[R-pkg-team] Bug#1097764: r-bioc-grohmm: ftbfs with GCC-15

[Matthias Klose]

Package: src:r-bioc-grohmm
Version: 1.40.3-2
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/r-bioc-grohmm_1.40.3-2_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

[...]
Check disk space
----------------

Sufficient free space for build

User Environment
----------------

APT_CONFIG=/var/lib/sbuild/apt.conf
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 r-bioc-grohmm
dpkg-buildpackage: info: source version 1.40.3-2
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Michael R. Crusoe <crusoe at debian.org>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
 debian/rules clean
dh clean --buildsystem R
   dh_auto_clean -O--buildsystem=R
   dh_autoreconf_clean -O--buildsystem=R
   dh_clean -O--buildsystem=R
 debian/rules binary
dh binary --buildsystem R
   dh_update_autotools_config -O--buildsystem=R
   dh_autoreconf -O--buildsystem=R
   dh_auto_configure -O--buildsystem=R
   dh_auto_build -O--buildsystem=R
   dh_auto_test -O--buildsystem=R
   create-stamp debian/debhelper-build-stamp
   dh_testroot -O--buildsystem=R
   dh_prep -O--buildsystem=R
   dh_auto_install --destdir=debian/r-bioc-grohmm/ -O--buildsystem=R
I: R Package: groHMM Version: 1.40.3
I: Building using R version 4.4.2-1
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Mon, 13 Jan 2025 21:17:46 +0100
	mkdir -p /build/reproducible-path/r-bioc-grohmm-1.40.3/debian/r-bioc-grohmm/usr/lib/R/site-library
	R CMD INSTALL -l /build/reproducible-path/r-bioc-grohmm-1.40.3/debian/r-bioc-grohmm/usr/lib/R/site-library --clean . "--built-timestamp='Mon, 13 Jan 2025 21:17:46 +0100'"
* installing *source* package ‘groHMM’ ...
** package ‘groHMM’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Debian 15-20250213-1) 15.0.1 20250213 (experimental) [master r15-7502-g26baa2c09b3]’
make[1]: Entering directory '/build/reproducible-path/r-bioc-grohmm-1.40.3/src'
gcc -I"/usr/share/R/include" -DNDEBUG       -fpic  -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2  -c AnnotateProbes.c -o AnnotateProbes.o
gcc -I"/usr/share/R/include" -DNDEBUG       -fpic  -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2  -c DecayAlgorithm.c -o DecayAlgorithm.o
DecayAlgorithm.c: In function ‘getTranscriptPositions’:
DecayAlgorithm.c:94:15: error: expected identifier or ‘(’ before ‘false’
   94 |     const int false= 0;
      |               ^~~~~
make[1]: *** [/usr/lib/R/etc/Makeconf:195: DecayAlgorithm.o] Error 1
make[1]: Leaving directory '/build/reproducible-path/r-bioc-grohmm-1.40.3/src'
make[1]: Entering directory '/build/reproducible-path/r-bioc-grohmm-1.40.3/src'
make[1]: Leaving directory '/build/reproducible-path/r-bioc-grohmm-1.40.3/src'
ERROR: compilation failed for package ‘groHMM’
* removing ‘/build/reproducible-path/r-bioc-grohmm-1.40.3/debian/r-bioc-grohmm/usr/lib/R/site-library/groHMM’
dh_auto_install: error: R CMD INSTALL -l /build/reproducible-path/r-bioc-grohmm-1.40.3/debian/r-bioc-grohmm/usr/lib/R/site-library --clean . "--built-timestamp='Mon, 13 Jan 2025 21:17:46 +0100'" returned exit code 1
make: *** [debian/rules:4: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2