Your message dated Sun, 26 Apr 2020 12:18:48 +0000
with message-id <[email protected]>
and subject line Bug#957536: fixed in mia 2.4.7-1
has caused the Debian Bug report #957536,
regarding mia: ftbfs with GCC-10
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
957536: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=957536
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:mia
Version: 2.4.6-5
Severity: normal
Tags: sid bullseye
User: [email protected]
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/mia_2.4.6-5_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
[...]
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/mia/2d/filter && /usr/bin/c++
-DBOOST_ALL_DYN_LINK -DBOOST_FILESYSTEM_VERSION=3 -DHAVE_CONFIG_H
-I/usr/include/eigen3 -I/usr/include/libxml2
-I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden
-DBOOST_TEST_DYN_LINK -o
CMakeFiles/test-2dimage-filter-shaped_mean.dir/test_shaped_mean.cc.o -c
/<<PKGBUILDDIR>>/mia/2d/filter/test_shaped_mean.cc
[ 30%] Linking CXX executable test-2dimage-filter-distance
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/mia/2d/filter && /usr/bin/cmake -E
cmake_link_script CMakeFiles/test-2dimage-filter-distance.dir/link.txt
--verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -fvisibility=hidden -Wl,-z,relro -Wl,-z,now
-Wl,--as-needed -fvisibility=hidden -rdynamic
CMakeFiles/test-2dimage-filter-distance.dir/test_distance.cc.o
CMakeFiles/2dimage-filter-distance-common.dir/distance.cc.o -o
test-2dimage-filter-distance
-Wl,-rpath,/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/mia/2d:/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/mia/core
-lboost_unit_test_framework ../libmia2dtest-2.4.so.6.0.0
../libmia2d-2.4.so.6.0.0 ../../core/libmiacore-2.4.so.6.0.0 -lgsl -lgslcblas
-lm -lboost_filesystem -lboost_system -lpthread -ldl -lfftw3f -lxml2
-lboost_unit_test_framework
/usr/bin/ld: CMakeFiles/test-2dimage-filter-distance.dir/test_distance.cc.o: in
function `test_distance_double::test_method()':
./obj-x86_64-linux-gnu/mia/2d/filter/./mia/core/filter.hh:263: undefined
reference to `std::shared_ptr<mia::C2DImage>
distance_2d_filter::C2DDistance::operator()<float>(mia::T2DImage<float> const&)
const'
/usr/bin/ld: CMakeFiles/test-2dimage-filter-distance.dir/test_distance.cc.o: in
function `filter<distance_2d_filter::C2DDistance, mia::C2DImage>':
./obj-x86_64-linux-gnu/mia/2d/filter/./mia/core/filter.hh:255: undefined
reference to `std::shared_ptr<mia::C2DImage>
distance_2d_filter::C2DDistance::operator()<signed char>(mia::T2DImage<signed
char> const&) const'
/usr/bin/ld: ./obj-x86_64-linux-gnu/mia/2d/filter/./mia/core/filter.hh:256:
undefined reference to `std::shared_ptr<mia::C2DImage>
distance_2d_filter::C2DDistance::operator()<unsigned
char>(mia::T2DImage<unsigned char> const&) const'
/usr/bin/ld: ./obj-x86_64-linux-gnu/mia/2d/filter/./mia/core/filter.hh:257:
undefined reference to `std::shared_ptr<mia::C2DImage>
distance_2d_filter::C2DDistance::operator()<short>(mia::T2DImage<short> const&)
const'
/usr/bin/ld: ./obj-x86_64-linux-gnu/mia/2d/filter/./mia/core/filter.hh:258:
undefined reference to `std::shared_ptr<mia::C2DImage>
distance_2d_filter::C2DDistance::operator()<unsigned
short>(mia::T2DImage<unsigned short> const&) const'
/usr/bin/ld: ./obj-x86_64-linux-gnu/mia/2d/filter/./mia/core/filter.hh:259:
undefined reference to `std::shared_ptr<mia::C2DImage>
distance_2d_filter::C2DDistance::operator()<int>(mia::T2DImage<int> const&)
const'
/usr/bin/ld: ./obj-x86_64-linux-gnu/mia/2d/filter/./mia/core/filter.hh:260:
undefined reference to `std::shared_ptr<mia::C2DImage>
distance_2d_filter::C2DDistance::operator()<unsigned
int>(mia::T2DImage<unsigned int> const&) const'
/usr/bin/ld: ./obj-x86_64-linux-gnu/mia/2d/filter/./mia/core/filter.hh:261:
undefined reference to `std::shared_ptr<mia::C2DImage>
distance_2d_filter::C2DDistance::operator()<long>(mia::T2DImage<long> const&)
const'
/usr/bin/ld: ./obj-x86_64-linux-gnu/mia/2d/filter/./mia/core/filter.hh:262:
undefined reference to `std::shared_ptr<mia::C2DImage>
distance_2d_filter::C2DDistance::operator()<unsigned
long>(mia::T2DImage<unsigned long> const&) const'
/usr/bin/ld: ./obj-x86_64-linux-gnu/mia/2d/filter/./mia/core/filter.hh:264:
undefined reference to `std::shared_ptr<mia::C2DImage>
distance_2d_filter::C2DDistance::operator()<double>(mia::T2DImage<double>
const&) const'
/usr/bin/ld: ./obj-x86_64-linux-gnu/mia/2d/filter/./mia/core/filter.hh:254:
undefined reference to `std::shared_ptr<mia::C2DImage>
distance_2d_filter::C2DDistance::operator()<bool>(mia::T2DImage<bool> const&)
const'
collect2: error: ld returned 1 exit status
make[4]: ***
[mia/2d/filter/CMakeFiles/test-2dimage-filter-distance.dir/build.make:97:
mia/2d/filter/test-2dimage-filter-distance] Error 1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[3]: *** [CMakeFiles/Makefile2:10579:
mia/2d/filter/CMakeFiles/test-2dimage-filter-distance.dir/all] Error 2
make[3]: *** Waiting for unfinished jobs....
[ 30%] Building CXX object mia/3d/CMakeFiles/mia3d.dir/similarity_profile.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/mia/3d && /usr/bin/c++
-DBOOST_ALL_DYN_LINK -DBOOST_FILESYSTEM_VERSION=3 -DHAVE_CONFIG_H
-Dmia3d_EXPORTS -I/usr/include/eigen3 -I/usr/include/libxml2
-I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden
-fPIC -o CMakeFiles/mia3d.dir/similarity_profile.cc.o -c
/<<PKGBUILDDIR>>/mia/3d/similarity_profile.cc
[ 30%] Linking CXX executable test-2dimage-filter-binarize
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/mia/2d/filter && /usr/bin/cmake -E
cmake_link_script CMakeFiles/test-2dimage-filter-binarize.dir/link.txt
--verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -fvisibility=hidden -Wl,-z,relro -Wl,-z,now
-Wl,--as-needed -fvisibility=hidden -rdynamic
CMakeFiles/test-2dimage-filter-binarize.dir/test_binarize.cc.o
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test-2dimage-filter-binarize
-Wl,-rpath,/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/mia/2d:/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/mia/core
-lboost_unit_test_framework ../libmia2dtest-2.4.so.6.0.0
../libmia2d-2.4.so.6.0.0 ../../core/libmiacore-2.4.so.6.0.0 -lgsl -lgslcblas
-lm -lboost_filesystem -lboost_system -lpthread -ldl -lfftw3f -lxml2
-lboost_unit_test_framework
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 30%] Built target test-2dimage-filter-binarize
[ 30%] Building CXX object
mia/3d/CMakeFiles/mia3d.dir/splinetransformpenalty.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/mia/3d && /usr/bin/c++
-DBOOST_ALL_DYN_LINK -DBOOST_FILESYSTEM_VERSION=3 -DHAVE_CONFIG_H
-Dmia3d_EXPORTS -I/usr/include/eigen3 -I/usr/include/libxml2
-I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden
-fPIC -o CMakeFiles/mia3d.dir/splinetransformpenalty.cc.o -c
/<<PKGBUILDDIR>>/mia/3d/splinetransformpenalty.cc
[ 30%] Linking CXX executable test-2dimage-filter-shaped_mean
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/mia/2d/filter && /usr/bin/cmake -E
cmake_link_script CMakeFiles/test-2dimage-filter-shaped_mean.dir/link.txt
--verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -fvisibility=hidden -Wl,-z,relro -Wl,-z,now
-Wl,--as-needed -fvisibility=hidden -rdynamic
CMakeFiles/test-2dimage-filter-shaped_mean.dir/test_shaped_mean.cc.o
CMakeFiles/2dimage-filter-shaped_mean-common.dir/shaped_mean.cc.o -o
test-2dimage-filter-shaped_mean
-Wl,-rpath,/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/mia/2d:/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/mia/core
-lboost_unit_test_framework ../libmia2dtest-2.4.so.6.0.0
../libmia2d-2.4.so.6.0.0 ../../core/libmiacore-2.4.so.6.0.0 -lgsl -lgslcblas
-lm -lboost_filesystem -lboost_system -lpthread -ldl -lfftw3f -lxml2
-lboost_unit_test_framework
[ 30%] Building CXX object mia/3d/CMakeFiles/mia3d.dir/stackdisttrans.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/mia/3d && /usr/bin/c++
-DBOOST_ALL_DYN_LINK -DBOOST_FILESYSTEM_VERSION=3 -DHAVE_CONFIG_H
