Package: src:r-bioc-rhdf5
Version: 2.46.1+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
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# see debian/hdf5-private/README
ln -s /<<PKGBUILDDIR>>/debian/hdf5-private/H5private.h
/<<PKGBUILDDIR>>/src/H5private.h
ln -s /<<PKGBUILDDIR>>/debian/hdf5-private/H5TSprivate.h
/<<PKGBUILDDIR>>/src/H5TSprivate.h
dh_auto_install # --no-parallel ... does not help
I: R Package: rhdf5 Version: 2.46.1
I: Building using R version 4.4.0-2
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Mon, 18 Dec 2023 13:37:02 +0100
mkdir -p
/<<BUILDDIR>>/r-bioc-rhdf5-2.46.1\+dfsg/debian/r-bioc-rhdf5/usr/lib/R/site-library
R CMD INSTALL -l
/<<BUILDDIR>>/r-bioc-rhdf5-2.46.1\+dfsg/debian/r-bioc-rhdf5/usr/lib/R/site-library
--clean . "--built-timestamp='Mon, 18 Dec 2023 13:37:02 +0100'"
* installing *source* package ‘rhdf5’ ...
** using staged installation
configure: creating ./config.status
config.status: creating src/external_filters.h
** libs
using C compiler: ‘gcc (Debian 13.2.0-25) 13.2.0’
using C++ compiler: ‘g++ (Debian 13.2.0-25) 13.2.0’
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
gcc -I"/usr/share/R/include" -DNDEBUG
-I'/usr/lib/R/site-library/Rhdf5lib/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 H5.c -o H5.o
gcc -I"/usr/share/R/include" -DNDEBUG
-I'/usr/lib/R/site-library/Rhdf5lib/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 H5A.c -o H5A.o
gcc -I"/usr/share/R/include" -DNDEBUG
-I'/usr/lib/R/site-library/Rhdf5lib/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 H5D.c -o H5D.o
gcc -I"/usr/share/R/include" -DNDEBUG
-I'/usr/lib/R/site-library/Rhdf5lib/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 H5E.c -o H5E.o
H5E.c: In function ‘_rhdf5PrintErrorR’:
H5E.c:117:19: error: format not a string literal and no format arguments
[-Werror=format-security]
117 | error(str);
| ^~~
H5E.c:119:34: error: format not a string literal and no format arguments
[-Werror=format-security]
119 | error(client_data.txt[0]);
| ~~~~~~~~~~~~~~~^~~
H5E.c: In function ‘_rhdf5PrintErrorRcompact’:
H5E.c:149:19: error: format not a string literal and no format arguments
[-Werror=format-security]
149 | error(str);
| ^~~
H5E.c:151:34: error: format not a string literal and no format arguments
[-Werror=format-security]
151 | error(client_data.txt[0]);
| ~~~~~~~~~~~~~~~^~~
cc1: some warnings being treated as errors
make[2]: *** [/usr/lib/R/etc/Makeconf:195: H5E.o] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
ERROR: compilation failed for package ‘rhdf5’
* removing ‘/<<PKGBUILDDIR>>/debian/r-bioc-rhdf5/usr/lib/R/site-library/rhdf5’
dh_auto_install: error: R CMD INSTALL -l
/<<BUILDDIR>>/r-bioc-rhdf5-2.46.1\+dfsg/debian/r-bioc-rhdf5/usr/lib/R/site-library
--clean . "--built-timestamp='Mon, 18 Dec 2023 13:37:02 +0100'" returned exit code 1
make[1]: *** [debian/rules:10: override_dh_auto_install] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:4: binary] Error 2
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.
