sci-biology:eugene-4.1:20160921-144425.log

sci-biology:eugene-4.1:20160921-144425.log (text/plain), 50.10 KB, created by Toralf Förster on 2016-09-21 17:06:52 UTC

 * Package:    sci-biology/eugene-4.1
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU
 * FEATURES:   preserve-libs sandbox userpriv usersandbox
>>> Unpacking source...
>>> Unpacking eugene-4.1.tar.gz to /var/tmp/portage/sci-biology/eugene-4.1/work
>>> Source unpacked in /var/tmp/portage/sci-biology/eugene-4.1/work
>>> Preparing source in /var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1 ...
 * Applying eugene-3.6-overflow.patch ...
 [ ok ]
 * Applying eugene-3.6-plugins.patch ...
 [ ok ]
 * Applying eugene-4.1-format-security.patch ...
 [ ok ]
 * Running eautoreconf in '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1' ...
 * Running aclocal ...
 [ ok ]
 * Running autoconf --force ...
 [ ok ]
 * Running autoheader ...
 [ ok ]
 * Running automake --add-missing --copy --force-missing ...
 [ ok ]
 * Running elibtoolize in: eugene-4.1/
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1 ...
./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-dependency-tracking --disable-silent-rules --libdir=/usr/lib64
checking for a BSD-compatible install... /usr/lib/portage/python3.4/ebuild-helpers/xattr/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of x86_64-pc-linux-gnu-g++... none
checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
checking whether we are using the GNU C compiler... yes
checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes
checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed
checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... yes
checking dependency style of x86_64-pc-linux-gnu-gcc... none
checking for gawk... (cached) gawk
checking whether ln -s works... yes
checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib
checking for main in -lc... yes
checking for main in -ldl... yes
checking for main in -lgcc... yes
checking for main in -lgd... yes
checking for main in -lm... yes
checking for main in -lpng... yes
checking for main in -lz... yes
checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking netdb.h usability... yes
checking netdb.h presence... yes
checking for netdb.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for strings.h... (cached) yes
checking for unistd.h... (cached) yes
checking values.h usability... yes
checking values.h presence... yes
checking for values.h... yes
checking getopt.h usability... yes
checking getopt.h presence... yes
checking for getopt.h... yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking whether struct tm is in sys/time.h or time.h... time.h
checking for size_t... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking whether lstat correctly handles trailing slash... yes
checking whether stat accepts an empty string... no
checking for floor... yes
checking for pow... yes
checking for sqrt... yes
checking for strchr... yes
checking for strspn... yes
checking for uname... yes
checking for getopt... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating README
config.status: creating src/Makefile
config.status: creating src/GDIF/Makefile
config.status: creating src/Parametrization/Makefile
config.status: creating src/SensorPlugins/Makefile
config.status: creating src/SensorPlugins/0_SensorTk/Makefile
config.status: creating src/SensorPlugins/0_SensorTk/GetData/Makefile
config.status: creating src/SensorPlugins/AnnotaStruct/Makefile
config.status: creating src/SensorPlugins/BlastX/Makefile
config.status: creating src/SensorPlugins/Est/Makefile
config.status: creating src/SensorPlugins/EuStop/Makefile
config.status: creating src/SensorPlugins/FrameShift/Makefile
config.status: creating src/SensorPlugins/GCPlot/Makefile
config.status: creating src/SensorPlugins/GFF/Makefile
config.status: creating src/SensorPlugins/GSplicer/Makefile
config.status: creating src/SensorPlugins/Homology/Makefile
config.status: creating src/SensorPlugins/IfElse/Makefile
config.status: creating src/SensorPlugins/MarkovConst/Makefile
config.status: creating src/SensorPlugins/MarkovIMM/Makefile
config.status: creating src/SensorPlugins/MarkovIMM/GetData/Makefile
config.status: creating src/SensorPlugins/MarkovProt/Makefile
config.status: creating src/SensorPlugins/MarkovProt/GetData/Makefile
config.status: creating src/SensorPlugins/NcRNA/Makefile
config.status: creating src/SensorPlugins/NG2/Makefile
config.status: creating src/SensorPlugins/NStart/Makefile
config.status: creating src/SensorPlugins/NStretch/Makefile
config.status: creating src/SensorPlugins/PatConst/Makefile
config.status: creating src/SensorPlugins/PepSignal/Makefile
config.status: creating src/SensorPlugins/ProStart/Makefile
config.status: creating src/SensorPlugins/Plotter/Makefile
config.status: creating src/SensorPlugins/QualData/Makefile
config.status: creating src/SensorPlugins/Repeat/Makefile
config.status: creating src/SensorPlugins/RibosomalFrameShift/Makefile
config.status: creating src/SensorPlugins/Riken/Makefile
config.status: creating src/SensorPlugins/SMachine/Makefile
config.status: creating src/SensorPlugins/SPred/Makefile
config.status: creating src/SensorPlugins/SpliceWAM/Makefile
config.status: creating src/SensorPlugins/StartWAM/Makefile
config.status: creating src/SensorPlugins/Tester/Makefile
config.status: creating src/SensorPlugins/Transcript/Makefile
config.status: creating plugins/Makefile
config.status: creating doc/Makefile
config.status: creating config.h
config.status: executing depfiles commands
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1 ...
