[R-pkg-team] Bug#1071341: r-bioc-genefilter: FTBFS: nd.c:75:21: error: format not a string literal and no format arguments

[Santiago Vila]

Package: src:r-bioc-genefilter
Version: 1.84.0-1
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-genefilter/ -O--buildsystem=R
I: R Package: genefilter Version: 1.84.0
I: Building using R version 4.4.0-2
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Thu, 30 Nov 2023 17:52:55 +0100
	mkdir -p /<<PKGBUILDDIR>>/debian/r-bioc-genefilter/usr/lib/R/site-library
	R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-bioc-genefilter/usr/lib/R/site-library --clean . "--built-timestamp='Thu, 30 Nov 2023 17:52:55 +0100'"
* installing *source* package ‘genefilter’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Debian 13.2.0-25) 13.2.0’
using Fortran compiler: ‘GNU Fortran (Debian 13.2.0-25) 13.2.0’
using C++ compiler: ‘g++ (Debian 13.2.0-25) 13.2.0’
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
g++ -std=gnu++17 -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 half_range_mode.cpp -o half_range_mode.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++
half_range_mode.cpp: In function ‘double half_range_mode(double*, double*, double, int)’:
half_range_mode.cpp:100:60: warning: format ‘%i’ expects argument of type ‘int’, but argument 5 has type ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wformat=]
   100 |     if (diag) Rprintf( "N = %i, N'' = %i, w = %.4f, |J| = %i\n", N, N_double_prime, w, J.size() );
       |                                                           ~^                           ~~~~~~~~
       |                                                            |                                 |
       |                                                            int                               std::vector<int>::size_type {aka long unsigned int}
       |                                                           %li
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 init.c -o init.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 nd.c -o nd.o
nd.c: In function ‘detectTies’:
nd.c:75:21: error: format not a string literal and no format arguments [-Werror=format-security]
    75 |             warning(msg_buf);
       |                     ^~~~~~~
cc1: some warnings being treated as errors
make[1]: *** [/usr/lib/R/etc/Makeconf:195: nd.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 ‘genefilter’
* removing ‘/<<PKGBUILDDIR>>/debian/r-bioc-genefilter/usr/lib/R/site-library/genefilter’
dh_auto_install: error: R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-bioc-genefilter/usr/lib/R/site-library --clean . "--built-timestamp='Thu, 30 Nov 2023 17:52:55 +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.