Debian Bug report logs - #984139
freebayes: ftbfs with GCC-11

Display info messages

Message #5 received at maintonly@bugs.debian.org (full text, mbox, reply):

From: Matthias Klose <doko@debian.org>

To: maintonly@bugs.debian.org

Subject: freebayes: ftbfs with GCC-11

Date: Wed, 03 Mar 2021 16:12:31 +0000

Package: src:freebayes
Version: 1.3.5-1
Severity: normal
Tags: sid bookworm
User: debian-gcc@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

Message #32 received at 984139-close@bugs.debian.org (full text, mbox, reply):

From: Debian FTP Masters <ftpmaster@ftp-master.debian.org>

To: 984139-close@bugs.debian.org

Subject: Bug#984139: fixed in libvcflib 1.0.2+dfsg-3

Date: Wed, 20 Oct 2021 17:03:47 +0000

Source: libvcflib
Source-Version: 1.0.2+dfsg-3
Done: Andreas Tille <tille@debian.org>

We believe that the bug you reported is fixed in the latest version of
libvcflib, 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 984139@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andreas Tille <tille@debian.org> (supplier of updated libvcflib 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 ftpmaster@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 1.8
Date: Wed, 20 Oct 2021 18:33:54 +0200
Source: libvcflib
Architecture: source
Version: 1.0.2+dfsg-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Closes: 984139
Changes:
 libvcflib (1.0.2+dfsg-3) unstable; urgency=medium
 .
   * Fix build with gcc-11
     Closes: #984139
   * Standards-Version: 4.6.0 (routine-update)
Checksums-Sha1:
 64e48141a6f95b0cbd0945223df9d5eacfb2e5d3 2290 libvcflib_1.0.2+dfsg-3.dsc
 34686f8d9643e3d99adc8b7a61016d339ccba6ab 9316 libvcflib_1.0.2+dfsg-3.debian.tar.xz
 43f94ab9110bd92ab0921763e4c7839611d1e73d 8604 libvcflib_1.0.2+dfsg-3_amd64.buildinfo
Checksums-Sha256:
 01b2fac52fc71e3260fd697c943a8c346ad4d01f43960f882ecba0b9d6307a35 2290 libvcflib_1.0.2+dfsg-3.dsc
 6f3bfe0247387891c1f5deb88bf5aa3be61028257c30270b2ae25601bbb89c20 9316 libvcflib_1.0.2+dfsg-3.debian.tar.xz
 7584fdbdddd7618324671f85ae2877a35bfb10534698c7db0bfbfcb711ff2b97 8604 libvcflib_1.0.2+dfsg-3_amd64.buildinfo
Files:
 99fc49903cbd85b83c9017e8a981e59d 2290 science optional libvcflib_1.0.2+dfsg-3.dsc
 06ba404513712d859c4193235f335c40 9316 science optional libvcflib_1.0.2+dfsg-3.debian.tar.xz
 9d6e3abacd0c6d40b3528b7cef665de1 8604 science optional libvcflib_1.0.2+dfsg-3_amd64.buildinfo

-----BEGIN PGP SIGNATURE-----
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=52S5
-----END PGP SIGNATURE-----

Send a report that this bug log contains spam.