make -j1 
(CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/config/missing autoheader)
rm -f stamp-h1
touch config.h.in
cd . && /bin/sh ./config.status config.h
config.status: creating config.h
config.status: config.h is unchanged
make  all-recursive
make[1]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1'
Making all in src
make[2]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src'
Making all in Parametrization
make[3]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/Parametrization'
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o ParaOptimization.o ParaOptimization.cc
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o OptiAlgorithm.o OptiAlgorithm.cc
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o Random.o Random.cc
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o LineSearch.o LineSearch.cc
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o Genetic.o Genetic.cc
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o CrossingOver.o CrossingOver.cc
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o Mutating.o Mutating.cc
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o Scaling.o Scaling.cc
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o Selecting.o Selecting.cc
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o Sharing.o Sharing.cc
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o SimulatedAnnealing.o SimulatedAnnealing.cc
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o Chromosome.o Chromosome.cc
rm -f libParametrization.a
ar cru libParametrization.a ParaOptimization.o OptiAlgorithm.o Random.o LineSearch.o Genetic.o CrossingOver.o Mutating.o Scaling.o Selecting.o Sharing.o SimulatedAnnealing.o Chromosome.o 
x86_64-pc-linux-gnu-ranlib libParametrization.a
make[3]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/Parametrization'
Making all in GDIF
make[3]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/GDIF'
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../..     -march=native -O2 -pipe -c -o gdIF.o gdIF.c
rm -f libGDIF.a
ar cru libGDIF.a gdIF.o 
x86_64-pc-linux-gnu-ranlib libGDIF.a
make[3]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/GDIF'
Making all in .
make[3]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src'
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..    -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -march=native -O2 -pipe -c -o AltEst.o AltEst.cc
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..    -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -march=native -O2 -pipe -c -o Attributes.o Attributes.cc
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..    -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -march=native -O2 -pipe -c -o BackP.o BackP.cc
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..    -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -march=native -O2 -pipe -c -o DAG.o DAG.cc
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..    -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -march=native -O2 -pipe -c -o DNASeq.o DNASeq.cc
DNASeq.cc: In constructor ‘DNASeq::DNASeq(char*)’:
DNASeq.cc:141:31: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
     fgets (Line, MAX_LINE, fp);
                               ^
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..    -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -march=native -O2 -pipe -c -o Dll.o Dll.cc
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..    -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -march=native -O2 -pipe -c -o EuGene.o EuGene.cc
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..    -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -march=native -O2 -pipe -c -o Gap.o Gap.cc
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..    -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -march=native -O2 -pipe -c -o GeneFeature.o GeneFeature.cc
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..    -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -march=native -O2 -pipe -c -o GeneFeatureSet.o GeneFeatureSet.cc
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..    -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -march=native -O2 -pipe -c -o Gff3Line.o Gff3Line.cc
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..    -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -march=native -O2 -pipe -c -o Hits.o Hits.cc
Hits.cc: In member function ‘Hits* Hits::ReadFromFile(FILE*, int*, int, int, int)’:
Hits.cc:167:77: warning: format ‘%a’ expects argument of type ‘float*’, but argument 11 has type ‘char*’ [-Wformat=]
                    &poids, &evalue, &phase, HitId, &HSPDeb, &HSPFin,HSP)) >= 8)
                                                                        ^
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..    -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -march=native -O2 -pipe -c -o Locus.o Locus.cc
