[Debian-med-packaging] Bug#984370: tvc: ftbfs with GCC-11

Wed Mar 3 16:18:03 GMT 2021

Package: src:tvc
Version: 5.0.3+git20151221.80e144e+dfsg-3
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/tvc_5.0.3+git20151221.80e144e+dfsg-3_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.

[...]
[ 66%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SigmaGenerator.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SigmaGenerator.cpp.o -c /<<PKGBUILDDIR>>/VariantCaller/EnsembleEval/SigmaGenerator.cpp
[ 67%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SkewGenerator.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SkewGenerator.cpp.o -c /<<PKGBUILDDIR>>/VariantCaller/EnsembleEval/SkewGenerator.cpp
[ 69%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/PosteriorInference.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/PosteriorInference.cpp.o -c /<<PKGBUILDDIR>>/VariantCaller/EnsembleEval/PosteriorInference.cpp
[ 70%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/ShortStack.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/ShortStack.cpp.o -c /<<PKGBUILDDIR>>/VariantCaller/EnsembleEval/ShortStack.cpp
[ 72%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/StackEngine.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/StackEngine.cpp.o -c /<<PKGBUILDDIR>>/VariantCaller/EnsembleEval/StackEngine.cpp
[ 73%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/CrossHypotheses.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/CrossHypotheses.cpp.o -c /<<PKGBUILDDIR>>/VariantCaller/EnsembleEval/CrossHypotheses.cpp
[ 75%] Building CXX object CMakeFiles/tvc.dir/external/vcflib/Variant.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/external/vcflib/Variant.cpp.o -c /<<PKGBUILDDIR>>/external/vcflib/Variant.cpp
[ 76%] Building CXX object CMakeFiles/tvc.dir/external/vcflib/split.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/external/vcflib/split.cpp.o -c /<<PKGBUILDDIR>>/external/vcflib/split.cpp
[ 78%] Building CXX object CMakeFiles/tvc.dir/external/vcflib/tabixpp/tabix.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/external/vcflib/tabixpp/tabix.cpp.o -c /<<PKGBUILDDIR>>/external/vcflib/tabixpp/tabix.cpp
[ 80%] Building C object CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o
/usr/bin/cc -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o -c /<<PKGBUILDDIR>>/external/vcflib/tabixpp/index.c
/<<PKGBUILDDIR>>/external/vcflib/tabixpp/index.c: In function ‘ti_index_core’:
/<<PKGBUILDDIR>>/external/vcflib/tabixpp/index.c:336:42: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int32_t’ {aka ‘int’} changes value from ‘last_bin = 4294967295’ to ‘-1’ [-Woverflow]
  336 |         save_bin = save_tid = last_tid = last_bin = 0xffffffffu;
      |                                          ^~~~~~~~
[ 81%] Building C object CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o
/usr/bin/cc -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o -c /<<PKGBUILDDIR>>/external/vcflib/tabixpp/bgzf.c
/<<PKGBUILDDIR>>/external/vcflib/tabixpp/bgzf.c: In function ‘_bgzf_check_EOF’:
/<<PKGBUILDDIR>>/external/vcflib/tabixpp/bgzf.c:678:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  678 |         fread(buf, 1, 28, fp->file);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 83%] Building CXX object CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o -c /<<PKGBUILDDIR>>/external/freebayes/src/AlleleParser.cpp
[ 84%] Building CXX object CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o -c /<<PKGBUILDDIR>>/BaseCaller/PIDloop.cpp
[ 86%] Building CXX object CMakeFiles/tvc.dir/BaseCaller/DPTreephaser.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/BaseCaller/DPTreephaser.cpp.o -c /<<PKGBUILDDIR>>/BaseCaller/DPTreephaser.cpp
[ 87%] Building CXX object CMakeFiles/tvc.dir/Calibration/LinearCalibrationModel.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/<<PKGBUILDDIR>>/external/vcflib -I/<<PKGBUILDDIR>>/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/<<PKGBUILDDIR>>/VariantCaller -I/<<PKGBUILDDIR>>/VariantCaller/FlowDistEval -I/<<PKGBUILDDIR>>/VariantCaller/EnsembleEval -I/<<PKGBUILDDIR>>/VariantCaller/Bookkeeping -I/<<PKGBUILDDIR>>/VariantCaller/Reads -I/<<PKGBUILDDIR>>/VariantCaller/Splice -I/<<PKGBUILDDIR>>/VariantCaller/Filter -I/<<PKGBUILDDIR>>/realignment -I/<<PKGBUILDDIR>>/file-io -I/<<PKGBUILDDIR>>/BaseCaller -I/<<PKGBUILDDIR>>/Calibration -I/<<PKGBUILDDIR>>/Util -I/<<PKGBUILDDIR>> -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -o CMakeFiles/tvc.dir/Calibration/LinearCalibrationModel.cpp.o -c /<<PKGBUILDDIR>>/Calibration/LinearCalibrationModel.cpp
