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fanglab / SMALR

SMALR: a framework for single-molecule level interrogation of the methylation status of SMRT reads.
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Install failure on MacOSX High Sierra #11

Closed yfuruta closed 6 years ago

yfuruta commented 6 years ago

Hi,

I ran install.sh after activating smalr_venv but got the following error. It looks like that it is the error during installing pysam and I posted the issue to pysam user group, but I also would like to post here just in case. Any help is highly appreciated!

Best, Yoshi

Cloning into 'SMALR'...
remote: Counting objects: 275, done.
remote: Compressing objects: 100% (10/10), done.
remote: Total 275 (delta 0), reused 9 (delta 0), pack-reused 265
Receiving objects: 100% (275/275), 38.03 MiB | 6.33 MiB/s, done.
Resolving deltas: 100% (158/158), done.
(smalr_venv) abl-users-imac-3:software Yoshi$ cd SMALR/
(smalr_venv) abl-users-imac-3:SMALR Yoshi$ ls
LICENSE     bin     setup.py    test
README.md   install.sh  smalr
(smalr_venv) abl-users-imac-3:SMALR Yoshi$ ./install.sh 
Installing Python package numpy...
Collecting numpy
  Using cached numpy-1.14.1-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Installing collected packages: numpy
Successfully installed numpy-1.14.1
Installing Python package cython...
Collecting cython
  Using cached Cython-0.27.3-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Installing collected packages: cython
Successfully installed cython-0.27.3
Installing Python package h5py...
Collecting h5py
  Using cached h5py-2.7.1-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting six (from h5py)
  Using cached six-1.11.0-py2.py3-none-any.whl
Requirement already satisfied: numpy>=1.7 in /Users/Yoshi/informatics/software/smalr_venv/lib/python2.7/site-packages (from h5py)
Installing collected packages: six, h5py
Successfully installed h5py-2.7.1 six-1.11.0
Cloning pbcore from https://github.com/PacificBiosciences/pbcore.git
Cloning into 'pbcore'...
remote: Counting objects: 6708, done.
remote: Compressing objects: 100% (24/24), done.
remote: Total 6708 (delta 11), reused 14 (delta 8), pack-reused 6675
Receiving objects: 100% (6708/6708), 40.64 MiB | 6.83 MiB/s, done.
Resolving deltas: 100% (4939/4939), done.
Installing pbcore...
running install
running bdist_egg
running egg_info
creating pbcore.egg-info
writing requirements to pbcore.egg-info/requires.txt
writing pbcore.egg-info/PKG-INFO
writing top-level names to pbcore.egg-info/top_level.txt
writing dependency_links to pbcore.egg-info/dependency_links.txt
writing entry points to pbcore.egg-info/entry_points.txt
writing manifest file 'pbcore.egg-info/SOURCES.txt'
reading manifest file 'pbcore.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'pbcore.egg-info/SOURCES.txt'
installing library code to build/bdist.macosx-10.6-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib
creating build/lib/pbcore
copying ./pbcore/sequence.py -> build/lib/pbcore
copying ./pbcore/__init__.py -> build/lib/pbcore
creating build/lib/pbcore/util
copying ./pbcore/util/__init__.py -> build/lib/pbcore/util
copying ./pbcore/util/ToolRunner.py -> build/lib/pbcore/util
copying ./pbcore/util/Process.py -> build/lib/pbcore/util
copying ./pbcore/util/decorators.py -> build/lib/pbcore/util
creating build/lib/pbcore/chemistry
copying ./pbcore/chemistry/__init__.py -> build/lib/pbcore/chemistry
copying ./pbcore/chemistry/chemistry.py -> build/lib/pbcore/chemistry
creating build/lib/pbcore/io
copying ./pbcore/io/VcfIO.py -> build/lib/pbcore/io
copying ./pbcore/io/FofnIO.py -> build/lib/pbcore/io
copying ./pbcore/io/rangeQueries.py -> build/lib/pbcore/io
copying ./pbcore/io/BasH5IO.py -> build/lib/pbcore/io
copying ./pbcore/io/opener.py -> build/lib/pbcore/io
copying ./pbcore/io/__init__.py -> build/lib/pbcore/io
copying ./pbcore/io/FastaIO.py -> build/lib/pbcore/io
copying ./pbcore/io/GffIO.py -> build/lib/pbcore/io
copying ./pbcore/io/FastqIO.py -> build/lib/pbcore/io
copying ./pbcore/io/BarcodeH5Reader.py -> build/lib/pbcore/io
copying ./pbcore/io/base.py -> build/lib/pbcore/io
copying ./pbcore/io/_utils.py -> build/lib/pbcore/io
creating build/lib/pbcore/model
copying ./pbcore/model/__init__.py -> build/lib/pbcore/model
copying ./pbcore/model/baseRegions.py -> build/lib/pbcore/model
creating build/lib/pbcore/data
copying ./pbcore/data/__init__.py -> build/lib/pbcore/data
creating build/lib/pbcore/io/dataset
copying ./pbcore/io/dataset/DataSetReader.py -> build/lib/pbcore/io/dataset
copying ./pbcore/io/dataset/DataSetWriter.py -> build/lib/pbcore/io/dataset
copying ./pbcore/io/dataset/DataSetIO.py -> build/lib/pbcore/io/dataset
copying ./pbcore/io/dataset/DataSetErrors.py -> build/lib/pbcore/io/dataset
copying ./pbcore/io/dataset/DataSetValidator.py -> build/lib/pbcore/io/dataset
copying ./pbcore/io/dataset/__init__.py -> build/lib/pbcore/io/dataset
copying ./pbcore/io/dataset/DataSetUtils.py -> build/lib/pbcore/io/dataset
copying ./pbcore/io/dataset/utils.py -> build/lib/pbcore/io/dataset
copying ./pbcore/io/dataset/DataSetMetaTypes.py -> build/lib/pbcore/io/dataset
copying ./pbcore/io/dataset/DataSetMembers.py -> build/lib/pbcore/io/dataset
creating build/lib/pbcore/io/align
copying ./pbcore/io/align/BlasrIO.py -> build/lib/pbcore/io/align
copying ./pbcore/io/align/_AlignmentMixin.py -> build/lib/pbcore/io/align
copying ./pbcore/io/align/__init__.py -> build/lib/pbcore/io/align
copying ./pbcore/io/align/BamIO.py -> build/lib/pbcore/io/align
copying ./pbcore/io/align/CmpH5IO.py -> build/lib/pbcore/io/align
copying ./pbcore/io/align/_bgzf.py -> build/lib/pbcore/io/align
copying ./pbcore/io/align/PacBioBamIndex.py -> build/lib/pbcore/io/align
copying ./pbcore/io/align/_BamSupport.py -> build/lib/pbcore/io/align
copying ./pbcore/io/align/BamAlignment.py -> build/lib/pbcore/io/align
creating build/lib/pbcore/io/dataset/pyxb
copying ./pbcore/io/dataset/pyxb/_pbpn.py -> build/lib/pbcore/io/dataset/pyxb
copying ./pbcore/io/dataset/pyxb/_pbrk.py -> build/lib/pbcore/io/dataset/pyxb
copying ./pbcore/io/dataset/pyxb/_pbds.py -> build/lib/pbcore/io/dataset/pyxb
copying ./pbcore/io/dataset/pyxb/_pbmeta.py -> build/lib/pbcore/io/dataset/pyxb
copying ./pbcore/io/dataset/pyxb/_pbbase.py -> build/lib/pbcore/io/dataset/pyxb
copying ./pbcore/io/dataset/pyxb/__init__.py -> build/lib/pbcore/io/dataset/pyxb
copying ./pbcore/io/dataset/pyxb/DataSetXsd.py -> build/lib/pbcore/io/dataset/pyxb
copying ./pbcore/io/dataset/pyxb/_pbsample.py -> build/lib/pbcore/io/dataset/pyxb
creating build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/__init__.py -> build/lib/pbcore/data/datasets
copying ./pbcore/data/m140912_020930_00114_c100702482550000001823141103261590_s1_p0.2.bax.h5 -> build/lib/pbcore/data
copying ./pbcore/data/m130731_192718_42129_c100564662550000001823085912221321_s1_p0.bas.h5 -> build/lib/pbcore/data
copying ./pbcore/data/m140307_221913_42203_c100626172550000001823119008061414_s1_p0.1.bc.h5 -> build/lib/pbcore/data
copying ./pbcore/data/m140307_221913_42203_c100626172550000001823119008061414_s1_p0.3.bc.h5 -> build/lib/pbcore/data
copying ./pbcore/data/m130731_192718_42129_c100564662550000001823085912221321_s1_p0.2.rgn.h5 -> build/lib/pbcore/data
copying ./pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.1.bax.h5 -> build/lib/pbcore/data
copying ./pbcore/data/m140307_221913_42203_c100626172550000001823119008061414_s1_p0.2.bc.h5 -> build/lib/pbcore/data