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..    -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -march=native -O2 -pipe -c -o MSensor.o MSensor.cc
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..    -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -march=native -O2 -pipe -c -o Param.o Param.cc
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..    -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -march=native -O2 -pipe -c -o PenaltyDist.o PenaltyDist.cc
PenaltyDist.cc: In member function ‘void PenaltyDist::LoadPenaltyDist(char*)’:
PenaltyDist.cc:116:48: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
   fscanf(Handle,"%d %lf\n",&FirstLen,&FirstPen);
                                                ^
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..    -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -march=native -O2 -pipe -c -o Prediction.o Prediction.cc
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..    -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -march=native -O2 -pipe -c -o Range.o Range.cc
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..    -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -march=native -O2 -pipe -c -o Sensor.o Sensor.cc
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..    -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -march=native -O2 -pipe -c -o State.o State.cc
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..    -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -march=native -O2 -pipe -c -o SoTerms.o SoTerms.cc
SoTerms.cc: In member function ‘void SoTerms::loadFile(char*)’:
SoTerms.cc:70:40: warning: format ‘%s’ expects argument of type ‘char*’, but argument 3 has type ‘char (*)[100]’ [-Wformat=]
       i = sscanf(line, "id: %s", &value);
                                        ^
SoTerms.cc:77:37: warning: format ‘%s’ expects argument of type ‘char*’, but argument 3 has type ‘char (*)[100]’ [-Wformat=]
  i = sscanf(line, "name: %s", &value);
                                     ^
SoTerms.cc:76:28: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  fgets (line, MAX_LINE, fp);
                            ^
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..    -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -march=native -O2 -pipe -c -o System.o System.cc
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..    -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -march=native -O2 -pipe -c -o Target.o Target.cc
x86_64-pc-linux-gnu-g++ -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -march=native -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o eugene AltEst.o Attributes.o BackP.o DAG.o DNASeq.o Dll.o EuGene.o Gap.o GeneFeature.o GeneFeatureSet.o Gff3Line.o Hits.o Locus.o MSensor.o Param.o PenaltyDist.o Prediction.o Range.o Sensor.o State.o SoTerms.o System.o Target.o Parametrization/libParametrization.a  GDIF/libGDIF.a -ldl -lz -lpng -lm -lgd -lgcc -ldl -lc 
make[3]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src'
Making all in SensorPlugins
make[3]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins'
Making all in 0_SensorTk
make[4]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/0_SensorTk'
Making all in GetData
make[5]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/0_SensorTk/GetData'
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../../..     -march=native -O2 -pipe -c -o WAMbuilder.o WAMbuilder.cc
In file included from WAMbuilder.cc:31:0:
../markov.cc: In function ‘int fichier2protmat(FILE*, ProtMat*&)’:
../markov.cc:908:29: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
   fscanf (fp, "%c", &tampon);
                             ^
../markov.cc:911:31: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf (fp, "%c", &tampon);
                               ^
../markov.cc:938:24: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf(fp,"%s",STR);
                        ^
In file included from WAMbuilder.cc:31:0:
../markov.cc: In member function ‘int TabChaine<CHAINE, T>::fichier2seq(FILE*, char*&) [with CHAINE = ChaineADN; T = int]’:
../markov.cc:396:3: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
   fgets (Line, 1000 , fp);
   ^~~~~
x86_64-pc-linux-gnu-g++  -march=native -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o egn_WAMbuilder WAMbuilder.o  -lz -lpng -lm -lgd -lgcc -ldl -lc 
make[5]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/0_SensorTk/GetData'
make[5]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/0_SensorTk'
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o BStrArray.o BStrArray.cc
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o WAM.o WAM.cc
In file included from WAM.cc:24:0:
markov.cc: In function ‘int fichier2protmat(FILE*, ProtMat*&)’:
markov.cc:908:29: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
   fscanf (fp, "%c", &tampon);
                             ^
