[Debian-med-packaging] Bug#957054: bowtie2: ftbfs with GCC-10
Matthias Klose
doko at debian.org
Fri Apr 17 11:57:23 BST 2020
Package: src:bowtie2
Version: 2.3.5.1-6
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/bowtie2_2.3.5.1-6_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
[...]
from aligner_driver.cpp:20:
/usr/include/tbb/tbb_config.h:653:134: note: ‘#pragma message: TBB Warning: Support for C++98/03 is deprecated. Please use the compiler that supports C++11 features at least.’
653 | #pragma message("TBB Warning: Support for C++98/03 is deprecated. Please use the compiler that supports C++11 features at least.")
| ^
In file included from threading.h:29,
from ds.h:30,
from random_util.h:25,
from aligner_seed2.h:101,
from aligner_driver.h:78,
from aligner_driver.cpp:20:
/usr/include/tbb/mutex.h:21:140: note: ‘#pragma message: TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.’
21 | #pragma message("TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.")
| ^
In file included from threading.h:32,
from ds.h:30,
from random_util.h:25,
from aligner_seed2.h:101,
from aligner_driver.h:78,
from aligner_driver.cpp:20:
/usr/include/tbb/atomic.h:21:141: note: ‘#pragma message: TBB Warning: tbb/atomic.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.’
21 | #pragma message("TBB Warning: tbb/atomic.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.")
| ^
In file included from /usr/include/tbb/internal/_deprecated_header_message_guard.h:17,
from /usr/include/tbb/mutex.h:17,
from threading.h:29,
from ds.h:30,
from bowtie_main.cpp:25:
/usr/include/tbb/tbb_config.h:653:134: note: ‘#pragma message: TBB Warning: Support for C++98/03 is deprecated. Please use the compiler that supports C++11 features at least.’
653 | #pragma message("TBB Warning: Support for C++98/03 is deprecated. Please use the compiler that supports C++11 features at least.")
| ^
In file included from threading.h:29,
from ds.h:30,
from bowtie_main.cpp:25:
/usr/include/tbb/mutex.h:21:140: note: ‘#pragma message: TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.’
21 | #pragma message("TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.")
| ^
In file included from threading.h:32,
from ds.h:30,
from bowtie_main.cpp:25:
/usr/include/tbb/atomic.h:21:141: note: ‘#pragma message: TBB Warning: tbb/atomic.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.’
21 | #pragma message("TBB Warning: tbb/atomic.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.")
| ^
make[2]: *** [Makefile:350: bowtie2-align-l] Error 1
In file included from /usr/include/tbb/internal/_deprecated_header_message_guard.h:17,
from /usr/include/tbb/mutex.h:17,
from threading.h:29,
from ds.h:30,
from bowtie_main.cpp:25:
/usr/include/tbb/tbb_config.h:653:134: note: ‘#pragma message: TBB Warning: Support for C++98/03 is deprecated. Please use the compiler that supports C++11 features at least.’
653 | #pragma message("TBB Warning: Support for C++98/03 is deprecated. Please use the compiler that supports C++11 features at least.")
| ^
In file included from threading.h:29,
from ds.h:30,
from bowtie_main.cpp:25:
/usr/include/tbb/mutex.h:21:140: note: ‘#pragma message: TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.’
21 | #pragma message("TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.")
| ^
In file included from threading.h:32,
from ds.h:30,
from bowtie_main.cpp:25:
/usr/include/tbb/atomic.h:21:141: note: ‘#pragma message: TBB Warning: tbb/atomic.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.’
21 | #pragma message("TBB Warning: tbb/atomic.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.")
| ^
make[2]: *** [Makefile:342: bowtie2-align-s] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j4 "INSTALL=install --strip-program=true" "EXTRA_FLAGS=-std=c++98 -Wl,-z,relro -Wl,-z,now" POPCNT_CAPABILITY=1 returned exit code 2
make[1]: *** [debian/rules:27: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:24: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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