Your message dated Sun, 03 May 2020 12:19:29 +0000
with message-id <[email protected]>
and subject line Bug#957836: fixed in spoa 3.0.2-4
has caused the Debian Bug report #957836,
regarding spoa: 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.)
--
957836: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=957836
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:spoa
Version: 3.0.1-1
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/spoa_3.0.1-1_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
[...]
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/alignment_engine.cpp:41:20: error: ‘invalid_argument’ is
not a member of ‘std’
41 | throw std::invalid_argument("[spoa::createAlignmentEngine]
error: "
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/alignment_engine.cpp:45:20: error: ‘invalid_argument’ is
not a member of ‘std’
45 | throw std::invalid_argument("[spoa::createAlignmentEngine]
error: "
| ^~~~~~~~~~~~~~~~
make[3]: *** [CMakeFiles/spoa.dir/build.make:66:
CMakeFiles/spoa.dir/src/alignment_engine.cpp.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[3]: *** [CMakeFiles/spoa_static.dir/build.make:66:
CMakeFiles/spoa_static.dir/src/alignment_engine.cpp.o] Error 1
make[3]: *** Waiting for unfinished jobs....
[ 31%] Building CXX object CMakeFiles/spoa_static.dir/src/graph.cpp.o
/usr/bin/c++ -I/<<PKGBUILDDIR>>/include
-I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/config -I/<<PKGBUILDDIR>>/src -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic
-O3 -DNDEBUG -std=c++11 -o CMakeFiles/spoa_static.dir/src/graph.cpp.o -c
/<<PKGBUILDDIR>>/src/graph.cpp
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp: In function
‘std::unique_ptr<spoa::AlignmentEngine>
spoa::createSimdAlignmentEngine(spoa::AlignmentType, spoa::AlignmentSubtype,
int8_t, int8_t, int8_t, int8_t, int8_t, int8_t)’:
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:293:74: warning: unused
parameter ‘type’ [-Wunused-parameter]
293 | std::unique_ptr<AlignmentEngine>
createSimdAlignmentEngine(AlignmentType type,
|
~~~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:294:22: warning: unused
parameter ‘subtype’ [-Wunused-parameter]
294 | AlignmentSubtype subtype, std::int8_t m, std::int8_t n, std::int8_t
g,
| ~~~~~~~~~~~~~~~~~^~~~~~~
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:294:43: warning: unused
parameter ‘m’ [-Wunused-parameter]
294 | AlignmentSubtype subtype, std::int8_t m, std::int8_t n, std::int8_t
g,
| ~~~~~~~~~~~~^
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:294:58: warning: unused
parameter ‘n’ [-Wunused-parameter]
294 | AlignmentSubtype subtype, std::int8_t m, std::int8_t n, std::int8_t
g,
| ~~~~~~~~~~~~^
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:294:73: warning: unused
parameter ‘g’ [-Wunused-parameter]
294 | AlignmentSubtype subtype, std::int8_t m, std::int8_t n, std::int8_t
g,
|
~~~~~~~~~~~~^
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:295:17: warning: unused
parameter ‘e’ [-Wunused-parameter]
295 | std::int8_t e, std::int8_t q, std::int8_t c) {
| ~~~~~~~~~~~~^
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:295:32: warning: unused
parameter ‘q’ [-Wunused-parameter]
295 | std::int8_t e, std::int8_t q, std::int8_t c) {
| ~~~~~~~~~~~~^
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:295:47: warning: unused
parameter ‘c’ [-Wunused-parameter]
295 | std::int8_t e, std::int8_t q, std::int8_t c) {
| ~~~~~~~~~~~~^
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp: In member function ‘virtual
void spoa::SimdAlignmentEngine::prealloc(uint32_t, uint32_t)’:
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:358:50: warning: unused
parameter ‘max_sequence_size’ [-Wunused-parameter]
358 | void SimdAlignmentEngine::prealloc(std::uint32_t max_sequence_size,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:359:19: warning: unused
parameter ‘alphabet_size’ [-Wunused-parameter]
359 | std::uint32_t alphabet_size) {
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp: In member function ‘void
spoa::SimdAlignmentEngine::realloc(uint32_t, uint32_t, uint32_t)’:
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:380:49: warning: unused
parameter ‘matrix_width’ [-Wunused-parameter]
380 | void SimdAlignmentEngine::realloc(std::uint32_t matrix_width,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:381:19: warning: unused
parameter ‘matrix_height’ [-Wunused-parameter]
381 | std::uint32_t matrix_height, std::uint32_t num_codes) {
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:381:48: warning: unused
parameter ‘num_codes’ [-Wunused-parameter]
381 | std::uint32_t matrix_height, std::uint32_t num_codes) {
| ~~~~~~~~~~~~~~^~~~~~~~~
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp: In member function ‘virtual
spoa::Alignment spoa::SimdAlignmentEngine::align(const char*, uint32_t, const
std::unique_ptr<spoa::Graph>&)’:
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:649:50: warning: unused
parameter ‘sequence’ [-Wunused-parameter]
649 | Alignment SimdAlignmentEngine::align(const char* sequence,
| ~~~~~~~~~~~~^~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:166: CMakeFiles/spoa.dir/all] Error 2
make[2]: *** Waiting for unfinished jobs....
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:139: CMakeFiles/spoa_static.dir/all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[1]: *** [Makefile:133: 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:13: build] Error 25
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: spoa
Source-Version: 3.0.2-4
Done: [email protected] (Michael R. Crusoe)
We believe that the bug you reported is fixed in the latest version of
spoa, 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.
Michael R. Crusoe <[email protected]> (supplier of updated spoa 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: SHA512
Format: 1.8
Date: Sun, 03 May 2020 14:02:30 +0200
Source: spoa
Architecture: source
Version: 3.0.2-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Michael R. Crusoe <[email protected]>
Closes: 957836
Changes:
spoa (3.0.2-4) unstable; urgency=medium
.
* Team upload.
* Mark libspoa{3,-dev} as Multi-Arch: same
* Simplify simde patch
.
[ Etienne Mollier ]
* Added patch for Gcc 10; assuming #959465 resolution:
Closes: #957836
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