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Gentoo's Bugzilla – Attachment 610360 Details for
Bug 707738
sci-biology/mafft-7.305 : fails to build with -fno-common or gcc-10
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sci-biology:mafft-7.305:20200131-230442.log
sci-biology:mafft-7.305:20200131-230442.log (text/plain), 11.87 KB, created by
Toralf Förster
on 2020-02-01 09:25:13 UTC
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Description:
sci-biology:mafft-7.305:20200131-230442.log
Filename:
MIME Type:
Creator:
Toralf Förster
Created:
2020-02-01 09:25:13 UTC
Size:
11.87 KB
patch
obsolete
> * Package: sci-biology/mafft-7.305 > * Repository: gentoo > * Maintainer: sci-biology@gentoo.org > * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU > * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox >>>> Unpacking source... >>>> Unpacking mafft-7.305-without-extensions-src.tgz to /var/tmp/portage/sci-biology/mafft-7.305/work >>>> Source unpacked in /var/tmp/portage/sci-biology/mafft-7.305/work >>>> Preparing source in /var/tmp/portage/sci-biology/mafft-7.305/work/mafft-7.305-without-extensions ... >>>> Source prepared. >>>> Configuring source in /var/tmp/portage/sci-biology/mafft-7.305/work/mafft-7.305-without-extensions ... >>>> Source configured. >>>> Compiling source in /var/tmp/portage/sci-biology/mafft-7.305/work/mafft-7.305-without-extensions ... >make -j1 ENABLE_MULTITHREAD= PREFIX=/usr CC=x86_64-pc-linux-gnu-gcc 'CFLAGS=-O2 -pipe -march=native -fno-common -Wno-unused-result' >cp mafftash_premafft.tmpl mafftash_premafft.pl >cp seekquencer_premafft.tmpl seekquencer_premafft.pl >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -Wno-unused-result -c mtxutl.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -Wno-unused-result -c io.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -Wno-unused-result -c mltaln9.c >In file included from /usr/include/stdio.h:867, > from mltaln.h:10, > from mltaln9.c:1: >In function âfgetsâ, > inlined from âcheck_guidetreefileâ at mltaln9.c:2708:2: >/usr/include/bits/stdio2.h:263:9: warning: call to â__fgets_chk_warnâ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] > 263 | return __fgets_chk_warn (__s, __bos (__s), __n, __stream); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -Wno-unused-result -c tddis.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -Wno-unused-result -c constants.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -Wno-unused-result -c nj.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -Wno-unused-result -c partSalignmm.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -Wno-unused-result -c Lalignmm.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -Wno-unused-result -c rna.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -Wno-unused-result -c Salignmm.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -Wno-unused-result -c Dalignmm.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -Wno-unused-result -c Falign.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -Wno-unused-result -c Falign_localhom.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -Wno-unused-result -c Galign11.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -Wno-unused-result -c MSalignmm.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -Wno-unused-result -c fftFunctions.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -Wno-unused-result -c fft.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -Wno-unused-result -c tditeration.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -Wno-unused-result -c dvtditr.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -Wno-unused-result -c defs.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -Wno-unused-result -c SAalignmm.c -o SAalignmm.o >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -Wno-unused-result -c treeOperation.c >x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -Wno-unused-result -c addfunctions.c >x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -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 MSalignmm.o fftFunctions.o fft.o tditeration.o dvtditr.o defs.o SAalignmm.o treeOperation.o addfunctions.o -O2 -pipe -march=native -fno-common -Wno-unused-result -lm >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: mltaln9.o:(.bss+0x0): multiple definition of `tsize'; io.o:(.bss+0x0): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: mltaln9.o:(.bss+0x4): multiple definition of `maxl'; io.o:(.bss+0x4): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: tddis.o:(.bss+0x0): multiple definition of `tsize'; io.o:(.bss+0x0): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: tddis.o:(.bss+0x4): multiple definition of `maxl'; io.o:(.bss+0x4): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: constants.o:(.bss+0x8): multiple definition of `tsize'; io.o:(.bss+0x0): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: constants.o:(.bss+0xc): multiple definition of `maxl'; io.o:(.bss+0x4): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: nj.o:(.bss+0x0): multiple definition of `tsize'; io.o:(.bss+0x0): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: nj.o:(.bss+0x4): multiple definition of `maxl'; io.o:(.bss+0x4): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: partSalignmm.o:(.bss+0x0): multiple definition of `tsize'; io.o:(.bss+0x0): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: partSalignmm.o:(.bss+0x4): multiple definition of `maxl'; io.o:(.bss+0x4): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: Lalignmm.o:(.bss+0x0): multiple definition of `tsize'; io.o:(.bss+0x0): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: Lalignmm.o:(.bss+0x4): multiple definition of `maxl'; io.o:(.bss+0x4): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: rna.o:(.bss+0x0): multiple definition of `tsize'; io.o:(.bss+0x0): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: rna.o:(.bss+0x4): multiple definition of `maxl'; io.o:(.bss+0x4): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: Salignmm.o:(.bss+0x0): multiple definition of `tsize'; io.o:(.bss+0x0): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: Salignmm.o:(.bss+0x4): multiple definition of `maxl'; io.o:(.bss+0x4): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: Dalignmm.o:(.bss+0x0): multiple definition of `tsize'; io.o:(.bss+0x0): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: Dalignmm.o:(.bss+0x4): multiple definition of `maxl'; io.o:(.bss+0x4): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: Falign.o:(.bss+0x0): multiple definition of `tsize'; io.o:(.bss+0x0): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: Falign.o:(.bss+0x4): multiple definition of `maxl'; io.o:(.bss+0x4): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: Falign_localhom.o:(.bss+0x0): multiple definition of `tsize'; io.o:(.bss+0x0): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: Falign_localhom.o:(.bss+0x4): multiple definition of `maxl'; io.o:(.bss+0x4): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: Galign11.o:(.bss+0x0): multiple definition of `tsize'; io.o:(.bss+0x0): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: Galign11.o:(.bss+0x4): multiple definition of `maxl'; io.o:(.bss+0x4): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: MSalignmm.o:(.bss+0x0): multiple definition of `tsize'; io.o:(.bss+0x0): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: MSalignmm.o:(.bss+0x4): multiple definition of `maxl'; io.o:(.bss+0x4): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: fftFunctions.o:(.bss+0x0): multiple definition of `tsize'; io.o:(.bss+0x0): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: fftFunctions.o:(.bss+0x4): multiple definition of `maxl'; io.o:(.bss+0x4): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: fft.o:(.bss+0x0): multiple definition of `tsize'; io.o:(.bss+0x0): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: fft.o:(.bss+0x4): multiple definition of `maxl'; io.o:(.bss+0x4): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: tditeration.o:(.bss+0x0): multiple definition of `tsize'; io.o:(.bss+0x0): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: tditeration.o:(.bss+0x4): multiple definition of `maxl'; io.o:(.bss+0x4): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: dvtditr.o:(.bss+0x0): multiple definition of `tsize'; io.o:(.bss+0x0): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: dvtditr.o:(.bss+0x4): multiple definition of `maxl'; io.o:(.bss+0x4): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: defs.o:(.bss+0x2fd0): multiple definition of `tsize'; io.o:(.bss+0x0): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: defs.o:(.bss+0x2fd4): multiple definition of `maxl'; io.o:(.bss+0x4): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: SAalignmm.o:(.bss+0x0): multiple definition of `tsize'; io.o:(.bss+0x0): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: SAalignmm.o:(.bss+0x4): multiple definition of `maxl'; io.o:(.bss+0x4): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: treeOperation.o:(.bss+0x0): multiple definition of `tsize'; io.o:(.bss+0x0): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: treeOperation.o:(.bss+0x4): multiple definition of `maxl'; io.o:(.bss+0x4): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: addfunctions.o:(.bss+0x0): multiple definition of `tsize'; io.o:(.bss+0x0): first defined here >/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: addfunctions.o:(.bss+0x4): multiple definition of `maxl'; io.o:(.bss+0x4): first defined here >collect2: error: ld returned 1 exit status >make: *** [Makefile:247: dvtditr] Error 1 > * ERROR: sci-biology/mafft-7.305::gentoo failed (compile phase): > * emake failed > * > * If you need support, post the output of `emerge --info '=sci-biology/mafft-7.305::gentoo'`, > * the complete build log and the output of `emerge -pqv '=sci-biology/mafft-7.305::gentoo'`. > * The complete build log is located at '/var/log/portage/sci-biology:mafft-7.305:20200131-230442.log'. > * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/mafft-7.305/temp/build.log'. > * The ebuild environment file is located at '/var/tmp/portage/sci-biology/mafft-7.305/temp/environment'. > * Working directory: '/var/tmp/portage/sci-biology/mafft-7.305/work/mafft-7.305-without-extensions/core' > * S: '/var/tmp/portage/sci-biology/mafft-7.305/work/mafft-7.305-without-extensions'
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