[Debian-med-packaging] Bug#984018: clonalorigin: ftbfs with GCC-11

Wed Mar 3 16:11:16 GMT 2021

Package: src:clonalorigin
Version: 1.0-4
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/clonalorigin_1.0-4_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.

[...]
 1826 |       max() _GLIBCXX_USE_NOEXCEPT { return __LDBL_MAX__; }
      |       ^~~
/usr/include/c++/11/limits:1826:7: error: expected ‘;’ at end of member declaration
 1826 |       max() _GLIBCXX_USE_NOEXCEPT { return __LDBL_MAX__; }
      |       ^~~
      |          ;
In file included from /usr/include/c++/11/cstdlib:41,
                 from /usr/include/c++/11/stdlib.h:36,
                 from /usr/include/gsl/gsl_rng.h:22,
                 from rng.h:4,
                 from rng.cpp:1:
/usr/include/c++/11/limits:1826:13: error: expected unqualified-id before ‘noexcept’
 1826 |       max() _GLIBCXX_USE_NOEXCEPT { return __LDBL_MAX__; }
      |             ^~~~~~~~~~~~~~~~~~~~~
In file included from rng.cpp:1:
/usr/include/c++/11/tr1/bessel_function.tcc: In function ‘void std::__detail::__bessel_jn(_Tp, _Tp, _Tp&, _Tp&, _Tp&, _Tp&)’:
rng.h:13:18: error: expected unqualified-id before ‘(’ token
   13 | #define max(a,b) ((a) >= (b) ? (a) : (b))
      |                  ^
/usr/include/c++/11/tr1/ell_integral.tcc: In function ‘_Tp std::__detail::__ellint_rf(_Tp, _Tp, _Tp)’:
rng.h:13:18: error: expected unqualified-id before ‘(’ token
   13 | #define max(a,b) ((a) >= (b) ? (a) : (b))
      |                  ^
rng.h:13:18: error: expected unqualified-id before ‘(’ token
   13 | #define max(a,b) ((a) >= (b) ? (a) : (b))
      |                  ^
/usr/include/c++/11/tr1/ell_integral.tcc: In function ‘_Tp std::__detail::__ellint_rd(_Tp, _Tp, _Tp)’:
rng.h:13:18: error: expected unqualified-id before ‘(’ token
   13 | #define max(a,b) ((a) >= (b) ? (a) : (b))
      |                  ^
rng.h:13:18: error: expected unqualified-id before ‘(’ token
   13 | #define max(a,b) ((a) >= (b) ? (a) : (b))
      |                  ^
/usr/include/c++/11/tr1/ell_integral.tcc: In function ‘_Tp std::__detail::__ellint_rj(_Tp, _Tp, _Tp, _Tp)’:
rng.h:13:18: error: expected unqualified-id before ‘(’ token
   13 | #define max(a,b) ((a) >= (b) ? (a) : (b))
      |                  ^
rng.h:13:18: error: expected unqualified-id before ‘(’ token
   13 | #define max(a,b) ((a) >= (b) ? (a) : (b))
      |                  ^
rng.h:13:18: error: expected unqualified-id before ‘(’ token
   13 | #define max(a,b) ((a) >= (b) ? (a) : (b))
      |                  ^
data.cpp: In constructor ‘weakarg::Data::Data(std::string)’:
data.cpp:50:40: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
   50 |             }else if(getNumber(tmpname)!=which){
      |                      ~~~~~~~~~~~~~~~~~~^~~~~~~
data.cpp: In member function ‘void weakarg::Data::subset(std::vector<int>, int)’:
data.cpp:169:14: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
  169 |   if (num<=0 &&seed>=0 || num<0) return;
      |       ~~~~~~~^~~~~~~~~
data.cpp:177:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  177 |     for(int i=0;i<numv.size();i++) if(numv[i]<tried.size()&&numv[i]>=0) {if(!tried[numv[i]]) {regions.push_back(numv[i]);tried[numv[i]]=true;}else{cerr<<"Warning: Duplicate blocks of "<<numv[i]<<" were specified and have been removed from the analysis."<<endl;}}else{cerr<<"Warning: Invalid blocks were specified and have been removed from the analysis."<<endl;}
      |                 ~^~~~~~~~~~~~
data.cpp:177:46: warning: comparison of integer expressions of different signedness: ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’} and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  177 |     for(int i=0;i<numv.size();i++) if(numv[i]<tried.size()&&numv[i]>=0) {if(!tried[numv[i]]) {regions.push_back(numv[i]);tried[numv[i]]=true;}else{cerr<<"Warning: Duplicate blocks of "<<numv[i]<<" were specified and have been removed from the analysis."<<endl;}}else{cerr<<"Warning: Invalid blocks were specified and have been removed from the analysis."<<endl;}
rng.cpp: In function ‘long unsigned int weakarg::seedrng(long unsigned int)’:
rng.cpp:40:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   40 |         fread(&tseed,sizeof(tseed),1,devrandom);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: *** [Makefile:688: warg-rng.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[3]: Leaving directory '/<<PKGBUILDDIR>>/warg/src'
make[2]: *** [Makefile:523: all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/warg/src'
make[1]: *** [Makefile:349: all-recursive] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>/warg'
dh_auto_build: error: cd warg && make -j4 returned exit code 2
make: *** [debian/rules:12: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2