[Debian-med-packaging] Bug#957542: minc-tools: ftbfs with GCC-10
Matthias Klose
doko at debian.org
Fri Apr 17 12:06:07 BST 2020
Package: src:minc-tools
Version: 2.3.00+dfsg-3
Severity: normal
Tags: sid bullseye
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-10
Please keep this issue open in the bug tracker for the package it
was filed for. If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.
The package fails to build in a test rebuild on at least amd64 with
gcc-10/g++-10, but succeeds to build with gcc-9/g++-9. The
severity of this report will be raised before the bullseye release,
so nothing has to be done for the buster release.
The full build log can be found at:
http://people.debian.org/~doko/logs/gcc10-20200225/minc-tools_2.3.00+dfsg-3_unstable_gcc10.log
The last lines of the build log are at the end of this report.
To build with GCC 10, either set CC=gcc-10 CXX=g++-10 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.
apt-get -t=experimental install g++
Common build failures are new warnings resulting in build failures with
-Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-10/porting_to.html
[...]
make -f conversion/CMakeFiles/upet2mnc.dir/build.make conversion/CMakeFiles/upet2mnc.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/conversion /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/conversion /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/conversion/CMakeFiles/upet2mnc.dir/DependInfo.cmake --color=
Scanning dependencies of target upet2mnc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make -f conversion/CMakeFiles/upet2mnc.dir/build.make conversion/CMakeFiles/upet2mnc.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 89%] Building C object conversion/CMakeFiles/upet2mnc.dir/micropet/upet2mnc.c.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/conversion && /usr/bin/cc -DHAVE_CONFIG_H -DHAVE_MINC1=1 -DHAVE_MINC2=1 -DMINC2=1 -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>>/conversion/Acr_nema -I/usr/include/nifti -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -o CMakeFiles/upet2mnc.dir/micropet/upet2mnc.c.o -c /<<PKGBUILDDIR>>/conversion/micropet/upet2mnc.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 89%] Built target nii2mnc
[ 89%] Building C object conversion/CMakeFiles/acr_nema.dir/Acr_nema/file_io.c.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/conversion && /usr/bin/cc -DHAVE_CONFIG_H -DHAVE_MINC1=1 -DHAVE_MINC2=1 -DMINC2=1 -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>>/conversion/Acr_nema -I/usr/include/nifti -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -o CMakeFiles/acr_nema.dir/Acr_nema/file_io.c.o -c /<<PKGBUILDDIR>>/conversion/Acr_nema/file_io.c
/<<PKGBUILDDIR>>/conversion/micropet/upet2mnc.c:419:36: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
419 | {NULL, ARGV_VERINFO, (char *) VERSIONSTR, (char *) NULL, NULL},
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/conversion/micropet/upet2mnc.c:16:38: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
16 | #define VERSIONSTR VERSION " built " __DATE__ " " __TIME__
| ^~~~~~~~
/<<PKGBUILDDIR>>/conversion/micropet/upet2mnc.c:419:36: note: in expansion of macro ‘VERSIONSTR’
419 | {NULL, ARGV_VERINFO, (char *) VERSIONSTR, (char *) NULL, NULL},
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/conversion/micropet/upet2mnc.c: In function ‘upet_to_minc’:
/<<PKGBUILDDIR>>/conversion/micropet/upet2mnc.c:537:19: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
537 | argv_tmp[1] = VERSIONSTR;
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/conversion/micropet/upet2mnc.c:16:38: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
16 | #define VERSIONSTR VERSION " built " __DATE__ " " __TIME__
| ^~~~~~~~
/<<PKGBUILDDIR>>/conversion/micropet/upet2mnc.c:537:19: note: in expansion of macro ‘VERSIONSTR’
537 | argv_tmp[1] = VERSIONSTR;
| ^~~~~~~~~~
[ 90%] Linking C executable minctoecat
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/conversion && /usr/bin/cmake -E cmake_link_script CMakeFiles/minctoecat.dir/link.txt --verbose=1
/usr/bin/cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -Wl,-z,relro -Wl,-z,now -Wl,-L/usr/lib/x86_64-linux-gnu/hdf5/serial -rdynamic CMakeFiles/minctoecat.dir/minctoecat/minctoecat.c.o CMakeFiles/minctoecat.dir/minctoecat/ecat_write.c.o CMakeFiles/minctoecat.dir/minctoecat/machine_indep.c.o -o minctoecat -lminc2 -lhdf5 -lpthread -lsz -lz -ldl -lm -lz -lm -ldl -lrt -lnetcdf -lminc2 -lminc2 -lhdf5 -lpthread -lsz -lz -ldl -lm -lz -lm -ldl -lrt -lnetcdf -lm -lminc2 -lhdf5 -lpthread -lsz -lz -ldl -lm -ldl -lrt -lnetcdf -lminc2 -lhdf5 -lpthread -lsz -lz -ldl -lm -lm -ldl -lrt -lnetcdf
/usr/bin/ld: CMakeFiles/minctoecat.dir/minctoecat/ecat_write.c.o:./obj-x86_64-linux-gnu/conversion/./conversion/minctoecat/ecat_write.h:42: multiple definition of `matrix_errno'; CMakeFiles/minctoecat.dir/minctoecat/minctoecat.c.o:./obj-x86_64-linux-gnu/conversion/./conversion/minctoecat/ecat_write.h:42: first defined here
