* Package: sci-biology/mothur-1.27.0-r1 * Repository: gentoo * Maintainer: sci-biology@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux mpi readline userland_GNU * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox * Using following Fortran compiler: * F77: x86_64-pc-linux-gnu-gfortran * FC: x86_64-pc-linux-gnu-gfortran >>> Unpacking source... >>> Unpacking mothur-1.27.0.zip to /var/tmp/portage/sci-biology/mothur-1.27.0-r1/work >>> Source unpacked in /var/tmp/portage/sci-biology/mothur-1.27.0-r1/work >>> Preparing source in /var/tmp/portage/sci-biology/mothur-1.27.0-r1/work/Mothur.source ... * Applying mothur-1.27.0-makefile.patch ... [ ok ] * Applying mothur-1.27.0-overflows.patch ... [ ok ] >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/mothur-1.27.0-r1/work/Mothur.source ... >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/mothur-1.27.0-r1/work/Mothur.source ... make -j1 USEMPI=yes USEREADLINE=yes x86_64-pc-linux-gnu-gfortran -c -O2 -pipe *.f mpicxx -O2 -pipe -march=native -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -DUSE_MPI -I. -DBIT_VERSION -c -o reportfile.o reportfile.cpp mpicxx -O2 -pipe -march=native -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -DUSE_MPI -I. -DBIT_VERSION -c -o pipelinepdscommand.o pipelinepdscommand.cpp mpicxx -O2 -pipe -march=native -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -DUSE_MPI -I. -DBIT_VERSION -c -o sharedjclass.o sharedjclass.cpp mpicxx -O2 -pipe -march=native -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -DUSE_MPI -I. -DBIT_VERSION -c -o rabundvector.o rabundvector.cpp mpicxx -O2 -pipe -march=native -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -DUSE_MPI -I. -DBIT_VERSION -c -o setlogfilecommand.o setlogfilecommand.cpp mpicxx -O2 -pipe -march=native -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -DUSE_MPI -I. -DBIT_VERSION -c -o kruskalwalliscommand.o kruskalwalliscommand.cpp mpicxx -O2 -pipe -march=native -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -DUSE_MPI -I. -DBIT_VERSION -c -o countgroupscommand.o countgroupscommand.cpp mpicxx -O2 -pipe -march=native -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -DUSE_MPI -I. -DBIT_VERSION -c -o getotulabelscommand.o getotulabelscommand.cpp mpicxx -O2 -pipe -march=native -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -DUSE_MPI -I. -DBIT_VERSION -c -o simpson.o simpson.cpp mpicxx -O2 -pipe -march=native -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -DUSE_MPI -I. -DBIT_VERSION -c -o removeseqscommand.o removeseqscommand.cpp mpicxx -O2 -pipe -march=native -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -DUSE_MPI -I. -DBIT_VERSION -c -o mempearson.o mempearson.cpp mpicxx -O2 -pipe -march=native -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -DUSE_MPI -I. -DBIT_VERSION -c -o venncommand.o venncommand.cpp mpicxx -O2 -pipe -march=native -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -DUSE_MPI -I. -DBIT_VERSION -c -o readphylip.o readphylip.cpp mpicxx -O2 -pipe -march=native -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -DUSE_MPI -I. -DBIT_VERSION -c -o weightedlinkage.o weightedlinkage.cpp mpicxx -O2 -pipe -march=native -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -DUSE_MPI -I. -DBIT_VERSION -c -o removerarecommand.o removerarecommand.cpp mpicxx -O2 -pipe -march=native -DRELEASE_DATE="\"8/8/2012\"" -DVERSION="\"1.27.0\"" -DUSE_READLINE -DUSE_MPI -I. -DBIT_VERSION -c -o classifyseqscommand.o classifyseqscommand.cpp classifyseqscommand.cpp: In member function ‘virtual int ClassifySeqsCommand::execute()’: classifyseqscommand.cpp:571:17: error: ‘MPI_MODE_CREATE’ was not declared in this scope int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; ^~~~~~~~~~~~~~~ classifyseqscommand.cpp:571:17: note: suggested alternative: ‘MPI_MODE_NOPUT’ int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; ^~~~~~~~~~~~~~~ MPI_MODE_NOPUT classifyseqscommand.cpp:571:33: error: ‘MPI_MODE_WRONLY’ was not declared in this scope int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; ^~~~~~~~~~~~~~~ classifyseqscommand.cpp:571:33: note: suggested alternative: ‘MPI_MODE_NOPUT’ int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; ^~~~~~~~~~~~~~~ MPI_MODE_NOPUT classifyseqscommand.cpp:572:16: error: ‘MPI_MODE_RDONLY’ was not declared in this scope int inMode=MPI_MODE_RDONLY; ^~~~~~~~~~~~~~~ classifyseqscommand.cpp:572:16: note: suggested alternative: ‘MPI_MODE_NOPUT’ int inMode=MPI_MODE_RDONLY; ^~~~~~~~~~~~~~~ MPI_MODE_NOPUT classifyseqscommand.cpp:586:5: error: ‘MPI_File_open’ was not declared in this scope MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer ^~~~~~~~~~~~~ classifyseqscommand.cpp:586:5: note: suggested alternative: ‘MPI_Free_mem’ MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer ^~~~~~~~~~~~~ MPI_Free_mem classifyseqscommand.cpp:591:52: error: ‘MPI_File_close’ was not declared in this scope if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPINewTax); MPI_File_close(&outMPIAcc); MPI_File_close(&outMPITempTax); delete