[Debian-med-packaging] Bug#957679: phyml: ftbfs with GCC-10

[Matthias Klose]

Package: src:phyml
Version: 3:3.3.20190909-1
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/phyml_3.3.20190909-1_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: bionj.o:(.bss+0x0): multiple definition of `TIME'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: bionj.o:(.bss+0x4): multiple definition of `CALL'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: models.o:(.bss+0x0): multiple definition of `TIME'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: models.o:(.bss+0x4): multiple definition of `CALL'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: free.o:(.bss+0x0): multiple definition of `TIME'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: free.o:(.bss+0x4): multiple definition of `CALL'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: help.o:(.bss+0x0): multiple definition of `TIME'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: help.o:(.bss+0x4): multiple definition of `CALL'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: simu.o:(.bss+0x0): multiple definition of `TIME'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: simu.o:(.bss+0x4): multiple definition of `CALL'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: eigen.o:(.bss+0x0): multiple definition of `TIME'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: eigen.o:(.bss+0x4): multiple definition of `CALL'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: pars.o:(.bss+0x0): multiple definition of `TIME'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: pars.o:(.bss+0x4): multiple definition of `CALL'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: alrt.o:(.bss+0x0): multiple definition of `TIME'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: alrt.o:(.bss+0x4): multiple definition of `CALL'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: interface.o:(.bss+0x0): multiple definition of `TIME'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: interface.o:(.bss+0x4): multiple definition of `CALL'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: cl.o:(.bss+0x0): multiple definition of `TIME'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: cl.o:(.bss+0x4): multiple definition of `CALL'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: spr.o:(.bss+0x0): multiple definition of `TIME'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: spr.o:(.bss+0x4): multiple definition of `CALL'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: draw.o:(.bss+0x0): multiple definition of `TIME'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: draw.o:(.bss+0x4): multiple definition of `CALL'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: stats.o:(.bss+0x0): multiple definition of `TIME'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: stats.o:(.bss+0x4): multiple definition of `CALL'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: rates.o:(.bss+0x0): multiple definition of `TIME'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: rates.o:(.bss+0x4): multiple definition of `CALL'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: mcmc.o:(.bss+0x0): multiple definition of `TIME'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: mcmc.o:(.bss+0x4): multiple definition of `CALL'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: times.o:(.bss+0x0): multiple definition of `TIME'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: times.o:(.bss+0x4): multiple definition of `CALL'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: tiporder.o:(.bss+0x0): multiple definition of `TIME'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: tiporder.o:(.bss+0x4): multiple definition of `CALL'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: m4.o:(.bss+0x0): multiple definition of `TIME'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: m4.o:(.bss+0x4): multiple definition of `CALL'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: io.o:(.bss+0x0): multiple definition of `TIME'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: io.o:(.bss+0x4): multiple definition of `CALL'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: make.o:(.bss+0x0): multiple definition of `TIME'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: make.o:(.bss+0x4): multiple definition of `CALL'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: nexus.o:(.bss+0x0): multiple definition of `TIME'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: nexus.o:(.bss+0x4): multiple definition of `CALL'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: init.o:(.bss+0x0): multiple definition of `TIME'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: init.o:(.bss+0x4): multiple definition of `CALL'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: xml.o:(.bss+0x0): multiple definition of `TIME'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: xml.o:(.bss+0x4): multiple definition of `CALL'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: date.o:(.bss+0x0): multiple definition of `TIME'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: date.o:(.bss+0x4): multiple definition of `CALL'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: sse.o:(.bss+0x0): multiple definition of `TIME'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: sse.o:(.bss+0x4): multiple definition of `CALL'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: avx.o:(.bss+0x0): multiple definition of `TIME'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: avx.o:(.bss+0x4): multiple definition of `CALL'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: tbe.o:(.bss+0x0): multiple definition of `TIME'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: tbe.o:(.bss+0x4): multiple definition of `CALL'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: ancestral.o:(.bss+0x0): multiple definition of `TIME'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: ancestral.o:(.bss+0x4): multiple definition of `CALL'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: mixt.o:(.bss+0x4): multiple definition of `TIME'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: mixt.o:(.bss+0x8): multiple definition of `CALL'; main.o:(.bss+0x4): first defined here
collect2: error: ld returned 1 exit status
make[4]: *** [Makefile:1664: phyml] Error 1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[3]: *** [Makefile:369: all-recursive] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: *** [Makefile:310: all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j4 "LDFLAGS=-Wl,-z,relro -Wl,-z,now" returned exit code 2
make[1]: *** [debian/rules:25: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:13: build] Error 2
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2