sci-biology:samstat-1.5.1:20201120-043744.log

sci-biology:samstat-1.5.1:20201120-043744.log (text/plain), 11.47 KB, created by Toralf Förster on 2020-11-20 15:55:12 UTC

 * Package:    sci-biology/samstat-1.5.1
 * Repository: science
 * Maintainer: [e-mail] [e-mail]
 * 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'