classify; return 0; } ^~~~~~~~~~~~~~ classifyseqscommand.cpp:591:52: note: suggested alternative: ‘MPI_Win_flush’ if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPINewTax); MPI_File_close(&outMPIAcc); MPI_File_close(&outMPITempTax); delete classify; return 0; } ^~~~~~~~~~~~~~ MPI_Win_flush classifyseqscommand.cpp:612:54: error: ‘MPI_File_close’ was not declared in this scope if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPINewTax); MPI_File_close(&outMPIAcc); MPI_File_close(&outMPITempTax); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete classify; return 0; } ^~~~~~~~~~~~~~ classifyseqscommand.cpp:612:54: note: suggested alternative: ‘MPI_Win_flush’ if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPINewTax); MPI_File_close(&outMPIAcc); MPI_File_close(&outMPITempTax); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete classify; return 0; } ^~~~~~~~~~~~~~ MPI_Win_flush classifyseqscommand.cpp:632:54: error: ‘MPI_File_close’ was not declared in this scope if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPINewTax); MPI_File_close(&outMPIAcc); MPI_File_close(&outMPITempTax); delete classify; return 0; } ^~~~~~~~~~~~~~ classifyseqscommand.cpp:632:54: note: suggested alternative: ‘MPI_Win_flush’ if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&inMPI); MPI_File_close(&outMPINewTax); MPI_File_close(&outMPIAcc); MPI_File_close(&outMPITempTax); delete classify; return 0; } ^~~~~~~~~~~~~~ MPI_Win_flush classifyseqscommand.cpp:639:5: error: ‘MPI_File_close’ was not declared in this scope MPI_File_close(&inMPI); ^~~~~~~~~~~~~~ classifyseqscommand.cpp:639:5: note: suggested alternative: ‘MPI_Win_flush’ MPI_File_close(&inMPI); ^~~~~~~~~~~~~~ MPI_Win_flush classifyseqscommand.cpp: In member function ‘int ClassifySeqsCommand::driverMPI(int, int, ADIOI_FileD*&, ADIOI_FileD*&, ADIOI_FileD*&, ADIOI_FileD*&, std::vector&)’: classifyseqscommand.cpp:1064:4: error: ‘MPI_File_read_at’ was not declared in this scope MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status); ^~~~~~~~~~~~~~~~ classifyseqscommand.cpp:1064:4: note: suggested alternative: ‘MPI_Aint_add’ MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status); ^~~~~~~~~~~~~~~~ MPI_Aint_add classifyseqscommand.cpp:1089:5: error: ‘MPI_File_write_shared’ was not declared in this scope MPI_File_write_shared(newFile, buf2, length, MPI_CHAR, &statusNew); ^~~~~~~~~~~~~~~~~~~~~ classifyseqscommand.cpp:1089:5: note: suggested alternative: ‘MPI_Win_allocate_shared’ MPI_File_write_shared(newFile, buf2, length, MPI_CHAR, &statusNew); ^~~~~~~~~~~~~~~~~~~~~ MPI_Win_allocate_shared classifyseqscommand.cpp: In member function ‘int ClassifySeqsCommand::MPIReadNamesFile(std::__cxx11::string)’: classifyseqscommand.cpp:1143:45: error: ‘MPI_MODE_RDONLY’ was not declared in this scope MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI); ^~~~~~~~~~~~~~~ classifyseqscommand.cpp:1143:45: note: suggested alternative: ‘MPI_MODE_NOPUT’ MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI); ^~~~~~~~~~~~~~~ MPI_MODE_NOPUT classifyseqscommand.cpp:1143:3: error: ‘MPI_File_open’ was not declared in this scope MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI); ^~~~~~~~~~~~~ classifyseqscommand.cpp:1143:3: note: suggested alternative: ‘MPI_Free_mem’ MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI); ^~~~~~~~~~~~~ MPI_Free_mem classifyseqscommand.cpp:1144:3: error: ‘MPI_File_get_size’ was not declared in this scope MPI_File_get_size(inMPI, &size); ^~~~~~~~~~~~~~~~~ classifyseqscommand.cpp:1144:3: note: suggested alternative: ‘MPI_Win_get_name’ MPI_File_get_size(inMPI, &size); ^~~~~~~~~~~~~~~~~ MPI_Win_get_name classifyseqscommand.cpp:1148:3: error: ‘MPI_File_read’ was not declared in this scope MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status); ^~~~~~~~~~~~~ classifyseqscommand.cpp:1148:3: note: suggested alternative: ‘MPI_Free_mem’ MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status); ^~~~~~~~~~~~~ MPI_Free_mem classifyseqscommand.cpp:1165:3: error: ‘MPI_File_close’ was not declared in this scope MPI_File_close(&inMPI); ^~~~~~~~~~~~~~ classifyseqscommand.cpp:1165:3: note: suggested alternative: ‘MPI_Win_flush’ MPI_File_close(&inMPI); ^~~~~~~~~~~~~~ MPI_Win_flush make: *** [makefile:113: classifyseqscommand.o] Error 1 * ERROR: sci-biology/mothur-1.27.0-r1::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-biology/mothur-1.27.0-r1::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-biology/mothur-1.27.0-r1::gentoo'`. * The complete build log is located at '/var/log/portage/sci-biology:mothur-1.27.0-r1:20190323-225202.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/mothur-1.27.0-r1/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/mothur-1.27.0-r1/temp/environment'. * Working directory: '/var/tmp/portage/sci-biology/mothur-1.27.0-r1/work/Mothur.source' * S: '/var/tmp/portage/sci-biology/mothur-1.27.0-r1/work/Mothur.source'