* Package: sci-biology/samstat-1.5.1 * Repository: science * Maintainer: mmokrejs@fold.natur.cuni.cz 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 samstat-1.5.1.tar.gz to /var/tmp/portage/sci-biology/samstat-1.5.1/work >>> Source unpacked in /var/tmp/portage/sci-biology/samstat-1.5.1/work >>> Preparing source in /var/tmp/portage/sci-biology/samstat-1.5.1/work/samstat-1.5.1 ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/samstat-1.5.1/work/samstat-1.5.1 ... ./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 --disable-silent-rules --docdir=/usr/share/doc/samstat-1.5.1 --htmldir=/usr/share/doc/samstat-1.5.1/html --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 a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether self tests are run under valgrind... no no checking for samtools... samtools checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no 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 whether x86_64-pc-linux-gnu-gcc understands -c and -o together... yes checking for style of include used by make... GNU checking dependency style of x86_64-pc-linux-gnu-gcc... none checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib 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 ctype.h usability... yes checking ctype.h presence... yes checking for ctype.h... yes checking getopt.h usability... yes checking getopt.h presence... yes checking for getopt.h... yes checking math.h usability... yes checking math.h presence... yes checking for math.h... yes checking stdio.h usability... yes checking stdio.h presence... yes checking for stdio.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for sys/stat.h... (cached) yes checking time.h usability... yes checking time.h presence... yes checking for time.h... yes checking for an ANSI C-conforming const... 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 that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating dev/Makefile config.status: creating src/Makefile config.status: creating lib/Makefile config.status: creating src/config.h config.status: executing depfiles commands Configuration: compiler: -O2 -pipe -march=native -fno-diagnostics-color -O2 -funroll-loops -Wall -std=gnu99 valgrind: >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/samstat-1.5.1/work/samstat-1.5.1 ... make -j1 Making all in lib make[1]: Entering directory '/var/tmp/portage/sci-biology/samstat-1.5.1/work/samstat-1.5.1/lib' x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../src -O2 -pipe -march=native -fno-diagnostics-color -O2 -funroll-loops -Wall -std=gnu99 -c -o kslib.o kslib.c rm -f libks.a ar cru libks.a kslib.o x86_64-pc-linux-gnu-ranlib libks.a make[1]: Leaving directory '/var/tmp/portage/sci-biology/samstat-1.5.1/work/samstat-1.5.1/lib' Making all in src make[1]: Entering directory '/var/tmp/portage/sci-biology/samstat-1.5.1/work/samstat-1.5.1/src' make all-am make[2]: Entering directory '/var/tmp/portage/sci-biology/samstat-1.5.1/work/samstat-1.5.1/src' x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../lib -O2 -pipe -march=native -fno-diagnostics-color -O2 -funroll-loops -Wall -std=gnu99 -c -o interface.o interface.c In file included from interface.c:34: interface.c: In function ‘interface’: interface.c:171:37: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context] 171 | MMALLOC(param->infile,sizeof(char*)* (argc-optind)); ../lib/kslib.h:26:38: note: in definition of macro ‘MMALLOC’ 26 | if (((p) = malloc(size)) == NULL && (size)) { \ | ^~~~ interface.c:47:6: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] 47 | int status; | ^~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../lib -O2 -pipe -march=native -fno-diagnostics-color -O2 -funroll-loops -Wall -std=gnu99 -c -o nuc_code.o nuc_code.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../lib -O2 -pipe -march=native -fno-diagnostics-color -O2 -funroll-loops -Wall -std=gnu99 -c -o misc.o misc.