sci-biology:autoeditor-1.20:20201119-151937.log

sci-biology:autoeditor-1.20:20201119-151937.log (text/plain), 34.07 KB, created by Toralf Förster on 2020-11-19 16:54:17 UTC

 * Package:    sci-biology/autoeditor-1.20
 * Repository: science
 * Maintainer: [e-mail] [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox
>>> Unpacking source...
>>> Unpacking autoEditor-1.20.tar.gz to /var/tmp/portage/sci-biology/autoeditor-1.20/work
>>> Source unpacked in /var/tmp/portage/sci-biology/autoeditor-1.20/work
>>> Preparing source in /var/tmp/portage/sci-biology/autoeditor-1.20/work/autoEditor-1.20 ...
 * Applying Makefile.patch ...
 [ ok ]
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/autoeditor-1.20/work/autoEditor-1.20 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/autoeditor-1.20/work/autoEditor-1.20 ...
make -j1 
cd libSlice-1.0; \
  CC=cc   \
  CXX=c++ \
  make;
make[1]: Entering directory '/var/tmp/portage/sci-biology/autoeditor-1.20/work/autoEditor-1.20/libSlice-1.0'
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE   -c -o getConsQC.o getConsQC.c
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE   -c -o getConsQV.o getConsQV.c
getConsQV.c: In function ‘libSlice_getConsensusRangeParam’:
getConsQV.c:1051:3: warning: implicit declaration of function ‘memset’ [-Wimplicit-function-declaration]
 1051 |   memset(*results, 0, len * sizeof(libSlice_Consensus *));
      |   ^~~~~~
getConsQV.c:1051:3: warning: incompatible implicit declaration of built-in function ‘memset’
getConsQV.c:19:1: note: include ‘<string.h>’ or provide a declaration of ‘memset’
   18 | #include "Slice.h"
  +++ |+#include <string.h>
   19 | 
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE   -c -o newmem.o newmem.c
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE   -c -o utility.o utility.c
ar rsv libSlice.a getConsQC.o getConsQV.o newmem.o utility.o
ar: creating libSlice.a
a - getConsQC.o
a - getConsQV.o
a - newmem.o
a - utility.o
make[1]: Leaving directory '/var/tmp/portage/sci-biology/autoeditor-1.20/work/autoEditor-1.20/libSlice-1.0'
c++ -O2 -pipe -march=native -fno-diagnostics-color  -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o Editor.o Editor.cc
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o autoEditor.o autoEditor.c
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o parseContig.o parseContig.c
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o parseQual.o parseQual.c
parseQual.c: In function ‘parseQual’:
parseQual.c:109:36: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 3 has type ‘off_t’ {aka ‘long int’} [-Wformat=]
  109 |             printf ( "%s offset:%lld\n", qvseq[i]->id, offset );
      |                                 ~~~^                   ~~~~~~
      |                                    |                   |
      |                                    long long int       off_t {aka long int}
      |                                 %ld
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o parseSeq.o parseSeq.c
parseSeq.c: In function ‘parseIndexedSeqs’:
parseSeq.c:59:36: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 3 has type ‘off_t’ {aka ‘long int’} [-Wformat=]
   59 |             printf ( "%s offset:%lld\n", seq[count]->id, offset );
      |                                 ~~~^                     ~~~~~~
      |                                    |                     |
      |                                    long long int         off_t {aka long int}
      |                                 %ld
parseSeq.c: In function ‘parseSeq’:
parseSeq.c:157:27: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  157 |             printf ( "%s %d\n", name, strlen ( name ) );
      |                          ~^           ~~~~~~~~~~~~~~~
      |                           |           |
      |                           int         size_t {aka long unsigned int}
      |                          %ld
parseSeq.c: In function ‘old_parseSeq’:
parseSeq.c:248:27: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  248 |             printf ( "%s %d\n", name, strlen ( name ) );
      |                          ~^           ~~~~~~~~~~~~~~~
      |                           |           |
      |                           int         size_t {aka long unsigned int}
      |                          %ld
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o compare.o compare.c
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o alignSeqs.o alignSeqs.c
alignSeqs.c: In function ‘alignQVSeqs2’:
alignSeqs.c:56:54: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘long unsigned int’ [-Wformat=]
   56 |         fprintf ( stderr, "%s line %d: Memory Full! %d requested.\n",
      |                                                     ~^
      |                                                      |
      |                                                      int
      |                                                     %ld
   57 |                   __FILE__, __LINE__, contigLen * sizeof ( unsigned short ) );
      |                                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                 |
      |                                                 long unsigned int
