--- Begin Message ---
Package: src:mafft
Version: 7.453-1
Severity: normal
Tags: sid bullseye
User: [email protected]
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/mafft_7.453-1_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
[...]
177 | fgets( gett, 999, dlfp );
| ^~~~~~~~~~~~~~~~~~~~~~~~
gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -c setdirection.c
In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33,
from /usr/include/stdio.h:27,
from mltaln.h:13,
from setdirection.c:1:
/usr/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE
are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use
_DEFAULT_SOURCE"
| ^~~~~~~
gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -c makedirectionlist.c
In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33,
from /usr/include/stdio.h:27,
from mltaln.h:13,
from makedirectionlist.c:1:
/usr/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE
are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use
_DEFAULT_SOURCE"
| ^~~~~~~
setdirection.c: In function ‘main’:
setdirection.c:132:3: warning: ignoring return value of ‘fgets’ declared with
attribute ‘warn_unused_result’ [-Wunused-result]
132 | fgets( line, 99, difp );
| ^~~~~~~~~~~~~~~~~~~~~~~
gcc -o version version.c -Denablemultithread -std=c99 -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now
-lm -lpthread
In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33,
from /usr/include/stdio.h:27,
from mltaln.h:13,
from version.c:1:
/usr/include/features.h:185:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE
are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
185 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use
_DEFAULT_SOURCE"
| ^~~~~~~
sed "s:_LIBDIR:/usr/lib/mafft/lib/mafft:" mafft.tmpl > mafft
sed "s:_BINDIR:/usr/lib/mafft/bin:" mafft-homologs.tmpl > mafft-homologs.rb
sed "s:_BINDIR:/usr/lib/mafft/bin:" mafft-sparsecore.tmpl > mafft-sparsecore.rb
gcc -o dvtditr mtxutl.o io.o mltaln9.o tddis.o constants.o nj.o partSalignmm.o
Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o
Lalign11.o genalign11.o MSalignmm.o fftFunctions.o fft.o tditeration.o
dvtditr.o defs.o SAalignmm.o treeOperation.o addfunctions.o
-Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread
gcc -o dndfast7 dndfast7.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o
Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now
-lm -lpthread
gcc -o dndblast dndblast.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o
Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now
-lm -lpthread
gcc -o sextet5 io.o constants.o mtxutl.o mltaln9.o tddis.o sextet5.o defs.o
Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now
-lm -lpthread
gcc -o mafft-distance io.o constants.o mtxutl.o mltaln9.o tddis.o
mafft-distance.o defs.o Galign11.o Lalign11.o genalign11.o -Denablemultithread
-std=c99 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro
-Wl,-z,now -lm -lpthread
gcc -o pairlocalalign mtxutl.o io.o mltaln9.o tddis.o constants.o
partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o MSalignmm.o
Galign11.o Lalign11.o genalign11.o MSalign11.o suboptalign11.o SAalignmm.o
pairlocalalignmain.o pairlocalalign.o defs.o fft.o fftFunctions.o
-Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread
gcc -o multi2hat3s mtxutl.o io.o mltaln9.o tddis.o constants.o multi2hat3s.o
defs.o fft.o fftFunctions.o Galign11.o Lalign11.o genalign11.o
-Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread
gcc -o pairash mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o
Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o MSalignmm.o Galign11.o
Lalign11.o genalign11.o MSalign11.o suboptalign11.o SAalignmm.o pairash.o
defs.o fft.o fftFunctions.o -Denablemultithread -std=c99 -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now
-lm -lpthread
gcc -o addsingle mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o
partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o
Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o addsingle.o
defs.o fft.o fftFunctions.o addfunctions.o -Denablemultithread -std=c99 -g
-O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now
-lm -lpthread
gcc -o splittbfast mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o
Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o
Lalign11.o genalign11.o SAalignmm.o MSalignmm.o splittbfast.o defs.o fft.o
fftFunctions.o -Denablemultithread -std=c99 -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now
-lm -lpthread
gcc -o disttbfast mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o
Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o
Lalign11.o genalign11.o SAalignmm.o MSalignmm.o disttbfast.o defs.o fft.o
