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.
