{"action":"created","issue":{"url":"https://api.github.com/repos/PacificBiosciences/blasr/issues/369","repository_url":"https://api.github.com/repos/PacificBiosciences/blasr","labels_url":"https://api.github.com/repos/PacificBiosciences/blasr/issues/369/labels{/name}","comments_url":"https://api.github.com/repos/PacificBiosciences/blasr/issues/369/comments","events_url":"https://api.github.com/repos/PacificBiosciences/blasr/issues/369/events","html_url":"https://github.com/PacificBiosciences/blasr/issues/369","id":250524452,"node_id":"MDU6SXNzdWUyNTA1MjQ0NTI=","number":369,"title":"make build-submodule fails","user":{"login":"samfux84","id":11944875,"node_id":"MDQ6VXNlcjExOTQ0ODc1","avatar_url":"https://avatars0.githubusercontent.com/u/11944875?v=4","gravatar_id":"","url":"https://api.github.com/users/samfux84","html_url":"https://github.com/samfux84","followers_url":"https://api.github.com/users/samfux84/followers","following_url":"https://api.github.com/users/samfux84/following{/other_user}","gists_url":"https://api.github.com/users/samfux84/gists{/gist_id}","starred_url":"https://api.github.com/users/samfux84/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/samfux84/subscriptions","organizations_url":"https://api.github.com/users/samfux84/orgs","repos_url":"https://api.github.com/users/samfux84/repos","events_url":"https://api.github.com/users/samfux84/events{/privacy}","received_events_url":"https://api.github.com/users/samfux84/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2017-08-16T06:32:21Z","updated_at":"2018-06-02T22:44:58Z","closed_at":"2018-06-02T22:44:58Z","author_association":"NONE","body":"Tried to install blasr following the instructions for make:\r\n\r\n1.) git clone git://github.com/PacificBiosciences/blasr.git blasr\r\n2.) git pull --rebase origin master && git submodule update --init\r\n3.) git submodule update --init\r\n4.) ./configure.py --shared --sub --no-pbbam HDF5_INCLUDE=/cluster/apps/hdf5/1.8.12/x86_64/gcc_4.8.2/serial/include HDF5_LIB=/cluster/apps/hdf5/1.8.12/x86_64/gcc_4.8.2/serial/lib\r\n\r\nOutput:\r\n```\r\n\r\n`uname`\r\nLinux\r\nwriting to '/cluster/apps/gdc/blasr/5.3/defines.mk':\r\n\"\"\"\r\nLIBPBDATA_LIB        ?= /cluster/apps/gdc/blasr/5.3/libcpp/pbdata\r\nLIBBLASR_LIBFLAGS    ?= -lblasr\r\nHDF5_LIB             ?= /cluster/apps/hdf5/1.8.12/x86_64/gcc_4.8.2/serial/lib\r\nDL_LIBFLAGS          ?= -ldl\r\nHDF5_INC             ?= /cluster/apps/hdf5/1.8.12/x86_64/gcc_4.8.2/serial/include\r\nLIBPBDATA_INC        ?= /cluster/apps/gdc/blasr/5.3/libcpp/pbdata\r\nLIBPBIHDF_LIBFLAGS   ?= -lpbihdf\r\nLIBPBIHDF_INC        ?= /cluster/apps/gdc/blasr/5.3/libcpp/hdf\r\nLIBBLASR_LIB         ?= /cluster/apps/gdc/blasr/5.3/libcpp/alignment\r\nSHELL                ?= bash\r\nRT_LIBFLAGS          ?= -lrt\r\nHDF5_LIBFLAGS        ?= -lhdf5_cpp -lhdf5\r\nLIBPBDATA_LIBFLAGS   ?= -lpbdata\r\nZLIB_LIBFLAGS        ?= -lz\r\nLIBBLASR_INC         ?= /cluster/apps/gdc/blasr/5.3/libcpp/alignment\r\nPTHREAD_LIBFLAGS     ?= -lpthread\r\nNOPBBAM              ?= 1\r\nLIBPBIHDF_LIB        ?= /cluster/apps/gdc/blasr/5.3/libcpp/hdf\r\nCXX                  := /cluster/apps/gcc/4.8.2/bin/g++\r\n\"\"\"\r\n----\r\n```\r\n\r\nmake build-submodule throws an error because of not finding pbdata header files:\r\n\r\n```\r\n[sfux@develop01 5.3]$ make build-submodule \r\nUnknown option: -C\r\nusage: git [--version] [--exec-path[=GIT_EXEC_PATH]] [--html-path]\r\n           [-p|--paginate|--no-pager] [--no-replace-objects]\r\n           [--bare] [--git-dir=GIT_DIR] [--work-tree=GIT_WORK_TREE]\r\n           [--help] COMMAND [ARGS]\r\nmake -C libcpp\r\nmake[1]: Entering directory `/cluster/apps/gdc/blasr/5.3/libcpp'\r\nmake libpbdata\r\nmake[2]: Entering directory `/cluster/apps/gdc/blasr/5.3/libcpp'\r\nmake -C /cluster/apps/gdc/blasr/5.3/libcpp//pbdata libconfig.h\r\nmake[3]: Entering directory `/cluster/apps/gdc/blasr/5.3/libcpp/pbdata'\r\necho \"Please run 'configure.py' with appropriate args to generate pbdata/libconfig.h\"\r\nPlease run 'configure.py' with appropriate args to generate pbdata/libconfig.h\r\nmake[3]: Leaving directory `/cluster/apps/gdc/blasr/5.3/libcpp/pbdata'\r\nmake -C /cluster/apps/gdc/blasr/5.3/libcpp//pbdata all\r\nmake[3]: Entering directory `/cluster/apps/gdc/blasr/5.3/libcpp/pbdata'\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c CCSSequence.cpp -o CCSSequence.