sci-biology:miranda-3.3a:20201119-153055.log

sci-biology:miranda-3.3a:20201119-153055.log (text/plain), 30.34 KB, created by Toralf Förster on 2020-11-19 16:54:05 UTC

 * Package:    sci-biology/miranda-3.3a
 * Repository: science
 * Maintainer: [e-mail]
 * 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'