Segmentation Fault on Doc.Write()

[mehersam]

We are getting segmentation fault errors when reading a SBOL2 file and then writing the read in file. The seg fault is happening on the write.

A simple C++ program was created that takes in a file on input and reads the file into a document and writes a new file out. To test this, a shell script was created that iterates through a series of SBOL2 files and calls the C++ program and then calls the libSBOLj jar file and compares the written file to the original read in file. However, a seg fault is thrown when attempting to write the file.

I am including a link to zip file with the C++ program along with the shell script and the results of running the script which shows the seg fault error.

result.txt Final_Testing_of_LibSBOL

[cjmyers]

This appears to be a windows only problem. I think paths on windows are a problem.

I can get the program and script working on Mac, but there are still a lot of errors. See attached Zip file and results. Here are some of the problems found:

1) Namespaces are getting dropped 2) Collections are getting dropped 3) GenericTopLevels are getting dropped 4) Some files simply get a segmentation fault 5) Several other files have differences in the output file.

Please use this to test your library. These bugs needed to be released before the library is safe to use.

Chris

ReadWriteTestlibSBOL.zip

[cjmyers]

This appears to be a windows only problem. I think paths on windows are a problem.

I can get the program and script working on Mac, but there are still a lot of errors. Results, C program, and script are attached (zip file on github issue tracker). Here are some of the problems found:

1) Namespaces are getting dropped 2) Collections are getting dropped 3) GenericTopLevels are getting dropped 4) Some files simply get a segmentation fault 5) Several other files have differences in the output file.

Please use this to test your library. These bugs needed to be released before the library is safe to use.

Chris

On Jan 4, 2017, at 5:22 PM, mehersam <notifications@github.com mailto:notifications@github.com> wrote:

We are getting segmentation fault errors when reading a SBOL2 file and then writing the read in file. The seg fault is happening on the write.

A simple C++ program was created that takes in a file on input and reads the file into a document and writes a new file out. To test this, a shell script was created that iterates through a series of SBOL2 files and calls the C++ program and then calls the libSBOLj jar file and compares the written file to the original read in file. However, a seg fault is thrown when attempting to write the file.

I am including a link to zip file with the C++ program along with the shell script and the results of running the script which shows the seg fault error.

result.txt https://github.com/SynBioDex/libSBOL/files/686161/result.txt Final_Testing_of_LibSBOL https://drive.google.com/open?id=0B_fQ3zF70irFd1NLeXV0SkhmNGs — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/SynBioDex/libSBOL/issues/114, or mute the thread https://github.com/notifications/unsubscribe-auth/ADWD93jRzZKwHmjSSZJOTaKZkcb193zJks5rPDe_gaJpZM4LbNyq.

SBOL2/AnnotationOutput.rdf Namespace {http://partsregistry.org} not found in outputFile Validation successful, no errors.

SBOL2/BBa_I0462.rdf Validation successful, no errors.

SBOL2/BBa_T9002.rdf ./script.sh: line 3: 87635 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f File is empty. Conversion failed.

SBOL2/CollectionOutput.rdf Collection http://parts.igem.org/Promoters/Catalog/Anderson not found in outputFile Validation successful, no errors.

SBOL2/ComponentDefinitionOutput.rdf Namespace {http://partsregistry.org} not found in outputFile Validation successful, no errors.

SBOL2/CreateAndRemoveCollections.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org} not found in outputFile Collection http://www.async.ece.utah.edu/myParts/1.0 not found in outputFile Validation successful, no errors.

SBOL2/CreateAndRemoveComponentDefinition.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org} not found in outputFile Validation successful, no errors.

SBOL2/CreateAndRemoveGenericTopLevel.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org} not found in outputFile GenericTopLevel http://www.async.ece.utah.edu/someGenTopLev/1.0 not found in outputFile Validation successful, no errors.

SBOL2/CreateAndRemoveModel.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org} not found in outputFile Collection http://www.async.ece.utah.edu/someSequence2/1.0 not found in outputFile Collection http://www.async.ece.utah.edu/someSequence1/1.0 not found in outputFile Collection http://www.async.ece.utah.edu/someSequence3/1.0 not found in outputFile Validation successful, no errors.

SBOL2/CreateAndRemoveModuleDefinition.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org} not found in outputFile Validation successful, no errors.

SBOL2/CutExample.rdf ./script.sh: line 3: 87652 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f File is empty. Conversion failed.

SBOL2/GenericTopLevelOutput.rdf Namespace {http://www.myapp.org} not found in outputFile GenericTopLevel http://www.partsregistry.org/gen/datasheet1 not found in outputFile Validation successful, no errors.

SBOL2/ModelOutput.rdf Validation successful, no errors.

SBOL2/ModuleDefinitionOutput.rdf ./script.sh: line 3: 87658 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f File is empty. Conversion failed.

SBOL2/RepressionModel.rdf ./script.sh: line 3: 87660 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f File is empty. Conversion failed.

SBOL2/SBOL1and2Test.rdf ./script.sh: line 3: 87662 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f Out/SBOL2/SBOL1and2Test.rdf (No such file or directory) I/O exception. java.io.FileNotFoundException: Out/SBOL2/SBOL1and2Test.rdf (No such file or directory) at java.io.FileInputStream.open(Native Method) at java.io.FileInputStream.(FileInputStream.java:146) at org.sbolstandard.core2.SBOLReader.read(SBOLReader.java:446) at org.sbolstandard.core2.SBOLReader.read(SBOLReader.java:379) at org.sbolstandard.core2.SBOLReader.read(SBOLReader.java:364) at org.sbolstandard.core2.SBOLValidate.validate(SBOLValidate.java:1568) at org.sbolstandard.core2.SBOLValidate.main(SBOLValidate.java:1816)

SBOL2/SBOLDocumentOutput.rdf Validation successful, no errors.

SBOL2/SequenceConstraintOutput.rdf Validation successful, no errors.

SBOL2/SequenceOutput.rdf Validation successful, no errors.

SBOL2/SimpleComponentDefinitionExample.rdf Validation successful, no errors.

SBOL2/SimpleModuleDefinition.rdf Validation successful, no errors.

SBOL2/igem1.rdf Namespace {http://www.w3.org/2000/01/rdf-schema#} not found in outputFile Namespace {http://sbolhub.org/} not found in outputFile Namespace {http://parts.igem.org/#} not found in outputFile Namespace {http://www.w3.org/2002/07/owl#} not found in outputFile Namespace {http://www.w3.org/2001/XMLSchema#} not found in outputFile Namespace {http://www.openrdf.org/schema/sesame#} not found in outputFile Namespace {http://www.w3.org/2005/xpath-functions#} not found in outputFile Collection http://sbolhub.org/col/igem_sbol2_151015212715 not found in outputFile Sequence http://parts.igem.org/Part:BBa_I742134#sequence not found in outputFile Sequence http://parts.igem.org/Part:BBa_I766203#sequence not found in outputFile GenericTopLevel http://sbolhub.org/gen/igem_sbol2_151015212715 not found in outputFile sbol-10402: The elements property of a Sequence is REQUIRED and MUST contain a String. Reference: SBOL Version 2.1.0 Section 7.6 on page 20 : http://parts.igem.org/Part:BBa_I742134#sequence

sbol-10402: The elements property of a Sequence is REQUIRED and MUST contain a String. Reference: SBOL Version 2.1.0 Section 7.6 on page 20 : http://parts.igem.org/Part:BBa_I766203#sequence

Validation failed.

SBOL2/igem2.rdf Namespace {http://www.w3.org/2000/01/rdf-schema#} not found in outputFile Namespace {http://sbolhub.org/} not found in outputFile Namespace {http://parts.igem.org/#} not found in outputFile Namespace {http://www.w3.org/2002/07/owl#} not found in outputFile Namespace {http://www.w3.org/2001/XMLSchema#} not found in outputFile Namespace {http://www.openrdf.org/schema/sesame#} not found in outputFile Namespace {http://www.w3.org/2005/xpath-functions#} not found in outputFile Collection http://sbolhub.org/col/igem_sbol2_151015212742 not found in outputFile Sequence http://parts.igem.org/Part:BBa_I716256#sequence not found in outputFile GenericTopLevel http://sbolhub.org/gen/igem_sbol2_151015212742 not found in outputFile sbol-10402: The elements property of a Sequence is REQUIRED and MUST contain a String. Reference: SBOL Version 2.1.0 Section 7.6 on page 20 : http://parts.igem.org/Part:BBa_I716256#sequence

Validation failed.

SBOL2/igem3.rdf Namespace {http://www.w3.org/2000/01/rdf-schema#} not found in outputFile Namespace {http://sbolhub.org/} not found in outputFile Namespace {http://parts.igem.org/#} not found in outputFile Namespace {http://www.w3.org/2002/07/owl#} not found in outputFile Namespace {http://www.w3.org/2001/XMLSchema#} not found in outputFile Namespace {http://www.openrdf.org/schema/sesame#} not found in outputFile Namespace {http://www.w3.org/2005/xpath-functions#} not found in outputFile Collection http://sbolhub.org/col/igem_sbol2_151015212923 not found in outputFile GenericTopLevel http://sbolhub.org/gen/igem_sbol2_151015212923 not found in outputFile Validation successful, no errors.

SBOL2/labhost_All.rdf Collection http://www.async.ece.utah.edu/Pichia_pastoris not found in outputFile Collection http://www.async.ece.utah.edu/Aspergillus_nidulans not found in outputFile Collection http://www.async.ece.utah.edu/Gram_negative_bacteria not found in outputFile Collection http://www.async.ece.utah.edu/Plant_Cells not found in outputFile Collection http://www.async.ece.utah.edu/Schizosaccharomyces_pombe not found in outputFile Collection http://www.async.ece.utah.edu/Mammalian_Cells not found in outputFile Collection http://www.async.ece.utah.edu/Drosophila_melanogaster not found in outputFile Collection http://www.async.ece.utah.edu/Saccharomyces_cerevisiae not found in outputFile Collection http://www.async.ece.utah.edu/Unspecified_labhost not found in outputFile Collection http://www.async.ece.utah.edu/Insect_Cells not found in outputFile Collection http://www.async.ece.utah.edu/Bacillus_subtilis not found in outputFile Collection http://www.async.ece.utah.edu/Escherichia_Coli not found in outputFile Collection http://www.async.ece.utah.edu/Kluyveromyces_lactis not found in outputFile ComponentDefinition http://www.async.ece.utah.edu/lac_UV5_promoter_003 differ. ComponentDefinition http://www.async.ece.utah.edu/lac_UV5_promoter_001 differ. ComponentDefinition http://www.async.ece.utah.edu/lac_UV5_promoter_002 differ. Validation successful, no errors.

SBOL2/labhost_Aspergillus_nidulans.rdf Collection http://www.async.ece.utah.edu/Aspergillus_nidulans not found in outputFile Validation successful, no errors.

SBOL2/labhost_Bacillus_subtilis.rdf Collection http://www.async.ece.utah.edu/Bacillus_subtilis not found in outputFile Validation successful, no errors.

SBOL2/labhost_Drosophila_melanogaster.rdf Collection http://www.async.ece.utah.edu/Drosophila_melanogaster not found in outputFile Validation successful, no errors.

SBOL2/labhost_Escherichia_Coli.rdf Collection http://www.async.ece.utah.edu/Escherichia_Coli not found in outputFile ComponentDefinition http://www.async.ece.utah.edu/lac_UV5_promoter_001 differ. ComponentDefinition http://www.async.ece.utah.edu/lac_UV5_promoter_002 differ. Validation successful, no errors.

SBOL2/labhost_Gram-negative_bacteria.rdf Collection http://www.async.ece.utah.edu/Gram_negative_bacteria not found in outputFile Validation successful, no errors.

SBOL2/labhost_Insect_Cells.rdf Collection http://www.async.ece.utah.edu/Insect_Cells not found in outputFile ComponentDefinition http://www.async.ece.utah.edu/lac_UV5_promoter_002 differ. Validation successful, no errors.

SBOL2/labhost_Kluyveromyces_lactis.rdf Collection http://www.async.ece.utah.edu/Kluyveromyces_lactis not found in outputFile Validation successful, no errors.

SBOL2/labhost_Mammalian_Cells.rdf Collection http://www.async.ece.utah.edu/Mammalian_Cells not found in outputFile ComponentDefinition http://www.async.ece.utah.edu/lac_UV5_promoter_002 differ. ComponentDefinition http://www.async.ece.utah.edu/lac_UV5_promoter_003 differ. Validation successful, no errors.