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c ChangeListID.cpp -o ChangeListID.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c CommandLineParser.cpp -o CommandLineParser.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c DNASequence.cpp -o DNASequence.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c FASTAReader.cpp -o FASTAReader.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c FASTASequence.cpp -o FASTASequence.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c FASTQReader.cpp -o FASTQReader.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c FASTQSequence.cpp -o FASTQSequence.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c GFFFile.cpp -o GFFFile.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c MD5Utils.cpp -o MD5Utils.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c NucConversion.cpp -o NucConversion.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c PackedDNASequence.cpp -o PackedDNASequence.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c ReverseCompressIndex.cpp -o ReverseCompressIndex.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c SMRTSequence.cpp -o SMRTSequence.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c StringUtils.cpp -o StringUtils.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c alignment/CmpAlignment.cpp -o CmpAlignment.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c amos/AfgBasWriter.cpp -o AfgBasWriter.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c loadpulses/MetricField.cpp -o MetricField.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c loadpulses/MovieAlnIndexLookupTable.cpp -o MovieAlnIndexLookupTable.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c metagenome/TitleTable.cpp -o TitleTable.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c qvs/QualityTransform.cpp -o QualityTransform.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c qvs/QualityValue.cpp -o QualityValue.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c reads/AcqParams.cpp -o AcqParams.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c reads/BaseFile.cpp -o BaseFile.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c reads/HoleXY.cpp -o HoleXY.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c reads/PulseBaseCommon.cpp -o PulseBaseCommon.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c reads/PulseFile.cpp -o PulseFile.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c reads/ReadType.cpp -o ReadType.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c reads/RegionAnnotation.cpp -o RegionAnnotation.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c reads/RegionAnnotations.cpp -o RegionAnnotations.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c reads/RegionTable.cpp -o RegionTable.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c reads/RegionTypeMap.cpp -o RegionTypeMap.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c reads/ScanData.cpp -o ScanData.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c reads/ZMWGroupEntry.cpp -o ZMWGroupEntry.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c saf/AlnGroup.cpp -o AlnGroup.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c saf/MovieInfo.cpp -o MovieInfo.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c saf/RefGroup.cpp -o RefGroup.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c saf/RefInfo.cpp -o RefInfo.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c sam/ReadGroup.cpp -o ReadGroup.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c sam/ReferenceSequence.cpp -o ReferenceSequence.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c sam/SAMAlignment.cpp -o SAMAlignment.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c sam/SAMHeader.cpp -o SAMHeader.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c sam/SAMKeywordValuePair.cpp -o SAMKeywordValuePair.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c utils/BitUtils.cpp -o BitUtils.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c utils/SMRTReadUtils.cpp -o SMRTReadUtils.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c utils/SMRTTitle.cpp -o SMRTTitle.