sci-biology:paml-4.4c-r1:20200127-132215.log

sci-biology:paml-4.4c-r1:20200127-132215.log (text/plain), 7.55 KB, created by Toralf Förster on 2020-01-27 17:38:15 UTC

 * Package:    sci-biology/paml-4.4c-r1
 * 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 paml4.4c.tar.gz to /var/tmp/portage/sci-biology/paml-4.4c-r1/work
>>> Source unpacked in /var/tmp/portage/sci-biology/paml-4.4c-r1/work
>>> Preparing source in /var/tmp/portage/sci-biology/paml-4.4c-r1/work/paml44 ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/paml-4.4c-r1/work/paml44 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/paml-4.4c-r1/work/paml44 ...
make -j1 -C src CC=x86_64-pc-linux-gnu-gcc 'CFLAGS=-O2 -pipe -march=native -fno-common -Wno-unused-result' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed' 
make: Entering directory '/var/tmp/portage/sci-biology/paml-4.4c-r1/work/paml44/src'
x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -O2 -pipe -march=native -fno-common -Wno-unused-result -o baseml baseml.c tools.c -lm 
In file included from baseml.c:129:
treesub.c: In function ‘ReadSeq’:
treesub.c:438:27: warning: passing argument 2 of ‘printsma’ from incompatible pointer type [-Wincompatible-pointer-types]
  438 |          printsma(fout,com.spname,com.z,com.ns,com.ls,com.ls,gap,com.seqtype,0,0,NULL);
      |                        ~~~^~~~~~~
      |                           |
      |                           unsigned char **
In file included from baseml.c:11:
paml.h:122:30: note: expected ‘char **’ but argument is of type ‘unsigned char **’
  122 | int printsma(FILE*fout, char*spname[], char*z[],
      |                         ~~~~~^~~~~~~~
In file included from baseml.c:129:
treesub.c:438:38: warning: passing argument 3 of ‘printsma’ from incompatible pointer type [-Wincompatible-pointer-types]
  438 |          printsma(fout,com.spname,com.z,com.ns,com.ls,com.ls,gap,com.seqtype,0,0,NULL);
      |                                   ~~~^~
      |                                      |
      |                                      unsigned char **
In file included from baseml.c:11:
paml.h:122:45: note: expected ‘char **’ but argument is of type ‘unsigned char **’
  122 | int printsma(FILE*fout, char*spname[], char*z[],
      |                                        ~~~~~^~~
In file included from baseml.c:129:
treesub.c:446:24: warning: passing argument 2 of ‘printsma’ from incompatible pointer type [-Wincompatible-pointer-types]
  446 |       printsma(fout,com.spname,com.z,com.ns,com.ls,com.ls,gap,com.seqtype,0,0,NULL);
      |                     ~~~^~~~~~~
      |                        |
      |                        unsigned char **
In file included from baseml.c:11:
paml.h:122:30: note: expected ‘char **’ but argument is of type ‘unsigned char **’
  122 | int printsma(FILE*fout, char*spname[], char*z[],
      |                         ~~~~~^~~~~~~~
In file included from baseml.c:129:
treesub.c:446:35: warning: passing argument 3 of ‘printsma’ from incompatible pointer type [-Wincompatible-pointer-types]
  446 |       printsma(fout,com.spname,com.z,com.ns,com.ls,com.ls,gap,com.seqtype,0,0,NULL);
      |                                ~~~^~
      |                                   |
      |                                   unsigned char **
In file included from baseml.c:11:
paml.h:122:45: note: expected ‘char **’ but argument is of type ‘unsigned char **’
  122 | int printsma(FILE*fout, char*spname[], char*z[],
      |                                        ~~~~~^~~
In file included from baseml.c:129:
treesub.c: In function ‘printPatterns’:
treesub.c:590:24: warning: passing argument 2 of ‘printsma’ from incompatible pointer type [-Wincompatible-pointer-types]
  590 |       printsma(fout,com.spname,com.z,com.ns, com.npatt,com.npatt, gap, com.seqtype, 1, 0, NULL);
      |                     ~~~^~~~~~~
      |                        |
      |                        unsigned char **
In file included from baseml.c:11:
paml.h:122:30: note: expected ‘char **’ but argument is of type ‘unsigned char **’
  122 | int printsma(FILE*fout, char*spname[], char*z[],
      |                         ~~~~~^~~~~~~~
In file included from baseml.c:129:
treesub.c:590:35: warning: passing argument 3 of ‘printsma’ from incompatible pointer type [-Wincompatible-pointer-types]
  590 |       printsma(fout,com.spname,com.z,com.ns, com.npatt,com.npatt, gap, com.seqtype, 1, 0, NULL);
      |                                ~~~^~
      |                                   |
      |                                   unsigned char **
In file included from baseml.c:11:
paml.h:122:45: note: expected ‘char **’ but argument is of type ‘unsigned char **’
  122 | int printsma(FILE*fout, char*spname[], char*z[],
      |                                        ~~~~~^~~
In file included from baseml.c:129:
treesub.c: In function ‘AllPatterns’:
treesub.c:811:24: warning: passing argument 2 of ‘printsma’ from incompatible pointer type [-Wincompatible-pointer-types]
  811 |       printsma(fout,com.spname,com.z,com.ns, com.ls, com.ls, gap, com.seqtype, 1, 0, NULL);
      |                     ~~~^~~~~~~
      |                        |
      |                        unsigned char **
In file included from baseml.c:11:
paml.h:122:30: note: expected ‘char **’ but argument is of type ‘unsigned char **’
  122 | int printsma(FILE*fout, char*spname[], char*z[],
      |                         ~~~~~^~~~~~~~
In file included from baseml.c:129:
treesub.c:811:35: warning: passing argument 3 of ‘printsma’ from incompatible pointer type [-Wincompatible-pointer-types]
  811 |       printsma(fout,com.spname,com.z,com.ns, com.ls, com.ls, gap, com.seqtype, 1, 0, NULL);
      |                                ~~~^~
      |                                   |
      |                                   unsigned char **
In file included from baseml.c:11:
paml.h:122:45: note: expected ‘char **’ but argument is of type ‘unsigned char **’
  122 | int printsma(FILE*fout, char*spname[], char*z[],
      |                                        ~~~~~^~~
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: /var/tmp/portage/sci-biology/paml-4.4c-r1/temp/ccu2aJRy.o:(.bss+0x4540): multiple definition of `OutTreeOptions'; /var/tmp/portage/sci-biology/paml-4.4c-r1/temp/ccr1nFqz.o:(.bss+0x32ed870): 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/paml-4.4c-r1/temp/ccu2aJRy.o:(.bss+0x4544): multiple definition of `DataTypes'; /var/tmp/portage/sci-biology/paml-4.4c-r1/temp/ccr1nFqz.o:(.bss+0x32ed874): first defined here
collect2: error: ld returned 1 exit status
make: *** [Makefile:23: baseml] Error 1
make: Leaving directory '/var/tmp/portage/sci-biology/paml-4.4c-r1/work/paml44/src'
 * ERROR: sci-biology/paml-4.4c-r1::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/paml-4.4c-r1::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/paml-4.4c-r1::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-biology:paml-4.4c-r1:20200127-132215.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/paml-4.4c-r1/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/paml-4.4c-r1/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/paml-4.4c-r1/work/paml44'
 * S: '/var/tmp/portage/sci-biology/paml-4.4c-r1/work/paml44'