sci-biology:lagan-2.0-r3:20200130-000914.log

sci-biology:lagan-2.0-r3:20200130-000914.log (text/plain), 4.94 KB, created by Toralf Förster on 2020-01-30 19:05:28 UTC

 * Package:    sci-biology/lagan-2.0-r3
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox
>>> Unpacking source...
>>> Unpacking lagan20.tar.gz to /var/tmp/portage/sci-biology/lagan-2.0-r3/work
>>> Source unpacked in /var/tmp/portage/sci-biology/lagan-2.0-r3/work
>>> Preparing source in /var/tmp/portage/sci-biology/lagan-2.0-r3/work/lagan20 ...
 * Applying lagan-2.0-flags.patch ...
 [ ok ]
 * Applying lagan-2.0-gcc4.3.patch ...
 [ ok ]
 * Applying lagan-2.0-fix-c++14.patch ...
 [ ok ]
 * Applying lagan-2.0-qa-implicit-declarations.patch ...
 [ ok ]
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/lagan-2.0-r3/work/lagan20 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/lagan-2.0-r3/work/lagan20 ...
make -j1 CC=x86_64-pc-linux-gnu-gcc CXX=x86_64-pc-linux-gnu-g++ 'CXXFLAGS=-O2 -pipe -march=native -fno-common' 'CFLAGS=-O2 -pipe -march=native -fno-common' 
make -C src
make[1]: Entering directory '/var/tmp/portage/sci-biology/lagan-2.0-r3/work/lagan20/src'
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -Wl,-O1 -Wl,--as-needed -o ../anchors anchors.c skiplist.c
anchors.c: In function ‘my_getline’:
anchors.c:232:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  232 |   fgets(temp, 1024, infile);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~
skiplist.c: In function ‘printSLE’:
skiplist.c:12:19: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘void *’ [-Wformat=]
   12 |   printf("  %d   %x\n", tbp->index, tbp->myelem);
      |                  ~^                 ~~~~~~~~~~~
      |                   |                    |
      |                   unsigned int         void *
      |                  %p
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -Wl,-O1 -Wl,--as-needed -o ../chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG
fchaos.c: In function ‘readfile’:
fchaos.c:344:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  344 |   fgets(temp, 255, input);
      |   ^~~~~~~~~~~~~~~~~~~~~~~
fchaos.c: In function ‘readSubstMatrix’:
fchaos.c:622:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  622 |       fscanf (file, "%d", &(substmatrix[(unsigned char) symbs[i]][(unsigned char) symbs[j]]));
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fchaos.c:627:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  627 |   fscanf (file, "%d", &gappenstart);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fchaos.c:628:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  628 |   fscanf (file, "%d", &gappenext);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
skiplist.c: In function ‘printSLE’:
skiplist.c:12:19: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘void *’ [-Wformat=]
   12 |   printf("  %d   %x\n", tbp->index, tbp->myelem);
      |                  ~^                 ~~~~~~~~~~~
      |                   |                    |
      |                   unsigned int         void *
      |                  %p
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: /var/tmp/portage/sci-biology/lagan-2.0-r3/temp/ccaWaStg.o:(.bss+0x20): multiple definition of `indeces'; /var/tmp/portage/sci-biology/lagan-2.0-r3/temp/ccI50tNk.o:(.bss+0x40080): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: /var/tmp/portage/sci-biology/lagan-2.0-r3/temp/ccI50tNk.o: in function `connectToPrev':
fchaos.c:(.text+0xc6c): undefined reference to `findPrev'
collect2: error: ld returned 1 exit status
make[1]: *** [Makefile:14: ../chaos] Error 1
make[1]: Leaving directory '/var/tmp/portage/sci-biology/lagan-2.0-r3/work/lagan20/src'
make: *** [Makefile:2: all] Error 2
 * ERROR: sci-biology/lagan-2.0-r3::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/lagan-2.0-r3::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/lagan-2.0-r3::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-biology:lagan-2.0-r3:20200130-000914.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/lagan-2.0-r3/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/lagan-2.0-r3/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/lagan-2.0-r3/work/lagan20'
 * S: '/var/tmp/portage/sci-biology/lagan-2.0-r3/work/lagan20'