[Debian-med-packaging] Bug#957851: sweed: ftbfs with GCC-10

[Matthias Klose]

Package: src:sweed
Version: 3.2.1+dfsg-1
Severity: normal
Tags: sid bullseye
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-10

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-10/g++-10, but succeeds to build with gcc-9/g++-9. The
severity of this report will be raised before the bullseye release,
so nothing has to be done for the buster release.

The full build log can be found at:
http://people.debian.org/~doko/logs/gcc10-20200225/sweed_3.2.1+dfsg-1_unstable_gcc10.log
The last lines of the build log are at the end of this report.

To build with GCC 10, either set CC=gcc-10 CXX=g++-10 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-10/porting_to.html

[...]
/usr/bin/ld: SweeD_Input.o:./SweeD.h:140: multiple definition of `nofTokens'; SweeD.o:./SweeD.h:140: first defined here
/usr/bin/ld: SweeD_Input.o:./SweeD.h:138: multiple definition of `map'; SweeD.o:./SweeD.h:138: first defined here
/usr/bin/ld: SweeD_Input.o:./SweeD.h:136: multiple definition of `mainTime0'; SweeD.o:./SweeD.h:136: first defined here
/usr/bin/ld: SweeD_Input.o:./SweeD.h:121: multiple definition of `borderTol'; SweeD.o:./SweeD.h:121: first defined here
/usr/bin/ld: SweeD_Input.o:./SweeD.h:119: multiple definition of `linkage_disequilibrium'; SweeD.o:./SweeD.h:119: first defined here
/usr/bin/ld: SweeD_Input.o:./SweeD.h:117: multiple definition of `bits_in_16bits'; SweeD.o:./SweeD.h:117: first defined here
/usr/bin/ld: SweeD_Kernel.o:./SweeD.h:225: multiple definition of `alignment'; SweeD.o:./SweeD.h:225: first defined here
/usr/bin/ld: SweeD_Kernel.o:./SweeD.h:257: multiple definition of `clr'; SweeD.o:./SweeD.h:257: first defined here
/usr/bin/ld: SweeD_Kernel.o:./SweeD.h:245: multiple definition of `factLUT'; SweeD.o:./SweeD.h:245: first defined here
/usr/bin/ld: SweeD_Kernel.o:./SweeD.h:235: multiple definition of `div6'; SweeD.o:./SweeD.h:235: first defined here
/usr/bin/ld: SweeD_Kernel.o:./SweeD.h:229: multiple definition of `rvLUT2'; SweeD.o:./SweeD.h:229: first defined here
/usr/bin/ld: SweeD_Kernel.o:./SweeD.h:228: multiple definition of `rvLUT'; SweeD.o:./SweeD.h:228: first defined here
/usr/bin/ld: SweeD_Kernel.o:./SweeD.h:227: multiple definition of `rv'; SweeD.o:./SweeD.h:227: first defined here
/usr/bin/ld: SweeD_Kernel.o:./SweeD.h:142: multiple definition of `nofSamples'; SweeD.o:./SweeD.h:142: first defined here
/usr/bin/ld: SweeD_Kernel.o:./SweeD.h:140: multiple definition of `nofTokens'; SweeD.o:./SweeD.h:140: first defined here
/usr/bin/ld: SweeD_Kernel.o:./SweeD.h:138: multiple definition of `map'; SweeD.o:./SweeD.h:138: first defined here
/usr/bin/ld: SweeD_Kernel.o:./SweeD.h:136: multiple definition of `mainTime0'; SweeD.o:./SweeD.h:136: first defined here
/usr/bin/ld: SweeD_Kernel.o:./SweeD.h:128: multiple definition of `runName'; SweeD.o:./SweeD.h:128: first defined here
/usr/bin/ld: SweeD_Kernel.o:./SweeD.h:126: multiple definition of `nxtVCFalignment'; SweeD.o:./SweeD.h:126: first defined here
/usr/bin/ld: SweeD_Kernel.o:./SweeD.h:125: multiple definition of `VCF_first_SNP'; SweeD.o:./SweeD.h:125: first defined here
/usr/bin/ld: SweeD_Kernel.o:./SweeD.h:124: multiple definition of `VCF_alignment_name'; SweeD.o:./SweeD.h:124: first defined here
/usr/bin/ld: SweeD_Kernel.o:./SweeD.h:123: multiple definition of `VCF_header_lines'; SweeD.o:./SweeD.h:123: first defined here
/usr/bin/ld: SweeD_Kernel.o:./SweeD.h:121: multiple definition of `borderTol'; SweeD.o:./SweeD.h:121: first defined here
/usr/bin/ld: SweeD_Kernel.o:./SweeD.h:119: multiple definition of `linkage_disequilibrium'; SweeD.o:./SweeD.h:119: first defined here
/usr/bin/ld: SweeD_Kernel.o:./SweeD.h:117: multiple definition of `bits_in_16bits'; SweeD.o:./SweeD.h:117: first defined here
/usr/bin/ld: SweeD_SFS.o:./SweeD.h:225: multiple definition of `alignment'; SweeD.o:./SweeD.h:225: first defined here
/usr/bin/ld: SweeD_SFS.o:./SweeD.h:245: multiple definition of `factLUT'; SweeD.o:./SweeD.h:245: first defined here
/usr/bin/ld: SweeD_SFS.o:./SweeD.h:257: multiple definition of `clr'; SweeD.o:./SweeD.h:257: first defined here
/usr/bin/ld: SweeD_SFS.o:./SweeD.h:235: multiple definition of `div6'; SweeD.o:./SweeD.h:235: first defined here
