Package: src:r-cran-rniftilib
Version: 0.0-35.r79-7
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configure.ac:2: warning: The macro `AC_CONFIG_HEADER' is obsolete.
configure.ac:2: You should run autoupdate.
./lib/autoconf/status.m4:719: AC_CONFIG_HEADER is expanded from...
configure.ac:2: the top level
configure.ac:10: warning: The macro `AC_HEADER_STDC' is obsolete.
configure.ac:10: You should run autoupdate.
./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from...
configure.ac:10: the top level
configure.ac:25: warning: The macro `CHECK_ZLIB' is obsolete.
configure.ac:25: You should run autoupdate.
aclocal.m4:81: CHECK_ZLIB is expanded from...
configure.ac:25: the top level
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-cran-rniftilib/ -O--buildsystem=R
I: R Package: Rniftilib Version: 0.0-35
I: Building using R version 4.4.0-2
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Fri, 22 Dec 2023 08:50:35 +0100
mkdir -p /<<PKGBUILDDIR>>/debian/r-cran-rniftilib/usr/lib/R/site-library
R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-cran-rniftilib/usr/lib/R/site-library
--clean . "--built-timestamp='Fri, 22 Dec 2023 08:50:35 +0100'"
* installing *source* package ‘Rniftilib’ ...
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether g++ -std=gnu++17 accepts -g... yes
checking for g++ -std=gnu++17 option to enable C++11 features... none needed
checking for gcc... gcc
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for inline... inline
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for GNU libc compatible malloc... yes
checking for pkg-config... /usr/bin/pkg-config
checking if zlib is wanted... yes
checking for inflateEnd in -lz... yes
checking for zlib.h... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating tools/config.h
** 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../tools -g -O2
-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
-Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -DHAVE_CONFIG_H -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 Rnifti.c -o Rnifti.o
Rnifti.c: In function ‘Rnifti_disp_lib_version’:
Rnifti.c:1670:67: warning: macro "__DATE__" might prevent reproducible builds
[-Wdate-time]
1670 | snprintf(buffer, 200, "%s, compiled %s", nifti_lib_version(),
__DATE__);
|
^~~~~~~~
gcc -I"/usr/share/R/include" -DNDEBUG -I../tools -g -O2
-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
-Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -DHAVE_CONFIG_H -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 nifti1_io.c -o nifti1_io.o
nifti1_io.c: In function ‘nifti_disp_lib_hist’:
nifti1_io.c:472:8: error: format not a string literal and no format arguments
[-Werror=format-security]
472 | Rprintf(gni_history[c]);
| ^~~~~~~
nifti1_io.c: In function ‘nifti_disp_matrix_orient’:
nifti1_io.c:1160:4: error: format not a string literal and no format arguments
[-Werror=format-security]
1160 | if ( mesg ) Rprintf(mesg); /* use stdout? */
| ^~
nifti1_io.c: In function ‘disp_nifti_1_header’:
nifti1_io.c:3536:4: error: format not a string literal and no format arguments
[-Werror=format-security]
3536 | if ( info ) Rprintf( info );
| ^~
nifti1_io.c: In function ‘nifti_image_infodump’:
nifti1_io.c:5153:4: error: format not a string literal and no format arguments
[-Werror=format-security]
5153 | if( str != NULL ){ REprintf(str); /*fputs(str,stderr)*/ ; free(str)
; }
| ^~
cc1: some warnings being treated as errors
make[1]: *** [/usr/lib/R/etc/Makeconf:195: nifti1_io.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 ‘Rniftilib’
* removing
‘/<<PKGBUILDDIR>>/debian/r-cran-rniftilib/usr/lib/R/site-library/Rniftilib’
dh_auto_install: error: R CMD INSTALL -l
/<<PKGBUILDDIR>>/debian/r-cran-rniftilib/usr/lib/R/site-library --clean .
"--built-timestamp='Fri, 22 Dec 2023 08:50:35 +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.
