sci-biology:recon-1.08:20200403-201259.log

sci-biology:recon-1.08:20200403-201259.log (text/plain), 6.89 KB, created by Toralf Förster on 2020-04-03 20:47:55 UTC

 * Package:    sci-biology/recon-1.08
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_musl kernel_linux userland_GNU
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox
>>> Unpacking source...
>>> Unpacking RECON-1.08.tar.gz to /var/tmp/portage/sci-biology/recon-1.08/work
>>> Source unpacked in /var/tmp/portage/sci-biology/recon-1.08/work
>>> Preparing source in /var/tmp/portage/sci-biology/recon-1.08/work/RECON-1.08 ...
 * Applying recon-1.08-buffer-overflow.patch ...
 [ ok ]
 * Applying recon-1.08-perl-shebangs.patch ...
 [ ok ]
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/recon-1.08/work/RECON-1.08 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/recon-1.08/work/RECON-1.08 ...
make -j1 CC=x86_64-gentoo-linux-musl-gcc 'CFLAGS=-O2 -pipe -march=native' -C src 
make: Entering directory '/var/tmp/portage/sci-biology/recon-1.08/work/RECON-1.08/src'
x86_64-gentoo-linux-musl-gcc -O2 -pipe -march=native  -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0  imagespread.c   -o imagespread
In file included from msps.h:3,
                 from imagespread.c:2:
bolts.h:13:1: error: unknown type name ‘int32_t’
   13 | int32_t seq_no;
      | ^~~~~~~
In file included from seqlist.h:2,
                 from msps.h:4,
                 from imagespread.c:2:
bolts.h:13:1: error: unknown type name ‘int32_t’
   13 | int32_t seq_no;
      | ^~~~~~~
In file included from msps.h:4,
                 from imagespread.c:2:
seqlist.h: In function ‘GetSeqNames’:
seqlist.h:39:9: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration]
   39 |  while (isspace(*name_start)) name_start++;
      |         ^~~~~~~
In file included from imagespread.c:2:
msps.h: At top level:
msps.h:12:3: error: unknown type name ‘int32_t’
   12 |   int32_t lb, rb;
      |   ^~~~~~~
msps.h:46:3: error: unknown type name ‘int32_t’
   46 |   int32_t score;
      |   ^~~~~~~
In file included from imagespread.c:2:
msps.h: In function ‘scan_msp’:
msps.h:112:5: error: unknown type name ‘int32_t’
  112 |     int32_t bd_tmp;
      |     ^~~~~~~
msps.h:116:25: warning: format ‘%ld’ expects argument of type ‘long int *’, but argument 3 has type ‘int *’ [-Wformat=]
  116 |     if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) {
      |                       ~~^                               ~~~~~~~~~~~
      |                         |                               |
      |                         long int *                      int *
      |                       %d
msps.h:116:32: warning: format ‘%ld’ expects argument of type ‘long int *’, but argument 5 has type ‘int *’ [-Wformat=]
  116 |     if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) {
      |                              ~~^                                                 ~~~~~~~~~~~~~~~~~~~
      |                                |                                                 |
      |                                long int *                                        int *
      |                              %d
msps.h:116:36: warning: format ‘%ld’ expects argument of type ‘long int *’, but argument 6 has type ‘int *’ [-Wformat=]
  116 |     if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) {
      |                                  ~~^                                                                  ~~~~~~~~~~~~~~~~~~~
      |                                    |                                                                  |
      |                                    long int *                                                         int *
      |                                  %d
msps.h:116:43: warning: format ‘%ld’ expects argument of type ‘long int *’, but argument 8 has type ‘int *’ [-Wformat=]
  116 |     if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) {
      |                                         ~~^                                                                                       ~~~~~~~~~~~~~~~~~~~
      |                                           |                                                                                       |
      |                                           long int *                                                                              int *
      |                                         %d
msps.h:116:47: warning: format ‘%ld’ expects argument of type ‘long int *’, but argument 9 has type ‘int *’ [-Wformat=]
  116 |     if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) {
      |                                             ~~^                                                                                                        ~~~~~~~~~~~~~~~~~~~
      |                                               |                                                                                                        |
      |                                               long int *                                                                                               int *
      |                                             %d
msps.h: In function ‘sing_cov’:
msps.h:197:3: error: unknown type name ‘int32_t’
  197 |   int32_t l1, l2, l, lb, rb;
      |   ^~~~~~~
msps.h: In function ‘doub_cov’:
msps.h:213:3: error: unknown type name ‘int32_t’
  213 |   int32_t l1, l2, l, lb, rb;
      |   ^~~~~~~
make: *** [<builtin>: imagespread] Error 1
make: Leaving directory '/var/tmp/portage/sci-biology/recon-1.08/work/RECON-1.08/src'
 * ERROR: sci-biology/recon-1.08::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/recon-1.08::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/recon-1.08::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-biology:recon-1.08:20200403-201259.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/recon-1.08/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/recon-1.08/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/recon-1.08/work/RECON-1.08'
 * S: '/var/tmp/portage/sci-biology/recon-1.08/work/RECON-1.08'