[Debian-med-packaging] Bug#1097774: raxml: ftbfs with GCC-15

Mon Feb 17 17:49:56 GMT 2025

Package: src:raxml
Version: 8.2.13+dfsg-1
Severity: important
Tags: sid forky
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-15

[This bug is NOT 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-15/g++-15, but succeeds to build with gcc-14/g++-14. The
severity of this report will be raised before the forky release.

The full build log can be found at:
http://qa-logs.debian.net/2025/02/16/amd64exp/raxml_8.2.13+dfsg-1_unstable_gccexp.log.gz
The last lines of the build log are at the end of this report.

To build with GCC 15, either set CC=gcc-15 CXX=g++-15 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

  apt-get -t=experimental install g++ 

GCC 15 now defaults to the C23/C++23 standards, exposing many FTBFS.
Other 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-15/porting_to.html

[...]

Command: dpkg-buildpackage --sanitize-env -us -uc -b
dpkg-buildpackage: info: source package raxml
dpkg-buildpackage: info: source version 8.2.13+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille at debian.org>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
 debian/rules clean
dh clean
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/reproducible-path/raxml-8.2.13+dfsg'
for mfile in Makefile.PTHREADS.gcc Makefile.SSE3.PTHREADS.gcc Makefile.AVX.PTHREADS.gcc; do /usr/bin/make -f ${mfile} clean ; done
make[2]: Entering directory '/build/reproducible-path/raxml-8.2.13+dfsg'
rm -f *.o raxmlHPC-PTHREADS
make[2]: Leaving directory '/build/reproducible-path/raxml-8.2.13+dfsg'
make[2]: Entering directory '/build/reproducible-path/raxml-8.2.13+dfsg'
rm -f *.o raxmlHPC-PTHREADS-SSE3
make[2]: Leaving directory '/build/reproducible-path/raxml-8.2.13+dfsg'
make[2]: Entering directory '/build/reproducible-path/raxml-8.2.13+dfsg'
rm -f *.o raxmlHPC-PTHREADS-AVX
make[2]: Leaving directory '/build/reproducible-path/raxml-8.2.13+dfsg'
rm -rf /build/reproducible-path/raxml-8.2.13+dfsg/debian/tmpbuild
make[1]: Leaving directory '/build/reproducible-path/raxml-8.2.13+dfsg'
   dh_clean
 debian/rules binary
dh binary
   dh_update_autotools_config
   dh_autoreconf
   debian/rules override_dh_auto_build
make[1]: Entering directory '/build/reproducible-path/raxml-8.2.13+dfsg'
mkdir -p /build/reproducible-path/raxml-8.2.13+dfsg/debian/tmpbuild
set -e ; for mfile in Makefile.PTHREADS.gcc Makefile.SSE3.PTHREADS.gcc Makefile.AVX.PTHREADS.gcc; do \
    dh_auto_build --buildsystem=makefile -- -f ${mfile} ; \
    curexe=`ls raxmlHPC* | head -n 1` ; \
    if [ -e /build/reproducible-path/raxml-8.2.13+dfsg/debian/tmpbuild/${curexe} ] ; then \
	echo "**** ERROR: ${curexe} was created before!!" && false ; \
    else \
	mv ${curexe} /build/reproducible-path/raxml-8.2.13+dfsg/debian/tmpbuild/${curexe} ; \
    fi ; \
    /usr/bin/make -f ${mfile} clean ; \
done
	make -j8 "INSTALL=install --strip-program=true" -f Makefile.PTHREADS.gcc
make[2]: Entering directory '/build/reproducible-path/raxml-8.2.13+dfsg'
rm -f *.o raxmlHPC-PTHREADS
gcc  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/raxml-8.2.13+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2  -D_USE_PTHREADS -msse  -Wdate-time -D_FORTIFY_SOURCE=2  -c -o axml.o axml.c
gcc  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/raxml-8.2.13+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2  -D_USE_PTHREADS -msse  -Wdate-time -D_FORTIFY_SOURCE=2  -c -o optimizeModel.o optimizeModel.c
gcc  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/raxml-8.2.13+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2  -D_USE_PTHREADS -msse  -Wdate-time -D_FORTIFY_SOURCE=2  -c -o multiple.o multiple.c
gcc  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/raxml-8.2.13+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2  -D_USE_PTHREADS -msse  -Wdate-time -D_FORTIFY_SOURCE=2  -c -o searchAlgo.o searchAlgo.c
gcc  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/raxml-8.2.13+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2  -D_USE_PTHREADS -msse  -Wdate-time -D_FORTIFY_SOURCE=2  -c -o topologies.o topologies.c
gcc  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/raxml-8.2.13+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2  -D_USE_PTHREADS -msse  -Wdate-time -D_FORTIFY_SOURCE=2  -c -o parsePartitions.o parsePartitions.c
gcc  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/raxml-8.2.13+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2  -D_USE_PTHREADS -msse  -Wdate-time -D_FORTIFY_SOURCE=2  -c -o treeIO.o treeIO.c
gcc  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/raxml-8.2.13+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2  -D_USE_PTHREADS -msse  -Wdate-time -D_FORTIFY_SOURCE=2  -c -o models.o models.c
gcc  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/raxml-8.2.13+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2  -D_USE_PTHREADS -msse  -Wdate-time -D_FORTIFY_SOURCE=2  -c -o bipartitionList.o bipartitionList.c
In file included from bipartitionList.c:46:
rmq.h:13:13: error: ‘bool’ cannot be defined via ‘typedef’
   13 | typedef int bool;
      |             ^~~~
rmq.h:13:13: note: ‘bool’ is a keyword with ‘-std=c23’ onwards
rmq.h:13:1: warning: useless type name in empty declaration
   13 | typedef int bool;
      | ^~~~~~~
make[2]: *** [<builtin>: bipartitionList.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: Leaving directory '/build/reproducible-path/raxml-8.2.13+dfsg'
dh_auto_build: error: make -j8 "INSTALL=install --strip-program=true" -f Makefile.PTHREADS.gcc returned exit code 2
make[1]: *** [debian/rules:33: override_dh_auto_build] Error 25
make[1]: Leaving directory '/build/reproducible-path/raxml-8.2.13+dfsg'
make: *** [debian/rules:25: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2