SBOL2/labhost_Pichia_pastoris.rdf Collection http://www.async.ece.utah.edu/Pichia_pastoris not found in outputFile Validation successful, no errors.

SBOL2/labhost_Plant_Cells.rdf Collection http://www.async.ece.utah.edu/Plant_Cells not found in outputFile ComponentDefinition http://www.async.ece.utah.edu/lac_UV5_promoter_002 differ. Validation successful, no errors.

SBOL2/labhost_Saccharomyces_cerevisiae.rdf Collection http://www.async.ece.utah.edu/Saccharomyces_cerevisiae not found in outputFile Validation successful, no errors.

SBOL2/labhost_Schizosaccharomyces_pombe.rdf Collection http://www.async.ece.utah.edu/Schizosaccharomyces_pombe not found in outputFile Validation successful, no errors.

SBOL2/labhost_Unspecified.rdf Collection http://www.async.ece.utah.edu/Unspecified_labhost not found in outputFile ComponentDefinition http://www.async.ece.utah.edu/lac_UV5_promoter_002 differ. Validation successful, no errors.

SBOL2/memberAnnotations.rdf ./script.sh: line 3: 87738 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f File is empty. Conversion failed.

SBOL2/multipleCollections_no_Members.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org} not found in outputFile Collection http://www.async.ece.utah.edu/myPart3/1.0 not found in outputFile Collection http://www.async.ece.utah.edu/myPart2/1.0 not found in outputFile Collection http://www.async.ece.utah.edu/myPart1/1.0 not found in outputFile Validation successful, no errors.

SBOL2/multipleGenericTopLevel.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org} not found in outputFile GenericTopLevel http://www.async.ece.utah.edu/GenericTopLevel3/1.0 not found in outputFile GenericTopLevel http://www.async.ece.utah.edu/GenericTopLevel1/1.0 not found in outputFile GenericTopLevel http://www.async.ece.utah.edu/GenericTopLevel2/1.0 not found in outputFile Validation successful, no errors.

SBOL2/multipleSequences.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org} not found in outputFile Validation successful, no errors.

SBOL2/namespace.rdf Validation successful, no errors.

SBOL2/new_AnnotationOutput.rdf Namespace {http://purl.org/dc/terms/#} not found in outputFile Namespace {http://purl.org/dc/terms/} not found in originalFile Validation successful, no errors.

SBOL2/new_BBa_I0462.rdf Serialization error: XML Parsing failed - no element found RAPTOR_LOG_LEVEL_ERROR -1, -1 http://sbols.org/v2# Serialization error: XML Parsing failed - no element found RAPTOR_LOG_LEVEL_ERROR -1, -1 http://sbols.org/v2# SBOL error 7:Missing namespace http://sbols.org/v2# SBOL error 7:Missing namespace http://www.w3.org/1999/02/22-rdf-syntax-ns# File is empty. Conversion failed.

SBOL2/pIKE_pTAK_cassettes 2.rdf SBOL error 12:File not found libc++abi.dylib: terminating with uncaught exception of type sbol::SBOLErrorCode ./script.sh: line 3: 87753 Abort trap: 6 ./ReadWriteTestlibSBOL $f Out/$f libSBOLj version 2.1.2 Description: validates the contents of an SBOL 2.0 document, can compare two documents, and can convert to/from SBOL 1.1, GenBank, and FASTA formats.

Usage: java --jar libSBOLj.jar [options] [-o -e ]

Options: -l specfies language (SBOL1/SBOL2/GenBank/FASTA) for output (default=SBOL2) -s select only this object and those it references -p used for converted objects -v used for converted objects -t uses types in URIs -n allow non-compliant URIs -i allow SBOL document to be incomplete -b check best practices -f fail on first error -d display detailed error trace

SBOL2/pIKE_pTAK_cassettes.rdf Collection http://www.async.ece.utah.edu/ToggleSwitchCassettes not found in outputFile Validation successful, no errors.

SBOL2/pIKE_pTAK_left_right_cassettes.rdf Collection http://www.async.ece.utah.edu/ToggleSwitchCassettes not found in outputFile Validation successful, no errors.

SBOL2/pIKE_pTAK_toggle_switches.rdf Validation successful, no errors.

SBOL2/partial_pIKE_left_cassette.rdf ./script.sh: line 3: 87774 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f File is empty. Conversion failed.

SBOL2/partial_pIKE_right_casette.rdf ./script.sh: line 3: 87776 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f File is empty. Conversion failed.

SBOL2/partial_pIKE_right_cassette.rdf ./script.sh: line 3: 87778 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f File is empty. Conversion failed.

SBOL2/partial_pTAK_left_cassette.rdf ./script.sh: line 3: 87780 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f File is empty. Conversion failed.

SBOL2/partial_pTAK_right_cassette.rdf ./script.sh: line 3: 87782 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f File is empty. Conversion failed.

SBOL2/sampleToggleSwitch.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org} not found in outputFile Collection http://www.async.ece.utah.edu/myParts/1/0 not found in outputFile ComponentDefinition http://www.async.ece.utah.edu/ptetlacI/1/0 differ. ->Component T not found in outputFile ->Component L not found in outputFile ->SequenceAnnotation p2_structAnnotate not found in outputFile ->SequenceAnnotation c2_structAnnotate not found in outputFile ->SequenceAnnotation http://sbols.org/c2_structAnnotate not found in originalFile ->SequenceAnnotation http://sbols.org/p2_structAnnotate not found in originalFile ComponentDefinition http://www.async.ece.utah.edu/pLactetR/1/0 not found in outputFile GenericTopLevel http://www.async.ece.utah.edu/GenericTopLevel/1/0 not found in outputFile sbol-11403: The Component referenced by the subject property of a SequenceConstraint MUST be contained by the ComponentDefinition that contains the SequenceConstraint. Reference: SBOL Version 2.1.0 Section 7.7.6 on page 36 : http://sbols.org/struct_constraint

Validation failed.

SBOL2/sequence1.rdf Namespace {http://www.ncbi.nlm.nih.gov} not found in outputFile Validation successful, no errors.

SBOL2/sequence2.rdf Namespace {http://www.ncbi.nlm.nih.gov} not found in outputFile Validation successful, no errors.

SBOL2/sequence3.rdf Namespace {http://www.ncbi.nlm.nih.gov} not found in outputFile Validation successful, no errors.

SBOL2/sequence4.rdf Namespace {http://www.ncbi.nlm.nih.gov} not found in outputFile Validation successful, no errors.

SBOL2/singleCollection.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org} not found in outputFile Collection http://www.async.ece.utah.edu/myParts/1.0 not found in outputFile Validation successful, no errors.

SBOL2/singleCompDef_withSeq.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org} not found in outputFile Validation successful, no errors.

SBOL2/singleComponentDefinition.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org} not found in outputFile Validation successful, no errors.

SBOL2/singleFunctionalComponent.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org} not found in outputFile Validation successful, no errors.

SBOL2/singleGenericTopLevel.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org} not found in outputFile GenericTopLevel http://www.async.ece.utah.edu/GenericTopLevel/1.0 not found in outputFile Validation successful, no errors.

SBOL2/singleModel.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org} not found in outputFile Model http://www.async.ece.utah.edu/ToggleModel/1.0 differ. Validation successful, no errors.

SBOL2/singleModuleDefinition.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org} not found in outputFile Validation successful, no errors.

SBOL2/singleSequence.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org} not found in outputFile Validation successful, no errors.

SBOL2/test_Collection_remove.rdf Namespace {http://partsregistry.org} not found in outputFile Validation successful, no errors.

SBOL2/test_ComponentDefinition_remove.rdf Namespace {http://partsregistry.org} not found in outputFile Validation successful, no errors.

SBOL2/test_GenericTopLevel_remove.rdf Namespace {http://partsregistry.org} not found in outputFile Validation successful, no errors.

SBOL2/test_Methods.rdf Namespace {http://partsregistry.org} not found in outputFile Validation successful, no errors.

SBOL2/test_Model_remove.rdf Namespace {http://partsregistry.org} not found in outputFile Validation successful, no errors.

SBOL2/test_ModuleDefinition_remove.rdf Namespace {http://partsregistry.org} not found in outputFile Validation successful, no errors.

SBOL2/test_Sequence_remove.rdf Namespace {http://partsregistry.org} not found in outputFile Validation successful, no errors.

SBOL2/toggle.rdf ./script.sh: line 3: 87830 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f File is empty. Conversion failed.

[bbartley]

Collections, Generic Locations are not currently implemented.  Additionally, Cut objects are serialized but not read.  These are all quick fixes, however. At least one seg-fault is caused by a namespace missing a prefix.  In the file SBOL1and2Test.rdf, the "http://sbols.org/v1#" namespace lacks a prefix.  Is this valid? There is another issue with namespaces in AnnotationOutput.rdf. The namespace xmlns:pr="http://partsregistry.org" is lacking a terminal delimiter such as '#' or '/'.  Is this valid?  It is not consistent with other namespaces and does not seem to parse correctly with RDF tools.  This is causing problems with how libSBOL parses data in extension namespaces. From: cjmyers notifications@github.com To: SynBioDex/libSBOL libSBOL@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Sent: Wednesday, January 4, 2017 7:32 PM Subject: Re: [SynBioDex/libSBOL] Segmentation Fault on Doc.Write() (#114)

This appears to be a windows only problem. I think paths on windows are a problem.

I can get the program and script working on Mac, but there are still a lot of errors. Results, C program, and script are attached (zip file on github issue tracker). Here are some of the problems found:

1) Namespaces are getting dropped 2) Collections are getting dropped 3) GenericTopLevels are getting dropped 4) Some files simply get a segmentation fault 5) Several other files have differences in the output file.

Please use this to test your library. These bugs needed to be released before the library is safe to use.

Chris

On Jan 4, 2017, at 5:22 PM, mehersam <notifications@github.com mailto:notifications@github.com> wrote:

We are getting segmentation fault errors when reading a SBOL2 file and then writing the read in file. The seg fault is happening on the write.

A simple C++ program was created that takes in a file on input and reads the file into a document and writes a new file out. To test this, a shell script was created that iterates through a series of SBOL2 files and calls the C++ program and then calls the libSBOLj jar file and compares the written file to the original read in file. However, a seg fault is thrown when attempting to write the file.

I am including a link to zip file with the C++ program along with the shell script and the results of running the script which shows the seg fault error.

result.txt https://github.com/SynBioDex/libSBOL/files/686161/result.txt Final_Testing_of_LibSBOL https://drive.google.com/open?id=0B_fQ3zF70irFd1NLeXV0SkhmNGs — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/SynBioDex/libSBOL/issues/114, or mute the thread https://github.com/notifications/unsubscribe-auth/ADWD93jRzZKwHmjSSZJOTaKZkcb193zJks5rPDe_gaJpZM4LbNyq.

SBOL2/AnnotationOutput.rdf Namespace {http://partsregistry.org} not found in outputFile Validation successful, no errors.

SBOL2/BBa_I0462.rdf Validation successful, no errors.

SBOL2/BBa_T9002.rdf ./script.sh: line 3: 87635 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f File is empty. Conversion failed.

SBOL2/CollectionOutput.rdf Collection http://parts.igem.org/Promoters/Catalog/Anderson not found in outputFile Validation successful, no errors.

SBOL2/ComponentDefinitionOutput.rdf Namespace {http://partsregistry.org} not found in outputFile Validation successful, no errors.

SBOL2/CreateAndRemoveCollections.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org} not found in outputFile Collection http://www.async.ece.utah.edu/myParts/1.0 not found in outputFile Validation successful, no errors.

SBOL2/CreateAndRemoveComponentDefinition.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org} not found in outputFile Validation successful, no errors.

SBOL2/CreateAndRemoveGenericTopLevel.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org} not found in outputFile GenericTopLevel http://www.async.ece.utah.edu/someGenTopLev/1.0 not found in outputFile Validation successful, no errors.

SBOL2/CreateAndRemoveModel.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org} not found in outputFile Collection http://www.async.ece.utah.edu/someSequence2/1.0 not found in outputFile Collection http://www.async.ece.utah.edu/someSequence1/1.0 not found in outputFile Collection http://www.async.ece.utah.edu/someSequence3/1.0 not found in outputFile Validation successful, no errors.

SBOL2/CreateAndRemoveModuleDefinition.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org} not found in outputFile Validation successful, no errors.