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -c utils/TimeUtils.cpp -o TimeUtils.o\r\nar rc libpbdata.a CCSSequence.o ChangeListID.o CommandLineParser.o DNASequence.o FASTAReader.o FASTASequence.o FASTQReader.o FASTQSequence.o GFFFile.o MD5Utils.o NucConversion.o PackedDNASequence.o ReverseCompressIndex.o SMRTSequence.o StringUtils.o CmpAlignment.o AfgBasWriter.o MetricField.o MovieAlnIndexLookupTable.o TitleTable.o QualityTransform.o QualityValue.o AcqParams.o BaseFile.o HoleXY.o PulseBaseCommon.o PulseFile.o ReadType.o RegionAnnotation.o RegionAnnotations.o RegionTable.o RegionTypeMap.o ScanData.o ZMWGroupEntry.o AlnGroup.o MovieInfo.o RefGroup.o RefInfo.o ReadGroup.o ReferenceSequence.o SAMAlignment.o SAMHeader.o SAMKeywordValuePair.o BitUtils.o SMRTReadUtils.o SMRTTitle.o TimeUtils.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c CCSSequence.cpp -o CCSSequence.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c ChangeListID.cpp -o ChangeListID.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c CommandLineParser.cpp -o CommandLineParser.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c DNASequence.cpp -o DNASequence.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c FASTAReader.cpp -o FASTAReader.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c FASTASequence.cpp -o FASTASequence.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c FASTQReader.cpp -o FASTQReader.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c FASTQSequence.cpp -o FASTQSequence.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c GFFFile.cpp -o GFFFile.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c MD5Utils.cpp -o MD5Utils.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c NucConversion.cpp -o NucConversion.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c PackedDNASequence.cpp -o PackedDNASequence.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c ReverseCompressIndex.cpp -o ReverseCompressIndex.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c SMRTSequence.cpp -o SMRTSequence.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c StringUtils.cpp -o StringUtils.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c alignment/CmpAlignment.cpp -o CmpAlignment.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c amos/AfgBasWriter.cpp -o AfgBasWriter.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c loadpulses/MetricField.cpp -o MetricField.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c loadpulses/MovieAlnIndexLookupTable.cpp -o MovieAlnIndexLookupTable.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c metagenome/TitleTable.cpp -o TitleTable.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c qvs/QualityTransform.cpp -o QualityTransform.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c qvs/QualityValue.cpp -o QualityValue.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c reads/AcqParams.cpp -o AcqParams.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c reads/BaseFile.cpp -o BaseFile.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c reads/HoleXY.cpp -o HoleXY.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c reads/PulseBaseCommon.cpp -o PulseBaseCommon.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c reads/PulseFile.cpp -o PulseFile.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c reads/ReadType.cpp -o ReadType.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c reads/RegionAnnotation.cpp -o RegionAnnotation.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c reads/RegionAnnotations.cpp -o RegionAnnotations.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c reads/RegionTable.cpp -o RegionTable.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c reads/RegionTypeMap.cpp -o RegionTypeMap.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c reads/ScanData.cpp -o ScanData.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c reads/ZMWGroupEntry.cpp -o ZMWGroupEntry.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c saf/AlnGroup.cpp -o AlnGroup.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c saf/MovieInfo.cpp -o MovieInfo.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c saf/RefGroup.cpp -o RefGroup.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c saf/RefInfo.cpp -o RefInfo.