copying ./pbcore/data/m130731_192718_42129_c100564662550000001823085912221321_s1_p0.1.bax.h5 -> build/lib/pbcore/data
copying ./pbcore/data/m110818_075520_42141_c100129202555500000315043109121112_s2_p0.bas.h5 -> build/lib/pbcore/data
copying ./pbcore/data/m130731_192718_42129_c100564662550000001823085912221321_s1_p0.3.bax.h5 -> build/lib/pbcore/data
copying ./pbcore/data/m130522_092457_42208_c100497142550000001823078008081323_s1_p0.2.bax.h5 -> build/lib/pbcore/data
copying ./pbcore/data/m110818_075520_42141_c100129202555500000315043109121112_s1_p0.bas.h5 -> build/lib/pbcore/data
copying ./pbcore/data/m130731_192718_42129_c100564662550000001823085912221321_s1_p0.1.rgn.h5 -> build/lib/pbcore/data
copying ./pbcore/data/m140912_020930_00114_c100702482550000001823141103261590_s1_p0.3.bax.h5 -> build/lib/pbcore/data
copying ./pbcore/data/m130731_192718_42129_c100564662550000001823085912221321_s1_p0.3.rgn.h5 -> build/lib/pbcore/data
copying ./pbcore/data/m140912_020930_00114_c100702482550000001823141103261590_s1_p0.1.bax.h5 -> build/lib/pbcore/data
copying ./pbcore/data/m130727_114215_42211_c100569412550000001823090301191423_s1_p0.1.ccs.h5 -> build/lib/pbcore/data
copying ./pbcore/data/m140912_020930_00114_c100702482550000001823141103261590_s1_p0.bas.h5 -> build/lib/pbcore/data
copying ./pbcore/data/m130522_092457_42208_c100497142550000001823078008081323_s1_p0.1.bax.h5 -> build/lib/pbcore/data
copying ./pbcore/data/m130522_092457_42208_c100497142550000001823078008081323_s1_p0.3.bax.h5 -> build/lib/pbcore/data
copying ./pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.cmp.h5 -> build/lib/pbcore/data
copying ./pbcore/data/m130731_192718_42129_c100564662550000001823085912221321_s1_p0.2.bax.h5 -> build/lib/pbcore/data
copying ./pbcore/data/aligned_reads_1.cmp.h5 -> build/lib/pbcore/data
copying ./pbcore/data/m130522_092457_42208_c100497142550000001823078008081323_s1_p0.bas.h5 -> build/lib/pbcore/data
copying ./pbcore/data/variants.gff -> build/lib/pbcore/data
copying ./pbcore/data/barcodes-ed65-450.fasta -> build/lib/pbcore/data
copying ./pbcore/data/Fluidigm_human_amplicons.fasta -> build/lib/pbcore/data
copying ./pbcore/data/Fluidigm_human_amplicons_tiny.fasta -> build/lib/pbcore/data
copying ./pbcore/data/Fluidigm_human_amplicons.fasta.fai -> build/lib/pbcore/data
copying ./pbcore/data/barcodes-ed65-450.fasta.fai -> build/lib/pbcore/data
copying ./pbcore/data/1.4_bas_files.fofn -> build/lib/pbcore/data
copying ./pbcore/data/2.3_bax_files.fofn -> build/lib/pbcore/data
copying ./pbcore/data/bc_files.fofn -> build/lib/pbcore/data
copying ./pbcore/data/2.1_ccs_files.fofn -> build/lib/pbcore/data
copying ./pbcore/data/2.0_bax_files.fofn -> build/lib/pbcore/data
copying ./pbcore/data/2.1_bax_files.fofn -> build/lib/pbcore/data
copying ./pbcore/data/blasr-output.m4 -> build/lib/pbcore/data
copying ./pbcore/data/weird.fa -> build/lib/pbcore/data
copying ./pbcore/data/lambdaNEB.fa -> build/lib/pbcore/data
copying ./pbcore/data/weird.fa.fai -> build/lib/pbcore/data
copying ./pbcore/data/lambdaNEB.fa.fai -> build/lib/pbcore/data
copying ./pbcore/data/blasr-output.m5 -> build/lib/pbcore/data
copying ./pbcore/data/empty.aligned_subreads.bam -> build/lib/pbcore/data
copying ./pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.bam -> build/lib/pbcore/data
copying ./pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.bam -> build/lib/pbcore/data
copying ./pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.scraps.bam -> build/lib/pbcore/data
copying ./pbcore/data/empty.ccs.bam -> build/lib/pbcore/data
copying ./pbcore/data/m130727_114215_42211_c100569412550000001823090301191423_s1_p0.ccs.bam -> build/lib/pbcore/data
copying ./pbcore/data/m130727_114215_42211_c100569412550000001823090301191423_s1_p0.ccs.bam.bai -> build/lib/pbcore/data
copying ./pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.bam.bai -> build/lib/pbcore/data
copying ./pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.scraps.bam.pbi -> build/lib/pbcore/data
copying ./pbcore/data/empty.ccs.bam.pbi -> build/lib/pbcore/data
copying ./pbcore/data/empty.aligned_subreads.bam.pbi -> build/lib/pbcore/data
copying ./pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.bam.pbi -> build/lib/pbcore/data
copying ./pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.bam.pbi -> build/lib/pbcore/data
copying ./pbcore/data/m130727_114215_42211_c100569412550000001823090301191423_s1_p0.ccs.bam.pbi -> build/lib/pbcore/data
copying ./pbcore/data/chemistry.xml -> build/lib/pbcore/data
creating build/lib/pbcore/chemistry/resources
copying ./pbcore/chemistry/resources/mapping.xml -> build/lib/pbcore/chemistry/resources
copying ./pbcore/data/datasets/pbalchemysim0.referenceset.xml -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.fake_bc.bam -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/pbalchemysim0.hdfsubreadset.xml -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/fofn.fofn -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.fake_bc.bam.bai -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/pbalchemysim0.subreadset.xml -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/pbalchemysim.hdfsubreadset.xml -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/transformed_rs_subread.dataset.xml -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/pbalchemysim1.subreadset.xml -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/pbalchemysim0.reference.fasta -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/contig.dataset.xml -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/pbalchemysim1.hdfsubreadset.xml -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.fake_bc.bam.pbi -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/pbalchemysim0.pbalign.bam -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/m150430_142051_Mon_p1_b25.sts.xml -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/pbalchemysim1.alignmentset.xml -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/reference.dataset.xml -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/pbalchemysim0.alignmentset.chunk1contigs.xml -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/m150616_053259_ethan_c100710482550000001823136404221563_s1_p0.sts.xml -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/subread.dataset.xml -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/pbalchemysim0.bas.h5 -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/ccsaligned.dataset.xml -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/pbalchemysim0.alignmentset.xml -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/pbalchemysim.alignmentset.xml -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/pbalchemysim0.reference.fasta.fai -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/pbalchemysim0.pbalign.bam.bai -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/pbalchemysim1.pbalign.bam -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/lambda.referenceset.xml -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/hdfsubread_dataset.xml -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/pbalchemysim1.subreads.bam.pbi -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/alignment.dataset.xml -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/pbalchemysim1.subreads.bam.bai -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/barcode.dataset.xml -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/pbalchemysim0.pbalign.bam.pbi -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/ccsread.dataset.xml -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/subreadSetWithStats.xml -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/pbalchemysim0.subreads.bam.pbi -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/pbalchemysim0.subreads.bam -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/empty_lambda.aligned.bam -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/empty_lambda.aligned.bam.pbi -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/pbalchemysim1.pbalign.bam.pbi -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/pbalchemysim0.alignmentset.chunk0contigs.xml -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/empty_lambda.aligned.bam.bai -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/pbalchemysim1.pbalign.bam.bai -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/lambda.alignmentset.xml -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/pbalchemysim1.bas.h5 -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/pbalchemysim0.subreads.bam.bai -> build/lib/pbcore/data/datasets