SBOL2/CutExample.rdf ./script.sh: line 3: 87652 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f File is empty. Conversion failed.

SBOL2/GenericTopLevelOutput.rdf Namespace {http://www.myapp.org} not found in outputFile GenericTopLevel http://www.partsregistry.org/gen/datasheet1 not found in outputFile Validation successful, no errors.

SBOL2/ModelOutput.rdf Validation successful, no errors.

SBOL2/ModuleDefinitionOutput.rdf ./script.sh: line 3: 87658 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f File is empty. Conversion failed.

SBOL2/RepressionModel.rdf ./script.sh: line 3: 87660 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f File is empty. Conversion failed.

SBOL2/SBOL1and2Test.rdf ./script.sh: line 3: 87662 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f Out/SBOL2/SBOL1and2Test.rdf (No such file or directory) I/O exception. java.io.FileNotFoundException: Out/SBOL2/SBOL1and2Test.rdf (No such file or directory) at java.io.FileInputStream.open(Native Method) at java.io.FileInputStream.(FileInputStream.java:146) at org.sbolstandard.core2.SBOLReader.read(SBOLReader.java:446) at org.sbolstandard.core2.SBOLReader.read(SBOLReader.java:379) at org.sbolstandard.core2.SBOLReader.read(SBOLReader.java:364) at org.sbolstandard.core2.SBOLValidate.validate(SBOLValidate.java:1568) at org.sbolstandard.core2.SBOLValidate.main(SBOLValidate.java:1816)

SBOL2/SBOLDocumentOutput.rdf Validation successful, no errors.

SBOL2/SequenceConstraintOutput.rdf Validation successful, no errors.

SBOL2/SequenceOutput.rdf Validation successful, no errors.

SBOL2/SimpleComponentDefinitionExample.rdf Validation successful, no errors.

SBOL2/SimpleModuleDefinition.rdf Validation successful, no errors.

SBOL2/igem1.rdf Namespace {http://www.w3.org/2000/01/rdf-schema#} not found in outputFile Namespace {http://sbolhub.org/} not found in outputFile Namespace {http://parts.igem.org/#} not found in outputFile Namespace {http://www.w3.org/2002/07/owl#} not found in outputFile Namespace {http://www.w3.org/2001/XMLSchema#} not found in outputFile Namespace {http://www.openrdf.org/schema/sesame#} not found in outputFile Namespace {http://www.w3.org/2005/xpath-functions#} not found in outputFile Collection http://sbolhub.org/col/igem_sbol2_151015212715 not found in outputFile Sequence http://parts.igem.org/Part:BBa_I742134#sequence not found in outputFile Sequence http://parts.igem.org/Part:BBa_I766203#sequence not found in outputFile GenericTopLevel http://sbolhub.org/gen/igem_sbol2_151015212715 not found in outputFile sbol-10402: The elements property of a Sequence is REQUIRED and MUST contain a String. Reference: SBOL Version 2.1.0 Section 7.6 on page 20 : http://parts.igem.org/Part:BBa_I742134#sequence

sbol-10402: The elements property of a Sequence is REQUIRED and MUST contain a String. Reference: SBOL Version 2.1.0 Section 7.6 on page 20 : http://parts.igem.org/Part:BBa_I766203#sequence

Validation failed.

SBOL2/igem2.rdf Namespace {http://www.w3.org/2000/01/rdf-schema#} not found in outputFile Namespace {http://sbolhub.org/} not found in outputFile Namespace {http://parts.igem.org/#} not found in outputFile Namespace {http://www.w3.org/2002/07/owl#} not found in outputFile Namespace {http://www.w3.org/2001/XMLSchema#} not found in outputFile Namespace {http://www.openrdf.org/schema/sesame#} not found in outputFile Namespace {http://www.w3.org/2005/xpath-functions#} not found in outputFile Collection http://sbolhub.org/col/igem_sbol2_151015212742 not found in outputFile Sequence http://parts.igem.org/Part:BBa_I716256#sequence not found in outputFile GenericTopLevel http://sbolhub.org/gen/igem_sbol2_151015212742 not found in outputFile sbol-10402: The elements property of a Sequence is REQUIRED and MUST contain a String. Reference: SBOL Version 2.1.0 Section 7.6 on page 20 : http://parts.igem.org/Part:BBa_I716256#sequence

Validation failed.

SBOL2/igem3.rdf Namespace {http://www.w3.org/2000/01/rdf-schema#} not found in outputFile Namespace {http://sbolhub.org/} not found in outputFile Namespace {http://parts.igem.org/#} not found in outputFile Namespace {http://www.w3.org/2002/07/owl#} not found in outputFile Namespace {http://www.w3.org/2001/XMLSchema#} not found in outputFile Namespace {http://www.openrdf.org/schema/sesame#} not found in outputFile Namespace {http://www.w3.org/2005/xpath-functions#} not found in outputFile Collection http://sbolhub.org/col/igem_sbol2_151015212923 not found in outputFile GenericTopLevel http://sbolhub.org/gen/igem_sbol2_151015212923 not found in outputFile Validation successful, no errors.

SBOL2/labhost_All.rdf Collection http://www.async.ece.utah.edu/Pichia_pastoris not found in outputFile Collection http://www.async.ece.utah.edu/Aspergillus_nidulans not found in outputFile Collection http://www.async.ece.utah.edu/Gram_negative_bacteria not found in outputFile Collection http://www.async.ece.utah.edu/Plant_Cells not found in outputFile Collection http://www.async.ece.utah.edu/Schizosaccharomyces_pombe not found in outputFile Collection http://www.async.ece.utah.edu/Mammalian_Cells not found in outputFile Collection http://www.async.ece.utah.edu/Drosophila_melanogaster not found in outputFile Collection http://www.async.ece.utah.edu/Saccharomyces_cerevisiae not found in outputFile Collection http://www.async.ece.utah.edu/Unspecified_labhost not found in outputFile Collection http://www.async.ece.utah.edu/Insect_Cells not found in outputFile Collection http://www.async.ece.utah.edu/Bacillus_subtilis not found in outputFile Collection http://www.async.ece.utah.edu/Escherichia_Coli not found in outputFile Collection http://www.async.ece.utah.edu/Kluyveromyces_lactis not found in outputFile ComponentDefinition http://www.async.ece.utah.edu/lac_UV5_promoter_003 differ. ComponentDefinition http://www.async.ece.utah.edu/lac_UV5_promoter_001 differ. ComponentDefinition http://www.async.ece.utah.edu/lac_UV5_promoter_002 differ. Validation successful, no errors.

SBOL2/labhost_Aspergillus_nidulans.rdf Collection http://www.async.ece.utah.edu/Aspergillus_nidulans not found in outputFile Validation successful, no errors.

SBOL2/labhost_Bacillus_subtilis.rdf Collection http://www.async.ece.utah.edu/Bacillus_subtilis not found in outputFile Validation successful, no errors.

SBOL2/labhost_Drosophila_melanogaster.rdf Collection http://www.async.ece.utah.edu/Drosophila_melanogaster not found in outputFile Validation successful, no errors.

SBOL2/labhost_Escherichia_Coli.rdf Collection http://www.async.ece.utah.edu/Escherichia_Coli not found in outputFile ComponentDefinition http://www.async.ece.utah.edu/lac_UV5_promoter_001 differ. ComponentDefinition http://www.async.ece.utah.edu/lac_UV5_promoter_002 differ. Validation successful, no errors.

SBOL2/labhost_Gram-negative_bacteria.rdf Collection http://www.async.ece.utah.edu/Gram_negative_bacteria not found in outputFile Validation successful, no errors.

SBOL2/labhost_Insect_Cells.rdf Collection http://www.async.ece.utah.edu/Insect_Cells not found in outputFile ComponentDefinition http://www.async.ece.utah.edu/lac_UV5_promoter_002 differ. Validation successful, no errors.

SBOL2/labhost_Kluyveromyces_lactis.rdf Collection http://www.async.ece.utah.edu/Kluyveromyces_lactis not found in outputFile Validation successful, no errors.

SBOL2/labhost_Mammalian_Cells.rdf Collection http://www.async.ece.utah.edu/Mammalian_Cells not found in outputFile ComponentDefinition http://www.async.ece.utah.edu/lac_UV5_promoter_002 differ. ComponentDefinition http://www.async.ece.utah.edu/lac_UV5_promoter_003 differ. Validation successful, no errors.

SBOL2/labhost_Pichia_pastoris.rdf Collection http://www.async.ece.utah.edu/Pichia_pastoris not found in outputFile Validation successful, no errors.

SBOL2/labhost_Plant_Cells.rdf Collection http://www.async.ece.utah.edu/Plant_Cells not found in outputFile ComponentDefinition http://www.async.ece.utah.edu/lac_UV5_promoter_002 differ. Validation successful, no errors.

SBOL2/labhost_Saccharomyces_cerevisiae.rdf Collection http://www.async.ece.utah.edu/Saccharomyces_cerevisiae not found in outputFile Validation successful, no errors.

SBOL2/labhost_Schizosaccharomyces_pombe.rdf Collection http://www.async.ece.utah.edu/Schizosaccharomyces_pombe not found in outputFile Validation successful, no errors.

SBOL2/labhost_Unspecified.rdf Collection http://www.async.ece.utah.edu/Unspecified_labhost not found in outputFile ComponentDefinition http://www.async.ece.utah.edu/lac_UV5_promoter_002 differ. Validation successful, no errors.

SBOL2/memberAnnotations.rdf ./script.sh: line 3: 87738 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f File is empty. Conversion failed.

SBOL2/multipleCollections_no_Members.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org} not found in outputFile Collection http://www.async.ece.utah.edu/myPart3/1.0 not found in outputFile Collection http://www.async.ece.utah.edu/myPart2/1.0 not found in outputFile Collection http://www.async.ece.utah.edu/myPart1/1.0 not found in outputFile Validation successful, no errors.

SBOL2/multipleGenericTopLevel.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org} not found in outputFile GenericTopLevel http://www.async.ece.utah.edu/GenericTopLevel3/1.0 not found in outputFile GenericTopLevel http://www.async.ece.utah.edu/GenericTopLevel1/1.0 not found in outputFile GenericTopLevel http://www.async.ece.utah.edu/GenericTopLevel2/1.0 not found in outputFile Validation successful, no errors.

SBOL2/multipleSequences.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org} not found in outputFile Validation successful, no errors.

SBOL2/namespace.rdf Validation successful, no errors.

SBOL2/new_AnnotationOutput.rdf Namespace {http://purl.org/dc/terms/#} not found in outputFile Namespace {http://purl.org/dc/terms/} not found in originalFile Validation successful, no errors.

SBOL2/new_BBa_I0462.rdf Serialization error: XML Parsing failed - no element found RAPTOR_LOG_LEVEL_ERROR -1, -1 http://sbols.org/v2# Serialization error: XML Parsing failed - no element found RAPTOR_LOG_LEVEL_ERROR -1, -1 http://sbols.org/v2# SBOL error 7:Missing namespace http://sbols.org/v2# SBOL error 7:Missing namespace http://www.w3.org/1999/02/22-rdf-syntax-ns# File is empty. Conversion failed.

SBOL2/pIKE_pTAK_cassettes 2.rdf SBOL error 12:File not found libc++abi.dylib: terminating with uncaught exception of type sbol::SBOLErrorCode ./script.sh: line 3: 87753 Abort trap: 6 ./ReadWriteTestlibSBOL $f Out/$f libSBOLj version 2.1.2 Description: validates the contents of an SBOL 2.0 document, can compare two documents, and can convert to/from SBOL 1.1, GenBank, and FASTA formats.

Usage: java --jar libSBOLj.jar [options] [-o -e ]

Options: -l specfies language (SBOL1/SBOL2/GenBank/FASTA) for output (default=SBOL2) -s select only this object and those it references -p used for converted objects -v used for converted objects -t uses types in URIs -n allow non-compliant URIs -i allow SBOL document to be incomplete -b check best practices -f fail on first error -d display detailed error trace

SBOL2/pIKE_pTAK_cassettes.rdf Collection http://www.async.ece.utah.edu/ToggleSwitchCassettes not found in outputFile Validation successful, no errors.

SBOL2/pIKE_pTAK_left_right_cassettes.rdf Collection http://www.async.ece.utah.edu/ToggleSwitchCassettes not found in outputFile Validation successful, no errors.

SBOL2/pIKE_pTAK_toggle_switches.rdf Validation successful, no errors.

SBOL2/partial_pIKE_left_cassette.rdf ./script.sh: line 3: 87774 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f File is empty. Conversion failed.