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o chqsortID.o chqsortID.c
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o binsearchID.o binsearchID.c
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o newmem.o newmem.c
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o stack.o stack.c
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o binsearchPos.o binsearchPos.c
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o emptyOutputFiles.o emptyOutputFiles.c
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o snifForGoodSignal.o snifForGoodSignal.c
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o recallCons.o recallCons.c
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o checkForGoodSignal.o checkForGoodSignal.c
checkForGoodSignal.c: In function ‘checkForGoodSignal’:
checkForGoodSignal.c:57:9: warning: variable ‘suppFailed’ set but not used [-Wunused-but-set-variable]
   57 |     int suppFailed = 0;
      |         ^~~~~~~~~~
checkForGoodSignal.c:56:9: warning: variable ‘maxValFailed’ set but not used [-Wunused-but-set-variable]
   56 |     int maxValFailed = 0;
      |         ^~~~~~~~~~~~
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o printData.o printData.c
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o getSeqPos.o getSeqPos.c
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o fOpen.o fOpen.c
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o indexSeqIDs.o indexSeqIDs.c
indexSeqIDs.c: In function ‘indexSeqIDs’:
indexSeqIDs.c:86:29: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 3 has type ‘off_t’ {aka ‘long int’} [-Wformat=]
   86 |             printf ( "%s %lld\n", ind[i]->id, ind[i]->offset );
      |                          ~~~^                 ~~~~~~~~~~~~~~
      |                             |                       |
      |                             long long int           off_t {aka long int}
      |                          %ld
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o freeData.o freeData.c
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o getChromFilePath.o getChromFilePath.c
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o getSignalPar.o getSignalPar.c
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o correctErrors.o correctErrors.c
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o getConsMult.o getConsMult.c
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o getAsmPos.o getAsmPos.c
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o corrInHomoErrors.o corrInHomoErrors.c
corrInHomoErrors.c: In function ‘correctInHomoDiscSlice’:
corrInHomoErrors.c:82:9: warning: variable ‘sign’ set but not used [-Wunused-but-set-variable]
   82 |     int sign = 1;
      |         ^~~~
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o corrSingleInHomoError.o corrSingleInHomoError.c
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o getInHomoBases.o getInHomoBases.c
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o corrInsertionErrors.o corrInsertionErrors.c
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o corrSingleInsertionError.o corrSingleInsertionError.c
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o getInsertionBases.o getInsertionBases.c
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o getSignalStats.o getSignalStats.c
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o getSignalParThresholds.o getSignalParThresholds.c
getSignalParThresholds.c: In function ‘getBasicSignalPar’:
getSignalParThresholds.c:117:5: warning: ignoring return value of ‘realloc’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  117 |     realloc ( locMax, j * sizeof ( unsigned short ) );
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
getSignalParThresholds.c:118:5: warning: ignoring return value of ‘realloc’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  118 |     realloc ( supp, k * sizeof ( unsigned short ) );
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
getSignalParThresholds.c:119:5: warning: ignoring return value of ‘realloc’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  119 |     realloc ( dist, l * sizeof ( unsigned short ) );
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o corrSingleDeletionError.o corrSingleDeletionError.c
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o corrGapSlice.o corrGapSlice.c
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o updateSeqData.o updateSeqData.c
updateSeqData.c: In function ‘updateSeqData’:
updateSeqData.c:157:69: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  157 |             printf ( "\nDEL: %s os->len:%d strlen(os->seq):%d oq->len:%ld\n",
      |                                                            ~^
      |                                                             |
      |                                                             int
      |                                                            %ld
  158 |                      corrData[corrElem]->seq_id, os->len, strlen ( os->seq ), oq->len );
      |                                                           ~~~~~~~~~~~~~~~~~~
      |                                                           |
      |                                                           size_t {aka long unsigned int}

