0x264): undefined reference to `tr_new_from_file'
/usr/bin/ld: ./src/util/./src/util/all_dists.c:100:(.text.startup+0x2b0): undefined reference to `phast_fopen'
/usr/bin/ld: ./src/util/./src/util/all_dists.c:100:(.text.startup+0x2c0): undefined reference to `tm_new_from_file'
/usr/bin/ld: ./src/util/./src/util/all_dists.c:101:(.text.startup+0x2cb): undefined reference to `tr_create_copy'
/usr/bin/ld: ./src/util/./src/util/all_dists.c:102:(.text.startup+0x2e0): undefined reference to `tm_free'
/usr/bin/ld: ./src/util/./src/util/all_dists.c:103:(.text.startup+0x2e8): undefined reference to `phast_fclose'
/usr/bin/ld: ./src/util/./src/util/all_dists.c:111:(.text.startup+0x32d): undefined reference to `lst_new_ptr'
/usr/bin/ld: ./src/util/./src/util/all_dists.c:112:(.text.startup+0x348): undefined reference to `smalloc'
/usr/bin/ld: ./src/util/./src/util/all_dists.c:113:(.text.startup+0x353): undefined reference to `smalloc'
/usr/bin/ld: ./src/util/./src/util/all_dists.c:115:(.text.startup+0x38a): undefined reference to `smalloc'
/usr/bin/ld: ./src/util/./src/util/all_dists.c:117:(.text.startup+0x3d8): undefined reference to `lst_new_dbl'
/usr/bin/ld: ./src/util/./src/util/all_dists.c:125:(.text.startup+0x49d): undefined reference to `lst_new_dbl'
/usr/bin/ld: ./src/util/./src/util/all_dists.c:138:(.text.startup+0x5f3): undefined reference to `die'
/usr/bin/ld: ./src/util/./src/util/all_dists.c:157:(.text.startup+0x8be): undefined reference to `tr_total_len'
/usr/bin/ld: all_dists.o: in function `lst_push':
./src/util/./src/../include/phast/lists.h:497:(.text.startup+0xa49): undefined reference to `srealloc'
/usr/bin/ld: ./src/util/./src/../include/phast/lists.h:497:(.text.startup+0xb02): undefined reference to `srealloc'
/usr/bin/ld: all_dists.o: in function `main':
./src/util/./src/util/all_dists.c:88:(.text.startup+0xba8): undefined reference to `str_append_charstr'
/usr/bin/ld: ./src/util/./src/util/all_dists.c:89:(.text.startup+0xbb5): undefined reference to `str_append_char'
/usr/bin/ld: ./src/util/./src/util/all_dists.c:80:(.text.startup+0xbef): undefined reference to `die'
/usr/bin/ld: all_dists.o: in function `lst_push':
./src/util/./src/../include/phast/lists.h:497:(.text.startup+0xc0b): undefined reference to `srealloc'
/usr/bin/ld: all_dists.o: in function `main':
./src/util/./src/util/all_dists.c:182:(.text.startup+0xd02): undefined reference to `lst_dbl_mean'
/usr/bin/ld: ./src/util/./src/util/all_dists.c:183:(.text.startup+0xd15): undefined reference to `lst_dbl_stdev'
/usr/bin/ld: ./src/util/./src/util/all_dists.c:184:(.text.startup+0xd2a): undefined reference to `lst_qsort_dbl'
/usr/bin/ld: ./src/util/./src/util/all_dists.c:185:(.text.startup+0xd44): undefined reference to `lst_dbl_quantiles'
/usr/bin/ld: ./src/util/./src/util/all_dists.c:195:(.text.startup+0xde1): undefined reference to `lst_dbl_mean'
/usr/bin/ld: ./src/util/./src/util/all_dists.c:196:(.text.startup+0xdee): undefined reference to `lst_dbl_stdev'
/usr/bin/ld: ./src/util/./src/util/all_dists.c:197:(.text.startup+0xdfe): undefined reference to `lst_qsort_dbl'
/usr/bin/ld: ./src/util/./src/util/all_dists.c:198:(.text.startup+0xe13): undefined reference to `lst_dbl_quantiles'
collect2: error: ld returned 1 exit status
make[3]: *** [Makefile:20: /<<PKGBUILDDIR>>/src/util/../../bin/all_dists] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/util'
make[2]: *** [Makefile:9: all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[1]: *** [Makefile:6: all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j8 "INSTALL=install --strip-program=true" returned exit code 2
make: *** [debian/rules:8: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2