SBOL2/partial_pIKE_right_casette.rdf ./script.sh: line 3: 87776 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f File is empty. Conversion failed.

SBOL2/partial_pIKE_right_cassette.rdf ./script.sh: line 3: 87778 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f File is empty. Conversion failed.

SBOL2/partial_pTAK_left_cassette.rdf ./script.sh: line 3: 87780 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f File is empty. Conversion failed.

SBOL2/partial_pTAK_right_cassette.rdf ./script.sh: line 3: 87782 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f File is empty. Conversion failed.

SBOL2/sampleToggleSwitch.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org} not found in outputFile Collection http://www.async.ece.utah.edu/myParts/1/0 not found in outputFile ComponentDefinition http://www.async.ece.utah.edu/ptetlacI/1/0 differ. ->Component T not found in outputFile ->Component L not found in outputFile ->SequenceAnnotation p2_structAnnotate not found in outputFile ->SequenceAnnotation c2_structAnnotate not found in outputFile ->SequenceAnnotation http://sbols.org/c2_structAnnotate not found in originalFile ->SequenceAnnotation http://sbols.org/p2_structAnnotate not found in originalFile ComponentDefinition http://www.async.ece.utah.edu/pLactetR/1/0 not found in outputFile GenericTopLevel http://www.async.ece.utah.edu/GenericTopLevel/1/0 not found in outputFile sbol-11403: The Component referenced by the subject property of a SequenceConstraint MUST be contained by the ComponentDefinition that contains the SequenceConstraint. Reference: SBOL Version 2.1.0 Section 7.7.6 on page 36 : http://sbols.org/struct_constraint

Validation failed.

SBOL2/sequence1.rdf Namespace {http://www.ncbi.nlm.nih.gov} not found in outputFile Validation successful, no errors.

SBOL2/sequence2.rdf Namespace {http://www.ncbi.nlm.nih.gov} not found in outputFile Validation successful, no errors.

SBOL2/sequence3.rdf Namespace {http://www.ncbi.nlm.nih.gov} not found in outputFile Validation successful, no errors.

SBOL2/sequence4.rdf Namespace {http://www.ncbi.nlm.nih.gov} not found in outputFile Validation successful, no errors.

SBOL2/singleCollection.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org} not found in outputFile Collection http://www.async.ece.utah.edu/myParts/1.0 not found in outputFile Validation successful, no errors.

SBOL2/singleCompDef_withSeq.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org} not found in outputFile Validation successful, no errors.

SBOL2/singleComponentDefinition.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org} not found in outputFile Validation successful, no errors.

SBOL2/singleFunctionalComponent.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org} not found in outputFile Validation successful, no errors.

SBOL2/singleGenericTopLevel.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org} not found in outputFile GenericTopLevel http://www.async.ece.utah.edu/GenericTopLevel/1.0 not found in outputFile Validation successful, no errors.

SBOL2/singleModel.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org} not found in outputFile Model http://www.async.ece.utah.edu/ToggleModel/1.0 differ. Validation successful, no errors.

SBOL2/singleModuleDefinition.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org} not found in outputFile Validation successful, no errors.

SBOL2/singleSequence.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org} not found in outputFile Validation successful, no errors.

SBOL2/test_Collection_remove.rdf Namespace {http://partsregistry.org} not found in outputFile Validation successful, no errors.

SBOL2/test_ComponentDefinition_remove.rdf Namespace {http://partsregistry.org} not found in outputFile Validation successful, no errors.

SBOL2/test_GenericTopLevel_remove.rdf Namespace {http://partsregistry.org} not found in outputFile Validation successful, no errors.

SBOL2/test_Methods.rdf Namespace {http://partsregistry.org} not found in outputFile Validation successful, no errors.

SBOL2/test_Model_remove.rdf Namespace {http://partsregistry.org} not found in outputFile Validation successful, no errors.

SBOL2/test_ModuleDefinition_remove.rdf Namespace {http://partsregistry.org} not found in outputFile Validation successful, no errors.

SBOL2/test_Sequence_remove.rdf Namespace {http://partsregistry.org} not found in outputFile Validation successful, no errors.

SBOL2/toggle.rdf ./script.sh: line 3: 87830 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f File is empty. Conversion failed.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

[cjmyers]

I updated the library on my machine, and now I'm getting the segmentation faults that Meher was seeing on writing I think. So, something you guys have done recently has broken writing.

I've also updated the namespaces to have a delimiter at the end in all cases. Attached is latest test directory. ReadWriteTestlibSBOL.zip

[cjmyers]

I updated the library on my machine, and now I'm getting the segmentation faults that Meher was seeing on writing I think. So, something you guys have done recently has broken writing.

I've also updated the namespaces to have a delimiter at the end in all cases. The latest test directory is posted to github issue.

Chris

On Jan 4, 2017, at 11:33 PM, bbartley <notifications@github.com mailto:notifications@github.com> wrote:

Collections, Generic Locations are not currently implemented. Additionally, Cut objects are serialized but not read. These are all quick fixes, however. At least one seg-fault is caused by a namespace missing a prefix. In the file SBOL1and2Test.rdf, the "http://sbols.org/v1# http://sbols.org/v1#" namespace lacks a prefix. Is this valid? There is another issue with namespaces in AnnotationOutput.rdf. The namespace xmlns:pr="http://partsregistry.org http://partsregistry.org/" is lacking a terminal delimiter such as '#' or '/'. Is this valid? It is not consistent with other namespaces and does not seem to parse correctly with RDF tools. This is causing problems with how libSBOL parses data in extension namespaces. From: cjmyers <notifications@github.com mailto:notifications@github.com> To: SynBioDex/libSBOL <libSBOL@noreply.github.com mailto:libSBOL@noreply.github.com> Cc: Subscribed <subscribed@noreply.github.com mailto:subscribed@noreply.github.com> Sent: Wednesday, January 4, 2017 7:32 PM Subject: Re: [SynBioDex/libSBOL] Segmentation Fault on Doc.Write() (#114)

This appears to be a windows only problem. I think paths on windows are a problem.

I can get the program and script working on Mac, but there are still a lot of errors. Results, C program, and script are attached (zip file on github issue tracker). Here are some of the problems found:

1) Namespaces are getting dropped 2) Collections are getting dropped 3) GenericTopLevels are getting dropped 4) Some files simply get a segmentation fault 5) Several other files have differences in the output file.

Please use this to test your library. These bugs needed to be released before the library is safe to use.

Chris

On Jan 4, 2017, at 5:22 PM, mehersam <notifications@github.com mailto:notifications@github.com <mailto:notifications@github.com mailto:notifications@github.com>> wrote:

We are getting segmentation fault errors when reading a SBOL2 file and then writing the read in file. The seg fault is happening on the write.

A simple C++ program was created that takes in a file on input and reads the file into a document and writes a new file out. To test this, a shell script was created that iterates through a series of SBOL2 files and calls the C++ program and then calls the libSBOLj jar file and compares the written file to the original read in file. However, a seg fault is thrown when attempting to write the file.

I am including a link to zip file with the C++ program along with the shell script and the results of running the script which shows the seg fault error.

result.txt <https://github.com/SynBioDex/libSBOL/files/686161/result.txt https://github.com/SynBioDex/libSBOL/files/686161/result.txt> Final_Testing_of_LibSBOL <https://drive.google.com/open?id=0B_fQ3zF70irFd1NLeXV0SkhmNGs https://drive.google.com/open?id=0B_fQ3zF70irFd1NLeXV0SkhmNGs> — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <https://github.com/SynBioDex/libSBOL/issues/114 https://github.com/SynBioDex/libSBOL/issues/114>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADWD93jRzZKwHmjSSZJOTaKZkcb193zJks5rPDe_gaJpZM4LbNyq https://github.com/notifications/unsubscribe-auth/ADWD93jRzZKwHmjSSZJOTaKZkcb193zJks5rPDe_gaJpZM4LbNyq>.

SBOL2/AnnotationOutput.rdf Namespace {http://partsregistry.org http://partsregistry.org/} not found in outputFile Validation successful, no errors.

SBOL2/BBa_I0462.rdf Validation successful, no errors.

SBOL2/BBa_T9002.rdf ./script.sh: line 3: 87635 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f File is empty. Conversion failed.

SBOL2/CollectionOutput.rdf Collection http://parts.igem.org/Promoters/Catalog/Anderson http://parts.igem.org/Promoters/Catalog/Anderson not found in outputFile Validation successful, no errors.

SBOL2/ComponentDefinitionOutput.rdf Namespace {http://partsregistry.org http://partsregistry.org/} not found in outputFile Validation successful, no errors.

SBOL2/CreateAndRemoveCollections.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org http://myannotation.org/} not found in outputFile Collection http://www.async.ece.utah.edu/myParts/1.0 http://www.async.ece.utah.edu/myParts/1.0 not found in outputFile Validation successful, no errors.

SBOL2/CreateAndRemoveComponentDefinition.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org http://myannotation.org/} not found in outputFile Validation successful, no errors.

SBOL2/CreateAndRemoveGenericTopLevel.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org http://myannotation.org/} not found in outputFile GenericTopLevel http://www.async.ece.utah.edu/someGenTopLev/1.0 http://www.async.ece.utah.edu/someGenTopLev/1.0 not found in outputFile Validation successful, no errors.

SBOL2/CreateAndRemoveModel.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org http://myannotation.org/} not found in outputFile Collection http://www.async.ece.utah.edu/someSequence2/1.0 http://www.async.ece.utah.edu/someSequence2/1.0 not found in outputFile Collection http://www.async.ece.utah.edu/someSequence1/1.0 http://www.async.ece.utah.edu/someSequence1/1.0 not found in outputFile Collection http://www.async.ece.utah.edu/someSequence3/1.0 http://www.async.ece.utah.edu/someSequence3/1.0 not found in outputFile Validation successful, no errors.

SBOL2/CreateAndRemoveModuleDefinition.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org http://myannotation.org/} not found in outputFile Validation successful, no errors.

SBOL2/CutExample.rdf ./script.sh: line 3: 87652 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f File is empty. Conversion failed.

SBOL2/GenericTopLevelOutput.rdf Namespace {http://www.myapp.org http://www.myapp.org/} not found in outputFile GenericTopLevel http://www.partsregistry.org/gen/datasheet1 http://www.partsregistry.org/gen/datasheet1 not found in outputFile Validation successful, no errors.

SBOL2/ModelOutput.rdf Validation successful, no errors.

SBOL2/ModuleDefinitionOutput.rdf ./script.sh: line 3: 87658 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f File is empty. Conversion failed.

SBOL2/RepressionModel.rdf ./script.sh: line 3: 87660 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f File is empty. Conversion failed.

SBOL2/SBOL1and2Test.rdf ./script.sh: line 3: 87662 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f Out/SBOL2/SBOL1and2Test.rdf (No such file or directory) I/O exception. java.io.FileNotFoundException: Out/SBOL2/SBOL1and2Test.rdf (No such file or directory) at java.io.FileInputStream.open(Native Method) at java.io.FileInputStream.(FileInputStream.java:146) at org.sbolstandard.core2.SBOLReader.read(SBOLReader.java:446) at org.sbolstandard.core2.SBOLReader.read(SBOLReader.java:379) at org.sbolstandard.core2.SBOLReader.read(SBOLReader.java:364) at org.sbolstandard.core2.SBOLValidate.validate(SBOLValidate.java:1568) at org.sbolstandard.core2.SBOLValidate.main(SBOLValidate.java:1816)

SBOL2/SBOLDocumentOutput.rdf Validation successful, no errors.

SBOL2/SequenceConstraintOutput.rdf Validation successful, no errors.

SBOL2/SequenceOutput.rdf Validation successful, no errors.

SBOL2/SimpleComponentDefinitionExample.rdf Validation successful, no errors.

SBOL2/SimpleModuleDefinition.rdf Validation successful, no errors.