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c sam/ReadGroup.cpp -o ReadGroup.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c sam/ReferenceSequence.cpp -o ReferenceSequence.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c sam/SAMAlignment.cpp -o SAMAlignment.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c sam/SAMHeader.cpp -o SAMHeader.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c sam/SAMKeywordValuePair.cpp -o SAMKeywordValuePair.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c utils/BitUtils.cpp -o BitUtils.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c utils/SMRTReadUtils.cpp -o SMRTReadUtils.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c utils/SMRTTitle.cpp -o SMRTTitle.shared.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra     -fPIC -c utils/TimeUtils.cpp -o TimeUtils.shared.o\r\nmake[3]: Leaving directory `/cluster/apps/gdc/blasr/5.3/libcpp/pbdata'\r\nmake[2]: Leaving directory `/cluster/apps/gdc/blasr/5.3/libcpp'\r\nmake libpbihdf\r\nmake[2]: Entering directory `/cluster/apps/gdc/blasr/5.3/libcpp'\r\nmake -C /cluster/apps/gdc/blasr/5.3/libcpp//hdf all\r\nmake[3]: Entering directory `/cluster/apps/gdc/blasr/5.3/libcpp/hdf'\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual     -c BufferedHDF2DArray.cpp -o BufferedHDF2DArray.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual     -c BufferedHDFArray.cpp -o BufferedHDFArray.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual     -c DatasetCollection.cpp -o DatasetCollection.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual     -c HDFAlnGroupGroup.cpp -o HDFAlnGroupGroup.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual     -c HDFAlnInfoGroup.cpp -o HDFAlnInfoGroup.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual     -c HDFAtom.cpp -o HDFAtom.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual     -c HDFAttributable.cpp -o HDFAttributable.o\r\n/cluster/apps/gcc/4.8.2/bin/g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual     -c HDFBaseCallsWriter.cpp -o HDFBaseCallsWriter.o\r\nHDFBaseCallsWriter.cpp:1:33: fatal error: ../pbdata/libconfig.h: No such file or directory\r\n #include \"../pbdata/libconfig.h\"\r\n                                 ^\r\ncompilation terminated.\r\nmake[3]: *** [HDFBaseCallsWriter.o] Error 1\r\nmake[3]: Leaving directory `/cluster/apps/gdc/blasr/5.3/libcpp/hdf'\r\nmake[2]: *** [libpbihdf] Error 2\r\nmake[2]: Leaving directory `/cluster/apps/gdc/blasr/5.3/libcpp'\r\nmake[1]: *** [all] Error 2\r\nmake[1]: Leaving directory `/cluster/apps/gdc/blasr/5.3/libcpp'\r\nmake: *** [build-submodule] Error 2\r\n[sfux@develop01 5.3]$\r\n```"},"comment":{"url":"https://api.github.com/repos/PacificBiosciences/blasr/issues/comments/394122216","html_url":"https://github.com/PacificBiosciences/blasr/issues/369#issuecomment-394122216","issue_url":"https://api.github.com/repos/PacificBiosciences/blasr/issues/369","id":394122216,"node_id":"MDEyOklzc3VlQ29tbWVudDM5NDEyMjIxNg==","user":{"login":"armintoepfer","id":1433286,"node_id":"MDQ6VXNlcjE0MzMyODY=","avatar_url":"https://avatars3.githubusercontent.com/u/1433286?v=4","gravatar_id":"","url":"https://api.github.com/users/armintoepfer","html_url":"https://github.com/armintoepfer","followers_url":"https://api.github.com/users/armintoepfer/followers","following_url":"https://api.github.com/users/armintoepfer/following{/other_user}","gists_url":"https://api.github.com/users/armintoepfer/gists{/gist_id}","starred_url":"https://api.github.com/users/armintoepfer/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/armintoepfer/subscriptions","organizations_url":"https://api.github.com/users/armintoepfer/orgs","repos_url":"https://api.github.com/users/armintoepfer/repos","events_url":"https://api.github.com/users/armintoepfer/events{/privacy}","received_events_url":"https://api.github.com/users/armintoepfer/received_events","type":"User","site_admin":false},"created_at":"2018-06-02T22:44:58Z","updated_at":"2018-06-02T22:44:58Z","author_association":"MEMBER","body":"We won't support source builds from now on, but provide the latest version on bioconda:\r\n`conda -c bioconda install blasr`"}}
{"actor":{"display_login":"armintoepfer"}}