* Package:    sci-biology/clustalw-mpi-0.13-r3:0
 * 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-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.
 * Clang 16 testing: this build is using a /etc/portage/bashrc hook (2022-11-24T21:47)!
 * Clang 16 testing: see https://wiki.gentoo.org/wiki/Modern_C_porting for more info.
>>> 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  -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS -Werror=implicit-function-declaration -Werror=implicit-int -c prfalign_mpi_pdiff.c
mpicc  -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS -Werror=implicit-function-declaration -Werror=implicit-int -c malign_mpi_progressive.c
mpicc  -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS -Werror=implicit-function-declaration -Werror=implicit-int -c sequence.c
mpicc  -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS -Werror=implicit-function-declaration -Werror=implicit-int -c clustalw-mpi.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));
      |           ^
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);
      |                                                 ^~~~~~~~~~~~~~~~~~~~~~~~~
mpicc  -pipe -march=native -fno-diagnostics-color -O2 -D_GLIBCXX_ASSERTIONS -Werror=implicit-function-declaration -Werror=implicit-int -c stupid.c
stupid.c: In function ‘mypdiff’:
stupid.c:347:17: error: implicit declaration of function ‘pforward_pass’ [-Werror=implicit-function-declaration]
  347 |                 pforward_pass(midi, t, tl, A, B, N, HH, DD);
      |                 ^~~~~~~~~~~~~
stupid.c:402:17: error: implicit declaration of function ‘preverse_pass’ [-Werror=implicit-function-declaration]
  402 |                 preverse_pass(midi, A, B, M, N, go2, RR, SS, gS);
      |                 ^~~~~~~~~~~~~
cc1: some warnings being treated as errors
make: *** [Makefile:52: stupid.o] Error 1 shuffle=2408644963
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)] = '-';
      |                                                ~~~~~~~~~~~~~~^~~~~
 * 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-r3:20221129-185501.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'