SBOL2/igem1.rdf Namespace {http://www.w3.org/2000/01/rdf-schema# http://www.w3.org/2000/01/rdf-schema#} not found in outputFile Namespace {http://sbolhub.org/ http://sbolhub.org/} not found in outputFile Namespace {http://parts.igem.org/# http://parts.igem.org/#} not found in outputFile Namespace {http://www.w3.org/2002/07/owl# http://www.w3.org/2002/07/owl#} not found in outputFile Namespace {http://www.w3.org/2001/XMLSchema# http://www.w3.org/2001/XMLSchema#} not found in outputFile Namespace {http://www.openrdf.org/schema/sesame# http://www.openrdf.org/schema/sesame#} not found in outputFile Namespace {http://www.w3.org/2005/xpath-functions# http://www.w3.org/2005/xpath-functions#} not found in outputFile Collection http://sbolhub.org/col/igem_sbol2_151015212715 http://sbolhub.org/col/igem_sbol2_151015212715 not found in outputFile Sequence http://parts.igem.org/Part:BBa_I742134#sequence http://parts.igem.org/Part:BBa_I742134#sequence not found in outputFile Sequence http://parts.igem.org/Part:BBa_I766203#sequence http://parts.igem.org/Part:BBa_I766203#sequence not found in outputFile GenericTopLevel http://sbolhub.org/gen/igem_sbol2_151015212715 http://sbolhub.org/gen/igem_sbol2_151015212715 not found in outputFile sbol-10402: The elements property of a Sequence is REQUIRED and MUST contain a String. Reference: SBOL Version 2.1.0 Section 7.6 on page 20 : http://parts.igem.org/Part:BBa_I742134#sequence http://parts.igem.org/Part:BBa_I742134#sequence

sbol-10402: The elements property of a Sequence is REQUIRED and MUST contain a String. Reference: SBOL Version 2.1.0 Section 7.6 on page 20 : http://parts.igem.org/Part:BBa_I766203#sequence http://parts.igem.org/Part:BBa_I766203#sequence

Validation failed.

SBOL2/igem2.rdf Namespace {http://www.w3.org/2000/01/rdf-schema# http://www.w3.org/2000/01/rdf-schema#} not found in outputFile Namespace {http://sbolhub.org/ http://sbolhub.org/} not found in outputFile Namespace {http://parts.igem.org/# http://parts.igem.org/#} not found in outputFile Namespace {http://www.w3.org/2002/07/owl# http://www.w3.org/2002/07/owl#} not found in outputFile Namespace {http://www.w3.org/2001/XMLSchema# http://www.w3.org/2001/XMLSchema#} not found in outputFile Namespace {http://www.openrdf.org/schema/sesame# http://www.openrdf.org/schema/sesame#} not found in outputFile Namespace {http://www.w3.org/2005/xpath-functions# http://www.w3.org/2005/xpath-functions#} not found in outputFile Collection http://sbolhub.org/col/igem_sbol2_151015212742 http://sbolhub.org/col/igem_sbol2_151015212742 not found in outputFile Sequence http://parts.igem.org/Part:BBa_I716256#sequence http://parts.igem.org/Part:BBa_I716256#sequence not found in outputFile GenericTopLevel http://sbolhub.org/gen/igem_sbol2_151015212742 http://sbolhub.org/gen/igem_sbol2_151015212742 not found in outputFile sbol-10402: The elements property of a Sequence is REQUIRED and MUST contain a String. Reference: SBOL Version 2.1.0 Section 7.6 on page 20 : http://parts.igem.org/Part:BBa_I716256#sequence http://parts.igem.org/Part:BBa_I716256#sequence

Validation failed.

SBOL2/igem3.rdf Namespace {http://www.w3.org/2000/01/rdf-schema# http://www.w3.org/2000/01/rdf-schema#} not found in outputFile Namespace {http://sbolhub.org/ http://sbolhub.org/} not found in outputFile Namespace {http://parts.igem.org/# http://parts.igem.org/#} not found in outputFile Namespace {http://www.w3.org/2002/07/owl# http://www.w3.org/2002/07/owl#} not found in outputFile Namespace {http://www.w3.org/2001/XMLSchema# http://www.w3.org/2001/XMLSchema#} not found in outputFile Namespace {http://www.openrdf.org/schema/sesame# http://www.openrdf.org/schema/sesame#} not found in outputFile Namespace {http://www.w3.org/2005/xpath-functions# http://www.w3.org/2005/xpath-functions#} not found in outputFile Collection http://sbolhub.org/col/igem_sbol2_151015212923 http://sbolhub.org/col/igem_sbol2_151015212923 not found in outputFile GenericTopLevel http://sbolhub.org/gen/igem_sbol2_151015212923 http://sbolhub.org/gen/igem_sbol2_151015212923 not found in outputFile Validation successful, no errors.

SBOL2/labhost_All.rdf Collection http://www.async.ece.utah.edu/Pichia_pastoris http://www.async.ece.utah.edu/Pichia_pastoris not found in outputFile Collection http://www.async.ece.utah.edu/Aspergillus_nidulans http://www.async.ece.utah.edu/Aspergillus_nidulans not found in outputFile Collection http://www.async.ece.utah.edu/Gram_negative_bacteria http://www.async.ece.utah.edu/Gram_negative_bacteria not found in outputFile Collection http://www.async.ece.utah.edu/Plant_Cells http://www.async.ece.utah.edu/Plant_Cells not found in outputFile Collection http://www.async.ece.utah.edu/Schizosaccharomyces_pombe http://www.async.ece.utah.edu/Schizosaccharomyces_pombe not found in outputFile Collection http://www.async.ece.utah.edu/Mammalian_Cells http://www.async.ece.utah.edu/Mammalian_Cells not found in outputFile Collection http://www.async.ece.utah.edu/Drosophila_melanogaster http://www.async.ece.utah.edu/Drosophila_melanogaster not found in outputFile Collection http://www.async.ece.utah.edu/Saccharomyces_cerevisiae http://www.async.ece.utah.edu/Saccharomyces_cerevisiae not found in outputFile Collection http://www.async.ece.utah.edu/Unspecified_labhost http://www.async.ece.utah.edu/Unspecified_labhost not found in outputFile Collection http://www.async.ece.utah.edu/Insect_Cells http://www.async.ece.utah.edu/Insect_Cells not found in outputFile Collection http://www.async.ece.utah.edu/Bacillus_subtilis http://www.async.ece.utah.edu/Bacillus_subtilis not found in outputFile Collection http://www.async.ece.utah.edu/Escherichia_Coli http://www.async.ece.utah.edu/Escherichia_Coli not found in outputFile Collection http://www.async.ece.utah.edu/Kluyveromyces_lactis http://www.async.ece.utah.edu/Kluyveromyces_lactis not found in outputFile ComponentDefinition http://www.async.ece.utah.edu/lac_UV5_promoter_003 http://www.async.ece.utah.edu/lac_UV5_promoter_003 differ. ComponentDefinition http://www.async.ece.utah.edu/lac_UV5_promoter_001 http://www.async.ece.utah.edu/lac_UV5_promoter_001 differ. ComponentDefinition http://www.async.ece.utah.edu/lac_UV5_promoter_002 http://www.async.ece.utah.edu/lac_UV5_promoter_002 differ. Validation successful, no errors.

SBOL2/labhost_Aspergillus_nidulans.rdf Collection http://www.async.ece.utah.edu/Aspergillus_nidulans http://www.async.ece.utah.edu/Aspergillus_nidulans not found in outputFile Validation successful, no errors.

SBOL2/labhost_Bacillus_subtilis.rdf Collection http://www.async.ece.utah.edu/Bacillus_subtilis http://www.async.ece.utah.edu/Bacillus_subtilis not found in outputFile Validation successful, no errors.

SBOL2/labhost_Drosophila_melanogaster.rdf Collection http://www.async.ece.utah.edu/Drosophila_melanogaster http://www.async.ece.utah.edu/Drosophila_melanogaster not found in outputFile Validation successful, no errors.

SBOL2/labhost_Escherichia_Coli.rdf Collection http://www.async.ece.utah.edu/Escherichia_Coli http://www.async.ece.utah.edu/Escherichia_Coli not found in outputFile ComponentDefinition http://www.async.ece.utah.edu/lac_UV5_promoter_001 http://www.async.ece.utah.edu/lac_UV5_promoter_001 differ. ComponentDefinition http://www.async.ece.utah.edu/lac_UV5_promoter_002 http://www.async.ece.utah.edu/lac_UV5_promoter_002 differ. Validation successful, no errors.

SBOL2/labhost_Gram-negative_bacteria.rdf Collection http://www.async.ece.utah.edu/Gram_negative_bacteria http://www.async.ece.utah.edu/Gram_negative_bacteria not found in outputFile Validation successful, no errors.

SBOL2/labhost_Insect_Cells.rdf Collection http://www.async.ece.utah.edu/Insect_Cells http://www.async.ece.utah.edu/Insect_Cells not found in outputFile ComponentDefinition http://www.async.ece.utah.edu/lac_UV5_promoter_002 http://www.async.ece.utah.edu/lac_UV5_promoter_002 differ. Validation successful, no errors.

SBOL2/labhost_Kluyveromyces_lactis.rdf Collection http://www.async.ece.utah.edu/Kluyveromyces_lactis http://www.async.ece.utah.edu/Kluyveromyces_lactis not found in outputFile Validation successful, no errors.

SBOL2/labhost_Mammalian_Cells.rdf Collection http://www.async.ece.utah.edu/Mammalian_Cells http://www.async.ece.utah.edu/Mammalian_Cells not found in outputFile ComponentDefinition http://www.async.ece.utah.edu/lac_UV5_promoter_002 http://www.async.ece.utah.edu/lac_UV5_promoter_002 differ. ComponentDefinition http://www.async.ece.utah.edu/lac_UV5_promoter_003 http://www.async.ece.utah.edu/lac_UV5_promoter_003 differ. Validation successful, no errors.

SBOL2/labhost_Pichia_pastoris.rdf Collection http://www.async.ece.utah.edu/Pichia_pastoris http://www.async.ece.utah.edu/Pichia_pastoris not found in outputFile Validation successful, no errors.

SBOL2/labhost_Plant_Cells.rdf Collection http://www.async.ece.utah.edu/Plant_Cells http://www.async.ece.utah.edu/Plant_Cells not found in outputFile ComponentDefinition http://www.async.ece.utah.edu/lac_UV5_promoter_002 http://www.async.ece.utah.edu/lac_UV5_promoter_002 differ. Validation successful, no errors.

SBOL2/labhost_Saccharomyces_cerevisiae.rdf Collection http://www.async.ece.utah.edu/Saccharomyces_cerevisiae http://www.async.ece.utah.edu/Saccharomyces_cerevisiae not found in outputFile Validation successful, no errors.

SBOL2/labhost_Schizosaccharomyces_pombe.rdf Collection http://www.async.ece.utah.edu/Schizosaccharomyces_pombe http://www.async.ece.utah.edu/Schizosaccharomyces_pombe not found in outputFile Validation successful, no errors.

SBOL2/labhost_Unspecified.rdf Collection http://www.async.ece.utah.edu/Unspecified_labhost http://www.async.ece.utah.edu/Unspecified_labhost not found in outputFile ComponentDefinition http://www.async.ece.utah.edu/lac_UV5_promoter_002 http://www.async.ece.utah.edu/lac_UV5_promoter_002 differ. Validation successful, no errors.

SBOL2/memberAnnotations.rdf ./script.sh: line 3: 87738 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f File is empty. Conversion failed.

SBOL2/multipleCollections_no_Members.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org http://myannotation.org/} not found in outputFile Collection http://www.async.ece.utah.edu/myPart3/1.0 http://www.async.ece.utah.edu/myPart3/1.0 not found in outputFile Collection http://www.async.ece.utah.edu/myPart2/1.0 http://www.async.ece.utah.edu/myPart2/1.0 not found in outputFile Collection http://www.async.ece.utah.edu/myPart1/1.0 http://www.async.ece.utah.edu/myPart1/1.0 not found in outputFile Validation successful, no errors.

SBOL2/multipleGenericTopLevel.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org http://myannotation.org/} not found in outputFile GenericTopLevel http://www.async.ece.utah.edu/GenericTopLevel3/1.0 http://www.async.ece.utah.edu/GenericTopLevel3/1.0 not found in outputFile GenericTopLevel http://www.async.ece.utah.edu/GenericTopLevel1/1.0 http://www.async.ece.utah.edu/GenericTopLevel1/1.0 not found in outputFile GenericTopLevel http://www.async.ece.utah.edu/GenericTopLevel2/1.0 http://www.async.ece.utah.edu/GenericTopLevel2/1.0 not found in outputFile Validation successful, no errors.

SBOL2/multipleSequences.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org http://myannotation.org/} not found in outputFile Validation successful, no errors.

SBOL2/namespace.rdf Validation successful, no errors.

