[Debian-med-packaging] Bug#984139: freebayes: ftbfs with GCC-11
Matthias Klose
doko at debian.org
Wed Mar 3 16:12:31 GMT 2021
Package: src:freebayes
Version: 1.3.5-1
Severity: normal
Tags: sid bookworm
User: debian-gcc at lists.debian.org
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/freebayes_1.3.5-1_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.
[...]
/usr/include/vcflib/../intervaltree/IntervalTree.h:250:85: error: ‘::min’ has not been declared; did you mean ‘std::min’?
250 | std::numeric_limits<Scalar>::min() };
| ^~~
| std::min
In file included from /usr/include/c++/11/algorithm:62,
from ../src/AlleleParser.h:11,
from ../src/AlleleParser.cpp:1:
/usr/include/c++/11/bits/stl_algo.h:3455:5: note: ‘std::min’ declared here
3455 | min(initializer_list<_Tp> __l, _Compare __comp)
| ^~~
In file included from ../src/BedReader.h:12,
from ../src/AlleleParser.h:20,
from ../src/AlleleParser.cpp:1:
/usr/include/vcflib/../intervaltree/IntervalTree.h: In member function ‘std::pair<bool, std::pair<_FIter, _FIter> > IntervalTree<Scalar, Value>::is_valid() const’:
/usr/include/vcflib/../intervaltree/IntervalTree.h:270:75: error: ‘numeric_limits’ is not a member of ‘std’
270 | std::pair<bool, std::pair<Scalar, Scalar>> result = {true, { std::numeric_limits<Scalar>::max(),
| ^~~~~~~~~~~~~~
/usr/include/vcflib/../intervaltree/IntervalTree.h:270:96: error: expected primary-expression before ‘>’ token
270 | std::pair<bool, std::pair<Scalar, Scalar>> result = {true, { std::numeric_limits<Scalar>::max(),
| ^
/usr/include/vcflib/../intervaltree/IntervalTree.h:270:99: error: ‘::max’ has not been declared; did you mean ‘std::max’?
270 | std::pair<bool, std::pair<Scalar, Scalar>> result = {true, { std::numeric_limits<Scalar>::max(),
| ^~~
| std::max
In file included from /usr/include/c++/11/algorithm:62,
from ../src/AlleleParser.h:11,
from ../src/AlleleParser.cpp:1:
/usr/include/c++/11/bits/stl_algo.h:3467:5: note: ‘std::max’ declared here
3467 | max(initializer_list<_Tp> __l, _Compare __comp)
| ^~~
In file included from ../src/BedReader.h:12,
from ../src/AlleleParser.h:20,
from ../src/AlleleParser.cpp:1:
/usr/include/vcflib/../intervaltree/IntervalTree.h:271:75: error: ‘numeric_limits’ is not a member of ‘std’
271 | std::numeric_limits<Scalar>::min() }};
| ^~~~~~~~~~~~~~
/usr/include/vcflib/../intervaltree/IntervalTree.h:271:96: error: expected primary-expression before ‘>’ token
271 | std::numeric_limits<Scalar>::min() }};
| ^
/usr/include/vcflib/../intervaltree/IntervalTree.h:271:99: error: ‘::min’ has not been declared; did you mean ‘std::min’?
271 | std::numeric_limits<Scalar>::min() }};
| ^~~
| std::min
In file included from /usr/include/c++/11/algorithm:62,
from ../src/AlleleParser.h:11,
from ../src/AlleleParser.cpp:1:
/usr/include/c++/11/bits/stl_algo.h:3455:5: note: ‘std::min’ declared here
3455 | min(initializer_list<_Tp> __l, _Compare __comp)
| ^~~
In file included from ../src/BedReader.h:12,
from ../src/AlleleParser.h:20,
from ../src/AlleleParser.cpp:1:
/usr/include/vcflib/../intervaltree/IntervalTree.h: In instantiation of ‘std::pair<bool, std::pair<_FIter, _FIter> > IntervalTree<Scalar, Value>::is_valid() const [with Scalar = int; Value = BedTarget*]’:
/usr/include/vcflib/../intervaltree/IntervalTree.h:115:13: required from ‘IntervalTree<Scalar, Value>::IntervalTree(IntervalTree<Scalar, Value>::interval_vector&&, std::size_t, std::size_t, std::size_t, Scalar, Scalar) [with Scalar = int; Value = BedTarget*; IntervalTree<Scalar, Value>::interval_vector = std::vector<Interval<int, BedTarget*>, std::allocator<Interval<int, BedTarget*> > >; std::size_t = long unsigned int]’
../src/BedReader.h:68:124: required from here
/usr/include/vcflib/../intervaltree/IntervalTree.h:270:52: error: could not convert ‘{true, {<expression error>, <expression error>}}’ from ‘<brace-enclosed initializer list>’ to ‘std::pair<bool, std::pair<int, int> >’
270 | std::pair<bool, std::pair<Scalar, Scalar>> result = {true, { std::numeric_limits<Scalar>::max(),
| ^~~~~~
| |
| <brace-enclosed initializer list>
[5/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Allele.cpp.o -MF libfreebayes_common.a.p/src_Allele.cpp.o.d -o libfreebayes_common.a.p/src_Allele.cpp.o -c ../src/Allele.cpp
../src/Allele.cpp: In member function ‘const short int Allele::currentQuality() const’:
../src/Allele.cpp:160:12: warning: enumeration value ‘ALLELE_GENOTYPE’ not handled in switch [-Wswitch]
160 | switch (this->type) {
| ^
../src/Allele.cpp:160:12: warning: enumeration value ‘ALLELE_NULL’ not handled in switch [-Wswitch]
ninja: build stopped: subcommand failed.
dh_auto_build: error: cd build && LC_ALL=C.UTF-8 ninja -j4 -v returned exit code 1
make: *** [debian/rules:6: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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