updateSeqData.c:316:69: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  316 |             printf ( "\nINS: %s os->len:%d strlen(os->seq):%d oq->len:%ld\n",
      |                                                            ~^
      |                                                             |
      |                                                             int
      |                                                            %ld
  317 |                      corrData[corrElem]->seq_id, os->len, strlen ( os->seq ), oq->len );
      |                                                           ~~~~~~~~~~~~~~~~~~
      |                                                           |
      |                                                           size_t {aka long unsigned int}

updateSeqData.c:442:82: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  442 | rintf ( "\nWARNING:%s seqPos:%d os->len:%d strlen(os->seq):%d\nos->seq:%s\n",
      |                                                            ~^
      |                                                             |
      |                                                             int
      |                                                            %ld
  443 |         s->id, seqPos, os->len, strlen ( os->seq ), os->seq );
      |                                 ~~~~~~~~~~~~~~~~~~           
      |                                 |
      |                                 size_t {aka long unsigned int}

cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o updateContigGapInd.o updateContigGapInd.c
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o getIncludeRegions.o getIncludeRegions.c
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o parseBCPos.o parseBCPos.c
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o getBCPos.o getBCPos.c
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o getTraceData.o getTraceData.c
cc -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o indexPos.o indexPos.c
indexPos.c: In function ‘indexPos’:
indexPos.c:93:32: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 4 has type ‘off_t’ {aka ‘long int’} [-Wformat=]
   93 |             printf ( "%d %s %lld\n", i, ind[i]->id, ind[i]->offset );
      |                             ~~~^                    ~~~~~~~~~~~~~~
      |                                |                          |
      |                                long long int              off_t {aka long int}
      |                             %ld
c++ -O2 -pipe -march=native -fno-diagnostics-color  -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT  -c -o TraceCache.o TraceCache.cc
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/include/g++-v10/ext/hash_map:60,
                 from TraceCache.cc:26:
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/include/g++-v10/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
   32 | #warning \
      |  ^~~~~~~
TraceCache.cc: In function ‘void insertTraceDataCache(const char*, Read*)’:
TraceCache.cc:117:14: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  117 |              "%s is already in the cache", seqname);
      |              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
TraceCache.cc:132:16: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  132 |                "Seqname %s not found in traceCache but last in queue!",
      |                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
TraceCache.cc: In function ‘void logCacheStatistics()’:
TraceCache.cc:173:33: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  173 |     logMsg(DEBUG_HIGH, "Cache", "Cache Size: %d", maxCacheSize);
      |                                 ^~~~~~~~~~~~~~~~
TraceCache.cc:174:33: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  174 |     logMsg(DEBUG_HIGH, "Cache", "Cache Hits: %d", cacheHit);
      |                                 ^~~~~~~~~~~~~~~~
TraceCache.cc:175:33: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  175 |     logMsg(DEBUG_HIGH, "Cache", "Cache Misses: %d", cacheMiss);
      |                                 ^~~~~~~~~~~~~~~~~~
TraceCache.cc:176:33: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  176 |     logMsg(DEBUG_HIGH, "Cache", "Cache Overflow: %d", cacheOverflow);
      |                                 ^~~~~~~~~~~~~~~~~~~~
c++ -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT -o autoEditor Editor.o autoEditor.o parseContig.o parseQual.o parseSeq.o compare.o alignSeqs.o chqsortID.o binsearchID.o newmem.o stack.o binsearchPos.o emptyOutputFiles.o snifForGoodSignal.o recallCons.o checkForGoodSignal.o printData.o getSeqPos.o fOpen.o indexSeqIDs.o freeData.o getChromFilePath.o getSignalPar.o correctErrors.o getConsMult.o getAsmPos.o corrInHomoErrors.o corrSingleInHomoError.o getInHomoBases.o corrInsertionErrors.o corrSingleInsertionError.o getInsertionBases.o getSignalStats.o getSignalParThresholds.o corrSingleDeletionError.o corrGapSlice.o updateSeqData.o updateContigGapInd.o getIncludeRegions.o parseBCPos.o getBCPos.o getTraceData.o indexPos.o TraceCache.o -lSlice -lTigrFoundation -lm -lstaden-read -lz ;                 \
  echo;                                                       \
  echo " *** A warning regarding tempnam is harmless. ***";   \
  echo;                                                       \
  echo "Now try 'make sample'";
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: libSlice-1.0/libSlice.a(getConsQV.o): in function `libSlice_calculateAmbiguityFlags':
getConsQV.c:(.text+0x1b0): undefined reference to `prToQV'
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: libSlice-1.0/libSlice.a(getConsQV.o): in function `libSlice_getConsensusParam':
getConsQV.c:(.text+0x915): undefined reference to `distributeQV'
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: getConsQV.c:(.text+0x984): undefined reference to `distributeQV'
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: getConsQV.c:(.text+0x9f3): undefined reference to `distributeQV'
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: getConsQV.c:(.text+0xa62): undefined reference to `distributeQV'
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: getConsQV.c:(.text+0xad1): undefined reference to `distributeQV'
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: getConsQV.c:(.text+0xcc6): undefined reference to `prToQV'
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: getConsQV.c:(.text+0xce1): undefined reference to `prToQV'
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: getConsQV.c:(.text+0xcfc): undefined reference to `prToQV'
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: getConsQV.c:(.text+0xd17): undefined reference to `prToQV'
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: getConsQV.c:(.text+0xd32): undefined reference to `prToQV'
collect2: error: ld returned 1 exit status

