[Debichem-devel] Bug#956998: apbs: ftbfs with GCC-10

Matthias Klose doko at debian.org
Fri Apr 17 11:56:24 BST 2020


Package: src:apbs
Version: 1.4-1
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/apbs_1.4-1_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: ../../lib/libapbs_pmgc.a(mgcsd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:70: multiple definition of `vol'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:70: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(mgcsd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:70: multiple definition of `conc3'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:70: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(mgcsd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:70: multiple definition of `conc2'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:70: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(mgcsd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:70: multiple definition of `conc1'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:70: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(mgcsd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:70: multiple definition of `v3'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:70: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(mgcsd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:70: multiple definition of `v2'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:70: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(mgcsd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:70: multiple definition of `v1'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:70: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(mgcsd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/generic/vhal.h:60: multiple definition of `data'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/generic/vhal.h:60: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(mlinpckd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/generic/vhal.h:60: multiple definition of `data'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/generic/vhal.h:60: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(newtond.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mgsubd.h:258: multiple definition of `cputme'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mgsubd.h:258: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(newtond.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mgsubd.h:258: multiple definition of `oh'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mgsubd.h:258: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(newtond.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mgsubd.h:258: multiple definition of `bf'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mgsubd.h:258: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(newtond.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:73: multiple definition of `sconc'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:73: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(newtond.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:72: multiple definition of `charge'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:72: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(newtond.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:71: multiple definition of `nion'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:71: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(newtond.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:70: multiple definition of `relSize'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:70: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(newtond.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:70: multiple definition of `vol'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:70: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(newtond.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:70: multiple definition of `conc3'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:70: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(newtond.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:70: multiple definition of `conc2'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:70: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(newtond.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:70: multiple definition of `conc1'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:70: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(newtond.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:70: multiple definition of `v3'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:70: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(newtond.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:70: multiple definition of `v2'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:70: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(newtond.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:70: multiple definition of `v1'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:70: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(newtond.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/generic/vhal.h:60: multiple definition of `data'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/generic/vhal.h:60: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(smoothd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:73: multiple definition of `sconc'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:73: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(smoothd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:72: multiple definition of `charge'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:72: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(smoothd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:71: multiple definition of `nion'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:71: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(smoothd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:70: multiple definition of `relSize'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:70: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(smoothd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:70: multiple definition of `vol'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:70: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(smoothd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:70: multiple definition of `conc3'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:70: first defined here
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/usr/bin/ld: ../../lib/libapbs_pmgc.a(smoothd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:70: multiple definition of `v3'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:70: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(smoothd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:70: multiple definition of `v2'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:70: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(smoothd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:70: multiple definition of `v1'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:70: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(smoothd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/generic/vhal.h:60: multiple definition of `data'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/generic/vhal.h:60: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(cgd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:73: multiple definition of `sconc'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:73: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(cgd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:72: multiple definition of `charge'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:72: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(cgd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:71: multiple definition of `nion'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:71: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(cgd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:70: multiple definition of `relSize'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:70: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(cgd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:70: multiple definition of `vol'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:70: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(cgd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:70: multiple definition of `conc3'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:70: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(cgd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:70: multiple definition of `conc2'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:70: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(cgd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:70: multiple definition of `conc1'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:70: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(cgd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:70: multiple definition of `v3'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:70: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(cgd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:70: multiple definition of `v2'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:70: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(cgd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:70: multiple definition of `v1'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:70: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(cgd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/generic/vhal.h:60: multiple definition of `data'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/generic/vhal.h:60: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(gsd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:73: multiple definition of `sconc'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:73: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(gsd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:72: multiple definition of `charge'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:72: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(gsd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:71: multiple definition of `nion'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:71: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(gsd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:70: multiple definition of `relSize'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:70: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(gsd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:70: multiple definition of `vol'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:70: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(gsd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:70: multiple definition of `conc3'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:70: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(gsd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:70: multiple definition of `conc2'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:70: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(gsd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:70: multiple definition of `conc1'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:70: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(gsd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:70: multiple definition of `v3'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:70: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(gsd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:70: multiple definition of `v2'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:70: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(gsd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/pmgc/mypdec.h:70: multiple definition of `v1'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/pmgc/mypdec.h:70: first defined here
/usr/bin/ld: ../../lib/libapbs_pmgc.a(gsd.c.o):./obj-x86_64-linux-gnu/src/pmgc/./src/generic/vhal.h:60: multiple definition of `data'; CMakeFiles/apbs.dir/main.c.o:./obj-x86_64-linux-gnu/src/./src/generic/vhal.h:60: first defined here
collect2: error: ld returned 1 exit status
make[3]: *** [src/CMakeFiles/apbs.dir/build.make:119: ../bin/apbs] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:161: src/CMakeFiles/apbs.dir/all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[1]: *** [Makefile:133: 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 returned exit code 2
make: *** [debian/rules:12: binary] Error 25
dpkg-buildpackage: error: fakeroot debian/rules binary subprocess returned exit status 2



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