/usr/bin/ld: SweeD_SFS.o:./SweeD.h:229: multiple definition of `rvLUT2'; SweeD.o:./SweeD.h:229: first defined here
/usr/bin/ld: SweeD_SFS.o:./SweeD.h:228: multiple definition of `rvLUT'; SweeD.o:./SweeD.h:228: first defined here
/usr/bin/ld: SweeD_SFS.o:./SweeD.h:227: multiple definition of `rv'; SweeD.o:./SweeD.h:227: first defined here
/usr/bin/ld: SweeD_SFS.o:./SweeD.h:142: multiple definition of `nofSamples'; SweeD.o:./SweeD.h:142: first defined here
/usr/bin/ld: SweeD_SFS.o:./SweeD.h:140: multiple definition of `nofTokens'; SweeD.o:./SweeD.h:140: first defined here
/usr/bin/ld: SweeD_SFS.o:./SweeD.h:138: multiple definition of `map'; SweeD.o:./SweeD.h:138: first defined here
/usr/bin/ld: SweeD_SFS.o:./SweeD.h:136: multiple definition of `mainTime0'; SweeD.o:./SweeD.h:136: first defined here
/usr/bin/ld: SweeD_SFS.o:./SweeD.h:128: multiple definition of `runName'; SweeD.o:./SweeD.h:128: first defined here
/usr/bin/ld: SweeD_SFS.o:./SweeD.h:126: multiple definition of `nxtVCFalignment'; SweeD.o:./SweeD.h:126: first defined here
/usr/bin/ld: SweeD_SFS.o:./SweeD.h:125: multiple definition of `VCF_first_SNP'; SweeD.o:./SweeD.h:125: first defined here
/usr/bin/ld: SweeD_SFS.o:./SweeD.h:124: multiple definition of `VCF_alignment_name'; SweeD.o:./SweeD.h:124: first defined here
/usr/bin/ld: SweeD_SFS.o:./SweeD.h:123: multiple definition of `VCF_header_lines'; SweeD.o:./SweeD.h:123: first defined here
/usr/bin/ld: SweeD_SFS.o:./SweeD.h:121: multiple definition of `borderTol'; SweeD.o:./SweeD.h:121: first defined here
/usr/bin/ld: SweeD_SFS.o:./SweeD.h:119: multiple definition of `linkage_disequilibrium'; SweeD.o:./SweeD.h:119: first defined here
/usr/bin/ld: SweeD_SFS.o:./SweeD.h:117: multiple definition of `bits_in_16bits'; SweeD.o:./SweeD.h:117: first defined here
/usr/bin/ld: SweeD_CLR.o:./SweeD.h:225: multiple definition of `alignment'; SweeD.o:./SweeD.h:225: first defined here
/usr/bin/ld: SweeD_CLR.o:./SweeD.h:257: multiple definition of `clr'; SweeD.o:./SweeD.h:257: first defined here
/usr/bin/ld: SweeD_CLR.o:./SweeD.h:245: multiple definition of `factLUT'; SweeD.o:./SweeD.h:245: first defined here
/usr/bin/ld: SweeD_CLR.o:./SweeD.h:228: multiple definition of `rvLUT'; SweeD.o:./SweeD.h:228: first defined here
/usr/bin/ld: SweeD_CLR.o:./SweeD.h:235: multiple definition of `div6'; SweeD.o:./SweeD.h:235: first defined here
/usr/bin/ld: SweeD_CLR.o:./SweeD.h:229: multiple definition of `rvLUT2'; SweeD.o:./SweeD.h:229: first defined here
/usr/bin/ld: SweeD_CLR.o:./SweeD.h:227: multiple definition of `rv'; SweeD.o:./SweeD.h:227: first defined here
/usr/bin/ld: SweeD_CLR.o:./SweeD.h:142: multiple definition of `nofSamples'; SweeD.o:./SweeD.h:142: first defined here
/usr/bin/ld: SweeD_CLR.o:./SweeD.h:140: multiple definition of `nofTokens'; SweeD.o:./SweeD.h:140: first defined here
/usr/bin/ld: SweeD_CLR.o:./SweeD.h:138: multiple definition of `map'; SweeD.o:./SweeD.h:138: first defined here
/usr/bin/ld: SweeD_CLR.o:./SweeD.h:136: multiple definition of `mainTime0'; SweeD.o:./SweeD.h:136: first defined here
/usr/bin/ld: SweeD_CLR.o:./SweeD.h:128: multiple definition of `runName'; SweeD.o:./SweeD.h:128: first defined here
/usr/bin/ld: SweeD_CLR.o:./SweeD.h:126: multiple definition of `nxtVCFalignment'; SweeD.o:./SweeD.h:126: first defined here
/usr/bin/ld: SweeD_CLR.o:./SweeD.h:125: multiple definition of `VCF_first_SNP'; SweeD.o:./SweeD.h:125: first defined here
/usr/bin/ld: SweeD_CLR.o:./SweeD.h:124: multiple definition of `VCF_alignment_name'; SweeD.o:./SweeD.h:124: first defined here
/usr/bin/ld: SweeD_CLR.o:./SweeD.h:123: multiple definition of `VCF_header_lines'; SweeD.o:./SweeD.h:123: first defined here
/usr/bin/ld: SweeD_CLR.o:./SweeD.h:121: multiple definition of `borderTol'; SweeD.o:./SweeD.h:121: first defined here
/usr/bin/ld: SweeD_CLR.o:./SweeD.h:119: multiple definition of `linkage_disequilibrium'; SweeD.o:./SweeD.h:119: first defined here
/usr/bin/ld: SweeD_CLR.o:./SweeD.h:117: multiple definition of `bits_in_16bits'; SweeD.o:./SweeD.h:117: first defined here
collect2: error: ld returned 1 exit status
make[2]: *** [Makefile.gcc:17: SweeD] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: *** [debian/rules:17: override_dh_auto_build] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:14: build] Error 2
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2