copying ./pbcore/data/datasets/pbalchemysim1.subreads.bam -> build/lib/pbcore/data/datasets
creating build/bdist.macosx-10.6-x86_64
creating build/bdist.macosx-10.6-x86_64/egg
creating build/bdist.macosx-10.6-x86_64/egg/pbcore
creating build/bdist.macosx-10.6-x86_64/egg/pbcore/util
copying build/lib/pbcore/util/__init__.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/util
copying build/lib/pbcore/util/ToolRunner.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/util
copying build/lib/pbcore/util/Process.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/util
copying build/lib/pbcore/util/decorators.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/util
creating build/bdist.macosx-10.6-x86_64/egg/pbcore/chemistry
creating build/bdist.macosx-10.6-x86_64/egg/pbcore/chemistry/resources
copying build/lib/pbcore/chemistry/resources/mapping.xml -> build/bdist.macosx-10.6-x86_64/egg/pbcore/chemistry/resources
copying build/lib/pbcore/chemistry/__init__.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/chemistry
copying build/lib/pbcore/chemistry/chemistry.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/chemistry
copying build/lib/pbcore/sequence.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore
creating build/bdist.macosx-10.6-x86_64/egg/pbcore/io
copying build/lib/pbcore/io/VcfIO.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/io
copying build/lib/pbcore/io/FofnIO.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/io
copying build/lib/pbcore/io/rangeQueries.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/io
copying build/lib/pbcore/io/BasH5IO.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/io
copying build/lib/pbcore/io/opener.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/io
creating build/bdist.macosx-10.6-x86_64/egg/pbcore/io/dataset
copying build/lib/pbcore/io/dataset/DataSetReader.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/io/dataset
copying build/lib/pbcore/io/dataset/DataSetWriter.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/io/dataset
copying build/lib/pbcore/io/dataset/DataSetIO.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/io/dataset
copying build/lib/pbcore/io/dataset/DataSetErrors.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/io/dataset
copying build/lib/pbcore/io/dataset/DataSetValidator.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/io/dataset
copying build/lib/pbcore/io/dataset/__init__.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/io/dataset
creating build/bdist.macosx-10.6-x86_64/egg/pbcore/io/dataset/pyxb
copying build/lib/pbcore/io/dataset/pyxb/_pbpn.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/io/dataset/pyxb
copying build/lib/pbcore/io/dataset/pyxb/_pbrk.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/io/dataset/pyxb
copying build/lib/pbcore/io/dataset/pyxb/_pbds.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/io/dataset/pyxb
copying build/lib/pbcore/io/dataset/pyxb/_pbmeta.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/io/dataset/pyxb
copying build/lib/pbcore/io/dataset/pyxb/_pbbase.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/io/dataset/pyxb
copying build/lib/pbcore/io/dataset/pyxb/__init__.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/io/dataset/pyxb
copying build/lib/pbcore/io/dataset/pyxb/DataSetXsd.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/io/dataset/pyxb
copying build/lib/pbcore/io/dataset/pyxb/_pbsample.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/io/dataset/pyxb
copying build/lib/pbcore/io/dataset/DataSetUtils.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/io/dataset
copying build/lib/pbcore/io/dataset/utils.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/io/dataset
copying build/lib/pbcore/io/dataset/DataSetMetaTypes.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/io/dataset
copying build/lib/pbcore/io/dataset/DataSetMembers.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/io/dataset
copying build/lib/pbcore/io/__init__.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/io
copying build/lib/pbcore/io/FastaIO.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/io
copying build/lib/pbcore/io/GffIO.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/io
creating build/bdist.macosx-10.6-x86_64/egg/pbcore/io/align
copying build/lib/pbcore/io/align/BlasrIO.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/io/align
copying build/lib/pbcore/io/align/_AlignmentMixin.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/io/align
copying build/lib/pbcore/io/align/__init__.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/io/align
copying build/lib/pbcore/io/align/BamIO.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/io/align
copying build/lib/pbcore/io/align/CmpH5IO.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/io/align
copying build/lib/pbcore/io/align/_bgzf.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/io/align
copying build/lib/pbcore/io/align/PacBioBamIndex.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/io/align
copying build/lib/pbcore/io/align/_BamSupport.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/io/align
copying build/lib/pbcore/io/align/BamAlignment.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/io/align
copying build/lib/pbcore/io/FastqIO.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/io
copying build/lib/pbcore/io/BarcodeH5Reader.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/io
copying build/lib/pbcore/io/base.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/io
copying build/lib/pbcore/io/_utils.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/io
copying build/lib/pbcore/__init__.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore
creating build/bdist.macosx-10.6-x86_64/egg/pbcore/model
copying build/lib/pbcore/model/__init__.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/model
copying build/lib/pbcore/model/baseRegions.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/model