SBOL2/new_AnnotationOutput.rdf Namespace {http://purl.org/dc/terms/# http://purl.org/dc/terms/#} not found in outputFile Namespace {http://purl.org/dc/terms/ http://purl.org/dc/terms/} not found in originalFile Validation successful, no errors.

SBOL2/new_BBa_I0462.rdf Serialization error: XML Parsing failed - no element found RAPTOR_LOG_LEVEL_ERROR -1, -1 http://sbols.org/v2# http://sbols.org/v2# Serialization error: XML Parsing failed - no element found RAPTOR_LOG_LEVEL_ERROR -1, -1 http://sbols.org/v2# http://sbols.org/v2# SBOL error 7:Missing namespace http://sbols.org/v2# http://sbols.org/v2# SBOL error 7:Missing namespace http://www.w3.org/1999/02/22-rdf-syntax-ns# http://www.w3.org/1999/02/22-rdf-syntax-ns# File is empty. Conversion failed.

SBOL2/pIKE_pTAK_cassettes 2.rdf SBOL error 12:File not found libc++abi.dylib: terminating with uncaught exception of type sbol::SBOLErrorCode ./script.sh: line 3: 87753 Abort trap: 6 ./ReadWriteTestlibSBOL $f Out/$f libSBOLj version 2.1.2 Description: validates the contents of an SBOL 2.0 document, can compare two documents, and can convert to/from SBOL 1.1, GenBank, and FASTA formats.

Usage: java --jar libSBOLj.jar [options] [-o -e ]

Options: -l specfies language (SBOL1/SBOL2/GenBank/FASTA) for output (default=SBOL2) -s select only this object and those it references -p used for converted objects -v used for converted objects -t uses types in URIs -n allow non-compliant URIs -i allow SBOL document to be incomplete -b check best practices -f fail on first error -d display detailed error trace

SBOL2/pIKE_pTAK_cassettes.rdf Collection http://www.async.ece.utah.edu/ToggleSwitchCassettes http://www.async.ece.utah.edu/ToggleSwitchCassettes not found in outputFile Validation successful, no errors.

SBOL2/pIKE_pTAK_left_right_cassettes.rdf Collection http://www.async.ece.utah.edu/ToggleSwitchCassettes http://www.async.ece.utah.edu/ToggleSwitchCassettes not found in outputFile Validation successful, no errors.

SBOL2/pIKE_pTAK_toggle_switches.rdf Validation successful, no errors.

SBOL2/partial_pIKE_left_cassette.rdf ./script.sh: line 3: 87774 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f File is empty. Conversion failed.

SBOL2/partial_pIKE_right_casette.rdf ./script.sh: line 3: 87776 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f File is empty. Conversion failed.

SBOL2/partial_pIKE_right_cassette.rdf ./script.sh: line 3: 87778 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f File is empty. Conversion failed.

SBOL2/partial_pTAK_left_cassette.rdf ./script.sh: line 3: 87780 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f File is empty. Conversion failed.

SBOL2/partial_pTAK_right_cassette.rdf ./script.sh: line 3: 87782 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f File is empty. Conversion failed.

SBOL2/sampleToggleSwitch.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org http://myannotation.org/} not found in outputFile Collection http://www.async.ece.utah.edu/myParts/1/0 http://www.async.ece.utah.edu/myParts/1/0 not found in outputFile ComponentDefinition http://www.async.ece.utah.edu/ptetlacI/1/0 http://www.async.ece.utah.edu/ptetlacI/1/0 differ. ->Component T not found in outputFile ->Component L not found in outputFile ->SequenceAnnotation p2_structAnnotate not found in outputFile ->SequenceAnnotation c2_structAnnotate not found in outputFile ->SequenceAnnotation http://sbols.org/c2_structAnnotate http://sbols.org/c2_structAnnotate not found in originalFile ->SequenceAnnotation http://sbols.org/p2_structAnnotate http://sbols.org/p2_structAnnotate not found in originalFile ComponentDefinition http://www.async.ece.utah.edu/pLactetR/1/0 http://www.async.ece.utah.edu/pLactetR/1/0 not found in outputFile GenericTopLevel http://www.async.ece.utah.edu/GenericTopLevel/1/0 http://www.async.ece.utah.edu/GenericTopLevel/1/0 not found in outputFile sbol-11403: The Component referenced by the subject property of a SequenceConstraint MUST be contained by the ComponentDefinition that contains the SequenceConstraint. Reference: SBOL Version 2.1.0 Section 7.7.6 on page 36 : http://sbols.org/struct_constraint http://sbols.org/struct_constraint

Validation failed.

SBOL2/sequence1.rdf Namespace {http://www.ncbi.nlm.nih.gov http://www.ncbi.nlm.nih.gov/} not found in outputFile Validation successful, no errors.

SBOL2/sequence2.rdf Namespace {http://www.ncbi.nlm.nih.gov http://www.ncbi.nlm.nih.gov/} not found in outputFile Validation successful, no errors.

SBOL2/sequence3.rdf Namespace {http://www.ncbi.nlm.nih.gov http://www.ncbi.nlm.nih.gov/} not found in outputFile Validation successful, no errors.

SBOL2/sequence4.rdf Namespace {http://www.ncbi.nlm.nih.gov http://www.ncbi.nlm.nih.gov/} not found in outputFile Validation successful, no errors.

SBOL2/singleCollection.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org http://myannotation.org/} not found in outputFile Collection http://www.async.ece.utah.edu/myParts/1.0 http://www.async.ece.utah.edu/myParts/1.0 not found in outputFile Validation successful, no errors.

SBOL2/singleCompDef_withSeq.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org http://myannotation.org/} not found in outputFile Validation successful, no errors.

SBOL2/singleComponentDefinition.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org http://myannotation.org/} not found in outputFile Validation successful, no errors.

SBOL2/singleFunctionalComponent.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org http://myannotation.org/} not found in outputFile Validation successful, no errors.

SBOL2/singleGenericTopLevel.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org http://myannotation.org/} not found in outputFile GenericTopLevel http://www.async.ece.utah.edu/GenericTopLevel/1.0 http://www.async.ece.utah.edu/GenericTopLevel/1.0 not found in outputFile Validation successful, no errors.

SBOL2/singleModel.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org http://myannotation.org/} not found in outputFile Model http://www.async.ece.utah.edu/ToggleModel/1.0 http://www.async.ece.utah.edu/ToggleModel/1.0 differ. Validation successful, no errors.

SBOL2/singleModuleDefinition.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org http://myannotation.org/} not found in outputFile Validation successful, no errors.

SBOL2/singleSequence.rdf Namespace {urn:bbn.com:tasbe:grn} not found in outputFile Namespace {http://myannotation.org http://myannotation.org/} not found in outputFile Validation successful, no errors.

SBOL2/test_Collection_remove.rdf Namespace {http://partsregistry.org http://partsregistry.org/} not found in outputFile Validation successful, no errors.

SBOL2/test_ComponentDefinition_remove.rdf Namespace {http://partsregistry.org http://partsregistry.org/} not found in outputFile Validation successful, no errors.

SBOL2/test_GenericTopLevel_remove.rdf Namespace {http://partsregistry.org http://partsregistry.org/} not found in outputFile Validation successful, no errors.

SBOL2/test_Methods.rdf Namespace {http://partsregistry.org http://partsregistry.org/} not found in outputFile Validation successful, no errors.

SBOL2/test_Model_remove.rdf Namespace {http://partsregistry.org http://partsregistry.org/} not found in outputFile Validation successful, no errors.

SBOL2/test_ModuleDefinition_remove.rdf Namespace {http://partsregistry.org http://partsregistry.org/} not found in outputFile Validation successful, no errors.

SBOL2/test_Sequence_remove.rdf Namespace {http://partsregistry.org http://partsregistry.org/} not found in outputFile Validation successful, no errors.

SBOL2/toggle.rdf ./script.sh: line 3: 87830 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f File is empty. Conversion failed.

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[kirichoi]

Issue seems fixed on commit e0038313afa2a1cc9992eb5a8689096f3bf253e4. Tested on Mac and Windows. There is a file called 'SBOL1and2Test.rdf' that fails, but this file also fails to be validated on online validator. In fact, multiple test files are actually invalid according to validator.

[cjmyers]

Which ones and which options? You should allow incomplete and non compliant Uris

Chris

Sent from my iPhone

On Jan 10, 2017, at 10:52 PM, Kiri Choi notifications@github.com wrote:

Issue seems fixed on commit e003831. Tested on Mac and Windows. There is a file called 'SBOL1and2Test.rdf' that fails, but this file also fails to be validated on online validator. In fact, multiple test files are actually invalid according to validator.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

[cjmyers]

This would not compile for me:

[myers@jiaqi ReadWriteTestlibSBOL]$ g++ -std=c++11 -I../libSBOL/source -I/usr/local/include/raptor2 -L/usr/local/lib -lraptor2 -ljsoncpp -lcurl -lsbol ReadWriteTestlibSBOL.cpp Undefined symbols for architecture x86_64: "sbol::URIProperty::get()", referenced from: sbol::Property<std::1::basic_string<char, std::__1::char_traits, std::1::allocator > >::write() in ReadWriteTestlibSBOL-809b7e.o sbol::Property::write() in ReadWriteTestlibSBOL-809b7e.o sbol::Property::write() in ReadWriteTestlibSBOL-809b7e.o sbol::Property::write() in ReadWriteTestlibSBOL-809b7e.o sbol::Property::write() in ReadWriteTestlibSBOL-809b7e.o sbol::Property::write() in ReadWriteTestlibSBOL-809b7e.o ld: symbol(s) not found for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation)

On Jan 10, 2017, at 10:52 PM, Kiri Choi notifications@github.com wrote:

Issue seems fixed on commit e003831 https://github.com/SynBioDex/libSBOL/commit/e0038313afa2a1cc9992eb5a8689096f3bf253e4. Tested on Mac and Windows. There is a file called 'SBOL1and2Test.rdf' that fails, but this file also fails to be validated on online validator. In fact, multiple test files are actually invalid according to validator.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/SynBioDex/libSBOL/issues/114#issuecomment-271723938, or mute the thread https://github.com/notifications/unsubscribe-auth/ADWD9x6KjA0GsIxrqRQvxdQpvF1BPQzTks5rRAuqgaJpZM4LbNyq.

[cjmyers]

I forgot make install. After that in compiled, but I still get write error:

[myers@jiaqi ReadWriteTestlibSBOL]$ ./script.sh SBOL2/AnnotationOutput.rdf ./script.sh: line 3: 97379 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f Out/SBOL2/AnnotationOutput.rdf (No such file or directory) I/O exception. java.io.FileNotFoundException: Out/SBOL2/AnnotationOutput.rdf (No such file or directory) at java.io.FileInputStream.open(Native Method) at java.io.FileInputStream.(FileInputStream.java:146) at org.sbolstandard.core2.SBOLReader.read(SBOLReader.java:446) at org.sbolstandard.core2.SBOLReader.read(SBOLReader.java:379) at org.sbolstandard.core2.SBOLReader.read(SBOLReader.java:364) at org.sbolstandard.core2.SBOLValidate.validate(SBOLValidate.java:1568) at org.sbolstandard.core2.SBOLValidate.main(SBOLValidate.java:1816)

On Jan 10, 2017, at 10:52 PM, Kiri Choi notifications@github.com wrote:

Issue seems fixed on commit e003831 https://github.com/SynBioDex/libSBOL/commit/e0038313afa2a1cc9992eb5a8689096f3bf253e4. Tested on Mac and Windows. There is a file called 'SBOL1and2Test.rdf' that fails, but this file also fails to be validated on online validator. In fact, multiple test files are actually invalid according to validator.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/SynBioDex/libSBOL/issues/114#issuecomment-271723938, or mute the thread https://github.com/notifications/unsubscribe-auth/ADWD9x6KjA0GsIxrqRQvxdQpvF1BPQzTks5rRAuqgaJpZM4LbNyq.

[mehersam]

This actually looks like a read error. I found that I had to keep my files in the exact same location as the .cpp file.

