* Package: sci-biology/miranda-3.3a * Repository: science * 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 miRanda-aug2010.tar.gz to /var/tmp/portage/sci-biology/miranda-3.3a/work >>> Source unpacked in /var/tmp/portage/sci-biology/miranda-3.3a/work >>> Preparing source in /var/tmp/portage/sci-biology/miranda-3.3a/work/miRanda-3.3a ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/miranda-3.3a/work/miRanda-3.3a ... * econf: updating miRanda-3.3a/config.sub with /usr/share/gnuconfig/config.sub * econf: updating miRanda-3.3a/config.guess with /usr/share/gnuconfig/config.guess ./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-dependency-tracking --libdir=/usr/lib64 checking for a BSD-compatible install... /usr/lib/portage/python3.7/ebuild-helpers/xattr/install -c checking whether build environment is sane... yes checking for gawk... gawk checking whether make sets $(MAKE)... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of x86_64-pc-linux-gnu-gcc... none checking for a BSD-compatible install... /usr/lib/portage/python3.7/ebuild-helpers/xattr/install -c checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib checking for main in -lm... yes checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for an ANSI C-conforming const... yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for size_t... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for working strtod... yes checking for memset... yes checking for sqrt... yes checking for strchr... yes checking for strdup... yes checking for strrchr... yes checking for strstr... yes configure: creating ./config.status config.status: creating Makefile config.status: creating RNAlib/H/Makefile config.status: creating RNAlib/Makefile config.status: creating man/Makefile config.status: creating src/Makefile config.status: creating config.h config.status: executing depfiles commands >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/miranda-3.3a/work/miRanda-3.3a ... make -j1 make all-recursive make[1]: Entering directory '/var/tmp/portage/sci-biology/miranda-3.3a/work/miRanda-3.3a' Making all in man make[2]: Entering directory '/var/tmp/portage/sci-biology/miranda-3.3a/work/miRanda-3.3a/man' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/var/tmp/portage/sci-biology/miranda-3.3a/work/miRanda-3.3a/man' Making all in RNAlib make[2]: Entering directory '/var/tmp/portage/sci-biology/miranda-3.3a/work/miRanda-3.3a/RNAlib' Making all in H make[3]: Entering directory '/var/tmp/portage/sci-biology/miranda-3.3a/work/miRanda-3.3a/RNAlib/H' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/var/tmp/portage/sci-biology/miranda-3.3a/work/miRanda-3.3a/RNAlib/H' make[3]: Entering directory '/var/tmp/portage/sci-biology/miranda-3.3a/work/miRanda-3.3a/RNAlib' x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I. -I.. -I./H -O2 -pipe -march=native -fno-diagnostics-color -c fold_vars.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I. -I.. -I./H -O2 -pipe -march=native -fno-diagnostics-color -c energy_par.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I. -I.. -I./H -O2 -pipe -march=native -fno-diagnostics-color -c utils.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I. -I.. -I./H -O2 -pipe -march=native -fno-diagnostics-color -c fold.c fold.c: In function ‘ML_Energy’: fold.c:1111:63: warning: iteration 8 invokes undefined behavior [-Waggressive-loop-optimizations] 1111 | for (x = 0; x <= NBPAIRS+1; x++) mlintern[x] = P->MLintern[x]; | ~~~~~~~~~~~^~~ fold.c:1111:5: note: within this loop 1111 | for (x = 0; x <= NBPAIRS+1; x++) mlintern[x] = P->MLintern[x]; | ^~~ fold.c:1108:32: warning: iteration 8 invokes undefined behavior [-Waggressive-loop-optimizations] 1108 | mlintern[x] = P->MLintern[x]-P->MLintern[1]; /* 0 or TerminalAU */ | ~~~~~~~~~~~^~~ fold.c:1107:5: note: within this loop 1107 | for (x = 0; x <= NBPAIRS+1; x++) | ^~~ fold.c:1111:50: warning: ‘__builtin_memcpy’ writing 36 bytes into a region of size 32 overflows the destination [-Wstringop-overflow=] 1111 | for (x = 0; x <= NBPAIRS+1; x++) mlintern[x] = P->MLintern[x]; | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I. -I.. -I./H -O2 -pipe -march=native -fno-diagnostics-color -c params.c rm -f libRNA.a ar cru libRNA.a fold_vars.o energy_par.o utils.o fold.o params.o x86_64-pc-linux-gnu-ranlib libRNA.a make[3]: Leaving directory '/var/tmp/portage/sci-biology/miranda-3.3a/work/miRanda-3.3a/RNAlib' make[2]: Leaving directory '/var/tmp/portage/sci-biology/miranda-3.3a/work/miRanda-3.3a/RNAlib' Making all in src make[2]: Entering directory '/var/tmp/portage/sci-biology/miranda-3.3a/work/miRanda-3.3a/src' x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../RNAlib/H/ -O2 -pipe -march=native -fno-diagnostics-color -c miranda.