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../lib -O2 -pipe -march=native -fno-diagnostics-color -O2 -funroll-loops -Wall -std=gnu99 -c -o main.o main.c main.c: In function ‘main’: main.c:104:6: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] 104 | int status; | ^~~~~~ In file included from main.c:25: main.c: In function ‘hmmdata_init’: main.c:854:39: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context] 854 | MMALLOC(hmm_data->length,sizeof(int) *size); ../lib/kslib.h:26:38: note: in definition of macro ‘MMALLOC’ 26 | if (((p) = malloc(size)) == NULL && (size)) { \ | ^~~~ main.c:855:41: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context] 855 | MMALLOC(hmm_data->weight,sizeof(float) *size); ../lib/kslib.h:26:38: note: in definition of macro ‘MMALLOC’ 26 | if (((p) = malloc(size)) == NULL && (size)) { \ | ^~~~ main.c:856:40: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context] 856 | MMALLOC(hmm_data->score,sizeof(float) *size); ../lib/kslib.h:26:38: note: in definition of macro ‘MMALLOC’ 26 | if (((p) = malloc(size)) == NULL && (size)) { \ | ^~~~ main.c:857:44: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context] 857 | MMALLOC(hmm_data->string , sizeof(char* ) * size); ../lib/kslib.h:26:38: note: in definition of macro ‘MMALLOC’ 26 | if (((p) = malloc(size)) == NULL && (size)) { \ | ^~~~ main.c:843:6: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] 843 | int status; | ^~~~~~ In file included from main.c:25: main.c: In function ‘init_samstat_hmm’: main.c:1071:44: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context] 1071 | MMALLOC(hmm->emissions[i], sizeof(float) * hmm->alphabet_len); ../lib/kslib.h:26:38: note: in definition of macro ‘MMALLOC’ 26 | if (((p) = malloc(size)) == NULL && (size)) { \ | ^~~~ main.c:1072:46: warning: ‘*’ in boolean context, suggest ‘&&’ instead [-Wint-in-bool-context] 1072 | MMALLOC(hmm->emissions_e[i], sizeof(float) * hmm->alphabet_len); ../lib/kslib.h:26:38: note: in definition of macro ‘MMALLOC’ 26 | if (((p) = malloc(size)) == NULL && (size)) { \ | ^~~~ main.c:1000:6: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] 1000 | int status; | ^~~~~~ main.c: In function ‘init_seq_stats’: main.c:1100:6: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] 1100 | int status; | ^~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../lib -O2 -pipe -march=native -fno-diagnostics-color -O2 -funroll-loops -Wall -std=gnu99 -c -o io.o io.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../lib -O2 -pipe -march=native -fno-diagnostics-color -O2 -funroll-loops -Wall -std=gnu99 -c -o hmm.o hmm.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../lib -O2 -pipe -march=native -fno-diagnostics-color -O2 -funroll-loops -Wall -std=gnu99 -c -o viz.o viz.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-diagnostics-color -O2 -funroll-loops -Wall -std=gnu99 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o samstat interface.o nuc_code.o misc.o main.o io.o hmm.o viz.o -lm -lpthread /var/tmp/portage/sci-biology/samstat-1.5.1/work/samstat-1.5.1/lib/libks.a /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: misc.o:(.bss+0x0): multiple definition of `rev_nuc_code'; nuc_code.o:(.bss+0x0): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: misc.o:(.bss+0x20): multiple definition of `nuc_code'; nuc_code.o:(.bss+0x20): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x20): multiple definition of `nuc_code'; nuc_code.o:(.bss+0x20): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x0): multiple definition of `rev_nuc_code'; nuc_code.o:(.bss+0x0): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: io.o:(.bss+0x20): multiple definition of `nuc_code'; nuc_code.o:(.bss+0x20): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: io.o:(.bss+0x0): multiple definition of `rev_nuc_code'; nuc_code.o:(.bss+0x0): first defined here collect2: error: ld returned 1 exit status make[2]: *** [Makefile:587: samstat] Error 1 make[2]: Leaving directory '/var/tmp/portage/sci-biology/samstat-1.5.1/work/samstat-1.5.1/src' make[1]: *** [Makefile:486: all] Error 2 make[1]: Leaving directory '/var/tmp/portage/sci-biology/samstat-1.5.1/work/samstat-1.5.1/src' make: *** [Makefile:334: all-recursive] Error 1 * ERROR: sci-biology/samstat-1.5.1::science failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-biology/samstat-1.5.1::science'`, * the complete build log and the output of `emerge -pqv '=sci-biology/samstat-1.5.1::science'`. * The complete build log is located at '/var/log/portage/sci-biology:samstat-1.5.1:20201120-043744.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/samstat-1.5.1/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/samstat-1.5.1/temp/environment'. * Working directory: '/var/tmp/portage/sci-biology/samstat-1.5.1/work/samstat-1.5.1' * S: '/var/tmp/portage/sci-biology/samstat-1.5.1/work/samstat-1.5.1'