[R-pkg-team] Bug#1071349: r-bioc-s4vectors: FTBFS: Rle_class.c:1136:17: error: format not a string literal and no format arguments

[Santiago Vila]

Package: src:r-bioc-s4vectors
Version: 0.40.2+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
    dh_auto_install --destdir=debian/r-bioc-s4vectors/ -O--buildsystem=R
I: R Package: S4Vectors Version: 0.40.2
I: Building using R version 4.4.0-2
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Wed, 29 Nov 2023 17:40:04 +0100
	mkdir -p /<<BUILDDIR>>/r-bioc-s4vectors-0.40.2\+dfsg/debian/r-bioc-s4vectors/usr/lib/R/site-library
	R CMD INSTALL -l /<<BUILDDIR>>/r-bioc-s4vectors-0.40.2\+dfsg/debian/r-bioc-s4vectors/usr/lib/R/site-library --clean . "--built-timestamp='Wed, 29 Nov 2023 17:40:04 +0100'"
* installing *source* package ‘S4Vectors’ ...
** 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       -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 AEbufs.c -o AEbufs.o
gcc -I"/usr/share/R/include" -DNDEBUG       -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 DataFrame_class.c -o DataFrame_class.o
gcc -I"/usr/share/R/include" -DNDEBUG       -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 Hits_class.c -o Hits_class.o
gcc -I"/usr/share/R/include" -DNDEBUG       -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 LLint_class.c -o LLint_class.o
gcc -I"/usr/share/R/include" -DNDEBUG       -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 List_class.c -o List_class.o
gcc -I"/usr/share/R/include" -DNDEBUG       -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 R_init_S4Vectors.c -o R_init_S4Vectors.o
gcc -I"/usr/share/R/include" -DNDEBUG       -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 Rle_class.c -o Rle_class.o
Rle_class.c: In function ‘_subset_Rle_by_ranges’:
Rle_class.c:1136:17: error: format not a string literal and no format arguments [-Werror=format-security]
  1136 |                 error(errmsg);
       |                 ^~~~~
Rle_class.c: In function ‘_subset_Rle_by_positions’:
Rle_class.c:1161:17: error: format not a string literal and no format arguments [-Werror=format-security]
  1161 |                 error(errmsg);
       |                 ^~~~~
Rle_class.c: In function ‘Rle_extract_range’:
Rle_class.c:1190:17: error: format not a string literal and no format arguments [-Werror=format-security]
  1190 |                 error(errmsg);
       |                 ^~~~~
cc1: some warnings being treated as errors
make[1]: *** [/usr/lib/R/etc/Makeconf:195: Rle_class.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 ‘S4Vectors’
* removing ‘/<<PKGBUILDDIR>>/debian/r-bioc-s4vectors/usr/lib/R/site-library/S4Vectors’
dh_auto_install: error: R CMD INSTALL -l /<<BUILDDIR>>/r-bioc-s4vectors-0.40.2\+dfsg/debian/r-bioc-s4vectors/usr/lib/R/site-library --clean . "--built-timestamp='Wed, 29 Nov 2023 17:40:04 +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.