sci-biology:clustalw-mpi-0.13-r3:20231205-025726.log

sci-biology:clustalw-mpi-0.13-r3:20231205-025726.log (text/plain), 9.45 KB, created by Toralf Förster on 2023-12-05 08:09:26 UTC

 * Package:    sci-biology/clustalw-mpi-0.13-r3:0
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux
 * 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-r3/work
>>> Source unpacked in /var/tmp/portage/sci-biology/clustalw-mpi-0.13-r3/work
>>> Preparing source in /var/tmp/portage/sci-biology/clustalw-mpi-0.13-r3/work/clustalw-mpi-0.13 ...
 * Applying clustalw-mpi-0.13-makefile.patch ...
 [ ok ]
 * Applying clustalw-mpi-0.13-fno-common.patch ...
 [ ok ]
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/clustalw-mpi-0.13-r3/work/clustalw-mpi-0.13 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/clustalw-mpi-0.13-r3/work/clustalw-mpi-0.13 ...
make -j4 
mpicc  -O2 -pipe -march=native -fno-diagnostics-color -c clustalw-mpi.c
mpicc  -O2 -pipe -march=native -fno-diagnostics-color -c interface.c
mpicc  -O2 -pipe -march=native -fno-diagnostics-color -c sequence.c
mpicc  -O2 -pipe -march=native -fno-diagnostics-color -c showpair.c
sequence.c: In function ‘get_clustal_seq’:
sequence.c:158:9: 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:163:46: 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:97:46: 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:724:33: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  724 |                                 fgets(line,MAXLINE+1,fin);
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~
sequence.c:752:33: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  752 |                                 fgets(line,MAXLINE+1,fin);
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~
sequence.c:760:25: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  760 |                         fgets(line,MAXLINE+1,fin);
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~
sequence.c:786:33: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  786 |                                 fgets(line,MAXLINE+1,fin);
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~
sequence.c:820:41: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  820 |                                         fgets(line,MAXLINE+1,fin);
      |                                         ^~~~~~~~~~~~~~~~~~~~~~~~~
sequence.c:824:41: 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:401:49: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  401 |                                                 fgets(line,MAXLINE+1,fin);
      |                                                 ^~~~~~~~~~~~~~~~~~~~~~~~~
sequence.c:406:49: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  406 |                                                 fgets(line,MAXLINE+1,fin);
      |                                                 ^~~~~~~~~~~~~~~~~~~~~~~~~
sequence.c:425:49: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  425 |                                                 fgets(line,MAXLINE+1,fin);
      |                                                 ^~~~~~~~~~~~~~~~~~~~~~~~~
sequence.c:430:49: 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:496:49: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  496 |                                                 fgets(line,MAXLINE+1,fin);
      |                                                 ^~~~~~~~~~~~~~~~~~~~~~~~~
sequence.c:501:49: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  501 |                                                 fgets(line,MAXLINE+1,fin);
      |                                                 ^~~~~~~~~~~~~~~~~~~~~~~~~
interface.c: In function ‘check_param’:
interface.c:207:27: error: ‘return’ with no value, in function returning non-void [-Wreturn-mismatch]
  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: error: ‘return’ with no value, in function returning non-void [-Wreturn-mismatch]
 3976 |    return;
      |    ^~~~~~
interface.c:3967:12: note: declared here
 3967 | static int myexit(int rval)
      |            ^~~~~~
interface.c: In function ‘open_output_file’:
interface.c:2178:25: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 2178 |                         fgets(temp, FILENAMELEN, stdin);
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
interface.c:2189:17: 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:3871:17: 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:2431:17: 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:2667:25: 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:2811:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
 2811 |                 fgets(temp, MAXLINE, stdin);
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~
interface.c:2840:17: 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-diagnostics-color -c malign.c
make: *** [Makefile:36: interface.o] Error 1
make: *** Waiting for unfinished jobs....
In function ‘get_seq’,
    inlined from ‘readseqs’ at sequence.c:988:9:
sequence.c:846:62: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  846 |                         for (i=0;i<offset;i++) seq[++(*len)] = '-';
      |                                                ~~~~~~~~~~~~~~^~~~~
In function ‘readseqs’:
cc1: note: destination object is likely at address zero
 * ERROR: sci-biology/clustalw-mpi-0.13-r3::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/clustalw-mpi-0.13-r3::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/clustalw-mpi-0.13-r3::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-biology:clustalw-mpi-0.13-r3:20231205-025726.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/clustalw-mpi-0.13-r3/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/clustalw-mpi-0.13-r3/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/clustalw-mpi-0.13-r3/work/clustalw-mpi-0.13'
 * S: '/var/tmp/portage/sci-biology/clustalw-mpi-0.13-r3/work/clustalw-mpi-0.13'