markov.cc:911:31: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf (fp, "%c", &tampon);
                               ^
markov.cc:938:24: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf(fp,"%s",STR);
                        ^
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o markov.o markov.cc
markov.cc: In function ‘int fichier2protmat(FILE*, ProtMat*&)’:
markov.cc:908:29: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
   fscanf (fp, "%c", &tampon);
                             ^
markov.cc:911:31: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf (fp, "%c", &tampon);
                               ^
markov.cc:938:24: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf(fp,"%s",STR);
                        ^
rm -f libSensorTk.a
ar cru libSensorTk.a BStrArray.o WAM.o markov.o 
x86_64-pc-linux-gnu-ranlib libSensorTk.a
make[5]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/0_SensorTk'
make[4]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/0_SensorTk'
Making all in AnnotaStruct
make[4]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/AnnotaStruct'
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o Sensor.AnnotaStruct.o Sensor.AnnotaStruct.cc
x86_64-pc-linux-gnu-g++ -rdynamic -fPIC -march=native -O2 -pipe -shared   -Wl,-O1 -Wl,--as-needed -o Sensor.AnnotaStruct.so Sensor.AnnotaStruct.o  -lz -lpng -lm -lgd -lgcc -ldl -lc 
make[4]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/AnnotaStruct'
Making all in BlastX
make[4]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/BlastX'
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o Sensor.BlastX.o Sensor.BlastX.cc
x86_64-pc-linux-gnu-g++ -rdynamic -fPIC -march=native -O2 -pipe -shared  -Wl,-O1 -Wl,--as-needed -o Sensor.BlastX.so Sensor.BlastX.o  -lz -lpng -lm -lgd -lgcc -ldl -lc 
make[4]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/BlastX'
Making all in Est
make[4]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/Est'
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o Sensor.Est.o Sensor.Est.cc
Sensor.Est.cc: In member function ‘void SensorEst::Print(char*)’:
Sensor.Est.cc:1300:40: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘std::vector<int>::size_type {aka long unsigned int}’ [-Wformat=]
   fprintf(fp, "vPos %d\n",  vPos.size());
                                        ^
Sensor.Est.cc:1306:50: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘std::vector<unsigned char>::size_type {aka long unsigned int}’ [-Wformat=]
   fprintf(fp, "vESTMatch %d\n",  vESTMatch.size());
                                                  ^
x86_64-pc-linux-gnu-g++ -rdynamic -fPIC -march=native -O2 -pipe -shared  -Wl,-O1 -Wl,--as-needed -o Sensor.Est.so Sensor.Est.o  -lz -lpng -lm -lgd -lgcc -ldl -lc 
make[4]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/Est'
Making all in EuStop
make[4]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/EuStop'
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o Sensor.EuStop.o Sensor.EuStop.cc
x86_64-pc-linux-gnu-g++ -rdynamic -fPIC -march=native -O2 -pipe -shared  -Wl,-O1 -Wl,--as-needed -o Sensor.EuStop.so Sensor.EuStop.o  -lz -lpng -lm -lgd -lgcc -ldl -lc 
make[4]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/EuStop'
Making all in FrameShift
make[4]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/FrameShift'
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o Sensor.FrameShift.o Sensor.FrameShift.cc
x86_64-pc-linux-gnu-g++ -rdynamic -fPIC -march=native -O2 -pipe -shared  -Wl,-O1 -Wl,--as-needed -o Sensor.FrameShift.so Sensor.FrameShift.o  -lz -lpng -lm -lgd -lgcc -ldl -lc 
make[4]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/FrameShift'
Making all in GCPlot
make[4]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/GCPlot'
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o Sensor.GCPlot.o Sensor.GCPlot.cc
x86_64-pc-linux-gnu-g++ -rdynamic -fPIC -march=native -O2 -pipe -shared  -Wl,-O1 -Wl,--as-needed -o Sensor.GCPlot.so Sensor.GCPlot.o  -lz -lpng -lm -lgd -lgcc -ldl -lc 
make[4]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/GCPlot'
Making all in GFF
make[4]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/GFF'
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o Sensor.GFF.o Sensor.GFF.cc
x86_64-pc-linux-gnu-g++ -rdynamic -fPIC -march=native -O2 -pipe -shared  -Wl,-O1 -Wl,--as-needed -o Sensor.GFF.so Sensor.GFF.o  -lz -lpng -lm -lgd -lgcc -ldl -lc 
make[4]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/GFF'
Making all in GSplicer
make[4]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/GSplicer'
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o Sensor.GSplicer.o Sensor.GSplicer.cc
x86_64-pc-linux-gnu-g++ -rdynamic -fPIC -march=native -O2 -pipe -shared  -Wl,-O1 -Wl,--as-needed -o Sensor.GSplicer.so Sensor.GSplicer.o  -lz -lpng -lm -lgd -lgcc -ldl -lc 
make[4]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/GSplicer'
Making all in Homology