 *** A warning regarding tempnam is harmless. ***

Now try 'make sample'
>>> Source compiled.
>>> Test phase [not enabled]: sci-biology/autoeditor-1.20

>>> Install sci-biology/autoeditor-1.20 into /var/tmp/portage/sci-biology/autoeditor-1.20/image/
make -j1 DESTDIR=/var/tmp/portage/sci-biology/autoeditor-1.20/image/ install 
c++ -Wall  -DUSE_ZLIB -DUSE_CPP_FRONTEND -IlibSlice-1.0 -LlibSlice-1.0  -I/usr/include/io_lib -L/usr/lib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_HAS_GETOPT -o autoEditor Editor.o autoEditor.o parseContig.o parseQual.o parseSeq.o compare.o alignSeqs.o chqsortID.o binsearchID.o newmem.o stack.o binsearchPos.o emptyOutputFiles.o snifForGoodSignal.o recallCons.o checkForGoodSignal.o printData.o getSeqPos.o fOpen.o indexSeqIDs.o freeData.o getChromFilePath.o getSignalPar.o correctErrors.o getConsMult.o getAsmPos.o corrInHomoErrors.o corrSingleInHomoError.o getInHomoBases.o corrInsertionErrors.o corrSingleInsertionError.o getInsertionBases.o getSignalStats.o getSignalParThresholds.o corrSingleDeletionError.o corrGapSlice.o updateSeqData.o updateContigGapInd.o getIncludeRegions.o parseBCPos.o getBCPos.o getTraceData.o indexPos.o TraceCache.o -lSlice -lTigrFoundation -lm -lstaden-read -lz ;                 \
  echo;                                                       \
  echo " *** A warning regarding tempnam is harmless. ***";   \
  echo;                                                       \
  echo "Now try 'make sample'";
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: libSlice-1.0/libSlice.a(getConsQV.o): in function `libSlice_calculateAmbiguityFlags':
getConsQV.c:(.text+0x1b0): undefined reference to `prToQV'
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: libSlice-1.0/libSlice.a(getConsQV.o): in function `libSlice_getConsensusParam':
getConsQV.c:(.text+0x915): undefined reference to `distributeQV'
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: getConsQV.c:(.text+0x984): undefined reference to `distributeQV'
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: getConsQV.c:(.text+0x9f3): undefined reference to `distributeQV'
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: getConsQV.c:(.text+0xa62): undefined reference to `distributeQV'
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: getConsQV.c:(.text+0xad1): undefined reference to `distributeQV'
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: getConsQV.c:(.text+0xcc6): undefined reference to `prToQV'
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: getConsQV.c:(.text+0xce1): undefined reference to `prToQV'
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: getConsQV.c:(.text+0xcfc): undefined reference to `prToQV'
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: getConsQV.c:(.text+0xd17): undefined reference to `prToQV'
/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: getConsQV.c:(.text+0xd32): undefined reference to `prToQV'
collect2: error: ld returned 1 exit status

 *** A warning regarding tempnam is harmless. ***

Now try 'make sample'
mkdir -p /var/tmp/portage/sci-biology/autoeditor-1.20/image//bin || exit
cp autoEditor /var/tmp/portage/sci-biology/autoeditor-1.20/image//bin/
cp: cannot stat 'autoEditor': No such file or directory
make: *** [Makefile:128: install] Error 1
 * ERROR: sci-biology/autoeditor-1.20::science failed (install phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/autoeditor-1.20::science'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/autoeditor-1.20::science'`.
 * The complete build log is located at '/var/log/portage/sci-biology:autoeditor-1.20:20201119-151937.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/autoeditor-1.20/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/autoeditor-1.20/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/autoeditor-1.20/work/autoEditor-1.20'
 * S: '/var/tmp/portage/sci-biology/autoeditor-1.20/work/autoEditor-1.20'