Package: src:r-bioc-rtracklayer
Version: 1.62.0-1
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
configure.ac:19: warning: AC_OUTPUT should be used without arguments.
configure.ac:19: You should run autoupdate.
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-rtracklayer/ -O--buildsystem=R
I: R Package: rtracklayer Version: 1.62.0
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 18:23:42 +0100
mkdir -p
/<<PKGBUILDDIR>>/debian/r-bioc-rtracklayer/usr/lib/R/site-library
R CMD INSTALL -l
/<<PKGBUILDDIR>>/debian/r-bioc-rtracklayer/usr/lib/R/site-library --clean .
"--built-timestamp='Thu, 30 Nov 2023 18:23:42 +0100'"
* installing *source* package ‘rtracklayer’ ...
** using staged installation
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for openssl >= 1.0... no
configure: creating ./config.status
config.status: creating src/Makevars
** 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 -D_FILE_OFFSET_BITS=64
-I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include'
-I'/usr/lib/R/site-library/XVector/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 S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64
-I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include'
-I'/usr/lib/R/site-library/XVector/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 -D_FILE_OFFSET_BITS=64
-I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include'
-I'/usr/lib/R/site-library/XVector/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 XVector_stubs.c -o XVector_stubs.o
gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64
-I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include'
-I'/usr/lib/R/site-library/XVector/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 R_init_rtracklayer.c -o R_init_rtracklayer.o
gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64
-I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include'
-I'/usr/lib/R/site-library/XVector/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 readGFF.c -o readGFF.o
gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64
-I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include'
-I'/usr/lib/R/site-library/XVector/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 bbiHelper.c -o bbiHelper.o
gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64
-I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include'
-I'/usr/lib/R/site-library/XVector/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 bigWig.c -o bigWig.o
gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64
-I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include'
-I'/usr/lib/R/site-library/XVector/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 bigBedHelper.c -o bigBedHelper.o
gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64
-I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include'
-I'/usr/lib/R/site-library/XVector/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 bigBed.c -o bigBed.o
gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64
-I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include'
-I'/usr/lib/R/site-library/XVector/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 chain_io.c -o chain_io.o
gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64
-I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include'
-I'/usr/lib/R/site-library/XVector/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 twoBit.c -o twoBit.o
gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64
-I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include'
-I'/usr/lib/R/site-library/XVector/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 handlers.c -o handlers.o
handlers.c: In function ‘R_warnHandler’:
handlers.c:10:11: error: format not a string literal and no format arguments
[-Werror=format-security]
10 | warning(warn_buf);
| ^~~~~~~~
cc1: some warnings being treated as errors
make[1]: *** [/usr/lib/R/etc/Makeconf:195: handlers.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 ‘rtracklayer’
* removing
‘/<<PKGBUILDDIR>>/debian/r-bioc-rtracklayer/usr/lib/R/site-library/rtracklayer’
dh_auto_install: error: R CMD INSTALL -l
/<<PKGBUILDDIR>>/debian/r-bioc-rtracklayer/usr/lib/R/site-library --clean .
"--built-timestamp='Thu, 30 Nov 2023 18:23:42 +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.