fftFunctions.o addfunctions.o -Denablemultithread -std=c99 -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now
-lm -lpthread
gcc -o tbfast mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o
partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o
Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o tbfast.o
defs.o fft.o fftFunctions.o addfunctions.o pairlocalalign.o MSalign11.o
-Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread
gcc -o nodepair mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o
partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o
Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o nodepair.o
defs.o fft.o fftFunctions.o addfunctions.o pairlocalalign.o MSalign11.o
-Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread
gcc -o mafft-profile io.o mtxutl.o mltaln9.o tddis.o constants.o partSalignmm.o
MSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o SAalignmm.o Galign11.o
Lalign11.o genalign11.o Falign.o Falign_localhom.o fftFunctions.o fft.o
mafft-profile.o defs.o -Denablemultithread -std=c99 -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now
-lm -lpthread
gcc -o f2cl mtxutl.o io.o f2cl.o constants.o defs.o -Denablemultithread
-std=c99 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro
-Wl,-z,now -lm -lpthread
gcc -o mccaskillwrap mtxutl.o io.o mccaskillwrap.o constants.o defs.o mltaln9.o
Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now
-lm -lpthread
gcc -o contrafoldwrap mtxutl.o io.o contrafoldwrap.o constants.o defs.o
mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g
-O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now
-lm -lpthread
gcc -o countlen mtxutl.o io.o countlen.o defs.o -Denablemultithread -std=c99
-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now
-lm -lpthread
gcc -o seq2regtable mtxutl.o io.o seq2regtable.o defs.o -Denablemultithread
-std=c99 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro
-Wl,-z,now -lm -lpthread
gcc -o regtable2seq mtxutl.o io.o regtable2seq.o defs.o mltaln9.o Galign11.o
Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now
-lm -lpthread
gcc -o score io.o mtxutl.o mltaln9.o score.o constants.o defs.o Galign11.o
Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now
-lm -lpthread
gcc -o getlag mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o
Lalignmm.o rna.o Salignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o
genalign11.o SAalignmm.o MSalignmm.o Dalignmm.o getlag.o defs.o fft.o
fftFunctions.o -Denablemultithread -std=c99 -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now
-lm -lpthread
gcc -o dndpre dndpre.o io.o constants.o mtxutl.o mltaln9.o defs.o Galign11.o
Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now
-lm -lpthread
gcc -o setcore mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o
Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o
Lalign11.o genalign11.o SAalignmm.o MSalignmm.o setcore.o defs.o fft.o
fftFunctions.o -Denablemultithread -std=c99 -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now
-lm -lpthread
gcc -o replaceu mtxutl.o io.o replaceu.o defs.o mltaln9.o Galign11.o Lalign11.o
genalign11.o -Denablemultithread -std=c99 -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now
-lm -lpthread
gcc -o restoreu mtxutl.o io.o restoreu.o defs.o mltaln9.o Galign11.o Lalign11.o
genalign11.o -Denablemultithread -std=c99 -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now
-lm -lpthread
gcc -o setdirection mtxutl.o io.o setdirection.o defs.o mltaln9.o Galign11.o
Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now
-lm -lpthread
gcc -o makedirectionlist mtxutl.o io.o mltaln9.o tddis.o constants.o
partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o
Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o
makedirectionlist.o defs.o fft.o fftFunctions.o addfunctions.o
-Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread
/usr/bin/ld: defs.o:(.bss+0x4): multiple definition of `nadd';
makedirectionlist.o:(.bss+0x10): first defined here
collect2: error: ld returned 1 exit status
make[2]: *** [Makefile:211: makedirectionlist] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>/core'
dh_auto_build: error: cd core && make -j4 "INSTALL=install
--strip-program=true" PREFIX=/usr/lib/mafft
ENABLE_MULTITHREAD=-Denablemultithread LIBDIR=/usr/lib/mafft/lib/mafft
"CFLAGS=-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2"
"LDFLAGS=-Wl,-z,relro -Wl,-z,now" returned exit code 2
make[1]: *** [debian/rules:14: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:11: build] Error 2
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2
--- End Message ---