creating build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/blasr-output.m5 -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/m140912_020930_00114_c100702482550000001823141103261590_s1_p0.2.bax.h5 -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/m130731_192718_42129_c100564662550000001823085912221321_s1_p0.bas.h5 -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/empty.aligned_subreads.bam -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/m140307_221913_42203_c100626172550000001823119008061414_s1_p0.1.bc.h5 -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/m140307_221913_42203_c100626172550000001823119008061414_s1_p0.3.bc.h5 -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/1.4_bas_files.fofn -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/blasr-output.m4 -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/weird.fa -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/2.3_bax_files.fofn -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/barcodes-ed65-450.fasta -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/bc_files.fofn -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/m130731_192718_42129_c100564662550000001823085912221321_s1_p0.2.rgn.h5 -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.1.bax.h5 -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/Fluidigm_human_amplicons.fasta.fai -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/m140307_221913_42203_c100626172550000001823119008061414_s1_p0.2.bc.h5 -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/m130731_192718_42129_c100564662550000001823085912221321_s1_p0.1.bax.h5 -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/2.1_ccs_files.fofn -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/m110818_075520_42141_c100129202555500000315043109121112_s2_p0.bas.h5 -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.bam -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/2.0_bax_files.fofn -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.scraps.bam.pbi -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/chemistry.xml -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
creating build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/pbalchemysim0.referenceset.xml -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.fake_bc.bam -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/pbalchemysim0.hdfsubreadset.xml -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/fofn.fofn -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.fake_bc.bam.bai -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/pbalchemysim0.subreadset.xml -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/pbalchemysim.hdfsubreadset.xml -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/transformed_rs_subread.dataset.xml -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/pbalchemysim1.subreadset.xml -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/pbalchemysim0.reference.fasta -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/contig.dataset.xml -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/pbalchemysim1.hdfsubreadset.xml -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.fake_bc.bam.pbi -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/pbalchemysim0.pbalign.bam -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/m150430_142051_Mon_p1_b25.sts.xml -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/pbalchemysim1.alignmentset.xml -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/reference.dataset.xml -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/pbalchemysim0.alignmentset.chunk1contigs.xml -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/m150616_053259_ethan_c100710482550000001823136404221563_s1_p0.sts.xml -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/__init__.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/subread.dataset.xml -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/pbalchemysim0.bas.h5 -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/ccsaligned.dataset.xml -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/pbalchemysim0.alignmentset.xml -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/pbalchemysim.alignmentset.xml -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/pbalchemysim0.reference.fasta.fai -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/pbalchemysim0.pbalign.bam.bai -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/pbalchemysim1.pbalign.bam -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/lambda.referenceset.xml -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/hdfsubread_dataset.xml -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/pbalchemysim1.subreads.bam.pbi -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/alignment.dataset.xml -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/pbalchemysim1.subreads.bam.bai -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/barcode.dataset.xml -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/pbalchemysim0.pbalign.bam.pbi -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/ccsread.dataset.xml -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/subreadSetWithStats.xml -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/pbalchemysim0.subreads.bam.pbi -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/pbalchemysim0.subreads.bam -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/empty_lambda.aligned.bam -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/empty_lambda.aligned.bam.pbi -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/pbalchemysim1.pbalign.bam.pbi -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/pbalchemysim0.alignmentset.chunk0contigs.xml -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/empty_lambda.aligned.bam.bai -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/pbalchemysim1.pbalign.bam.bai -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/lambda.alignmentset.xml -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/pbalchemysim1.bas.h5 -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/pbalchemysim0.subreads.bam.bai -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/datasets/pbalchemysim1.subreads.bam -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets
copying build/lib/pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.bam -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/__init__.py -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/2.1_bax_files.fofn -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/empty.ccs.bam.pbi -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/m130731_192718_42129_c100564662550000001823085912221321_s1_p0.3.bax.h5 -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/m130522_092457_42208_c100497142550000001823078008081323_s1_p0.2.bax.h5 -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/barcodes-ed65-450.fasta.fai -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/m110818_075520_42141_c100129202555500000315043109121112_s1_p0.bas.h5 -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/empty.aligned_subreads.bam.pbi -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/lambdaNEB.fa -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/weird.fa.fai -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.bam.pbi -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/m130731_192718_42129_c100564662550000001823085912221321_s1_p0.1.rgn.h5 -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/lambdaNEB.fa.fai -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.scraps.bam -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/m140912_020930_00114_c100702482550000001823141103261590_s1_p0.3.bax.h5 -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/m130731_192718_42129_c100564662550000001823085912221321_s1_p0.3.rgn.h5 -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/m140912_020930_00114_c100702482550000001823141103261590_s1_p0.1.bax.h5 -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/m130727_114215_42211_c100569412550000001823090301191423_s1_p0.1.ccs.h5 -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/empty.ccs.bam -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/m140912_020930_00114_c100702482550000001823141103261590_s1_p0.bas.h5 -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/Fluidigm_human_amplicons.fasta -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/Fluidigm_human_amplicons_tiny.fasta -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/variants.gff -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.bam.pbi -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/m130727_114215_42211_c100569412550000001823090301191423_s1_p0.ccs.bam -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/m130522_092457_42208_c100497142550000001823078008081323_s1_p0.1.bax.h5 -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/m130727_114215_42211_c100569412550000001823090301191423_s1_p0.ccs.bam.pbi -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/m130522_092457_42208_c100497142550000001823078008081323_s1_p0.3.bax.h5 -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/m130727_114215_42211_c100569412550000001823090301191423_s1_p0.ccs.bam.bai -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.cmp.h5 -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/m130731_192718_42129_c100564662550000001823085912221321_s1_p0.2.bax.h5 -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/aligned_reads_1.cmp.h5 -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.bam.bai -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
copying build/lib/pbcore/data/m130522_092457_42208_c100497142550000001823078008081323_s1_p0.bas.h5 -> build/bdist.macosx-10.6-x86_64/egg/pbcore/data
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/util/__init__.py to __init__.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/util/ToolRunner.py to ToolRunner.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/util/Process.py to Process.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/util/decorators.py to decorators.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/chemistry/__init__.py to __init__.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/chemistry/chemistry.py to chemistry.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/sequence.py to sequence.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/io/VcfIO.py to VcfIO.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/io/FofnIO.py to FofnIO.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/io/rangeQueries.py to rangeQueries.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/io/BasH5IO.py to BasH5IO.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/io/opener.py to opener.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/io/dataset/DataSetReader.py to DataSetReader.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/io/dataset/DataSetWriter.py to DataSetWriter.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/io/dataset/DataSetIO.py to DataSetIO.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/io/dataset/DataSetErrors.py to DataSetErrors.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/io/dataset/DataSetValidator.py to DataSetValidator.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/io/dataset/__init__.py to __init__.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/io/dataset/pyxb/_pbpn.py to _pbpn.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/io/dataset/pyxb/_pbrk.py to _pbrk.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/io/dataset/pyxb/_pbds.py to _pbds.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/io/dataset/pyxb/_pbmeta.py to _pbmeta.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/io/dataset/pyxb/_pbbase.py to _pbbase.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/io/dataset/pyxb/__init__.py to __init__.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/io/dataset/pyxb/DataSetXsd.py to DataSetXsd.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/io/dataset/pyxb/_pbsample.py to _pbsample.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/io/dataset/DataSetUtils.py to DataSetUtils.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/io/dataset/utils.py to utils.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/io/dataset/DataSetMetaTypes.py to DataSetMetaTypes.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/io/dataset/DataSetMembers.py to DataSetMembers.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/io/__init__.py to __init__.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/io/FastaIO.py to FastaIO.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/io/GffIO.py to GffIO.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/io/align/BlasrIO.py to BlasrIO.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/io/align/_AlignmentMixin.py to _AlignmentMixin.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/io/align/__init__.py to __init__.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/io/align/BamIO.py to BamIO.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/io/align/CmpH5IO.py to CmpH5IO.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/io/align/_bgzf.py to _bgzf.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/io/align/PacBioBamIndex.py to PacBioBamIndex.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/io/align/_BamSupport.py to _BamSupport.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/io/align/BamAlignment.py to BamAlignment.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/io/FastqIO.py to FastqIO.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/io/BarcodeH5Reader.py to BarcodeH5Reader.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/io/base.py to base.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/io/_utils.py to _utils.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/__init__.py to __init__.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/model/__init__.py to __init__.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/model/baseRegions.py to baseRegions.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/data/datasets/__init__.py to __init__.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/pbcore/data/__init__.py to __init__.pyc
creating build/bdist.macosx-10.6-x86_64/egg/EGG-INFO
copying pbcore.egg-info/PKG-INFO -> build/bdist.macosx-10.6-x86_64/egg/EGG-INFO
copying pbcore.egg-info/SOURCES.txt -> build/bdist.macosx-10.6-x86_64/egg/EGG-INFO
copying pbcore.egg-info/dependency_links.txt -> build/bdist.macosx-10.6-x86_64/egg/EGG-INFO
copying pbcore.egg-info/entry_points.txt -> build/bdist.macosx-10.6-x86_64/egg/EGG-INFO
copying pbcore.egg-info/not-zip-safe -> build/bdist.macosx-10.6-x86_64/egg/EGG-INFO
copying pbcore.egg-info/requires.txt -> build/bdist.macosx-10.6-x86_64/egg/EGG-INFO
copying pbcore.egg-info/top_level.txt -> build/bdist.macosx-10.6-x86_64/egg/EGG-INFO
creating dist
creating 'dist/pbcore-1.4.2-py2.7.egg' and adding 'build/bdist.macosx-10.6-x86_64/egg' to it
removing 'build/bdist.macosx-10.6-x86_64/egg' (and everything under it)
Processing pbcore-1.4.2-py2.7.egg
creating /Users/Yoshi/informatics/software/smalr_venv/lib/python2.7/site-packages/pbcore-1.4.2-py2.7.egg
Extracting pbcore-1.4.2-py2.7.egg to /Users/Yoshi/informatics/software/smalr_venv/lib/python2.7/site-packages
Adding pbcore 1.4.2 to easy-install.pth file
Installing .open script to /Users/Yoshi/informatics/software/smalr_venv/bin

