[R-pkg-team] Bug#1071353: r-bioc-xvector: FTBFS: RDS_random_access.c:136:17: error: format not a string literal and no format arguments

Santiago Vila sanvila at debian.org
Fri May 17 21:41:12 BST 2024


Package: src:r-bioc-xvector
Version: 0.42.0-1
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-xvector/ -O--buildsystem=R
I: R Package: XVector Version: 0.42.0
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 00:31:07 +0000
	mkdir -p /<<PKGBUILDDIR>>/debian/r-bioc-xvector/usr/lib/R/site-library
	R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-bioc-xvector/usr/lib/R/site-library --clean . "--built-timestamp='Thu, 30 Nov 2023 00:31:07 +0000'"
* installing *source* package ‘XVector’ ...
** 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/IRanges/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 IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/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 Ocopy_byteblocks.c -o Ocopy_byteblocks.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/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 RDS_random_access.c -o RDS_random_access.o
RDS_random_access.c: In function ‘RDS_read_chars’:
RDS_random_access.c:136:17: error: format not a string literal and no format arguments [-Werror=format-security]
   136 |                 error(errmsg);
       |                 ^~~~~
RDS_random_access.c: In function ‘RDS_read_vector_length’:
RDS_random_access.c:218:17: error: format not a string literal and no format arguments [-Werror=format-security]
   218 |                 error(errmsg);
       |                 ^~~~~
RDS_random_access.c:226:17: error: format not a string literal and no format arguments [-Werror=format-security]
   226 |                 error(errmsg);
       |                 ^~~~~
RDS_random_access.c: In function ‘RDS_read_string’:
RDS_random_access.c:277:17: error: format not a string literal and no format arguments [-Werror=format-security]
   277 |                 error(errmsg);
       |                 ^~~~~
RDS_random_access.c:283:25: error: format not a string literal and no format arguments [-Werror=format-security]
   283 |                         error(errmsg);
       |                         ^~~~~
RDS_random_access.c: In function ‘RDS_read_atomic_vector’:
RDS_random_access.c:360:17: error: format not a string literal and no format arguments [-Werror=format-security]
   360 |                 error(errmsg);
       |                 ^~~~~
RDS_random_access.c: In function ‘RDS_read_attrib_separator’:
RDS_random_access.c:406:17: error: format not a string literal and no format arguments [-Werror=format-security]
   406 |                 error(errmsg);
       |                 ^~~~~
RDS_random_access.c: In function ‘RDS_read_symbol’:
RDS_random_access.c:428:17: error: format not a string literal and no format arguments [-Werror=format-security]
   428 |                 error(errmsg);
       |                 ^~~~~
RDS_random_access.c: In function ‘RDS_read_object’:
RDS_random_access.c:497:17: error: format not a string literal and no format arguments [-Werror=format-security]
   497 |                 error(errmsg);
       |                 ^~~~~
RDS_random_access.c: In function ‘RDS_read_file_header’:
RDS_random_access.c:559:17: error: format not a string literal and no format arguments [-Werror=format-security]
   559 |                 error(errmsg);
       |                 ^~~~~
RDS_random_access.c: In function ‘extract_top_level_object_type’:
RDS_random_access.c:618:17: error: format not a string literal and no format arguments [-Werror=format-security]
   618 |                 error(errmsg);
       |                 ^~~~~
RDS_random_access.c: In function ‘RDS_read_atom_at_offset’:
RDS_random_access.c:675:17: error: format not a string literal and no format arguments [-Werror=format-security]
   675 |                 error(errmsg);
       |                 ^~~~~
RDS_random_access.c:698:17: error: format not a string literal and no format arguments [-Werror=format-security]
   698 |                 error(errmsg);
       |                 ^~~~~
RDS_random_access.c: In function ‘RDS_extract_subvector’:
RDS_random_access.c:772:17: error: format not a string literal and no format arguments [-Werror=format-security]
   772 |                 error(errmsg);
       |                 ^~~~~
cc1: some warnings being treated as errors
make[1]: *** [/usr/lib/R/etc/Makeconf:195: RDS_random_access.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 ‘XVector’
* removing ‘/<<PKGBUILDDIR>>/debian/r-bioc-xvector/usr/lib/R/site-library/XVector’
dh_auto_install: error: R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-bioc-xvector/usr/lib/R/site-library --clean . "--built-timestamp='Thu, 30 Nov 2023 00:31:07 +0000'" 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.



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