* 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 ‘fgets’, inlined from ‘check_guidetreefile’ at mltaln9.c:2708:2: /usr/include/bits/stdio2.h:263:9: warning: call to ‘__fgets_chk_warn’ 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'