make[4]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/Homology'
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o Sensor.Homology.o Sensor.Homology.cc
In file included from Sensor.Homology.h:25:0,
                 from Sensor.Homology.cc:29:
../0_SensorTk/markov.cc: In function ‘int fichier2protmat(FILE*, ProtMat*&)’:
../0_SensorTk/markov.cc:908:29: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
   fscanf (fp, "%c", &tampon);
                             ^
../0_SensorTk/markov.cc:911:31: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf (fp, "%c", &tampon);
                               ^
../0_SensorTk/markov.cc:938:24: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf(fp,"%s",STR);
                        ^
Sensor.Homology.cc: In member function ‘void SensorHomology::ReadHomology(char*, DNASeq*, int, ProtMat*)’:
Sensor.Homology.cc:206:28: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
      fscanf(ftblastx,"%*s");
                            ^
x86_64-pc-linux-gnu-g++ -rdynamic -fPIC -march=native -O2 -pipe -shared  -Wl,-O1 -Wl,--as-needed -o Sensor.Homology.so Sensor.Homology.o  -lz -lpng -lm -lgd -lgcc -ldl -lc 
make[4]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/Homology'
Making all in IfElse
make[4]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/IfElse'
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o Sensor.IfElse.o Sensor.IfElse.cc
x86_64-pc-linux-gnu-g++ -rdynamic -fPIC -march=native -O2 -pipe -shared   -Wl,-O1 -Wl,--as-needed -o Sensor.IfElse.so Sensor.IfElse.o  -lz -lpng -lm -lgd -lgcc -ldl -lc 
make[4]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/IfElse'
Making all in MarkovConst
make[4]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/MarkovConst'
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o Sensor.MarkovConst.o Sensor.MarkovConst.cc
x86_64-pc-linux-gnu-g++ -rdynamic -fPIC -march=native -O2 -pipe -shared   -Wl,-O1 -Wl,--as-needed -o Sensor.MarkovConst.so Sensor.MarkovConst.o  -lz -lpng -lm -lgd -lgcc -ldl -lc 
make[4]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/MarkovConst'
Making all in MarkovIMM
make[4]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/MarkovIMM'
Making all in GetData
make[5]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/MarkovIMM/GetData'
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../../..     -march=native -O2 -pipe -c -o TrainIMM.o TrainIMM.cc
x86_64-pc-linux-gnu-g++  -march=native -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o egn_TrainIMM TrainIMM.o  -lz -lpng -lm -lgd -lgcc -ldl -lc 
make[5]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/MarkovIMM/GetData'
make[5]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/MarkovIMM'
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o Sensor.MarkovIMM.o Sensor.MarkovIMM.cc
x86_64-pc-linux-gnu-g++ -rdynamic -fPIC -march=native -O2 -pipe -shared   -Wl,-O1 -Wl,--as-needed -o Sensor.MarkovIMM.so Sensor.MarkovIMM.o  -lz -lpng -lm -lgd -lgcc -ldl -lc 
make[5]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/MarkovIMM'
make[4]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/MarkovIMM'
Making all in MarkovProt
make[4]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/MarkovProt'
Making all in GetData
make[5]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/MarkovProt/GetData'
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../../..     -march=native -O2 -pipe -c -o buildMarkovProt.o buildMarkovProt.cc
buildMarkovProt.cc:38:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
 char* MATRIXfile = "SwissProt41.noFragm.mininfo1000.order2.usi.bin";  // outfile matrix
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from buildMarkovProt.cc:31:0:
../../0_SensorTk/markov.cc: In function ‘int fichier2protmat(FILE*, ProtMat*&)’:
../../0_SensorTk/markov.cc:908:29: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
   fscanf (fp, "%c", &tampon);
                             ^
../../0_SensorTk/markov.cc:911:31: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf (fp, "%c", &tampon);
                               ^
../../0_SensorTk/markov.cc:938:24: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf(fp,"%s",STR);
                        ^
In file included from buildMarkovProt.cc:31:0:
../../0_SensorTk/markov.cc: In member function ‘int TabChaine<CHAINE, T>::fichier2seq(FILE*, char*&) [with CHAINE = ChainePROT21; T = int]’:
../../0_SensorTk/markov.cc:396:3: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
   fgets (Line, 1000 , fp);
   ^~~~~
x86_64-pc-linux-gnu-g++  -march=native -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o egn_buildMarkovProt buildMarkovProt.o  -lz -lpng -lm -lgd -lgcc -ldl -lc 
make[5]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/MarkovProt/GetData'
make[5]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/MarkovProt'
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o Sensor.MarkovProt.o Sensor.MarkovProt.cc
