[Debian-med-packaging] Bug#957194: fastlink: ftbfs with GCC-10

[Matthias Klose]

Package: src:fastlink
Version: 4.1P-fix100+dfsg-2
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/fastlink_4.1P-fix100+dfsg-2_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: lodscore.o:./4.1P/src/commondefs.h:864: multiple definition of `continue_'; loiostuff.o:./4.1P/src/commondefs.h:864: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:674: multiple definition of `maxmemcount'; loiostuff.o:./4.1P/src/commondefs.h:674: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:674: multiple definition of `memcount'; loiostuff.o:./4.1P/src/commondefs.h:674: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:671: multiple definition of `ped_nuscales'; loiostuff.o:./4.1P/src/commondefs.h:671: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:640: multiple definition of `looplastgen'; loiostuff.o:./4.1P/src/commondefs.h:640: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:637: multiple definition of `loopfirstgen'; loiostuff.o:./4.1P/src/commondefs.h:637: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:626: multiple definition of `loopfile'; loiostuff.o:./4.1P/src/commondefs.h:626: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:624: multiple definition of `speedfile'; loiostuff.o:./4.1P/src/commondefs.h:624: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:624: multiple definition of `ipedfile'; loiostuff.o:./4.1P/src/commondefs.h:624: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:622: multiple definition of `disfreqs'; loiostuff.o:./4.1P/src/commondefs.h:622: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:619: multiple definition of `risk'; loiostuff.o:./4.1P/src/commondefs.h:619: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:618: multiple definition of `segscale'; loiostuff.o:./4.1P/src/commondefs.h:618: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:614: multiple definition of `lastpriv'; loiostuff.o:./4.1P/src/commondefs.h:614: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:614: multiple definition of `risksys'; loiostuff.o:./4.1P/src/commondefs.h:614: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:612: multiple definition of `riskall'; loiostuff.o:./4.1P/src/commondefs.h:612: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:608: multiple definition of `segval'; loiostuff.o:./4.1P/src/commondefs.h:608: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:607: multiple definition of `tempseg2'; loiostuff.o:./4.1P/src/commondefs.h:607: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:607: multiple definition of `tempseg'; loiostuff.o:./4.1P/src/commondefs.h:607: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:606: multiple definition of `segindex'; loiostuff.o:./4.1P/src/commondefs.h:606: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:604: multiple definition of `genenumber'; loiostuff.o:./4.1P/src/commondefs.h:604: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:603: multiple definition of `muthap'; loiostuff.o:./4.1P/src/commondefs.h:603: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:600: multiple definition of `numCopies'; loiostuff.o:./4.1P/src/commondefs.h:600: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:599: multiple definition of `looppers'; loiostuff.o:./4.1P/src/commondefs.h:599: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:594: multiple definition of `phapcache1'; loiostuff.o:./4.1P/src/commondefs.h:594: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:586: multiple definition of `qsumcache'; loiostuff.o:./4.1P/src/commondefs.h:586: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:586: multiple definition of `psumcache'; loiostuff.o:./4.1P/src/commondefs.h:586: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:581: multiple definition of `gene'; loiostuff.o:./4.1P/src/commondefs.h:581: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:580: multiple definition of `flag'; loiostuff.o:./4.1P/src/commondefs.h:580: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:578: multiple definition of `nonzgens'; loiostuff.o:./4.1P/src/commondefs.h:578: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:577: multiple definition of `order'; loiostuff.o:./4.1P/src/commondefs.h:577: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:574: multiple definition of `probend'; loiostuff.o:./4.1P/src/commondefs.h:574: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:574: multiple definition of `probstart'; loiostuff.o:./4.1P/src/commondefs.h:574: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:573: multiple definition of `segstart'; loiostuff.o:./4.1P/src/commondefs.h:573: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:572: multiple definition of `nchild'; loiostuff.o:./4.1P/src/commondefs.h:572: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:571: multiple definition of `childarray'; loiostuff.o:./4.1P/src/commondefs.h:571: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:569: multiple definition of `thischild'; loiostuff.o:./4.1P/src/commondefs.h:569: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:567: multiple definition of `malechild'; loiostuff.o:./4.1P/src/commondefs.h:567: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:564: multiple definition of `riskmale'; loiostuff.o:./4.1P/src/commondefs.h:564: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:563: multiple definition of `risk2'; loiostuff.o:./4.1P/src/commondefs.h:563: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:563: multiple definition of `risk1'; loiostuff.o:./4.1P/src/commondefs.h:563: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:563: multiple definition of `rare'; loiostuff.o:./4.1P/src/commondefs.h:563: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:561: multiple definition of `thispath'; loiostuff.o:./4.1P/src/commondefs.h:561: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:554: multiple definition of `invgenenum2'; loiostuff.o:./4.1P/src/commondefs.h:554: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:554: multiple definition of `invgenenum1'; loiostuff.o:./4.1P/src/commondefs.h:554: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:550: multiple definition of `hind'; loiostuff.o:./4.1P/src/commondefs.h:550: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:549: multiple definition of `haps2'; loiostuff.o:./4.1P/src/commondefs.h:549: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:549: multiple definition of `haps1'; loiostuff.o:./4.1P/src/commondefs.h:549: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:548: multiple definition of `fence'; loiostuff.o:./4.1P/src/commondefs.h:548: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:548: multiple definition of `base'; loiostuff.o:./4.1P/src/commondefs.h:548: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:547: multiple definition of `currentfence'; loiostuff.o:./4.1P/src/commondefs.h:547: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:536: multiple definition of `maxfemgen'; loiostuff.o:./4.1P/src/commondefs.h:536: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:536: multiple definition of `maxhaplo'; loiostuff.o:./4.1P/src/commondefs.h:536: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:532: multiple definition of `mymaxped'; loiostuff.o:./4.1P/src/commondefs.h:532: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:531: multiple definition of `pedidx2num'; loiostuff.o:./4.1P/src/commondefs.h:531: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:530: multiple definition of `currentped'; loiostuff.o:./4.1P/src/commondefs.h:530: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:529: multiple definition of `ped_loc_all'; loiostuff.o:./4.1P/src/commondefs.h:529: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:518: multiple definition of `ped_must_change_locations'; loiostuff.o:./4.1P/src/commondefs.h:518: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:513: multiple definition of `ped_new_allele_count'; loiostuff.o:./4.1P/src/commondefs.h:513: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:493: multiple definition of `gfemaletheta'; loiostuff.o:./4.1P/src/commondefs.h:493: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:493: multiple definition of `gmaletheta'; loiostuff.o:./4.1P/src/commondefs.h:493: first defined here
/usr/bin/ld: lodscore.o:./4.1P/src/commondefs.h:356: multiple definition of `approxarray'; loiostuff.o:./4.1P/src/commondefs.h:356: first defined here
collect2: error: ld returned 1 exit status
make[2]: *** [Makefile:661: lodscore] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: Leaving directory '/<<PKGBUILDDIR>>/4.1P/src'
dh_auto_build: error: cd 4.1P/src && make -j4 "INSTALL=install --strip-program=true" "CFLAGS=-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security" "DEBIANLDFLAGS=-Wl,-z,relro -Wl,-z,now" returned exit code 2
make[1]: *** [debian/rules:12: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:6: build] Error 2
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2