* Package:    sci-biology/clustalw-mpi-0.13-r2
 * 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 clustalw-mpi-0.13.tar.gz to /var/tmp/portage/sci-biology/clustalw-mpi-0.13-r2/work
>>> Source unpacked in /var/tmp/portage/sci-biology/clustalw-mpi-0.13-r2/work
>>> Preparing source in /var/tmp/portage/sci-biology/clustalw-mpi-0.13-r2/work/clustalw-mpi-0.13 ...
 * Applying 0.13-gentoo.patch ...
 [ ok ]
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/clustalw-mpi-0.13-r2/work/clustalw-mpi-0.13 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/clustalw-mpi-0.13-r2/work/clustalw-mpi-0.13 ...
make -j1 
mpicc  -O2 -pipe -march=native -fno-common -c clustalw-mpi.c
mpicc  -O2 -pipe -march=native -fno-common -c interface.c
interface.c: In function ‘check_param’:
interface.c:207:20: warning: ‘return’ with no value, in function returning non-void
  207 |  if(args[0]==NULL) return;
      |                    ^~~~~~
interface.c:195:13: note: declared here
  195 | static sint check_param(char **args,char *params[], char *param_arg[])
      |             ^~~~~~~~~~~
interface.c: In function ‘myexit’:
interface.c:3976:4: warning: ‘return’ with no value, in function returning non-void
 3976 |    return;
      |    ^~~~~~
interface.c:3967:12: note: declared here
 3967 | static int myexit(int rval)
      |            ^~~~~~
interface.c: In function ‘open_output_file’:
interface.c:2178:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
 2178 |    fgets(temp, FILENAMELEN, stdin);
      |    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
interface.c:2189:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
 2189 |   fgets(temp, FILENAMELEN, stdin);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
interface.c: In function ‘create_parameter_output’:
interface.c:3871:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
 3871 |   fgets(temp, FILENAMELEN, stdin);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
interface.c: In function ‘new_sequence_align’:
interface.c:2431:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
 2431 |   fgets(temp, MAXLINE, stdin);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~
interface.c: In function ‘get_tree’:
interface.c:2667:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
 2667 |       fgets(temp, MAXLINE, stdin);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~
interface.c: In function ‘profile_align’:
interface.c:2811:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
 2811 |   fgets(temp, MAXLINE, stdin);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~
interface.c:2840:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
 2840 |   fgets(temp, MAXLINE, stdin);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~
mpicc  -O2 -pipe -march=native -fno-common -c sequence.c
sequence.c: In function ‘get_clustal_seq’:
sequence.c:158:2: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  158 |  fgets(line,MAXLINE+1,fin); /* read the title line...ignore it */
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~
sequence.c:163:25: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  163 |    for(i=1;i<seqno;i++) fgets(line,MAXLINE+1,fin);
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~
sequence.c: In function ‘get_msf_seq’:
sequence.c:97:25: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
   97 |    for(i=1;i<seqno;i++) fgets(line,MAXLINE+1,fin);
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~
sequence.c: In function ‘get_seq’:
sequence.c:724:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  724 |     fgets(line,MAXLINE+1,fin);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~
sequence.c:752:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  752 |     fgets(line,MAXLINE+1,fin);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~
sequence.c:760:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  760 |    fgets(line,MAXLINE+1,fin);
      |    ^~~~~~~~~~~~~~~~~~~~~~~~~
sequence.c:786:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  786 |     fgets(line,MAXLINE+1,fin);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~
sequence.c:820:6: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  820 |      fgets(line,MAXLINE+1,fin);
      |      ^~~~~~~~~~~~~~~~~~~~~~~~~
sequence.c:824:6: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  824 |      fgets(line,MAXLINE+1,fin);
      |      ^~~~~~~~~~~~~~~~~~~~~~~~~
sequence.c: In function ‘get_embl_ss’:
sequence.c:401:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  401 |       fgets(line,MAXLINE+1,fin);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~
sequence.c:406:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  406 |       fgets(line,MAXLINE+1,fin);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~
sequence.c:425:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  425 |       fgets(line,MAXLINE+1,fin);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~
sequence.c:430:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  430 |       fgets(line,MAXLINE+1,fin);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~
sequence.c: In function ‘get_rsf_ss’:
sequence.c:496:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  496 |       fgets(line,MAXLINE+1,fin);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~