/usr/bin/ld: CMakeFiles/minctoecat.dir/minctoecat/ecat_write.c.o:./obj-x86_64-linux-gnu/conversion/./conversion/minctoecat/ecat_write.h:44: multiple definition of `matrix_errtxt'; CMakeFiles/minctoecat.dir/minctoecat/minctoecat.c.o:./obj-x86_64-linux-gnu/conversion/./conversion/minctoecat/ecat_write.h:44: first defined here
/usr/bin/ld: CMakeFiles/minctoecat.dir/minctoecat/machine_indep.c.o:./obj-x86_64-linux-gnu/conversion/./conversion/minctoecat/ecat_write.h:44: multiple definition of `matrix_errtxt'; CMakeFiles/minctoecat.dir/minctoecat/minctoecat.c.o:./obj-x86_64-linux-gnu/conversion/./conversion/minctoecat/ecat_write.h:44: first defined here
/usr/bin/ld: CMakeFiles/minctoecat.dir/minctoecat/machine_indep.c.o:./obj-x86_64-linux-gnu/conversion/./conversion/minctoecat/ecat_write.h:42: multiple definition of `matrix_errno'; CMakeFiles/minctoecat.dir/minctoecat/minctoecat.c.o:./obj-x86_64-linux-gnu/conversion/./conversion/minctoecat/ecat_write.h:42: first defined here
[ 91%] Building C object conversion/CMakeFiles/acr_nema.dir/Acr_nema/globals.c.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/conversion && /usr/bin/cc -DHAVE_CONFIG_H -DHAVE_MINC1=1 -DHAVE_MINC2=1 -DMINC2=1 -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>>/conversion/Acr_nema -I/usr/include/nifti -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -o CMakeFiles/acr_nema.dir/Acr_nema/globals.c.o -c /<<PKGBUILDDIR>>/conversion/Acr_nema/globals.c
[ 92%] Building C object conversion/CMakeFiles/acr_nema.dir/Acr_nema/group.c.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/conversion && /usr/bin/cc -DHAVE_CONFIG_H -DHAVE_MINC1=1 -DHAVE_MINC2=1 -DMINC2=1 -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>>/conversion/Acr_nema -I/usr/include/nifti -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -o CMakeFiles/acr_nema.dir/Acr_nema/group.c.o -c /<<PKGBUILDDIR>>/conversion/Acr_nema/group.c
collect2: error: ld returned 1 exit status
make[3]: *** [conversion/CMakeFiles/minctoecat.dir/build.make:147: conversion/minctoecat] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:2110: conversion/CMakeFiles/minctoecat.dir/all] Error 2
make[2]: *** Waiting for unfinished jobs....
[ 93%] Building C object conversion/CMakeFiles/acr_nema.dir/Acr_nema/message.c.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/conversion && /usr/bin/cc -DHAVE_CONFIG_H -DHAVE_MINC1=1 -DHAVE_MINC2=1 -DMINC2=1 -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>>/conversion/Acr_nema -I/usr/include/nifti -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -o CMakeFiles/acr_nema.dir/Acr_nema/message.c.o -c /<<PKGBUILDDIR>>/conversion/Acr_nema/message.c
[ 93%] Linking C executable upet2mnc
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/conversion && /usr/bin/cmake -E cmake_link_script CMakeFiles/upet2mnc.dir/link.txt --verbose=1
/usr/bin/cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -Wl,-z,relro -Wl,-z,now -Wl,-L/usr/lib/x86_64-linux-gnu/hdf5/serial -rdynamic CMakeFiles/upet2mnc.dir/micropet/upet2mnc.c.o -o upet2mnc -lminc2 -lhdf5 -lpthread -lsz -lz -ldl -lm -lz -lm -ldl -lrt -lnetcdf -ldl -lm -lm -ldl -lrt -lnetcdf
[ 93%] Building C object conversion/CMakeFiles/acr_nema.dir/Acr_nema/value_repr.c.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/conversion && /usr/bin/cc -DHAVE_CONFIG_H -DHAVE_MINC1=1 -DHAVE_MINC2=1 -DMINC2=1 -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>>/conversion/Acr_nema -I/usr/include/nifti -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -o CMakeFiles/acr_nema.dir/Acr_nema/value_repr.c.o -c /<<PKGBUILDDIR>>/conversion/Acr_nema/value_repr.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 93%] Built target upet2mnc
[ 94%] Linking C static library libacr_nema.a
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/conversion && /usr/bin/cmake -P CMakeFiles/acr_nema.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/conversion && /usr/bin/cmake -E cmake_link_script CMakeFiles/acr_nema.dir/link.txt --verbose=1
/usr/bin/ar qc libacr_nema.a CMakeFiles/acr_nema.dir/Acr_nema/acr_io.c.o CMakeFiles/acr_nema.dir/Acr_nema/dicom_client_routines.c.o CMakeFiles/acr_nema.dir/Acr_nema/dicom_network.c.o CMakeFiles/acr_nema.dir/Acr_nema/element.c.o CMakeFiles/acr_nema.dir/Acr_nema/file_io.c.o CMakeFiles/acr_nema.dir/Acr_nema/globals.c.o CMakeFiles/acr_nema.dir/Acr_nema/group.c.o CMakeFiles/acr_nema.dir/Acr_nema/message.c.o CMakeFiles/acr_nema.dir/Acr_nema/value_repr.c.o
/usr/bin/ranlib libacr_nema.a
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 94%] Built target acr_nema
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[1]: *** [Makefile:166: all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" returned exit code 2
make: *** [debian/rules:22: build] Error 25
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2
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