[Debian-med-packaging] Bug#1097906: soapaligner: ftbfs with GCC-15

[Matthias Klose]

Package: src:soapaligner
Version: 2.20-5
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/soapaligner_2.20-5_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

[...]
HOME=/sbuild-nonexistent
LANG=C.UTF-8
LC_ALL=C.UTF-8
LOGNAME=user42
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SHELL=/bin/sh
USER=user42

dpkg-buildpackage
-----------------

Command: dpkg-buildpackage --sanitize-env -us -uc -b
dpkg-buildpackage: info: source package soapaligner
dpkg-buildpackage: info: source version 2.20-5
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Nilesh Patra <npatra974 at gmail.com>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
 debian/rules clean
dh clean
   dh_auto_clean
	make -j8 clean
make[1]: Entering directory '/build/reproducible-path/soapaligner-2.20'
rm -f *.o soap
make[1]: Leaving directory '/build/reproducible-path/soapaligner-2.20'
   dh_clean
	rm -f debian/debhelper-build-stamp
	rm -rf debian/.debhelper/
	rm -f -- debian/soapaligner.substvars debian/files
	rm -fr -- debian/soapaligner/ debian/tmp/
	find .  \( \( \
		\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
	        \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
		 -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
		 -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
		 -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
		\) -exec rm -f {} + \) -o \
		\( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \)
 debian/rules binary
dh binary
   dh_update_autotools_config
   dh_autoreconf
   dh_auto_configure
   dh_auto_build
	make -j8 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/build/reproducible-path/soapaligner-2.20'
cc -c -flto -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapaligner-2.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -maccumulate-outgoing-args -fomit-frame-pointer -DPTHREADS -DMAKE_TIME=\""SOURCE_DATE_EPOCH"\" SeqIO.c -o SeqIO.o
cc -c -flto -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapaligner-2.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -maccumulate-outgoing-args -fomit-frame-pointer -DPTHREADS -DMAKE_TIME=\""SOURCE_DATE_EPOCH"\" MiscUtilities.c -o MiscUtilities.o
cc -c -flto -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapaligner-2.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -maccumulate-outgoing-args -fomit-frame-pointer -DPTHREADS -DMAKE_TIME=\""SOURCE_DATE_EPOCH"\" MemManager.c -o MemManager.o
cc -c -flto -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapaligner-2.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -maccumulate-outgoing-args -fomit-frame-pointer -DPTHREADS -DMAKE_TIME=\""SOURCE_DATE_EPOCH"\" TextConverter.c -o TextConverter.o
cc -c -flto -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapaligner-2.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -maccumulate-outgoing-args -fomit-frame-pointer -DPTHREADS -DMAKE_TIME=\""SOURCE_DATE_EPOCH"\" r250.c -o r250.o
cc -c -flto -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapaligner-2.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -maccumulate-outgoing-args -fomit-frame-pointer -DPTHREADS -DMAKE_TIME=\""SOURCE_DATE_EPOCH"\" DNACount.c -o DNACount.o
cc -c -flto -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapaligner-2.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -maccumulate-outgoing-args -fomit-frame-pointer -DPTHREADS -DMAKE_TIME=\""SOURCE_DATE_EPOCH"\" HSP.c -o HSP.o
cc -c -flto -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapaligner-2.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -maccumulate-outgoing-args -fomit-frame-pointer -DPTHREADS -DMAKE_TIME=\""SOURCE_DATE_EPOCH"\" Timing.c -o Timing.o
r250.c:31:21: error: conflicting types for ‘randlcg’; have ‘unsigned int(int)’
   31 | static unsigned int randlcg(int sd)       /* returns a random unsigned integer */
      |                     ^~~~~~~
r250.c:19:21: note: previous declaration of ‘randlcg’ with type ‘unsigned int(void)’
   19 | static unsigned int randlcg();
      |                     ^~~~~~~
r250.c: In function ‘randlcg’:
r250.c:33:41: warning: overflow in conversion from ‘long int’ to ‘int’ changes value from ‘548781581296767’ to ‘724984959’ [-Woverflow]
   33 |                 static int quotient1  = LONG_MAX / 16807L;
      |                                         ^~~~~~~~
make[1]: *** [Makefile:45: r250.o] Error 1
make[1]: *** Waiting for unfinished jobs....
make[1]: Leaving directory '/build/reproducible-path/soapaligner-2.20'
dh_auto_build: error: make -j8 "INSTALL=install --strip-program=true" returned exit code 2
make: *** [debian/rules:14: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2