Your message dated Mon, 06 Sep 2021 14:48:41 +0000
with message-id <[email protected]>
and subject line Bug#984079: fixed in khmer 2.1.2+dfsg-9
has caused the Debian Bug report #984079,
regarding khmer: ftbfs with GCC-11
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
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--
984079: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=984079
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:khmer
Version: 2.1.2+dfsg-8
Severity: normal
Tags: sid bookworm
User: [email protected]
Usertags: ftbfs-gcc-11
[This bug is not targeted to the upcoming bullseye release]
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-11/g++-11, but succeeds to build with gcc-10/g++-10. The
severity of this report will be raised before the bookworm release,
so nothing has to be done for the bullseye release.
The full build log can be found at:
http://people.debian.org/~doko/logs/20210228/filtered/gcc11/khmer_2.1.2+dfsg-8_unstable_gcc11.log
The last lines of the build log are at the end of this report.
To build with GCC 11, either set CC=gcc-11 CXX=g++-11 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-11/porting_to.html
GCC 11 defaults to the GNU++17 standard. If your package installs
header files in /usr/include, please don't work around C++17 issues
by choosing a lower C++ standard for the package build, but fix these
issues to build with the C++17 standard.
[...]
src/oxli/hashtable.cc:512:1: required from here
src/oxli/hashtable.cc:103:18: warning: catching polymorphic type ‘struct
oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=]
103 | } catch (NoMoreReadsAvailable) {
| ^~~~~~~~~~~~~~~~~~~~
src/oxli/hashtable.cc: In instantiation of ‘void
oxli::Hashtable::consume_seqfile_banding(oxli::read_parsers::ReadParserPtr<SeqIO>&,
unsigned int, unsigned int, unsigned int&, long long unsigned int&) [with
SeqIO = oxli::read_parsers::FastxReader;
oxli::read_parsers::ReadParserPtr<SeqIO> =
std::unique_ptr<oxli::read_parsers::ReadParser<oxli::read_parsers::FastxReader>
>]’:
src/oxli/hashtable.cc:529:1: required from here
src/oxli/hashtable.cc:133:18: warning: catching polymorphic type ‘struct
oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=]
133 | } catch (NoMoreReadsAvailable) {
| ^~~~~~~~~~~~~~~~~~~~
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g
-fwrapv -O2 -Wall -g
-ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=.
-fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2
-DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude
-Ithird-party/seqan/core/include -Ithird-party/smhasher
-I/usr/include/python3.9 -c src/oxli/hllcounter.cc -o
build/temp.linux-x86_64-3.9/src/oxli/hllcounter.o -O3 -std=c++11 -pedantic
-fopenmp
src/oxli/hllcounter.cc: In instantiation of ‘void
oxli::HLLCounter::consume_seqfile(oxli::read_parsers::ReadParserPtr<SeqIO>&,
bool, unsigned int&, long long unsigned int&) [with SeqIO =
oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr<SeqIO> =
std::unique_ptr<oxli::read_parsers::ReadParser<oxli::read_parsers::FastxReader>
>]’:
src/oxli/hllcounter.cc:524:1: required from here
src/oxli/hllcounter.cc:428:40: warning: catching polymorphic type ‘struct
oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=]
428 | } catch (read_parsers::NoMoreReadsAvailable) {
| ^~~~~~~~~~~~~~~~~~~~
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g
-fwrapv -O2 -Wall -g
-ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=.
-fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2
-DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude
-Ithird-party/seqan/core/include -Ithird-party/smhasher
-I/usr/include/python3.9 -c src/oxli/kmer_filters.cc -o
build/temp.linux-x86_64-3.9/src/oxli/kmer_filters.o -O3 -std=c++11 -pedantic
-fopenmp
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g
-fwrapv -O2 -Wall -g
-ffile-prefix-map=/build/python3.9-RNBry6/python3.9-3.9.2=.
-fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2
-DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude
-Ithird-party/seqan/core/include -Ithird-party/smhasher
-I/usr/include/python3.9 -c src/oxli/kmer_hash.cc -o
build/temp.linux-x86_64-3.9/src/oxli/kmer_hash.o -O3 -std=c++11 -pedantic
-fopenmp
src/oxli/kmer_hash.cc: In function ‘std::pair<long unsigned int, long unsigned
int> oxli::compute_band_interval(unsigned int, unsigned int)’:
src/oxli/kmer_hash.cc:226:31: error: ‘numeric_limits’ is not a member of ‘std’
226 | uint64_t band_size = std::numeric_limits<uint64_t>::max() /
num_bands;
| ^~~~~~~~~~~~~~
src/oxli/kmer_hash.cc:226:54: error: expected primary-expression before ‘>’
token
226 | uint64_t band_size = std::numeric_limits<uint64_t>::max() /
num_bands;
| ^
src/oxli/kmer_hash.cc:226:61: error: no matching function for call to ‘max()’
226 | uint64_t band_size = std::numeric_limits<uint64_t>::max() /
num_bands;
| ^
In file included from /usr/include/c++/11/algorithm:61,
from src/oxli/kmer_hash.cc:41:
/usr/include/c++/11/bits/stl_algobase.h:254:5: note: candidate: ‘template<class
_Tp> const _Tp& std::max(const _Tp&, const _Tp&)’
254 | max(const _Tp& __a, const _Tp& __b)
| ^~~
/usr/include/c++/11/bits/stl_algobase.h:254:5: note: template argument
deduction/substitution failed:
src/oxli/kmer_hash.cc:226:61: note: candidate expects 2 arguments, 0 provided
226 | uint64_t band_size = std::numeric_limits<uint64_t>::max() /
num_bands;
| ^
In file included from /usr/include/c++/11/algorithm:61,
from src/oxli/kmer_hash.cc:41:
/usr/include/c++/11/bits/stl_algobase.h:300:5: note: candidate: ‘template<class
_Tp, class _Compare> const _Tp& std::max(const _Tp&, const _Tp&, _Compare)’
300 | max(const _Tp& __a, const _Tp& __b, _Compare __comp)
| ^~~
/usr/include/c++/11/bits/stl_algobase.h:300:5: note: template argument
deduction/substitution failed:
src/oxli/kmer_hash.cc:226:61: note: candidate expects 3 arguments, 0 provided
226 | uint64_t band_size = std::numeric_limits<uint64_t>::max() /
num_bands;
| ^
In file included from /usr/include/c++/11/algorithm:62,
from src/oxli/kmer_hash.cc:41:
/usr/include/c++/11/bits/stl_algo.h:3461:5: note: candidate: ‘template<class
_Tp> _Tp std::max(std::initializer_list<_Tp>)’
3461 | max(initializer_list<_Tp> __l)
| ^~~
/usr/include/c++/11/bits/stl_algo.h:3461:5: note: template argument
deduction/substitution failed:
src/oxli/kmer_hash.cc:226:61: note: candidate expects 1 argument, 0 provided
226 | uint64_t band_size = std::numeric_limits<uint64_t>::max() /
num_bands;
| ^
In file included from /usr/include/c++/11/algorithm:62,
from src/oxli/kmer_hash.cc:41:
/usr/include/c++/11/bits/stl_algo.h:3467:5: note: candidate: ‘template<class
_Tp, class _Compare> _Tp std::max(std::initializer_list<_Tp>, _Compare)’
3467 | max(initializer_list<_Tp> __l, _Compare __comp)
| ^~~
/usr/include/c++/11/bits/stl_algo.h:3467:5: note: template argument
deduction/substitution failed:
src/oxli/kmer_hash.cc:226:61: note: candidate expects 2 arguments, 0 provided
226 | uint64_t band_size = std::numeric_limits<uint64_t>::max() /
num_bands;
| ^
error: command '/usr/bin/x86_64-linux-gnu-gcc' failed with exit code 1
E: pybuild pybuild:353: build: plugin distutils failed with: exit code=1:
/usr/bin/python3 setup.py build
dh_auto_build: error: pybuild --build --test-pytest -i python{version} -p 3.9
returned exit code 13
make[1]: *** [debian/rules:19: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:16: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: khmer
Source-Version: 2.1.2+dfsg-9
Done: Nilesh Patra <[email protected]>
We believe that the bug you reported is fixed in the latest version of
khmer, 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.
Nilesh Patra <[email protected]> (supplier of updated khmer 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: Mon, 06 Sep 2021 14:34:23 +0000
Source: khmer
Architecture: source
Version: 2.1.2+dfsg-9
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Nilesh Patra <[email protected]>
Closes: 984079
Changes:
khmer (2.1.2+dfsg-9) unstable; urgency=medium
.
[ Nilesh Patra ]
* Team Upload.
* debian/patches/gcc11.patch: Fix gcc-11 FTBFS (Closes: #984079)
* d/salsa-ci.yml: Disable reprotest and i386 build
* d/clean: Clean more files
.
[ Steffen Moeller ]
* Fix watchfile to detect new versions on github (routine-update)
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--- End Message ---