Installed /Users/Yoshi/informatics/software/smalr_venv/lib/python2.7/site-packages/pbcore-1.4.2-py2.7.egg
Processing dependencies for pbcore==1.4.2
Searching for pysam>=0.9.0
Reading https://pypi.python.org/simple/pysam/
Downloading https://pypi.python.org/packages/d8/78/8b3fad13d3bd8787c0d922056061727c2a0cf91c45a836c98342594dd293/pysam-0.14.tar.gz#md5=fb187f3fb005ec21f8a844b3a53d7e38
Best match: pysam 0.14
Processing pysam-0.14.tar.gz
Writing /var/folders/55/s9g3y_713q7cs2gcfhmkm6qm0000gn/T/easy_install-D7k3GR/pysam-0.14/setup.cfg
Running pysam-0.14/setup.py -q bdist_egg --dist-dir /var/folders/55/s9g3y_713q7cs2gcfhmkm6qm0000gn/T/easy_install-D7k3GR/pysam-0.14/egg-dist-tmp-l4hiAl
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is shared
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
checking for gcc... gcc
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 gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking for grep that handles long lines and -e... /usr/bin/grep
checking for C compiler warning flags... -Wall
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for _LARGEFILE_SOURCE value needed for large files... no
checking shared library type for unknown-Darwin... Darwin dylib
checking how to run the C preprocessor... gcc -E
checking for egrep... /usr/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 for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking whether fdatasync is declared... no
checking for library containing log... none required
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing recv... none required
checking for bzlib.h... yes
checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
checking for lzma.h... yes
checking for lzma_easy_buffer_encode in -llzma... yes
checking for curl_easy_pause in -lcurl... yes
checking for CCHmac... yes
checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes
configure: creating ./config.status
config.status: creating config.mk
config.status: creating htslib.pc.tmp
config.status: creating config.h
# pysam: htslib configure options: --enable-libcurl
make: ./version.sh: Command not found
make: ./version.sh: Command not found
# pysam: htslib_config LIBS=-llzma -lbz2 -lz -lcurl
# pysam: htslib_config PLATFORM=Darwin
# pysam: htslib_config LIBHTS_OBJS=kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o hfile_libcurl.o hfile_gcs.o hfile_s3.o
# pysam: htslib_config LDFLAGS=
# pysam: config_option: ENABLE_PLUGINS=0
# pysam: config_option: HAVE_COMMONCRYPTO=1
# pysam: config_option: HAVE_GMTIME_R=1
# pysam: config_option: HAVE_HMAC=0
# pysam: config_option: HAVE_IRODS=0
# pysam: config_option: HAVE_LIBCURL=1
# pysam: config_option: HAVE_MMAP=1
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'bcftools/__init__.py' not found (or not a regular file)
package init file 'samtools/win32/__init__.py' not found (or not a regular file)
package init file 'htslib/__init__.py' not found (or not a regular file)
package init file 'htslib/htslib/__init__.py' not found (or not a regular file)
warning: no files found matching 'KNOWN_BUGS'
warning: no files found matching 'THANKS'
warning: no files found matching 'samtools/configure'
warning: no files found matching 'samtools/config.mk.in'
warning: no files found matching 'samtools/config.h.in'
warning: no files found matching 'htslib/win/*.c'
warning: no files found matching 'htslib/win/*.h'

