[Debian-med-packaging] Bug#984055: fastqtl: ftbfs with GCC-11

[Matthias Klose]

Package: src:fastqtl
Version: 2.184+dfsg-7
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/fastqtl_2.184+dfsg-7_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.

[...]
      |         ^~~~
In file included from src/analysisPermutationSequence.cpp:17:
src/data.h: In member function ‘double data::getCorrelation(std::vector<float>&, std::vector<float>&)’:
src/data.h:170:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
  170 |         case 3: sum0 += vec1[i+2] * vec2[i+2];
src/data.h:171:9: note: here
  171 |         case 2: sum0 += vec1[i+1] * vec2[i+1];
      |         ^~~~
src/data.h:171:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
  171 |         case 2: sum0 += vec1[i+1] * vec2[i+1];
src/data.h:172:9: note: here
  172 |         case 1: sum0 += vec1[i+0] * vec2[i+0];
      |         ^~~~
src/df.cpp:24:9: error: reference to ‘data’ is ambiguous
   24 |         data * D;
      |         ^~~~
In file included from /usr/include/c++/11/string:54,
                 from src/utils/utils.h:44,
                 from src/data.h:25,
                 from src/df.cpp:17:
/usr/include/c++/11/bits/range_access.h:318:5: note: candidates are: ‘template<class _Tp> constexpr const _Tp* std::data(std::initializer_list<_Tp>)’
  318 |     data(initializer_list<_Tp> __il) noexcept
      |     ^~~~
/usr/include/c++/11/bits/range_access.h:309:5: note:                 ‘template<class _Tp, long unsigned int _Nm> constexpr _Tp* std::data(_Tp (&)[_Nm])’
  309 |     data(_Tp (&__array)[_Nm]) noexcept
      |     ^~~~
/usr/include/c++/11/bits/range_access.h:299:5: note:                 ‘template<class _Container> constexpr decltype (__cont.data()) std::data(const _Container&)’
  299 |     data(const _Container& __cont) noexcept(noexcept(__cont.data()))
      |     ^~~~
/usr/include/c++/11/bits/range_access.h:289:5: note:                 ‘template<class _Container> constexpr decltype (__cont.data()) std::data(_Container&)’
  289 |     data(_Container& __cont) noexcept(noexcept(__cont.data()))
      |     ^~~~
In file included from src/df.cpp:17:
src/data.h:30:7: note:                 ‘class data’
   30 | class data {
      |       ^~~~
src/df.cpp:28:31: error: expected ‘)’ before ‘*’ token
   28 |         data_to_function (data * _D, int _n, double * _C) {
      |                          ~    ^~
      |                               )
src/df.cpp: In function ‘double degreeOfFreedom(const gsl_vector*, void*)’:
src/df.cpp:41:30: error: ‘struct data_to_function’ has no member named ‘D’
   41 |                 pval[c] = d->D->getPvalue(d->C[c], gsl_vector_get(v, 0));
      |                              ^
src/df.cpp: In member function ‘int data::learnDF(std::vector<double>&, double&)’:
src/df.cpp:65:84: error: new initializer expression list treated as compound expression [-fpermissive]
   65 |         data_to_function * par  = new data_to_function (this, corr.size(), &corr[0]);
      |                                                                                    ^
src/df.cpp:65:57: warning: left operand of comma operator has no effect [-Wunused-value]
   65 |         data_to_function * par  = new data_to_function (this, corr.size(), &corr[0]);
      |                                                         ^~~~
src/df.cpp:65:84: error: no matching function for call to ‘data_to_function::data_to_function(__gnu_cxx::__alloc_traits<std::allocator<double>, double>::value_type*)’
   65 |         data_to_function * par  = new data_to_function (this, corr.size(), &corr[0]);
      |                                                                                    ^
src/df.cpp:23:8: note: candidate: ‘data_to_function::data_to_function()’
   23 | struct data_to_function {
      |        ^~~~~~~~~~~~~~~~
src/df.cpp:23:8: note:   candidate expects 0 arguments, 1 provided
src/df.cpp:23:8: note: candidate: ‘constexpr data_to_function::data_to_function(const data_to_function&)’
src/df.cpp:23:8: note:   no known conversion for argument 1 from ‘__gnu_cxx::__alloc_traits<std::allocator<double>, double>::value_type*’ {aka ‘double*’} to ‘const data_to_function&’
src/df.cpp:23:8: note: candidate: ‘constexpr data_to_function::data_to_function(data_to_function&&)’
src/df.cpp:23:8: note:   no known conversion for argument 1 from ‘__gnu_cxx::__alloc_traits<std::allocator<double>, double>::value_type*’ {aka ‘double*’} to ‘data_to_function&&’
make[2]: *** [Makefile:97: obj/df.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j4 "INSTALL=install --strip-program=true" "CXXFLAGS=-g  -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security" returned exit code 2
make[1]: *** [debian/rules:14: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:9: build] Error 2
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2