[Debian-med-packaging] Bug#966127: embassy-phylip: FTBFS with GCC 10: multiple definition of ... due to -fno-common

[Andreas Beckmann]

Source: embassy-phylip
Version: 3.69.660-3
Severity: serious
Tags: ftbfs sid bullseye
Justification: fails to build from source
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-10

Hi,

embassy-phylip started to FTBFS when GCC 10 was made the default compiler:

/bin/bash ../libtool  --tag=CC   --mode=link gcc    -g -O2 -fdebug-prefix-map=/build/embassy-phylip-3.69.660=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/lib/emboss/include -I/usr/lib/emboss/include/epcre -I/usr/lib/emboss/include/eplplo
t -L/usr/lib/emboss/lib -Wl,--rpath,/usr/lib/emboss/lib  -O2   -Wl,-z,relro -Wl,--as-needed -o fclique clique.o disc.o phylip.o -L/usr/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre  -leplplot -lX11  -lXaw -lXt -lm  -lgd -lpng -lz -lm
/bin/bash ../libtool  --tag=CC   --mode=link gcc    -g -O2 -fdebug-prefix-map=/build/embassy-phylip-3.69.660=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/lib/emboss/include -I/usr/lib/emboss/include/epcre -I/usr/lib/emboss/include/eplplot -L/usr/lib/emboss/lib -Wl,--rpath,/usr/lib/emboss/lib  -O2   -Wl,-z,relro -Wl,--as-needed -o fconsense consense.o cons.o phylip.o -L/usr/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre  -leplplot -lX11  -lXaw -lXt -lm  -lgd -lpng -lz -lm
/bin/bash ../libtool  --tag=CC   --mode=link gcc    -g -O2 -fdebug-prefix-map=/build/embassy-phylip-3.69.660=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/lib/emboss/include -I/usr/lib/emboss/include/epcre -I/usr/lib/emboss/include/eplplot -L/usr/lib/emboss/lib -Wl,--rpath,/usr/lib/emboss/lib  -O2   -Wl,-z,relro -Wl,--as-needed -o fcontml contml.o cont.o phylip.o -L/usr/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre  -leplplot -lX11  -lXaw -lXt -lm  -lgd -lpng -lz -lm
libtool: link: gcc -g -O2 -fdebug-prefix-map=/build/embassy-phylip-3.69.660=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/lib/emboss/include -I/usr/lib/emboss/include/epcre -I/usr/lib/emboss/include/eplplot -Wl,--rpath -Wl,/usr/lib/emboss/lib -O2 -Wl,-z -Wl,relro -Wl,--as-needed -o fclique clique.o disc.o phylip.o  -L/usr/lib/emboss/lib -L/usr/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre -leplplot -lX11 -lXaw -lXt -lgd -lpng -lz -lm
/usr/bin/ld: disc.o:./src/disc.c:4: multiple definition of `phylostates'; clique.o:./src/clique.c:12: first defined here
/usr/bin/ld: phylip.o:./src/phylip.c:43: multiple definition of `embossouttree'; clique.o:./src/clique.c:76: first defined here
/usr/bin/ld: phylip.o:./src/phylip.c:40: multiple definition of `embossoutfile'; clique.o:./src/clique.c:75: first defined here
libtool: link: gcc -g -O2 -fdebug-prefix-map=/build/embassy-phylip-3.69.660=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/lib/emboss/include -I/usr/lib/emboss/include/epcre -I/usr/lib/emboss/include/eplplot -Wl,--rpath -Wl,/usr/lib/emboss/lib -O2 -Wl,-z -Wl,relro -Wl,--as-needed -o fconsense consense.o cons.o phylip.o  -L/usr/lib/emboss/lib -L/usr/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre -leplplot -lX11 -lXaw -lXt -lgd -lpng -lz -lm
/usr/bin/ld: phylip.o:./src/phylip.c:43: multiple definition of `embossouttree'; consense.o:./src/consense.c:23: first defined here
/usr/bin/ld: phylip.o:./src/phylip.c:40: multiple definition of `embossoutfile'; consense.o:./src/consense.c:22: first defined here
libtool: link: gcc -g -O2 -fdebug-prefix-map=/build/embassy-phylip-3.69.660=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/lib/emboss/include -I/usr/lib/emboss/include/epcre -I/usr/lib/emboss/include/eplplot -Wl,--rpath -Wl,/usr/lib/emboss/lib -O2 -Wl,-z -Wl,relro -Wl,--as-needed -o fcontml contml.o cont.o phylip.o  -L/usr/lib/emboss/lib -L/usr/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre -leplplot -lX11 -lXaw -lXt -lgd -lpng -lz -lm
/usr/bin/ld: phylip.o:./src/phylip.c:43: multiple definition of `embossouttree'; contml.o:./src/contml.c:73: first defined here
/usr/bin/ld: phylip.o:./src/phylip.c:40: multiple definition of `embossoutfile'; contml.o:./src/contml.c:72: first defined here
collect2: error: ld returned 1 exit status
make[3]: *** [Makefile:1193: fclique] Error 1
make[3]: *** Waiting for unfinished jobs....
collect2: error: ld returned 1 exit status
make[3]: *** [Makefile:1197: fconsense] Error 1
collect2: error: ld returned 1 exit status
make[3]: *** [Makefile:1201: fcontml] Error 1
make[3]: Leaving directory '/build/embassy-phylip-3.69.660/src'
make[2]: *** [Makefile:1093: all] Error 2
make[2]: Leaving directory '/build/embassy-phylip-3.69.660/src'
make[1]: *** [Makefile:425: all-recursive] Error 1
make[1]: Leaving directory '/build/embassy-phylip-3.69.660'
dh_auto_build: error: make -j3 returned exit code 2
make: *** [debian/rules:7: build] Error 25

More information about the corresponding GCC change can be found here:
https://gcc.gnu.org/gcc-10/porting_to.html
"Default to -fno-common"


Andreas