gcc: error: @loader_path: No such file or directory
gcc: error: unrecognized command line option '-rpath'
error: Setup script exited with error: command 'gcc' failed with exit status 1

Installing SMALR...
running install
running bdist_egg
running egg_info
creating smalr.egg-info
writing requirements to smalr.egg-info/requires.txt
writing smalr.egg-info/PKG-INFO
writing top-level names to smalr.egg-info/top_level.txt
writing dependency_links to smalr.egg-info/dependency_links.txt
writing manifest file 'smalr.egg-info/SOURCES.txt'
reading manifest file 'smalr.egg-info/SOURCES.txt'
writing manifest file 'smalr.egg-info/SOURCES.txt'
installing library code to build/bdist.macosx-10.6-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib
creating build/lib/smalr
copying smalr/smalr_multicontig.py -> build/lib/smalr
copying smalr/CCS_aligner.py -> build/lib/smalr
copying smalr/smalr.py -> build/lib/smalr
copying smalr/__init__.py -> build/lib/smalr
copying smalr/sam_parser.py -> build/lib/smalr
copying smalr/SmalrConfig.py -> build/lib/smalr
copying smalr/parse_mol_aligns.py -> build/lib/smalr
creating build/lib/smalr/R
copying smalr/R/call_motifFinder.r -> build/lib/smalr/R
copying smalr/R/motifFinder.r -> build/lib/smalr/R
creating build/bdist.macosx-10.6-x86_64
creating build/bdist.macosx-10.6-x86_64/egg
creating build/bdist.macosx-10.6-x86_64/egg/smalr
copying build/lib/smalr/smalr_multicontig.py -> build/bdist.macosx-10.6-x86_64/egg/smalr
copying build/lib/smalr/CCS_aligner.py -> build/bdist.macosx-10.6-x86_64/egg/smalr
creating build/bdist.macosx-10.6-x86_64/egg/smalr/R
copying build/lib/smalr/R/call_motifFinder.r -> build/bdist.macosx-10.6-x86_64/egg/smalr/R
copying build/lib/smalr/R/motifFinder.r -> build/bdist.macosx-10.6-x86_64/egg/smalr/R
copying build/lib/smalr/smalr.py -> build/bdist.macosx-10.6-x86_64/egg/smalr
copying build/lib/smalr/__init__.py -> build/bdist.macosx-10.6-x86_64/egg/smalr
copying build/lib/smalr/sam_parser.py -> build/bdist.macosx-10.6-x86_64/egg/smalr
copying build/lib/smalr/SmalrConfig.py -> build/bdist.macosx-10.6-x86_64/egg/smalr
copying build/lib/smalr/parse_mol_aligns.py -> build/bdist.macosx-10.6-x86_64/egg/smalr
byte-compiling build/bdist.macosx-10.6-x86_64/egg/smalr/smalr_multicontig.py to smalr_multicontig.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/smalr/CCS_aligner.py to CCS_aligner.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/smalr/smalr.py to smalr.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/smalr/__init__.py to __init__.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/smalr/sam_parser.py to sam_parser.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/smalr/SmalrConfig.py to SmalrConfig.pyc
byte-compiling build/bdist.macosx-10.6-x86_64/egg/smalr/parse_mol_aligns.py to parse_mol_aligns.pyc
creating build/bdist.macosx-10.6-x86_64/egg/EGG-INFO
installing scripts to build/bdist.macosx-10.6-x86_64/egg/EGG-INFO/scripts
running install_scripts
running build_scripts
creating build/scripts-2.7
copying bin/smalr -> build/scripts-2.7
copying and adjusting bin/call_smalr.py -> build/scripts-2.7
changing mode of build/scripts-2.7/smalr from 644 to 755
changing mode of build/scripts-2.7/call_smalr.py from 644 to 755
creating build/bdist.macosx-10.6-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/smalr -> build/bdist.macosx-10.6-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/call_smalr.py -> build/bdist.macosx-10.6-x86_64/egg/EGG-INFO/scripts
changing mode of build/bdist.macosx-10.6-x86_64/egg/EGG-INFO/scripts/smalr to 755
changing mode of build/bdist.macosx-10.6-x86_64/egg/EGG-INFO/scripts/call_smalr.py to 755
copying smalr.egg-info/PKG-INFO -> build/bdist.macosx-10.6-x86_64/egg/EGG-INFO
copying smalr.egg-info/SOURCES.txt -> build/bdist.macosx-10.6-x86_64/egg/EGG-INFO
copying smalr.egg-info/dependency_links.txt -> build/bdist.macosx-10.6-x86_64/egg/EGG-INFO
copying smalr.egg-info/not-zip-safe -> build/bdist.macosx-10.6-x86_64/egg/EGG-INFO
copying smalr.egg-info/requires.txt -> build/bdist.macosx-10.6-x86_64/egg/EGG-INFO
copying smalr.egg-info/top_level.txt -> build/bdist.macosx-10.6-x86_64/egg/EGG-INFO
creating dist
creating 'dist/smalr-1.0.1-py2.7.egg' and adding 'build/bdist.macosx-10.6-x86_64/egg' to it
removing 'build/bdist.macosx-10.6-x86_64/egg' (and everything under it)
Processing smalr-1.0.1-py2.7.egg
creating /Users/Yoshi/informatics/software/smalr_venv/lib/python2.7/site-packages/smalr-1.0.1-py2.7.egg
Extracting smalr-1.0.1-py2.7.egg to /Users/Yoshi/informatics/software/smalr_venv/lib/python2.7/site-packages
Adding smalr 1.0.1 to easy-install.pth file
Installing smalr script to /Users/Yoshi/informatics/software/smalr_venv/bin
Installing call_smalr.py script to /Users/Yoshi/informatics/software/smalr_venv/bin

