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:
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[...]
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
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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.