-Dmia3d_EXPORTS -I/usr/include/eigen3 -I/usr/include/libxml2
-I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden
-fPIC -o CMakeFiles/mia3d.dir/stackdisttrans.cc.o -c
/<<PKGBUILDDIR>>/mia/3d/stackdisttrans.cc
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 30%] Built target test-2dimage-filter-shaped_mean
[ 30%] Building CXX object mia/3d/CMakeFiles/mia3d.dir/timestep.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/mia/3d && /usr/bin/c++
-DBOOST_ALL_DYN_LINK -DBOOST_FILESYSTEM_VERSION=3 -DHAVE_CONFIG_H
-Dmia3d_EXPORTS -I/usr/include/eigen3 -I/usr/include/libxml2
-I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden
-fPIC -o CMakeFiles/mia3d.dir/timestep.cc.o -c
/<<PKGBUILDDIR>>/mia/3d/timestep.cc
[ 31%] Building CXX object mia/3d/CMakeFiles/mia3d.dir/trackpoint.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/mia/3d && /usr/bin/c++
-DBOOST_ALL_DYN_LINK -DBOOST_FILESYSTEM_VERSION=3 -DHAVE_CONFIG_H
-Dmia3d_EXPORTS -I/usr/include/eigen3 -I/usr/include/libxml2
-I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden
-fPIC -o CMakeFiles/mia3d.dir/trackpoint.cc.o -c
/<<PKGBUILDDIR>>/mia/3d/trackpoint.cc
[ 31%] Building CXX object mia/3d/CMakeFiles/mia3d.dir/transform.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/mia/3d && /usr/bin/c++
-DBOOST_ALL_DYN_LINK -DBOOST_FILESYSTEM_VERSION=3 -DHAVE_CONFIG_H
-Dmia3d_EXPORTS -I/usr/include/eigen3 -I/usr/include/libxml2
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-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden
-fPIC -o CMakeFiles/mia3d.dir/transform.cc.o -c
/<<PKGBUILDDIR>>/mia/3d/transform.cc
[ 31%] Building CXX object mia/3d/CMakeFiles/mia3d.dir/transformfactory.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/mia/3d && /usr/bin/c++
-DBOOST_ALL_DYN_LINK -DBOOST_FILESYSTEM_VERSION=3 -DHAVE_CONFIG_H
-Dmia3d_EXPORTS -I/usr/include/eigen3 -I/usr/include/libxml2
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[ 31%] Building CXX object mia/3d/CMakeFiles/mia3d.dir/transformio.cc.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/mia/3d && /usr/bin/c++
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-I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -g -O2
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[ 31%] Building CXX object mia/3d/CMakeFiles/mia3d.dir/vectorfield.cc.o
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[ 31%] Building CXX object mia/3d/CMakeFiles/mia3d.dir/vfregularizer.cc.o
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-lm -lboost_filesystem -lboost_system -lpthread -ldl -lfftw3f -lxml2
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/mia/3d && /usr/bin/cmake -E
cmake_symlink_library libmia3d-2.4.so.6.0.0 libmia3d-2.4.so.6 libmia3d-2.4.so
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 31%] Built target mia3d
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [Makefile:144: all] Error 2
make[2]: 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[1]: *** [debian/rules:51: override_dh_auto_build-arch] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:32: build] Error 2
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: mia
Source-Version: 2.4.7-1
Done: Gert Wollny <[email protected]>
We believe that the bug you reported is fixed in the latest version of
mia, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Gert Wollny <[email protected]> (supplier of updated mia package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Sun, 26 Apr 2020 14:00:20 +0200
Source: mia
Architecture: source
Version: 2.4.7-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <[email protected]>
Changed-By: Gert Wollny <[email protected]>
Closes: 957536
Changes:
mia (2.4.7-1) unstable; urgency=medium
.
* New upstream version 2.4.7 Closes: #957536
* d/control: Update mailinglist
* d/p: remove patches applied upstream
* d/rules: disable nipype because it is currently not available on python3
* d/rules: remove --as-needed
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