In file included from Sensor.MarkovProt.h:26:0,
                 from Sensor.MarkovProt.cc:20:
../0_SensorTk/markov.cc: In function ‘int fichier2protmat(FILE*, ProtMat*&)’:
../0_SensorTk/markov.cc:908:29: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
   fscanf (fp, "%c", &tampon);
                             ^
../0_SensorTk/markov.cc:911:31: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf (fp, "%c", &tampon);
                               ^
../0_SensorTk/markov.cc:938:24: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf(fp,"%s",STR);
                        ^
x86_64-pc-linux-gnu-g++ -rdynamic -fPIC -march=native -O2 -pipe -shared   -Wl,-O1 -Wl,--as-needed -o Sensor.MarkovProt.so Sensor.MarkovProt.o  -lz -lpng -lm -lgd -lgcc -ldl -lc 
make[5]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/MarkovProt'
make[4]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/MarkovProt'
Making all in NG2
make[4]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/NG2'
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o Sensor.NG2.o Sensor.NG2.cc
Sensor.NG2.cc: In member function ‘void SensorNG2::ReadNG2F(char*, int)’:
Sensor.NG2.cc:122:31: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
   fgets(buf,FILENAME_MAX-1,fp);
                               ^
Sensor.NG2.cc: In member function ‘void SensorNG2::ReadNG2R(char*, int)’:
Sensor.NG2.cc:163:31: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
   fgets(buf,FILENAME_MAX-1,fp);
                               ^
x86_64-pc-linux-gnu-g++ -rdynamic -fPIC -march=native -O2 -pipe -shared   -Wl,-O1 -Wl,--as-needed -o Sensor.NG2.so Sensor.NG2.o  -lz -lpng -lm -lgd -lgcc -ldl -lc 
make[4]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/NG2'
Making all in NStart
make[4]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/NStart'
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o Sensor.NStart.o Sensor.NStart.cc
x86_64-pc-linux-gnu-g++ -rdynamic -fPIC -march=native -O2 -pipe -shared   -Wl,-O1 -Wl,--as-needed -o Sensor.NStart.so Sensor.NStart.o  -lz -lpng -lm -lgd -lgcc -ldl -lc 
make[4]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/NStart'
Making all in PatConst
make[4]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/PatConst'
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o Sensor.PatConst.o Sensor.PatConst.cc
x86_64-pc-linux-gnu-g++ -rdynamic -fPIC -march=native -O2 -pipe -shared   -Wl,-O1 -Wl,--as-needed -o Sensor.PatConst.so Sensor.PatConst.o  -lz -lpng -lm -lgd -lgcc -ldl -lc 
make[4]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/PatConst'
Making all in PepSignal
make[4]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/PepSignal'
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o Sensor.PepSignal.o Sensor.PepSignal.cc
x86_64-pc-linux-gnu-g++ -rdynamic -fPIC -march=native -O2 -pipe -shared   -Wl,-O1 -Wl,--as-needed -o Sensor.PepSignal.so Sensor.PepSignal.o  -lz -lpng -lm -lgd -lgcc -ldl -lc 
make[4]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/PepSignal'
Making all in Plotter
make[4]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/Plotter'
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o Sensor.Plotter.o Sensor.Plotter.cc
x86_64-pc-linux-gnu-g++ -rdynamic -fPIC -march=native -O2 -pipe -shared   -Wl,-O1 -Wl,--as-needed -o Sensor.Plotter.so Sensor.Plotter.o  -lz -lpng -lm -lgd -lgcc -ldl -lc 
make[4]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/Plotter'
Making all in ProStart
make[4]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/ProStart'
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o Sensor.ProStart.o Sensor.ProStart.cc
Sensor.ProStart.cc: In member function ‘void SensorProStart::ReadScore()’:
Sensor.ProStart.cc:139:30: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
      fscanf ( Data,"%lf",&e );
                              ^
Sensor.ProStart.cc:152:47: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
   fscanf ( Data, "%*d %lf %lf %*f\n", &e, &f );
                                               ^
x86_64-pc-linux-gnu-g++ -rdynamic -fPIC -march=native -O2 -pipe -shared  -Wl,-O1 -Wl,--as-needed -o Sensor.ProStart.so Sensor.ProStart.o  -lz -lpng -lm -lgd -lgcc -ldl -lc 
make[4]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/ProStart'
Making all in Repeat
make[4]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/Repeat'
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o Sensor.Repeat.o Sensor.Repeat.cc
x86_64-pc-linux-gnu-g++ -rdynamic -fPIC -march=native -O2 -pipe -shared   -Wl,-O1 -Wl,--as-needed -o Sensor.Repeat.so Sensor.Repeat.o  -lz -lpng -lm -lgd -lgcc -ldl -lc 
make[4]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/Repeat'
Making all in RibosomalFrameShift
make[4]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/RibosomalFrameShift'
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o Sensor.RibosomalFrameShift.o Sensor.RibosomalFrameShift.cc