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../RNAlib/H/ -O2 -pipe -march=native -fno-diagnostics-color -c output.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../RNAlib/H/ -O2 -pipe -march=native -fno-diagnostics-color -c scan.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../RNAlib/H/ -O2 -pipe -march=native -fno-diagnostics-color -c seqio.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../RNAlib/H/ -O2 -pipe -march=native -fno-diagnostics-color -c swat.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../RNAlib/H/ -O2 -pipe -march=native -fno-diagnostics-color -c pairs.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../RNAlib/H/ -O2 -pipe -march=native -fno-diagnostics-color -c thermo.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../RNAlib/H/ -O2 -pipe -march=native -fno-diagnostics-color -c utils.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I. -I.. -I../RNAlib/H/ -O2 -pipe -march=native -fno-diagnostics-color -c ExpString.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-diagnostics-color -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o miranda miranda.o output.o scan.o seqio.o swat.o pairs.o thermo.o utils.o ExpString.o ../RNAlib/libRNA.a -lm -lm /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: output.o:(.bss+0x28): multiple definition of `score_threshold'; miranda.o:(.bss+0x28): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: output.o:(.bss+0x20): multiple definition of `energy_threshold'; miranda.o:(.bss+0x20): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: output.o:(.bss+0x48): multiple definition of `scale'; miranda.o:(.bss+0x48): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: output.o:(.bss+0x44): multiple definition of `strict'; miranda.o:(.bss+0x44): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: output.o:(.bss+0x30): multiple definition of `gap_extend'; miranda.o:(.bss+0x30): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: output.o:(.bss+0x38): multiple definition of `gap_open'; miranda.o:(.bss+0x38): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: output.o:(.bss+0x8): multiple definition of `outfile'; miranda.o:(.bss+0x8): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: output.o:(.bss+0xc): multiple definition of `verbosity'; miranda.o:(.bss+0xc): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: output.o:(.bss+0x4): multiple definition of `truncated'; miranda.o:(.bss+0x4): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: output.o:(.bss+0x10): multiple definition of `no_energy'; miranda.o:(.bss+0x10): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: output.o:(.bss+0x0): multiple definition of `restricted'; miranda.o:(.bss+0x0): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: output.o:(.bss+0x40): multiple definition of `debug'; miranda.o:(.bss+0x40): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: output.o:(.bss+0x14): multiple definition of `key_value_pairs'; miranda.o:(.bss+0x14): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: output.o:(.bss+0x18): multiple definition of `length_3p_for_weighting'; miranda.o:(.bss+0x18): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: output.o:(.bss+0x1c): multiple definition of `length_5p_for_weighting'; miranda.o:(.bss+0x1c): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: scan.o:(.bss+0x44): multiple definition of `strict'; miranda.o:(.bss+0x44): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: scan.o:(.bss+0x10): multiple definition of `no_energy'; miranda.o:(.bss+0x10): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: scan.o:(.bss+0x20): multiple definition of `energy_threshold'; miranda.o:(.bss+0x20): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: scan.o:(.bss+0x28): multiple definition of `score_threshold'; miranda.o:(.bss+0x28): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: scan.o:(.bss+0x40): multiple definition of `debug'; miranda.o:(.bss+0x40): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: scan.o:(.bss+0x14): multiple definition of `key_value_pairs'; miranda.o:(.bss+0x14): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: scan.o:(.bss+0xc): multiple definition of `verbosity'; miranda.o:(.bss+0xc): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: scan.o:(.bss+0x0): multiple definition of `restricted'; miranda.o:(.bss+0x0): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: scan.o:(.bss+0x4): multiple definition of `truncated'; miranda.o:(.bss+0x4): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: scan.o:(.bss+0x1c): multiple definition of `length_5p_for_weighting'; miranda.o:(.bss+0x1c): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: scan.o:(.bss+0x18): multiple definition of `length_3p_for_weighting'; miranda.o:(.bss+0x18): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: scan.o:(.bss+0x8): multiple definition of `outfile'; miranda.o:(.bss+0x8): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: scan.o:(.bss+0x30): multiple definition of `gap_extend'; miranda.o:(.bss+0x30): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: scan.o:(.bss+0x38): multiple definition of `gap_open'; miranda.o:(.bss+0x38): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: scan.o:(.bss+0x48): multiple definition of `scale'; miranda.o:(.bss+0x48): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: seqio.o:(.bss+0x120): multiple definition of `restricted'; miranda.o:(.bss+0x0): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: seqio.o:(.bss+0x124): multiple definition of `truncated'; miranda.o:(.bss+0x4): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: seqio.o:(.bss+0x128): multiple definition of `outfile'; miranda.o:(.bss+0x8): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: seqio.o:(.bss+0x12c): multiple definition of `verbosity'; miranda.o:(.bss+0xc): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: seqio.o:(.bss+0x130): multiple definition of `no_energy'; miranda.o:(.bss+0x10): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: seqio.o:(.bss+0x134): multiple definition of `key_value_pairs'; miranda.o:(.bss+0x14): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: seqio.o:(.bss+0x138): multiple definition of `length_3p_for_weighting'; miranda.o:(.bss+0x18): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: seqio.o:(.bss+0x13c): multiple definition of `length_5p_for_weighting'; miranda.o:(.bss+0x1c): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: seqio.o:(.bss+0x140): multiple definition of `energy_threshold'; miranda.o:(.bss+0x20): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: seqio.o:(.bss+0x148): multiple definition of `score_threshold'; miranda.o:(.bss+0x28): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: seqio.o:(.bss+0x150): multiple definition of `gap_extend'; miranda.o:(.bss+0x30): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: seqio.o:(.bss+0x158): multiple definition of `gap_open'; miranda.o:(.bss+0x38): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: seqio.o:(.bss+0x160): multiple definition of `debug'; miranda.o:(.bss+0x40): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: seqio.o:(.bss+0x164): multiple definition of `strict'; miranda.o:(.bss+0x44): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: seqio.o:(.bss+0x168): multiple definition of `scale'; miranda.o:(.bss+0x48): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: swat.o:(.bss+0x568): multiple definition of `scale'; miranda.o:(.bss+0x48): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: swat.o:(.bss+0x538): multiple definition of `length_3p_for_weighting'; miranda.o:(.bss+0x18): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: swat.o:(.bss+0x558): multiple definition of `gap_open'; miranda.o:(.bss+0x38): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: swat.o:(.bss+0x550): multiple definition of `gap_extend'; miranda.o:(.bss+0x30): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: swat.o:(.bss+0x548): multiple definition of `score_threshold'; miranda.o:(.bss+0x28): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: swat.o:(.bss+0x520): multiple definition of `restricted'; miranda.o:(.bss+0x0): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: swat.o:(.bss+0x524): multiple definition of `truncated'; miranda.o:(.bss+0x4): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: swat.o:(.bss+0x528): multiple definition of `outfile'; miranda.o:(.bss+0x8): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: swat.o:(.bss+0x52c): multiple definition of `verbosity'; miranda.o:(.bss+0xc): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: swat.o:(.bss+0x530): multiple definition of `no_energy'; miranda.o:(.bss+0x10): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: swat.o:(.bss+0x534): multiple definition of `key_value_pairs'; miranda.o:(.bss+0x14): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: swat.o:(.bss+0x53c): multiple definition of `length_5p_for_weighting'; miranda.o:(.bss+0x1c): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: swat.o:(.bss+0x540): multiple definition of `energy_threshold'; miranda.o:(.bss+0x20): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: swat.o:(.bss+0x560): multiple definition of `debug'; miranda.o:(.bss+0x40): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: swat.o:(.bss+0x564): multiple definition of `strict'; miranda.o:(.bss+0x44): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: pairs.o:(.bss+0x0): multiple definition of `restricted'; miranda.o:(.bss+0x0): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: pairs.o:(.bss+0x4): multiple definition of `truncated'; miranda.o:(.bss+0x4): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: pairs.o:(.bss+0x8): multiple definition of `outfile'; miranda.o:(.bss+0x8): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: pairs.o:(.bss+0xc): multiple definition of `verbosity'; miranda.o:(.bss+0xc): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: pairs.o:(.bss+0x10): multiple definition of `no_energy'; miranda.o:(.bss+0x10): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: pairs.o:(.bss+0x14): multiple definition of `key_value_pairs'; miranda.o:(.bss+0x14): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: pairs.o:(.bss+0x18): multiple definition of `length_3p_for_weighting'; miranda.o:(.bss+0x18): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: pairs.o:(.bss+0x1c): multiple definition of `length_5p_for_weighting'; miranda.o:(.bss+0x1c): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: pairs.o:(.bss+0x20): multiple definition of `energy_threshold'; miranda.o:(.bss+0x20): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: pairs.o:(.bss+0x28): multiple definition of `score_threshold'; miranda.o:(.bss+0x28): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: pairs.o:(.bss+0x30): multiple definition of `gap_extend'; miranda.o:(.bss+0x30): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: pairs.o:(.bss+0x38): multiple definition of `gap_open'; miranda.o:(.bss+0x38): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: pairs.o:(.bss+0x40): multiple definition of `debug'; miranda.o:(.bss+0x40): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: pairs.o:(.bss+0x44): multiple definition of `strict'; miranda.o:(.bss+0x44): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: pairs.o:(.bss+0x48): multiple definition of `scale'; miranda.o:(.bss+0x48): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: thermo.o:(.bss+0x0): multiple definition of `restricted'; miranda.o:(.bss+0x0): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: thermo.o:(.bss+0x4): multiple definition of `truncated'; miranda.o:(.bss+0x4): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: thermo.o:(.bss+0x8): multiple definition of `outfile'; miranda.o:(.bss+0x8): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: thermo.o:(.bss+0xc): multiple definition of `verbosity'; miranda.o:(.bss+0xc): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: thermo.o:(.bss+0x10): multiple definition of `no_energy'; miranda.o:(.bss+0x10): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: thermo.o:(.bss+0x14): multiple definition of `key_value_pairs'; miranda.o:(.bss+0x14): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: thermo.o:(.bss+0x18): multiple definition of `length_3p_for_weighting'; miranda.o:(.bss+0x18): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: thermo.o:(.bss+0x1c): multiple definition of `length_5p_for_weighting'; miranda.o:(.bss+0x1c): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: thermo.o:(.bss+0x20): multiple definition of `energy_threshold'; miranda.o:(.bss+0x20): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: thermo.o:(.bss+0x28): multiple definition of `score_threshold'; miranda.o:(.bss+0x28): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: thermo.o:(.bss+0x30): multiple definition of `gap_extend'; miranda.o:(.bss+0x30): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: thermo.o:(.bss+0x38): multiple definition of `gap_open'; miranda.o:(.bss+0x38): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: thermo.o:(.bss+0x40): multiple definition of `debug'; miranda.o:(.bss+0x40): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: thermo.o:(.bss+0x44): multiple definition of `strict'; miranda.o:(.bss+0x44): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: thermo.o:(.bss+0x48): multiple definition of `scale'; miranda.o:(.bss+0x48): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: utils.o:(.bss+0x0): multiple definition of `restricted'; miranda.o:(.bss+0x0): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: utils.o:(.bss+0x4): multiple definition of `truncated'; miranda.o:(.bss+0x4): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: utils.o:(.bss+0x8): multiple definition of `outfile'; miranda.o:(.bss+0x8): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: utils.o:(.bss+0xc): multiple definition of `verbosity'; miranda.o:(.bss+0xc): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: utils.o:(.bss+0x10): multiple definition of `no_energy'; miranda.o:(.bss+0x10): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: utils.o:(.bss+0x14): multiple definition of `key_value_pairs'; miranda.o:(.bss+0x14): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: utils.o:(.bss+0x18): multiple definition of `length_3p_for_weighting'; miranda.o:(.bss+0x18): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: utils.o:(.bss+0x1c): multiple definition of `length_5p_for_weighting'; miranda.o:(.bss+0x1c): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: utils.o:(.bss+0x20): multiple definition of `energy_threshold'; miranda.o:(.bss+0x20): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: utils.o:(.bss+0x28): multiple definition of `score_threshold'; miranda.o:(.bss+0x28): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: utils.o:(.bss+0x30): multiple definition of `gap_extend'; miranda.o:(.bss+0x30): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: utils.o:(.bss+0x38): multiple definition of `gap_open'; miranda.o:(.bss+0x38): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: utils.o:(.bss+0x40): multiple definition of `debug'; miranda.o:(.bss+0x40): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: utils.o:(.bss+0x44): multiple definition of `strict'; miranda.o:(.bss+0x44): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: utils.o:(.bss+0x48): multiple definition of `scale'; miranda.o:(.bss+0x48): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ExpString.o:(.bss+0x0): multiple definition of `restricted'; miranda.o:(.bss+0x0): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ExpString.o:(.bss+0x4): multiple definition of `truncated'; miranda.o:(.bss+0x4): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ExpString.o:(.bss+0x8): multiple definition of `outfile'; miranda.o:(.bss+0x8): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ExpString.o:(.bss+0xc): multiple definition of `verbosity'; miranda.o:(.bss+0xc): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ExpString.o:(.bss+0x10): multiple definition of `no_energy'; miranda.o:(.bss+0x10): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ExpString.o:(.bss+0x14): multiple definition of `key_value_pairs'; miranda.o:(.bss+0x14): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ExpString.o:(.bss+0x18): multiple definition of `length_3p_for_weighting'; miranda.o:(.bss+0x18): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ExpString.o:(.bss+0x1c): multiple definition of `length_5p_for_weighting'; miranda.o:(.bss+0x1c): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ExpString.o:(.bss+0x20): multiple definition of `energy_threshold'; miranda.o:(.bss+0x20): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ExpString.o:(.bss+0x28): multiple definition of `score_threshold'; miranda.o:(.bss+0x28): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ExpString.o:(.bss+0x30): multiple definition of `gap_extend'; miranda.o:(.bss+0x30): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ExpString.o:(.bss+0x38): multiple definition of `gap_open'; miranda.o:(.bss+0x38): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ExpString.o:(.bss+0x40): multiple definition of `debug'; miranda.o:(.bss+0x40): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ExpString.o:(.bss+0x44): multiple definition of `strict'; miranda.o:(.bss+0x44): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ExpString.o:(.bss+0x48): multiple definition of `scale'; miranda.o:(.bss+0x48): first defined here collect2: error: ld returned 1 exit status make[2]: *** [Makefile:267: miranda] Error 1 make[2]: Leaving directory '/var/tmp/portage/sci-biology/miranda-3.3a/work/miRanda-3.3a/src' make[1]: *** [Makefile:270: all-recursive] Error 1 make[1]: Leaving directory '/var/tmp/portage/sci-biology/miranda-3.3a/work/miRanda-3.3a' make: *** [Makefile:208: all] Error 2 * ERROR: sci-biology/miranda-3.3a::science failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-biology/miranda-3.3a::science'`, * the complete build log and the output of `emerge -pqv '=sci-biology/miranda-3.3a::science'`. * The complete build log is located at '/var/log/portage/sci-biology:miranda-3.3a:20201119-153055.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/miranda-3.3a/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/miranda-3.3a/temp/environment'. * Working directory: '/var/tmp/portage/sci-biology/miranda-3.3a/work/miRanda-3.3a' * S: '/var/tmp/portage/sci-biology/miranda-3.3a/work/miRanda-3.3a'