[Debian-med-packaging] Bug#957783: seaview: ftbfs with GCC-10

[Matthias Klose]

Package: src:seaview
Version: 1:4.7-1
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/seaview_4.7-1_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

[...]
g++  -c -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_XFT -I/usr/include/freetype2 -DFLTK1 -Dunix -Icsrc -I. -DNO_PDF -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -fPIC -Dunix -O3 -I.  -Icsrc    -DNO_PDF FL/Fl_Native_File_Chooser_FLTK.cxx
gcc -c  -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_XFT -I/usr/include/freetype2 -DFLTK1 -Dunix -Icsrc -I. -DNO_PDF -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -fPIC -Dunix -Icsrc csrc/raa_acnuc.c
gcc -c  -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_XFT -I/usr/include/freetype2 -DFLTK1 -Dunix -Icsrc -I. -DNO_PDF -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -fPIC -Dunix -Icsrc csrc/parser.c
gcc -c  -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_XFT -I/usr/include/freetype2 -DFLTK1 -Dunix -Icsrc -I. -DNO_PDF -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -fPIC -Dunix -Icsrc csrc/md5.c
gcc -c  -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_XFT -I/usr/include/freetype2 -DFLTK1 -Dunix -Icsrc -I. -DNO_PDF -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -fPIC -Dunix -Icsrc csrc/zsockr.c
gcc -c  -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_XFT -I/usr/include/freetype2 -DFLTK1 -Dunix -Icsrc -I. -DNO_PDF -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -fPIC -Dunix -Icsrc csrc/misc_acnuc.c
gcc -c  -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_XFT -I/usr/include/freetype2 -DFLTK1 -Dunix -Icsrc -I. -DNO_PDF -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -fPIC -Dunix -Icsrc csrc/dnapars.c
gcc -c  -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_XFT -I/usr/include/freetype2 -DFLTK1 -Dunix -Icsrc -I. -DNO_PDF -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -fPIC -Dunix -Icsrc csrc/protpars.c
gcc -c  -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_XFT -I/usr/include/freetype2 -DFLTK1 -Dunix -Icsrc -I. -DNO_PDF -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -fPIC -Dunix -Icsrc csrc/seq.c
gcc -c  -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_XFT -I/usr/include/freetype2 -DFLTK1 -Dunix -Icsrc -I. -DNO_PDF -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -fPIC -Dunix -Icsrc csrc/phylip.c
gcc -c  -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_XFT -I/usr/include/freetype2 -DFLTK1 -Dunix -Icsrc -I. -DNO_PDF -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -fPIC -Dunix -Icsrc csrc/lwl.c
gcc -c  -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_XFT -I/usr/include/freetype2 -DFLTK1 -Dunix -Icsrc -I. -DNO_PDF -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -fPIC -Dunix -Icsrc csrc/bionj.c
gcc -c  -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_XFT -I/usr/include/freetype2 -DFLTK1 -Dunix -Icsrc -I. -DNO_PDF -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -fPIC -Dunix -Icsrc csrc/phyml_util.c
g++ -o seaview  -Wl,-z,relro -Wl,-z,now -Wl,--as-needed seaview.o custom.o use_mase_files.o regions.o load_seq.o align.o xfmatpt.o comlines.o resource.o nexus.o viewasprots.o racnuc_fetch.o concatenate.o statistics.o trees.o treedraw.o addbootstrap.o least_squares_brl.o pseudoterminal.o unrooted.o pdf_or_ps.o svg.o threads.o tbe.o Fl_Native_File_Chooser_FLTK.o raa_acnuc.o parser.o md5.o zsockr.o misc_acnuc.o dnapars.o protpars.o seq.o phylip.o lwl.o bionj.o phyml_util.o  `fltk-config --use-images --ldflags` -ldl -lpthread -lz 
/usr/bin/ld: dnapars.o:./csrc/dnapars.c:114: multiple definition of `progname'; seaview.o:./seaview.cxx:238: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:109: multiple definition of `chars'; dnapars.o:./csrc/dnapars.c:84: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:112: multiple definition of `usertree'; dnapars.o:./csrc/dnapars.c:88: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:118: multiple definition of `threshwt'; dnapars.o:./csrc/dnapars.c:107: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:123: multiple definition of `fsteps'; dnapars.o:./csrc/dnapars.c:103: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:137: multiple definition of `nsteps'; dnapars.o:./csrc/dnapars.c:102: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:133: multiple definition of `minwhich'; dnapars.o:./csrc/dnapars.c:99: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:116: multiple definition of `treenode'; dnapars.o:./csrc/dnapars.c:93: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:108: multiple definition of `root'; dnapars.o:./csrc/dnapars.c:83: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:135: multiple definition of `recompute'; dnapars.o:./csrc/dnapars.c:101: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:127: multiple definition of `temp1'; dnapars.o:./csrc/dnapars.c:110: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:127: multiple definition of `temp'; dnapars.o:./csrc/dnapars.c:110: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:138: multiple definition of `place'; dnapars.o:./csrc/dnapars.c:105: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:135: multiple definition of `lastrearr'; dnapars.o:./csrc/dnapars.c:101: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:136: multiple definition of `there'; dnapars.o:./csrc/dnapars.c:104: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:124: multiple definition of `bestrees'; dnapars.o:./csrc/dnapars.c:106: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:139: multiple definition of `names'; dnapars.o:./csrc/dnapars.c:112: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:112: multiple definition of `trout'; dnapars.o:./csrc/dnapars.c:89: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:109: multiple definition of `col'; dnapars.o:./csrc/dnapars.c:84: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:120: multiple definition of `enterorder'; dnapars.o:./csrc/dnapars.c:94: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:112: multiple definition of `jumble'; dnapars.o:./csrc/dnapars.c:88: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:109: multiple definition of `njumble'; dnapars.o:./csrc/dnapars.c:84: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:109: multiple definition of `jumb'; dnapars.o:./csrc/dnapars.c:84: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:119: multiple definition of `seed'; dnapars.o:./csrc/dnapars.c:92: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:130: multiple definition of `progname'; seaview.o:./seaview.cxx:238: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:126: multiple definition of `garbage'; dnapars.o:./csrc/dnapars.c:109: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:113: multiple definition of `mulsets'; dnapars.o:./csrc/dnapars.c:89: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:109: multiple definition of `msets'; dnapars.o:./csrc/dnapars.c:84: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:113: multiple definition of `firstset'; dnapars.o:./csrc/dnapars.c:89: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:112: multiple definition of `thresh'; dnapars.o:./csrc/dnapars.c:88: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:112: multiple definition of `weights'; dnapars.o:./csrc/dnapars.c:88: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:112: multiple definition of `progress'; dnapars.o:./csrc/dnapars.c:89: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:112: multiple definition of `stepbox'; dnapars.o:./csrc/dnapars.c:89: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:113: multiple definition of `ancseq'; dnapars.o:./csrc/dnapars.c:89: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:107: multiple definition of `outtreename'; dnapars.o:./csrc/dnapars.c:80: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:109: multiple definition of `ith'; dnapars.o:./csrc/dnapars.c:84: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:113: multiple definition of `justwts'; dnapars.o:./csrc/dnapars.c:89: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:117: multiple definition of `threshold'; dnapars.o:./csrc/dnapars.c:87: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:111: multiple definition of `inseed0'; dnapars.o:./csrc/dnapars.c:86: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:111: multiple definition of `inseed'; dnapars.o:./csrc/dnapars.c:86: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:107: multiple definition of `weightfilename'; dnapars.o:./csrc/dnapars.c:81: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:107: multiple definition of `intreename'; dnapars.o:./csrc/dnapars.c:80: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:107: multiple definition of `outfilename'; dnapars.o:./csrc/dnapars.c:80: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:107: multiple definition of `infilename'; dnapars.o:./csrc/dnapars.c:80: first defined here
/usr/bin/ld: protpars.o:./csrc/phylip.h:366: multiple definition of `firstplotblock'; dnapars.o:./csrc/phylip.h:366: first defined here
/usr/bin/ld: protpars.o:./csrc/phylip.h:345: multiple definition of `javarun'; dnapars.o:./csrc/phylip.h:345: first defined here
/usr/bin/ld: seq.o:./csrc/phylip.h:366: multiple definition of `firstplotblock'; dnapars.o:./csrc/phylip.h:366: first defined here
/usr/bin/ld: seq.o:./csrc/phylip.h:345: multiple definition of `javarun'; dnapars.o:./csrc/phylip.h:345: first defined here
/usr/bin/ld: phylip.o:./csrc/phylip.h:345: multiple definition of `javarun'; dnapars.o:./csrc/phylip.h:345: first defined here
/usr/bin/ld: phylip.o:./csrc/phylip.h:366: multiple definition of `firstplotblock'; dnapars.o:./csrc/phylip.h:366: first defined here
collect2: error: ld returned 1 exit status
make[1]: *** [Makefile:46: seaview] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j4 "INSTALL=install --strip-program=true" returned exit code 2
make: *** [debian/rules:18: build] Error 25
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2