[R-pkg-team] Bug#1071345: r-bioc-rhdf5: FTBFS: H5E.c:117:19: error: format not a string literal and no format arguments

[Santiago Vila]

Package: src:r-bioc-rhdf5
Version: 2.46.1+dfsg-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
    debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# see debian/hdf5-private/README
ln -s /<<PKGBUILDDIR>>/debian/hdf5-private/H5private.h   /<<PKGBUILDDIR>>/src/H5private.h
ln -s /<<PKGBUILDDIR>>/debian/hdf5-private/H5TSprivate.h /<<PKGBUILDDIR>>/src/H5TSprivate.h
dh_auto_install # --no-parallel ... does not help
I: R Package: rhdf5 Version: 2.46.1
I: Building using R version 4.4.0-2
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Mon, 18 Dec 2023 13:37:02 +0100
	mkdir -p /<<BUILDDIR>>/r-bioc-rhdf5-2.46.1\+dfsg/debian/r-bioc-rhdf5/usr/lib/R/site-library
	R CMD INSTALL -l /<<BUILDDIR>>/r-bioc-rhdf5-2.46.1\+dfsg/debian/r-bioc-rhdf5/usr/lib/R/site-library --clean . "--built-timestamp='Mon, 18 Dec 2023 13:37:02 +0100'"
* installing *source* package ‘rhdf5’ ...
** using staged installation
configure: creating ./config.status
config.status: creating src/external_filters.h
** libs
using C compiler: ‘gcc (Debian 13.2.0-25) 13.2.0’
using C++ compiler: ‘g++ (Debian 13.2.0-25) 13.2.0’
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
gcc -I"/usr/share/R/include" -DNDEBUG  -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 H5.c -o H5.o
gcc -I"/usr/share/R/include" -DNDEBUG  -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 H5A.c -o H5A.o
gcc -I"/usr/share/R/include" -DNDEBUG  -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 H5D.c -o H5D.o
gcc -I"/usr/share/R/include" -DNDEBUG  -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 H5E.c -o H5E.o
H5E.c: In function ‘_rhdf5PrintErrorR’:
H5E.c:117:19: error: format not a string literal and no format arguments [-Werror=format-security]
   117 |             error(str);
       |                   ^~~
H5E.c:119:34: error: format not a string literal and no format arguments [-Werror=format-security]
   119 |             error(client_data.txt[0]);
       |                   ~~~~~~~~~~~~~~~^~~
H5E.c: In function ‘_rhdf5PrintErrorRcompact’:
H5E.c:149:19: error: format not a string literal and no format arguments [-Werror=format-security]
   149 |             error(str);
       |                   ^~~
H5E.c:151:34: error: format not a string literal and no format arguments [-Werror=format-security]
   151 |             error(client_data.txt[0]);
       |                   ~~~~~~~~~~~~~~~^~~
cc1: some warnings being treated as errors
make[2]: *** [/usr/lib/R/etc/Makeconf:195: H5E.o] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
ERROR: compilation failed for package ‘rhdf5’
* removing ‘/<<PKGBUILDDIR>>/debian/r-bioc-rhdf5/usr/lib/R/site-library/rhdf5’
dh_auto_install: error: R CMD INSTALL -l /<<BUILDDIR>>/r-bioc-rhdf5-2.46.1\+dfsg/debian/r-bioc-rhdf5/usr/lib/R/site-library --clean . "--built-timestamp='Mon, 18 Dec 2023 13:37:02 +0100'" returned exit code 1
make[1]: *** [debian/rules:10: override_dh_auto_install] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:4: binary] Error 2
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.