x86_64-pc-linux-gnu-g++ -rdynamic -fPIC -march=native -O2 -pipe -shared   -Wl,-O1 -Wl,--as-needed -o Sensor.RibosomalFrameShift.so Sensor.RibosomalFrameShift.o  -lz -lpng -lm -lgd -lgcc -ldl -lc 
make[4]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/RibosomalFrameShift'
Making all in Riken
make[4]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/Riken'
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o Sensor.Riken.o Sensor.Riken.cc
Sensor.Riken.cc: In constructor ‘SensorRiken::SensorRiken(int, DNASeq*)’:
Sensor.Riken.cc:95:61: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘std::vector<RAFLgene>::size_type {aka long unsigned int}’ [-Wformat=]
   fprintf(stderr, "%d RAFL EST pairs read, ", RAFLtmp.size());
                                                             ^
Sensor.Riken.cc:151:46: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘std::vector<RAFLgene>::size_type {aka long unsigned int}’ [-Wformat=]
   fprintf(stderr,"resulting %d\n",RAFL.size());
                                              ^
x86_64-pc-linux-gnu-g++ -rdynamic -fPIC -march=native -O2 -pipe -shared   -Wl,-O1 -Wl,--as-needed -o Sensor.Riken.so Sensor.Riken.o  -lz -lpng -lm -lgd -lgcc -ldl -lc 
make[4]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/Riken'
Making all in SMachine
make[4]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/SMachine'
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o Sensor.SMachine.o Sensor.SMachine.cc
Sensor.SMachine.cc: In member function ‘void SensorSMachine::ReadSMachineSplices(char*, int)’:
Sensor.SMachine.cc:200:87: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t {aka long unsigned int}’ [-Wformat=]
 tf(stderr, "Error in SpliceMachine splice site file %s, line %d\n", name, len);
                                                                              ^
Sensor.SMachine.cc:174:33: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
   fgets(buf, FILENAME_MAX-1, fp);
                                 ^
Sensor.SMachine.cc: In member function ‘void SensorSMachine::SpliceMachine()’:
Sensor.SMachine.cc:398:13: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result]
   system(s1);
             ^
x86_64-pc-linux-gnu-g++ -rdynamic -fPIC -march=native -O2 -pipe -shared   -Wl,-O1 -Wl,--as-needed -o Sensor.SMachine.so Sensor.SMachine.o  -lz -lpng -lm -lgd -lgcc -ldl -lc 
make[4]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/SMachine'
Making all in SPred
make[4]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/SPred'
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o Sensor.SPred.o Sensor.SPred.cc
x86_64-pc-linux-gnu-g++ -rdynamic -fPIC -march=native -O2 -pipe -shared   -Wl,-O1 -Wl,--as-needed -o Sensor.SPred.so Sensor.SPred.o  -lz -lpng -lm -lgd -lgcc -ldl -lc 
make[4]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/SPred'
Making all in SpliceWAM
make[4]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/SpliceWAM'
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o Sensor.SpliceWAM.o Sensor.SpliceWAM.cc
In file included from ../0_SensorTk/WAM.cc:24:0,
                 from Sensor.SpliceWAM.h:26,
                 from Sensor.SpliceWAM.cc:22:
../0_SensorTk/markov.cc: In function ‘int fichier2protmat(FILE*, ProtMat*&)’:
../0_SensorTk/markov.cc:908:29: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
   fscanf (fp, "%c", &tampon);
                             ^
../0_SensorTk/markov.cc:911:31: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf (fp, "%c", &tampon);
                               ^
../0_SensorTk/markov.cc:938:24: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf(fp,"%s",STR);
                        ^
x86_64-pc-linux-gnu-g++ -rdynamic -fPIC -march=native -O2 -pipe -shared   -Wl,-O1 -Wl,--as-needed -o Sensor.SpliceWAM.so Sensor.SpliceWAM.o  -lz -lpng -lm -lgd -lgcc -ldl -lc 
make[4]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/SpliceWAM'
Making all in StartWAM
make[4]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/StartWAM'
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o Sensor.StartWAM.o Sensor.StartWAM.cc
In file included from ../0_SensorTk/WAM.cc:24:0,
                 from Sensor.StartWAM.h:25,
                 from Sensor.StartWAM.cc:22:
../0_SensorTk/markov.cc: In function ‘int fichier2protmat(FILE*, ProtMat*&)’:
../0_SensorTk/markov.cc:908:29: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
   fscanf (fp, "%c", &tampon);
                             ^
../0_SensorTk/markov.cc:911:31: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf (fp, "%c", &tampon);
                               ^
../0_SensorTk/markov.cc:938:24: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
     fscanf(fp,"%s",STR);
                        ^
x86_64-pc-linux-gnu-g++ -rdynamic -fPIC -march=native -O2 -pipe -shared   -Wl,-O1 -Wl,--as-needed -o Sensor.StartWAM.so Sensor.StartWAM.o  -lz -lpng -lm -lgd -lgcc -ldl -lc 