Installed /Users/Yoshi/informatics/software/smalr_venv/lib/python2.7/site-packages/smalr-1.0.1-py2.7.egg
Processing dependencies for smalr==1.0.1
Searching for pysam>=0.9.0
Reading https://pypi.python.org/simple/pysam/
Downloading https://pypi.python.org/packages/d8/78/8b3fad13d3bd8787c0d922056061727c2a0cf91c45a836c98342594dd293/pysam-0.14.tar.gz#md5=fb187f3fb005ec21f8a844b3a53d7e38
Best match: pysam 0.14
Processing pysam-0.14.tar.gz
Writing /var/folders/55/s9g3y_713q7cs2gcfhmkm6qm0000gn/T/easy_install-hlpVZM/pysam-0.14/setup.cfg
Running pysam-0.14/setup.py -q bdist_egg --dist-dir /var/folders/55/s9g3y_713q7cs2gcfhmkm6qm0000gn/T/easy_install-hlpVZM/pysam-0.14/egg-dist-tmp-zciIdW
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is shared
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
checking for gcc... gcc
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 gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking for grep that handles long lines and -e... /usr/bin/grep
checking for C compiler warning flags... -Wall
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for _LARGEFILE_SOURCE value needed for large files... no
checking shared library type for unknown-Darwin... Darwin dylib
checking how to run the C preprocessor... gcc -E
checking for egrep... /usr/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 for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking whether fdatasync is declared... no
checking for library containing log... none required
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing recv... none required
checking for bzlib.h... yes
checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
checking for lzma.h... yes
checking for lzma_easy_buffer_encode in -llzma... yes
checking for curl_easy_pause in -lcurl... yes
checking for CCHmac... yes
checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes
configure: creating ./config.status
config.status: creating config.mk
config.status: creating htslib.pc.tmp
config.status: creating config.h
# pysam: htslib configure options: --enable-libcurl
make: ./version.sh: Command not found
make: ./version.sh: Command not found
# pysam: htslib_config LIBS=-llzma -lbz2 -lz -lcurl
# pysam: htslib_config PLATFORM=Darwin
# pysam: htslib_config LIBHTS_OBJS=kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o hfile_libcurl.o hfile_gcs.o hfile_s3.o
# pysam: htslib_config LDFLAGS=
# pysam: config_option: ENABLE_PLUGINS=0
# pysam: config_option: HAVE_COMMONCRYPTO=1
# pysam: config_option: HAVE_GMTIME_R=1
# pysam: config_option: HAVE_HMAC=0
# pysam: config_option: HAVE_IRODS=0
# pysam: config_option: HAVE_LIBCURL=1
# pysam: config_option: HAVE_MMAP=1
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'bcftools/__init__.py' not found (or not a regular file)
package init file 'samtools/win32/__init__.py' not found (or not a regular file)
package init file 'htslib/__init__.py' not found (or not a regular file)
package init file 'htslib/htslib/__init__.py' not found (or not a regular file)
warning: no files found matching 'KNOWN_BUGS'
warning: no files found matching 'THANKS'
warning: no files found matching 'samtools/configure'
warning: no files found matching 'samtools/config.mk.in'
warning: no files found matching 'samtools/config.h.in'
warning: no files found matching 'htslib/win/*.c'
warning: no files found matching 'htslib/win/*.h'

gcc: error: @loader_path: No such file or directory
gcc: error: unrecognized command line option '-rpath'
error: Setup script exited with error: command 'gcc' failed with exit status 1
yfuruta commented 6 years ago

Solved by installing pysam with conda, adding sys.path to PYTHONPATH, loading the PYTHONPATH after entering smalrenv.

jbeaulaurier commented 6 years ago

Hi Yoshi,

Very glad to hear this. I wasn't able to replicate this problem and investigating online didn't reveal any answers. But please let me know if you have any other issues.

Best, John