{"action":"created","issue":{"url":"https://api.github.com/repos/PacificBiosciences/blasr/issues/92","labels_url":"https://api.github.com/repos/PacificBiosciences/blasr/issues/92/labels{/name}","comments_url":"https://api.github.com/repos/PacificBiosciences/blasr/issues/92/comments","events_url":"https://api.github.com/repos/PacificBiosciences/blasr/issues/92/events","html_url":"https://github.com/PacificBiosciences/blasr/issues/92","id":100035186,"number":92,"title":"OSX linking error","user":{"login":"armintoepfer","id":1433286,"avatar_url":"https://avatars.githubusercontent.com/u/1433286?v=3","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},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-08-10T10:54:16Z","updated_at":"2015-08-10T14:58:17Z","closed_at":null,"body":"I get a linking error on OSX 10.10.4 w/ clang, building the submodules.\r\n\r\n```sh\r\nc++ -shared -fPIC -o libpbdata.so -Wl,-soname,libpbdata.so CCSSequence.shared.o ChangeListID.shared.o CommandLineParser.shared.o DNASequence.shared.o FASTAReader.shared.o FASTASequence.shared.o FASTQReader.shared.o FASTQSequence.shared.o GFFFile.shared.o MD5Utils.shared.o NucConversion.shared.o PackedDNASequence.shared.o ReverseCompressIndex.shared.o SMRTSequence.shared.o StringUtils.shared.o reads/BaseFile.shared.o reads/HoleXY.shared.o reads/PulseBaseCommon.shared.o reads/PulseFile.shared.o reads/ReadType.shared.o reads/RegionTable.shared.o reads/ScanData.shared.o reads/ZMWGroupEntry.shared.o metagenome/TitleTable.shared.o qvs/QualityTransform.shared.o qvs/QualityValue.shared.o saf/AlnGroup.shared.o saf/MovieInfo.shared.o saf/RefGroup.shared.o saf/RefInfo.shared.o utils/BitUtils.shared.o utils/SMRTReadUtils.shared.o utils/SMRTTitle.shared.o loadpulses/MetricField.shared.o loadpulses/MovieAlnIndexLookupTable.shared.o alignment/CmpAlignment.shared.o amos/AfgBasWriter.shared.o sam/ReadGroup.shared.o sam/ReferenceSequence.shared.o sam/SAMAlignment.shared.o sam/SAMHeader.shared.o sam/SAMKeywordValuePair.shared.o\r\nld: unknown option: -soname\r\n```\r\n\r\nHere is my blasr/defines.mk:\r\n```sh\r\n$ cat defines.mk\r\nLIBBLASR_LIBFLAGS    ?= -lblasr\r\nSHELL                ?= bash\r\nLIBPBIHDF_INCLUDE    ?= /Users/atoepfer/tools/blasr/libcpp/hdf\r\nDL_LIBFLAGS          ?= -ldl\r\nLIBPBDATA_INCLUDE    ?= /Users/atoepfer/tools/blasr/libcpp/pbdata\r\nLIBPBIHDF_LIBFLAGS   ?= -lpbihdf\r\nLIBPBDATA_LIB        ?= /Users/atoepfer/tools/blasr/libcpp/pbdata\r\nLIBBLASR_INCLUDE     ?= /Users/atoepfer/tools/blasr/libcpp/alignment\r\nLIBBLASR_LIB         ?= /Users/atoepfer/tools/blasr/libcpp/alignment\r\nHDF5_LIB             ?= /usr/local/Cellar/hdf5/1.8.14/lib/\r\nRT_LIBFLAGS          ?= -lrt\r\nHDF5_LIBFLAGS        ?= -lhdf5_cpp -lhdf5\r\nLIBPBDATA_LIBFLAGS   ?= -lpbdata\r\nZLIB_LIBFLAGS        ?= -lz\r\nHDF5_INCLUDE         ?= /usr/local/Cellar/hdf5/1.8.14/include\r\nPTHREAD_LIBFLAGS     ?= -lpthread\r\nLIBPBIHDF_LIB        ?= /Users/atoepfer/tools/blasr/libcpp/hdf\r\nLDFLAGS+=-static\r\n```\r\n\r\nAnd the blasr/libcpp/defines.mk:\r\n```sh\r\n$ cat libcpp/defines.mk\r\n\r\nHDF5_INCLUDE:=/usr/local/Cellar/hdf5/1.8.14/include\r\nHDF5_LIB:=/usr/local/Cellar/hdf5/1.8.14/lib//libhdf5.so\r\n#CPPFLAGS+=-I../pbdata -I../hdf -I../alignment\r\nLIBPBDATA_INCLUDE     ?=../pbdata\r\nLIBPBIHDF_INCLUDE     ?=../hdf\r\nLIBBLASR_INCLUDE      ?=../alignment\r\nLIBPBDATA_LIB     ?=../pbdata/libpbdata.so\r\nLIBPBIHDF_LIB     ?=../hdf/libpbihdf.so\r\nLIBBLASR_LIB      ?=../alignment/libblasr.so\r\n```\r\n\r\nDo you need anything else?"},"comment":{"url":"https://api.github.com/repos/PacificBiosciences/blasr/issues/comments/129481968","html_url":"https://github.com/PacificBiosciences/blasr/issues/92#issuecomment-129481968","issue_url":"https://api.github.com/repos/PacificBiosciences/blasr/issues/92","id":129481968,"user":{"login":"pb-cdunn","id":12086299,"avatar_url":"https://avatars.githubusercontent.com/u/12086299?v=3","gravatar_id":"","url":"https://api.github.com/users/pb-cdunn","html_url":"https://github.com/pb-cdunn","followers_url":"https://api.github.com/users/pb-cdunn/followers","following_url":"https://api.github.com/users/pb-cdunn/following{/other_user}","gists_url":"https://api.github.com/users/pb-cdunn/gists{/gist_id}","starred_url":"https://api.github.com/users/pb-cdunn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pb-cdunn/subscriptions","organizations_url":"https://api.github.com/users/pb-cdunn/orgs","repos_url":"https://api.github.com/users/pb-cdunn/repos","events_url":"https://api.github.com/users/pb-cdunn/events{/privacy}","received_events_url":"https://api.github.com/users/pb-cdunn/received_events","type":"User","site_admin":false},"created_at":"2015-08-10T14:58:17Z","updated_at":"2015-08-10T14:58:17Z","body":"That was needed for mobs.  We can use `-install_name` on OSX, but we'll need to detect OSX. This will take a few minutes....\r\n\r\nBtw, I just got a follow-up note from TravisCI-support about the availability of osx build machines, so we might soon be able to test osx regularly."}}