make[4]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/StartWAM'
Making all in Tester
make[4]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/Tester'
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../..    -rdynamic -fPIC -march=native -O2 -pipe -c -o Sensor.Tester.o Sensor.Tester.cc
Sensor.Tester.cc: In function ‘int isinf(double)’:
Sensor.Tester.cc:22:28: error: ‘int isinf(double)’ conflicts with a previous declaration
 inline int (isinf)(double r) { return isinf(r); }
                            ^
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/math.h:36:0,
                 from Sensor.Tester.cc:21:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:618:3: note: previous declaration ‘constexpr bool std::isinf(double)’
   isinf(double __x)
   ^~~~~
Sensor.Tester.cc: In function ‘int isinf(double)’:
Sensor.Tester.cc:22:46: error: call of overloaded ‘isinf(double&)’ is ambiguous
 inline int (isinf)(double r) { return isinf(r); }
                                              ^
Sensor.Tester.cc:22:13: note: candidate: int isinf(double)
 inline int (isinf)(double r) { return isinf(r); }
             ^~~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/math.h:36:0,
                 from Sensor.Tester.cc:21:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:623:3: note: candidate: constexpr bool std::isinf(long double)
   isinf(long double __x)
   ^~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:618:3: note: candidate: constexpr bool std::isinf(double)
   isinf(double __x)
   ^~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:610:3: note: candidate: constexpr bool std::isinf(float)
   isinf(float __x)
   ^~~~~
Sensor.Tester.cc: In function ‘int isnan(double)’:
Sensor.Tester.cc:23:28: error: ‘int isnan(double)’ conflicts with a previous declaration
 inline int (isnan)(double r) { return isnan(r); }
                            ^
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/math.h:36:0,
                 from Sensor.Tester.cc:21:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:643:3: note: previous declaration ‘constexpr bool std::isnan(double)’
   isnan(double __x)
   ^~~~~
Sensor.Tester.cc: In function ‘int isnan(double)’:
Sensor.Tester.cc:23:46: error: call of overloaded ‘isnan(double&)’ is ambiguous
 inline int (isnan)(double r) { return isnan(r); }
                                              ^
Sensor.Tester.cc:23:13: note: candidate: int isnan(double)
 inline int (isnan)(double r) { return isnan(r); }
             ^~~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/math.h:36:0,
                 from Sensor.Tester.cc:21:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:648:3: note: candidate: constexpr bool std::isnan(long double)
   isnan(long double __x)
   ^~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:643:3: note: candidate: constexpr bool std::isnan(double)
   isnan(double __x)
   ^~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:635:3: note: candidate: constexpr bool std::isnan(float)
   isnan(float __x)
   ^~~~~
Sensor.Tester.cc: In member function ‘void SensorTester::UpdateThreshold(double)’:
Sensor.Tester.cc:896:14: error: call of overloaded ‘isnan(double&)’ is ambiguous
   if (isnan(t))
              ^
Sensor.Tester.cc:23:13: note: candidate: int isnan(double)
 inline int (isnan)(double r) { return isnan(r); }
             ^~~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/math.h:36:0,
                 from Sensor.Tester.cc:21:
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:648:3: note: candidate: constexpr bool std::isnan(long double)
   isnan(long double __x)
   ^~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:643:3: note: candidate: constexpr bool std::isnan(double)
   isnan(double __x)
   ^~~~~
/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:635:3: note: candidate: constexpr bool std::isnan(float)
   isnan(float __x)
   ^~~~~
make[4]: *** [Makefile:347: Sensor.Tester.o] Error 1
make[4]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins/Tester'
make[3]: *** [Makefile:335: all-recursive] Error 1
make[3]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src/SensorPlugins'
make[2]: *** [Makefile:481: all-recursive] Error 1
make[2]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1/src'
make[1]: *** [Makefile:461: all-recursive] Error 1
make[1]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1'
make: *** [Makefile:400: all] Error 2
 * ERROR: sci-biology/eugene-4.1::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/eugene-4.1::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/eugene-4.1::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-biology:eugene-4.1:20160921-144425.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/eugene-4.1/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/eugene-4.1/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1'
 * S: '/var/tmp/portage/sci-biology/eugene-4.1/work/eugene-4.1'