In file included from /usr/include/c++/11/map:60,
                 from /<<PKGBUILDDIR>>/external/freebayes/src/AlleleParser.h:6,
                 from /<<PKGBUILDDIR>>/external/freebayes/src/AlleleParser.cpp:1:
/usr/include/c++/11/bits/stl_tree.h: In instantiation of ‘static const _Key& std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_S_key(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_Const_Link_type) [with _Key = Allele; _Val = std::pair<const Allele, AlleleDetails>; _KeyOfValue = std::_Select1st<std::pair<const Allele, AlleleDetails> >; _Compare = AllelePositionCompare; _Alloc = std::allocator<std::pair<const Allele, AlleleDetails> >; std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_Const_Link_type = const std::_Rb_tree_node<std::pair<const Allele, AlleleDetails> >*]’:
/usr/include/c++/11/bits/stl_tree.h:2433:62:   required from ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const Allele&>, std::tuple<>}; _Key = Allele; _Val = std::pair<const Allele, AlleleDetails>; _KeyOfValue = std::_Select1st<std::pair<const Allele, AlleleDetails> >; _Compare = AllelePositionCompare; _Alloc = std::allocator<std::pair<const Allele, AlleleDetails> >; std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator = std::_Rb_tree<Allele, std::pair<const Allele, AlleleDetails>, std::_Select1st<std::pair<const Allele, AlleleDetails> >, AllelePositionCompare, std::allocator<std::pair<const Allele, AlleleDetails> > >::iterator; std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator = std::_Rb_tree<Allele, std::pair<const Allele, AlleleDetails>, std::_Select1st<std::pair<const Allele, AlleleDetails> >, AllelePositionCompare, std::allocator<std::pair<const Allele, AlleleDetails> > >::const_iterator]’
/usr/include/c++/11/bits/stl_map.h:501:37:   required from ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = Allele; _Tp = AlleleDetails; _Compare = AllelePositionCompare; _Alloc = std::allocator<std::pair<const Allele, AlleleDetails> >; std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type = AlleleDetails; std::map<_Key, _Tp, _Compare, _Alloc>::key_type = Allele]’
/<<PKGBUILDDIR>>/external/freebayes/src/AlleleParser.cpp:479:23:   required from here
/usr/include/c++/11/bits/stl_tree.h:770:15: error: static assertion failed: comparison object must be invocable as const
  770 |               is_invocable_v<const _Compare&, const _Key&, const _Key&>,
      |               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_tree.h:770:15: note: ‘std::is_invocable_v<const AllelePositionCompare&, const Allele&, const Allele&>’ evaluates to false
make[3]: *** [CMakeFiles/tvc.dir/build.make:514: CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o] Error 1
make[3]: *** Waiting for unfinished jobs....
/<<PKGBUILDDIR>>/Calibration/LinearCalibrationModel.cpp: In member function ‘void LinearCalibrationModel::SaveModelFileToBamComments(std::vector<std::__cxx11::basic_string<char> >&, const string&) const’:
/<<PKGBUILDDIR>>/Calibration/LinearCalibrationModel.cpp:708:20: warning: ‘FastWriter’ is deprecated: Use StreamWriterBuilder instead [-Wdeprecated-declarations]
  708 |   Json::FastWriter writer;
      |                    ^~~~~~
In file included from /usr/include/jsoncpp/json/json.h:13,
                 from /<<PKGBUILDDIR>>/Calibration/CalibrationHelper.h:23,
                 from /<<PKGBUILDDIR>>/Calibration/LinearCalibrationModel.h:16,
                 from /<<PKGBUILDDIR>>/Calibration/LinearCalibrationModel.cpp:13:
/usr/include/jsoncpp/json/writer.h:168:70: note: declared here
  168 | class JSONCPP_DEPRECATED("Use StreamWriterBuilder instead") JSON_API FastWriter
      |                                                                      ^~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:156: CMakeFiles/tvc.dir/all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[1]: *** [Makefile:163: 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" VERBOSE=1 returned exit code 2
make: *** [debian/rules:18: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2