[R-pkg-team] Bug#1071342: r-bioc-hdf5array: FTBFS: H5DSetDescriptor.c:1182:17: error: format not a string literal and no format arguments

[Santiago Vila]

Package: src:r-bioc-hdf5array
Version: 1.30.1-1
Severity: serious
Tags: ftbfs

Dear maintainer:

During a rebuild of all packages in unstable, your package failed to build:

--------------------------------------------------------------------------------
[...]
  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-hdf5array/ -O--buildsystem=R
I: R Package: HDF5Array Version: 1.30.1
I: Building using R version 4.4.0-2
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Tue, 20 Feb 2024 14:26:16 +0100
	mkdir -p /<<PKGBUILDDIR>>/debian/r-bioc-hdf5array/usr/lib/R/site-library
	R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-bioc-hdf5array/usr/lib/R/site-library --clean . "--built-timestamp='Tue, 20 Feb 2024 14:26:16 +0100'"
* installing *source* package ‘HDF5Array’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Debian 13.2.0-25) 13.2.0’
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/Rhdf5lib/include'     -fpic  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/Rhdf5lib/include'     -fpic  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2  -c H5File.c -o H5File.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/Rhdf5lib/include'     -fpic  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2  -c global_errmsg_buf.c -o global_errmsg_buf.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/Rhdf5lib/include'     -fpic  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2  -c H5DSetDescriptor.c -o H5DSetDescriptor.o
H5DSetDescriptor.c: In function ‘C_new_H5DSetDescriptor_xp’:
H5DSetDescriptor.c:1182:17: error: format not a string literal and no format arguments [-Werror=format-security]
  1182 |                 error(_HDF5Array_global_errmsg_buf());
       |                 ^~~~~
cc1: some warnings being treated as errors
make[1]: *** [/usr/lib/R/etc/Makeconf:195: H5DSetDescriptor.o] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
ERROR: compilation failed for package ‘HDF5Array’
* removing ‘/<<PKGBUILDDIR>>/debian/r-bioc-hdf5array/usr/lib/R/site-library/HDF5Array’
dh_auto_install: error: R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-bioc-hdf5array/usr/lib/R/site-library --clean . "--built-timestamp='Tue, 20 Feb 2024 14:26:16 +0100'" returned exit code 1
make: *** [debian/rules:4: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------

The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:

https://people.debian.org/~sanvila/build-logs/202405/

About the archive rebuild: The build was made on virtual machines
of type m6a.large and r6a.large from AWS, using sbuild and a
reduced chroot with only build-essential packages.

If you could not reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.

If this is really a bug in one of the build-depends, please use
reassign and affects, so that this is still visible in the BTS web
page for this package.

Thanks.