sequence.c:501:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  501 |       fgets(line,MAXLINE+1,fin);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~
mpicc  -O2 -pipe -march=native -fno-common -c showpair.c
mpicc  -O2 -pipe -march=native -fno-common -c malign.c
mpicc  -O2 -pipe -march=native -fno-common -c malign_mpi_progressive.c
malign_mpi_progressive.c: In function ‘key_compare’:
malign_mpi_progressive.c:843:11: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
  843 |     v1 = *(int *) (*((int *) e1));
      |           ^
malign_mpi_progressive.c:844:11: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
  844 |     v2 = *(int *) (*((int *) e2));
      |           ^
mpicc  -O2 -pipe -march=native -fno-common -c malign_mpi_pdiff.c
mpicc  -O2 -pipe -march=native -fno-common -c util.c
util.c: In function ‘getstr’:
util.c:179:2: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  179 |  fgets(outstr, MAXLINE, stdin);
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
util.c: In function ‘getreal’:
util.c:193:10: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  193 |          fgets(line, MAXLINE, stdin);
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~
util.c: In function ‘getint’:
util.c:221:10: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  221 |          fgets(line, MAXLINE, stdin);
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~
util.c: In function ‘do_system’:
util.c:244:3: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result]
  244 |   system(line);
      |   ^~~~~~~~~~~~
mpicc  -DSERIAL_NJTREE -O2 -pipe -march=native -fno-common -c trees.c
mpicc  -O2 -pipe -march=native -fno-common -c gcgcheck.c
mpicc  -O2 -pipe -march=native -fno-common -c prfalign_mpi_pdiff.c
mpicc  -O2 -pipe -march=native -fno-common -c prfalign_mpi_progressive.c
mpicc  -DDYNAMIC_SCHEDULING_PAIRALIGN  -O2 -pipe -march=native -fno-common -c pairalign_new.c
mpicc  -O2 -pipe -march=native -fno-common -c calcgapcoeff.c
mpicc  -O2 -pipe -march=native -fno-common -c calcprf1.c
mpicc  -O2 -pipe -march=native -fno-common -c calcprf2.c
mpicc  -O2 -pipe -march=native -fno-common -c calctree.c
calctree.c: In function ‘create_tree’:
calctree.c:362:8: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  362 |        fscanf(fd,"%f",&dist);
      |        ^~~~~~~~~~~~~~~~~~~~~
mpicc  -O2 -pipe -march=native -fno-common -c readmat.c
mpicc  -O2 -pipe -march=native -fno-common -c alnscore.c
mpicc  -O2 -pipe -march=native -fno-common -c random.c
mpicc  -DDYNAMIC_SCHEDULING_PAIRALIGN  -O2 -pipe -march=native -fno-common -c parallel_compare.c
mpicc  -O2 -pipe -march=native -fno-common -c prfalign.c
mpicc  -O2 -pipe -march=native -fno-common -c stupid.c
stupid.c: In function ‘mypdiff’:
stupid.c:347:3: warning: implicit declaration of function ‘pforward_pass’ [-Wimplicit-function-declaration]
  347 |   pforward_pass(midi, t, tl, A, B, N, HH, DD);
      |   ^~~~~~~~~~~~~
stupid.c:402:3: warning: implicit declaration of function ‘preverse_pass’ [-Wimplicit-function-declaration]
  402 |   preverse_pass(midi, A, B, M, N, go2, RR, SS, gS);
      |   ^~~~~~~~~~~~~
mpicc  -Wl,-O1 -Wl,--as-needed -o clustalw-mpi clustalw-mpi.o interface.o sequence.o showpair.o malign.o malign_mpi_progressive.o malign_mpi_pdiff.o util.o trees.o gcgcheck.o prfalign_mpi_pdiff.o prfalign_mpi_progressive.o pairalign_new.o calcgapcoeff.o calcprf1.o calcprf2.o calctree.o readmat.o alnscore.o random.o parallel_compare.o prfalign.o stupid.o -lm 
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: parallel_compare.o:(.bss+0x2c): multiple definition of `ktup'; showpair.o:(.bss+0x34): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: parallel_compare.o:(.bss+0x0): multiple definition of `zzd'; showpair.o:(.bss+0x0): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: parallel_compare.o:(.bss+0x8): multiple definition of `zzc'; showpair.o:(.bss+0x8): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: parallel_compare.o:(.bss+0x10): multiple definition of `zzb'; showpair.o:(.bss+0x10): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: parallel_compare.o:(.bss+0x18): multiple definition of `zza'; showpair.o:(.bss+0x18): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: parallel_compare.o:(.bss+0x20): multiple definition of `signif'; showpair.o:(.bss+0x28): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: parallel_compare.o:(.bss+0x28): multiple definition of `window'; showpair.o:(.bss+0x30): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: parallel_compare.o:(.bss+0x24): multiple definition of `wind_gap'; showpair.o:(.bss+0x2c): first defined here
collect2: error: ld returned 1 exit status
make: *** [Makefile:33: clustalw-mpi] Error 1
 * ERROR: sci-biology/clustalw-mpi-0.13-r2::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/clustalw-mpi-0.13-r2::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/clustalw-mpi-0.13-r2::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-biology:clustalw-mpi-0.13-r2:20200128-142727.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/clustalw-mpi-0.13-r2/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/clustalw-mpi-0.13-r2/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/clustalw-mpi-0.13-r2/work/clustalw-mpi-0.13'
 * S: '/var/tmp/portage/sci-biology/clustalw-mpi-0.13-r2/work/clustalw-mpi-0.13'