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Gentoo's Bugzilla – Attachment 447206 Details for
Bug 594700
sci-biology/eugene-4.1 : Sensor.Tester.cc:22:28: error: ‘int isinf(double)’ conflicts with a previous declaration
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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
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hide
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Description:
sci-biology:eugene-4.1:20160921-144425.log
Filename:
MIME Type:
Creator:
Toralf Förster
Created:
2016-09-21 17:06:52 UTC
Size:
50.10 KB
patch
obsolete
> * Package: sci-biology/eugene-4.1 > * Repository: gentoo > * Maintainer: sci-biology@gentoo.org > * 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 âDNASeq::DNASeq(char*)â: >DNASeq.cc:141:31: warning: ignoring return value of âchar* fgets(char*, int, FILE*)â, 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 âHits* Hits::ReadFromFile(FILE*, int*, int, int, int)â: >Hits.cc:167:77: warning: format â%aâ expects argument of type âfloat*â, but argument 11 has type âchar*â [-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 âvoid PenaltyDist::LoadPenaltyDist(char*)â: >PenaltyDist.cc:116:48: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â, 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 âvoid SoTerms::loadFile(char*)â: >SoTerms.cc:70:40: warning: format â%sâ expects argument of type âchar*â, but argument 3 has type âchar (*)[100]â [-Wformat=] > i = sscanf(line, "id: %s", &value); > ^ >SoTerms.cc:77:37: warning: format â%sâ expects argument of type âchar*â, but argument 3 has type âchar (*)[100]â [-Wformat=] > i = sscanf(line, "name: %s", &value); > ^ >SoTerms.cc:76:28: warning: ignoring return value of âchar* fgets(char*, int, FILE*)â, 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 âint fichier2protmat(FILE*, ProtMat*&)â: >../markov.cc:908:29: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â, declared with attribute warn_unused_result [-Wunused-result] > fscanf (fp, "%c", &tampon); > ^ >../markov.cc:911:31: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â, declared with attribute warn_unused_result [-Wunused-result] > fscanf (fp, "%c", &tampon); > ^ >../markov.cc:938:24: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â, 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 âint TabChaine<CHAINE, T>::fichier2seq(FILE*, char*&) [with CHAINE = ChaineADN; T = int]â: >../markov.cc:396:3: warning: ignoring return value of âchar* fgets(char*, int, FILE*)â, 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 âint fichier2protmat(FILE*, ProtMat*&)â: >markov.cc:908:29: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â, declared with attribute warn_unused_result [-Wunused-result] > fscanf (fp, "%c", &tampon); > ^ >markov.cc:911:31: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â, declared with attribute warn_unused_result [-Wunused-result] > fscanf (fp, "%c", &tampon); > ^ >markov.cc:938:24: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â, 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 âint fichier2protmat(FILE*, ProtMat*&)â: >markov.cc:908:29: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â, declared with attribute warn_unused_result [-Wunused-result] > fscanf (fp, "%c", &tampon); > ^ >markov.cc:911:31: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â, declared with attribute warn_unused_result [-Wunused-result] > fscanf (fp, "%c", &tampon); > ^ >markov.cc:938:24: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â, 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 âvoid SensorEst::Print(char*)â: >Sensor.Est.cc:1300:40: warning: format â%dâ expects argument of type âintâ, but argument 3 has type âstd::vector<int>::size_type {aka long unsigned int}â [-Wformat=] > fprintf(fp, "vPos %d\n", vPos.size()); > ^ >Sensor.Est.cc:1306:50: warning: format â%dâ expects argument of type âintâ, but argument 3 has type âstd::vector<unsigned char>::size_type {aka long unsigned int}â [-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 âint fichier2protmat(FILE*, ProtMat*&)â: >../0_SensorTk/markov.cc:908:29: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â, declared with attribute warn_unused_result [-Wunused-result] > fscanf (fp, "%c", &tampon); > ^ >../0_SensorTk/markov.cc:911:31: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â, declared with attribute warn_unused_result [-Wunused-result] > fscanf (fp, "%c", &tampon); > ^ >../0_SensorTk/markov.cc:938:24: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â, declared with attribute warn_unused_result [-Wunused-result] > fscanf(fp,"%s",STR); > ^ >Sensor.Homology.cc: In member function âvoid SensorHomology::ReadHomology(char*, DNASeq*, int, ProtMat*)â: >Sensor.Homology.cc:206:28: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â, 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 âchar*â [-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 âint fichier2protmat(FILE*, ProtMat*&)â: >../../0_SensorTk/markov.cc:908:29: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â, declared with attribute warn_unused_result [-Wunused-result] > fscanf (fp, "%c", &tampon); > ^ >../../0_SensorTk/markov.cc:911:31: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â, declared with attribute warn_unused_result [-Wunused-result] > fscanf (fp, "%c", &tampon); > ^ >../../0_SensorTk/markov.cc:938:24: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â, 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 âint TabChaine<CHAINE, T>::fichier2seq(FILE*, char*&) [with CHAINE = ChainePROT21; T = int]â: >../../0_SensorTk/markov.cc:396:3: warning: ignoring return value of âchar* fgets(char*, int, FILE*)â, 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 âint fichier2protmat(FILE*, ProtMat*&)â: >../0_SensorTk/markov.cc:908:29: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â, declared with attribute warn_unused_result [-Wunused-result] > fscanf (fp, "%c", &tampon); > ^ >../0_SensorTk/markov.cc:911:31: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â, declared with attribute warn_unused_result [-Wunused-result] > fscanf (fp, "%c", &tampon); > ^ >../0_SensorTk/markov.cc:938:24: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â, 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 âvoid SensorNG2::ReadNG2F(char*, int)â: >Sensor.NG2.cc:122:31: warning: ignoring return value of âchar* fgets(char*, int, FILE*)â, declared with attribute warn_unused_result [-Wunused-result] > fgets(buf,FILENAME_MAX-1,fp); > ^ >Sensor.NG2.cc: In member function âvoid SensorNG2::ReadNG2R(char*, int)â: >Sensor.NG2.cc:163:31: warning: ignoring return value of âchar* fgets(char*, int, FILE*)â, 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 âvoid SensorProStart::ReadScore()â: >Sensor.ProStart.cc:139:30: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â, declared with attribute warn_unused_result [-Wunused-result] > fscanf ( Data,"%lf",&e ); > ^ >Sensor.ProStart.cc:152:47: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â, 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 âSensorRiken::SensorRiken(int, DNASeq*)â: >Sensor.Riken.cc:95:61: warning: format â%dâ expects argument of type âintâ, but argument 3 has type âstd::vector<RAFLgene>::size_type {aka long unsigned int}â [-Wformat=] > fprintf(stderr, "%d RAFL EST pairs read, ", RAFLtmp.size()); > ^ >Sensor.Riken.cc:151:46: warning: format â%dâ expects argument of type âintâ, but argument 3 has type âstd::vector<RAFLgene>::size_type {aka long unsigned int}â [-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 âvoid SensorSMachine::ReadSMachineSplices(char*, int)â: >Sensor.SMachine.cc:200:87: warning: format â%dâ expects argument of type âintâ, but argument 4 has type âsize_t {aka long unsigned int}â [-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 âchar* fgets(char*, int, FILE*)â, declared with attribute warn_unused_result [-Wunused-result] > fgets(buf, FILENAME_MAX-1, fp); > ^ >Sensor.SMachine.cc: In member function âvoid SensorSMachine::SpliceMachine()â: >Sensor.SMachine.cc:398:13: warning: ignoring return value of âint system(const char*)â, 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 âint fichier2protmat(FILE*, ProtMat*&)â: >../0_SensorTk/markov.cc:908:29: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â, declared with attribute warn_unused_result [-Wunused-result] > fscanf (fp, "%c", &tampon); > ^ >../0_SensorTk/markov.cc:911:31: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â, declared with attribute warn_unused_result [-Wunused-result] > fscanf (fp, "%c", &tampon); > ^ >../0_SensorTk/markov.cc:938:24: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â, 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 âint fichier2protmat(FILE*, ProtMat*&)â: >../0_SensorTk/markov.cc:908:29: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â, declared with attribute warn_unused_result [-Wunused-result] > fscanf (fp, "%c", &tampon); > ^ >../0_SensorTk/markov.cc:911:31: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â, declared with attribute warn_unused_result [-Wunused-result] > fscanf (fp, "%c", &tampon); > ^ >../0_SensorTk/markov.cc:938:24: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â, 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 âint isinf(double)â: >Sensor.Tester.cc:22:28: error: âint isinf(double)â 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 âconstexpr bool std::isinf(double)â > isinf(double __x) > ^~~~~ >Sensor.Tester.cc: In function âint isinf(double)â: >Sensor.Tester.cc:22:46: error: call of overloaded âisinf(double&)â 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 âint isnan(double)â: >Sensor.Tester.cc:23:28: error: âint isnan(double)â 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 âconstexpr bool std::isnan(double)â > isnan(double __x) > ^~~~~ >Sensor.Tester.cc: In function âint isnan(double)â: >Sensor.Tester.cc:23:46: error: call of overloaded âisnan(double&)â 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 âvoid SensorTester::UpdateThreshold(double)â: >Sensor.Tester.cc:896:14: error: call of overloaded âisnan(double&)â 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'
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