Best,

Meher Samineni mehersam251@gmail.com 801-654-8841

On Tue, Jan 10, 2017 at 4:48 PM, cjmyers notifications@github.com wrote:

I forgot make install. After that in compiled, but I still get write error:

[myers@jiaqi ReadWriteTestlibSBOL]$ ./script.sh SBOL2/AnnotationOutput.rdf ./script.sh: line 3: 97379 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f Out/SBOL2/AnnotationOutput.rdf (No such file or directory) I/O exception. java.io.FileNotFoundException: Out/SBOL2/AnnotationOutput.rdf (No such file or directory) at java.io.FileInputStream.open(Native Method) at java.io.FileInputStream.(FileInputStream.java:146) at org.sbolstandard.core2.SBOLReader.read(SBOLReader.java:446) at org.sbolstandard.core2.SBOLReader.read(SBOLReader.java:379) at org.sbolstandard.core2.SBOLReader.read(SBOLReader.java:364) at org.sbolstandard.core2.SBOLValidate.validate(SBOLValidate.java:1568) at org.sbolstandard.core2.SBOLValidate.main(SBOLValidate.java:1816)

On Jan 10, 2017, at 10:52 PM, Kiri Choi notifications@github.com wrote:

Issue seems fixed on commit e003831 https://github.com/SynBioDex/ libSBOL/commit/e0038313afa2a1cc9992eb5a8689096f3bf253e4. Tested on Mac and Windows. There is a file called 'SBOL1and2Test.rdf' that fails, but this file also fails to be validated on online validator. In fact, multiple test files are actually invalid according to validator.

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[bbartley]

This possibly looks like a mismatch between the binary and the headers.  If you are using the latest snapshot from the develop branch, you might need to rebuild libsbol and make install it to update the binary.  The command line works and the test file compiles on my machine. B

  From: cjmyers <notifications@github.com>

To: SynBioDex/libSBOL libSBOL@noreply.github.com Cc: bbartley bartleyba@yahoo.com; Comment comment@noreply.github.com Sent: Tuesday, January 10, 2017 3:44 PM Subject: Re: [SynBioDex/libSBOL] Segmentation Fault on Doc.Write() (#114)

This would not compile for me:

[myers@jiaqi ReadWriteTestlibSBOL]$ g++ -std=c++11 -I../libSBOL/source -I/usr/local/include/raptor2 -L/usr/local/lib -lraptor2 -ljsoncpp -lcurl -lsbol ReadWriteTestlibSBOL.cpp Undefined symbols for architecture x86_64: "sbol::URIProperty::get()", referenced from: sbol::Property<std::1::basic_string<char, std::__1::char_traits, std::1::allocator > >::write() in ReadWriteTestlibSBOL-809b7e.o sbol::Property::write() in ReadWriteTestlibSBOL-809b7e.o sbol::Property::write() in ReadWriteTestlibSBOL-809b7e.o sbol::Property::write() in ReadWriteTestlibSBOL-809b7e.o sbol::Property::write() in ReadWriteTestlibSBOL-809b7e.o sbol::Property::write() in ReadWriteTestlibSBOL-809b7e.o ld: symbol(s) not found for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation)

On Jan 10, 2017, at 10:52 PM, Kiri Choi notifications@github.com wrote:

Issue seems fixed on commit e003831 https://github.com/SynBioDex/libSBOL/commit/e0038313afa2a1cc9992eb5a8689096f3bf253e4. Tested on Mac and Windows. There is a file called 'SBOL1and2Test.rdf' that fails, but this file also fails to be validated on online validator. In fact, multiple test files are actually invalid according to validator.

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[kirichoi]

Allowing incomplete and non compliant Uris seems to fix it. The file 'SBOL1and2Test.rdf' still fails, which is not that surprising actually. We can talk about this tomorrow. Other files work okay.

[cjmyers]

The read error is from libSBOLj because the libSBOL program is seg faulting and not producing any output for me. My configure is SBOL_BUILD_64 on and SBOL_BUILD_STATIC on, everything else is off.

Chris

On Jan 10, 2017, at 11:51 PM, mehersam notifications@github.com wrote:

This actually looks like a read error. I found that I had to keep my files in the exact same location as the .cpp file.

Best,

Meher Samineni mehersam251@gmail.com 801-654-8841

On Tue, Jan 10, 2017 at 4:48 PM, cjmyers notifications@github.com wrote:

I forgot make install. After that in compiled, but I still get write error:

[myers@jiaqi ReadWriteTestlibSBOL]$ ./script.sh SBOL2/AnnotationOutput.rdf ./script.sh: line 3: 97379 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f Out/SBOL2/AnnotationOutput.rdf (No such file or directory) I/O exception. java.io.FileNotFoundException: Out/SBOL2/AnnotationOutput.rdf (No such file or directory) at java.io.FileInputStream.open(Native Method) at java.io.FileInputStream.(FileInputStream.java:146) at org.sbolstandard.core2.SBOLReader.read(SBOLReader.java:446) at org.sbolstandard.core2.SBOLReader.read(SBOLReader.java:379) at org.sbolstandard.core2.SBOLReader.read(SBOLReader.java:364) at org.sbolstandard.core2.SBOLValidate.validate(SBOLValidate.java:1568) at org.sbolstandard.core2.SBOLValidate.main(SBOLValidate.java:1816)

On Jan 10, 2017, at 10:52 PM, Kiri Choi notifications@github.com wrote:

Issue seems fixed on commit e003831 https://github.com/SynBioDex/ libSBOL/commit/e0038313afa2a1cc9992eb5a8689096f3bf253e4. Tested on Mac and Windows. There is a file called 'SBOL1and2Test.rdf' that fails, but this file also fails to be validated on online validator. In fact, multiple test files are actually invalid according to validator.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub < https://github.com/SynBioDex/libSBOL/issues/114#issuecomment-271723938>, or mute the thread https://github.com/notifications/unsubscribe-auth/ ADWD9x6KjA0GsIxrqRQvxdQpvF1BPQzTks5rRAuqgaJpZM4LbNyq.

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[cjmyers]

I just tried to build SHARED, and I get linker errors:

[ 9%] Linking CXX shared library ../release/library/libsbol.dylib ld: warning: object file (/usr/local/lib/libjsoncpp.a(json_writer.cpp.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libjsoncpp.a(json_value.cpp.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libjsoncpp.a(json_reader.cpp.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_iostream.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_parse.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_serialize.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_statement.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_uri.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_general.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_namespace.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_term.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_avltree.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_concepts.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(snprintf.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_sequence.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_stringbuffer.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_rfc2396.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_www.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_grddl.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_guess.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(ntriples_parse.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_librdfa.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_rdfxml.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_rss.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(turtle_parser.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_serialize_rss.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_serialize_dot.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_serialize_html.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_serialize_json.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_serialize_ntriples.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_serialize_rdfxml.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_serialize_rdfxmla.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_serialize_turtle.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_libxml.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_log.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_qname.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_ntriples.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_option.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_sax2.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_escaped.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_syntax_description.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_xml.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_abbrev.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_rss_common.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_set.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_json_writer.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_turtle_writer.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_xml_writer.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(context.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(triple.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(rdfa.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_locator.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_memstr.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(sort_r.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(turtle_common.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_unicode.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(raptor_www_curl.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(turtle_lexer.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/opt/local/lib/libxslt.a(transform.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/opt/local/lib/libxslt.a(extensions.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/opt/local/lib/libxslt.a(security.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/opt/local/lib/libxslt.a(xslt.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/opt/local/lib/libxslt.a(xsltutils.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(subject.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(lists.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(rdfa_utils.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(iri.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(curie.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(language.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/usr/local/lib/libraptor2.a(namespace.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/opt/local/lib/libxslt.a(keys.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/opt/local/lib/libxslt.a(pattern.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/opt/local/lib/libxslt.a(attributes.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/opt/local/lib/libxslt.a(templates.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/opt/local/lib/libxslt.a(attrvt.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/opt/local/lib/libxslt.a(namespaces.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/opt/local/lib/libxslt.a(extra.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/opt/local/lib/libxslt.a(documents.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/opt/local/lib/libxslt.a(variables.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/opt/local/lib/libxslt.a(preproc.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/opt/local/lib/libxslt.a(imports.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/opt/local/lib/libxslt.a(xsltlocale.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/opt/local/lib/libxslt.a(numbers.o)) was built for newer OSX version (10.11) than being linked (10.9) ld: warning: object file (/opt/local/lib/libxslt.a(functions.o)) was built for newer OSX version (10.11) than being linked (10.9) Undefined symbols for architecture x86_64: "_CFArrayAppendValue", referenced from: _append_cert_to_array in libcurl.a(libcurl_la-darwinssl.o) "_CFArrayCreate", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) "_CFArrayCreateMutable", referenced from: _darwinssl_connect_step2 in libcurl.a(libcurl_la-darwinssl.o) "_CFArrayGetCount", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) "_CFArrayGetValueAtIndex", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) "_CFDataCreate", referenced from: _append_cert_to_array in libcurl.a(libcurl_la-darwinssl.o) "_CFDictionaryCreate", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) "_CFDictionaryGetValue", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) "_CFRelease", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) _Curl_darwinssl_close in libcurl.a(libcurl_la-darwinssl.o) _darwinssl_connect_step2 in libcurl.a(libcurl_la-darwinssl.o) _append_cert_to_array in libcurl.a(libcurl_la-darwinssl.o) "_CFRetain", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) "_CFStringCreateWithCString", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) "_CFStringGetCString", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) _append_cert_to_array in libcurl.a(libcurl_la-darwinssl.o) "_CFURLCreateDataAndPropertiesFromResource", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) "_CFURLCreateFromFileSystemRepresentation", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) "_SSLClose", referenced from: _Curl_darwinssl_close in libcurl.a(libcurl_la-darwinssl.o) "_SSLCopyPeerTrust", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) _darwinssl_connect_step2 in libcurl.a(libcurl_la-darwinssl.o) "_SSLCreateContext", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) "_SSLGetBufferedReadSize", referenced from: _Curl_darwinssl_data_pending in libcurl.a(libcurl_la-darwinssl.o) "_SSLGetNegotiatedCipher", referenced from: _darwinssl_connect_step2 in libcurl.a(libcurl_la-darwinssl.o) "_SSLGetNegotiatedProtocolVersion", referenced from: _darwinssl_connect_step2 in libcurl.a(libcurl_la-darwinssl.o) "_SSLGetNumberSupportedCiphers", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) "_SSLGetSessionState", referenced from: _Curl_darwinssl_check_cxn in libcurl.a(libcurl_la-darwinssl.o) "_SSLGetSupportedCiphers", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) "_SSLHandshake", referenced from: _darwinssl_connect_step2 in libcurl.a(libcurl_la-darwinssl.o) "_SSLRead", referenced from: _darwinssl_recv in libcurl.a(libcurl_la-darwinssl.o) "_SSLSetCertificate", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) "_SSLSetConnection", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) "_SSLSetEnableCertVerify", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) "_SSLSetEnabledCiphers", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) "_SSLSetIOFuncs", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) "_SSLSetPeerDomainName", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) "_SSLSetPeerID", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) "_SSLSetProtocolVersionMax", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) "_SSLSetProtocolVersionMin", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) "_SSLSetSessionOption", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) "_SSLWrite", referenced from: _darwinssl_send in libcurl.a(libcurl_la-darwinssl.o) "_SecCertificateCopyLongDescription", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) _append_cert_to_array in libcurl.a(libcurl_la-darwinssl.o) "_SecCertificateCreateWithData", referenced from: _append_cert_to_array in libcurl.a(libcurl_la-darwinssl.o) "_SecIdentityCopyCertificate", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) "_SecItemCopyMatching", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) "_SecPKCS12Import", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) "_SecPolicyCreateSSL", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) "_SecTrustEvaluate", referenced from: _darwinssl_connect_step2 in libcurl.a(libcurl_la-darwinssl.o) "_SecTrustGetCertificateAtIndex", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) "_SecTrustGetCertificateCount", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) "_SecTrustSetAnchorCertificates", referenced from: _darwinssl_connect_step2 in libcurl.a(libcurl_la-darwinssl.o) "_SecTrustSetAnchorCertificatesOnly", referenced from: _darwinssl_connect_step2 in libcurl.a(libcurl_la-darwinssl.o) "_ber_free", referenced from: _Curl_ldap in libcurl.a(libcurl_la-ldap.o) "_htmlCreatePushParserCtxt", referenced from: _raptor_grddl_parse_chunk in libraptor2.a(raptor_grddl.o) "_htmlCtxtUseOptions", referenced from: _raptor_grddl_parse_chunk in libraptor2.a(raptor_grddl.o) "_htmlDocContentDumpFormatOutput", referenced from: _xsltSaveResultTo in libxslt.a(xsltutils.o) "_htmlDocContentDumpOutput", referenced from: _xsltSaveResultTo in libxslt.a(xsltutils.o) "_htmlFreeParserCtxt", referenced from: _raptor_grddl_parse_terminate in libraptor2.a(raptor_grddl.o) _raptor_grddl_parse_chunk in libraptor2.a(raptor_grddl.o) "_htmlNewDoc", referenced from: _xsltDocumentElem in libxslt.a(transform.o) _xsltApplyStylesheetInternal in libxslt.a(transform.o) "_htmlNewDocNoDtD", referenced from: _xsltDocumentElem in libxslt.a(transform.o) "_htmlParseChunk", referenced from: _raptor_grddl_parse_chunk in libraptor2.a(raptor_grddl.o) "_htmlSetMetaEncoding", referenced from: _xsltSaveResultTo in libxslt.a(xsltutils.o) "_inflate", referenced from: _inflate_stream in libcurl.a(libcurl_la-content_encoding.o) "_inflateEnd", referenced from: _inflate_stream in libcurl.a(libcurl_la-content_encoding.o) _Curl_unencode_gzip_write in libcurl.a(libcurl_la-content_encoding.o) _Curl_unencode_cleanup in libcurl.a(libcurl_la-content_encoding.o) "inflateInit2", referenced from: _inflate_stream in libcurl.a(libcurl_la-content_encoding.o) _Curl_unencode_gzip_write in libcurl.a(libcurl_la-content_encoding.o) "inflateInit", referenced from: _Curl_unencode_deflate_write in libcurl.a(libcurl_la-content_encoding.o) "_inputPush", referenced from: _xsltDocDefaultLoaderFunc in libxslt.a(documents.o) "_kCFAllocatorDefault", referenced from: _darwinssl_connect_step2 in libcurl.a(libcurl_la-darwinssl.o) _append_cert_to_array in libcurl.a(libcurl_la-darwinssl.o) "_kCFBooleanTrue", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) "_kCFCopyStringDictionaryKeyCallBacks", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) "_kCFTypeArrayCallBacks", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) _darwinssl_connect_step2 in libcurl.a(libcurl_la-darwinssl.o) "_kCFTypeDictionaryValueCallBacks", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) "_kSecClass", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) "_kSecClassIdentity", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) "_kSecImportExportPassphrase", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) "_kSecImportItemIdentity", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) "_kSecMatchLimit", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) "_kSecMatchLimitOne", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) "_kSecMatchPolicy", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) "_kSecReturnRef", referenced from: _darwinssl_connect_common in libcurl.a(libcurl_la-darwinssl.o) "_ldap_err2string", referenced from: _Curl_ldap in libcurl.a(libcurl_la-ldap.o) "_ldap_first_attribute", referenced from: _Curl_ldap in libcurl.a(libcurl_la-ldap.o) "_ldap_first_entry", referenced from: _Curl_ldap in libcurl.a(libcurl_la-ldap.o) "_ldap_free_urldesc", referenced from: _Curl_ldap in libcurl.a(libcurl_la-ldap.o) "_ldap_get_dn", referenced from: _Curl_ldap in libcurl.a(libcurl_la-ldap.o) "_ldap_get_values_len", referenced from: _Curl_ldap in libcurl.a(libcurl_la-ldap.o) "_ldap_init", referenced from: _Curl_ldap in libcurl.a(libcurl_la-ldap.o) "_ldap_memfree", referenced from: _Curl_ldap in libcurl.a(libcurl_la-ldap.o) "_ldap_msgfree", referenced from: _Curl_ldap in libcurl.a(libcurl_la-ldap.o) "_ldap_next_attribute", referenced from: _Curl_ldap in libcurl.a(libcurl_la-ldap.o) "_ldap_next_entry", referenced from: _Curl_ldap in libcurl.a(libcurl_la-ldap.o) "_ldap_search_s", referenced from: _Curl_ldap in libcurl.a(libcurl_la-ldap.o) "_ldap_set_option", referenced from: _Curl_ldap in libcurl.a(libcurl_la-ldap.o) "_ldap_simple_bind_s", referenced from: _Curl_ldap in libcurl.a(libcurl_la-ldap.o) "_ldap_unbind_s", referenced from: _Curl_ldap in libcurl.a(libcurl_la-ldap.o) "_ldap_url_parse", referenced from: _Curl_ldap in libcurl.a(libcurl_la-ldap.o) "_ldap_value_free_len", referenced from: _Curl_ldap in libcurl.a(libcurl_la-ldap.o) "_valuePop", referenced from: _xsltDocumentFunction in libxslt.a(functions.o) _xsltKeyFunction in libxslt.a(functions.o) _xsltUnparsedEntityURIFunction in libxslt.a(functions.o) _xsltFormatNumberFunction in libxslt.a(functions.o) _xsltGenerateIdFunction in libxslt.a(functions.o) _xsltSystemPropertyFunction in libxslt.a(functions.o) _xsltElementAvailableFunction in libxslt.a(functions.o) ... "_valuePush", referenced from: _xsltDocumentFunction in libxslt.a(functions.o) _xsltKeyFunction in libxslt.a(functions.o) _xsltUnparsedEntityURIFunction in libxslt.a(functions.o) _xsltFormatNumberFunction in libxslt.a(functions.o) _xsltGenerateIdFunction in libxslt.a(functions.o) _xsltSystemPropertyFunction in libxslt.a(functions.o) _xsltElementAvailableFunction in libxslt.a(functions.o) ... "_xmlAddChild", referenced from: _xsltCopyTextString in libxslt.a(transform.o) _xsltCopyTreeInternal in libxslt.a(transform.o) _xsltCopy in libxslt.a(transform.o) _xsltCopyText in libxslt.a(transform.o) _xsltShallowCopyElem in libxslt.a(transform.o) _xsltText in libxslt.a(transform.o) _xsltElement in libxslt.a(transform.o) ... "_xmlAddChildList", referenced from: _raptor_libxml_getEntity in libraptor2.a(raptor_libxml.o) "_xmlAddID", referenced from: _xsltAttributeInternal in libxslt.a(attributes.o) _xsltAttrListTemplateProcess in libxslt.a(templates.o) "_xmlAddPrevSibling", referenced from: _xsltParseTemplateContent in libxslt.a(xslt.o) "_xmlAllocOutputBuffer", referenced from: _xsltSaveResultToString in libxslt.a(xsltutils.o) "_xmlBufContent", referenced from: _xsltSaveResultToString in libxslt.a(xsltutils.o) "_xmlBufUse", referenced from: _xsltSaveResultToString in libxslt.a(xsltutils.o) "_xmlBufferAdd", referenced from: _xsltFormatNumberConversion in libxslt.a(numbers.o) "_xmlBufferCCat", referenced from: _xsltNumberFormat in libxslt.a(numbers.o) _xsltNumberFormatInsertNumbers in libxslt.a(numbers.o) _xsltNumberFormatAlpha in libxslt.a(numbers.o) _xsltNumberFormatRoman in libxslt.a(numbers.o) "_xmlBufferCat", referenced from: _xsltNumberFormat in libxslt.a(numbers.o) _xsltNumberFormatInsertNumbers in libxslt.a(numbers.o) _xsltNumberFormatDecimal in libxslt.a(numbers.o) "_xmlBufferContent", referenced from: _xsltNumberFormat in libxslt.a(numbers.o) _xsltFormatNumberConversion in libxslt.a(numbers.o) "_xmlBufferCreate", referenced from: _xsltNumberFormat in libxslt.a(numbers.o) _xsltFormatNumberConversion in libxslt.a(numbers.o) "_xmlBufferFree", referenced from: _xsltNumberFormat in libxslt.a(numbers.o) _xsltFormatNumberConversion in libxslt.a(numbers.o) "_xmlBuildURI", referenced from: _xsltDocumentElem in libxslt.a(transform.o) _xsltLoadStylesheetPI in libxslt.a(xslt.o) _xsltParseStylesheetImport in libxslt.a(imports.o) _xsltParseStylesheetInclude in libxslt.a(imports.o) _xsltDocumentFunction in libxslt.a(functions.o) "_xmlCharInRange", referenced from: _xsltScanNCName in libxslt.a(pattern.o) _xsltNumberFormatTokenize in libxslt.a(numbers.o) "_xmlCheckFilename", referenced from: _xsltExtModuleRegisterDynamic in libxslt.a(extensions.o) "_xmlCleanupParser", referenced from: _raptor_libxml_finish in libraptor2.a(raptor_libxml.o) "_xmlCopyCharMultiByte", referenced from: _xsltNumberFormatDecimal in libxslt.a(numbers.o) "_xmlCreateIntSubset", referenced from: _xsltDocumentElem in libxslt.a(transform.o) _xsltApplyStylesheetInternal in libxslt.a(transform.o) "_xmlCreatePushParserCtxt", referenced from: _raptor_grddl_parse_chunk in libraptor2.a(raptor_grddl.o) _raptor_grddl_uri_xml_parse_bytes in libraptor2.a(raptor_grddl.o) _raptor_sax2_parse_chunk in libraptor2.a(raptor_sax2.o) "_xmlCreateURI", referenced from: _xsltCheckWrite in libxslt.a(security.o) "_xmlCtxtUseOptions", referenced from: _raptor_grddl_parse_chunk in libraptor2.a(raptor_grddl.o) _raptor_grddl_uri_xml_parse_bytes in libraptor2.a(raptor_grddl.o) _raptor_sax2_parse_chunk in libraptor2.a(raptor_sax2.o) _xsltDocDefaultLoaderFunc in libxslt.a(documents.o) "_xmlDetectCharEncoding", referenced from: _raptor_grddl_parse_chunk in libraptor2.a(raptor_grddl.o) "_xmlDictCreate", referenced from: _xsltNewStylesheet in libxslt.a(xslt.o) "_xmlDictCreateSub", referenced from: _xsltNewTransformContext in libxslt.a(transform.o) "_xmlDictFree", referenced from: _xsltFreeTransformContext in libxslt.a(transform.o) _xsltFreeStylesheet in libxslt.a(xslt.o) _xsltParseStylesheetImportedDoc in libxslt.a(xslt.o) _xsltDocDefaultLoaderFunc in libxslt.a(documents.o) "_xmlDictLookup", referenced from: _xsltElement in libxslt.a(transform.o) _xsltApplyStylesheetInternal in libxslt.a(transform.o) _xsltParseTemplateContent in libxslt.a(xslt.o) _xsltParseStylesheetProcess in libxslt.a(xslt.o) _xsltPrecomputeStylesheet in libxslt.a(xslt.o) _xsltGetCNsProp in libxslt.a(xsltutils.o) _xsltSplitQName in libxslt.a(xsltutils.o) ... "_xmlDictOwns", referenced from: _xsltCopyText in libxslt.a(transform.o) _xsltParseTemplateContent in libxslt.a(xslt.o) _xsltPrecomputeStylesheet in libxslt.a(xslt.o) _xsltAttrTemplateProcess in libxslt.a(templates.o) _xsltAttrListTemplateProcess in libxslt.a(templates.o) "_xmlDictQLookup", referenced from: _xsltDocumentElem in libxslt.a(transform.o) _xsltApplyStylesheetInternal in libxslt.a(transform.o) "_xmlDictReference", referenced from: _xsltDocumentElem in libxslt.a(transform.o) _xsltApplyStylesheetInternal in libxslt.a(transform.o) _xsltParseStylesheetImportedDoc in libxslt.a(xslt.o) _xsltLoadStylesheetPI in libxslt.a(xslt.o) _xsltDocDefaultLoaderFunc in libxslt.a(documents.o) _xsltCreateRVT in libxslt.a(variables.o) "_xmlDocCopyNode", referenced from: _xsltCopyTreeInternal in libxslt.a(transform.o) _xsltShallowCopyElem in libxslt.a(transform.o) _xsltLoadStylesheetPI in libxslt.a(xslt.o) "_xmlDocDumpFormatMemory", referenced from: _raptor_grddl_parse_chunk in libraptor2.a(raptor_grddl.o) "_xmlDocGetRootElement", referenced from: _raptor_grddl_parse_chunk in libraptor2.a(raptor_grddl.o) _xsltDocumentElem in libxslt.a(transform.o) _xsltApplyStylesheetInternal in libxslt.a(transform.o) _xsltFreeStylesheet in libxslt.a(xslt.o) _xsltParseStylesheetProcess in libxslt.a(xslt.o) _xsltPrecomputeStylesheet in libxslt.a(xslt.o) _xsltParseStylesheetImportedDoc in libxslt.a(xslt.o) ... "_xmlDocSetRootElement", referenced from: _xsltGetProfileInformation in libxslt.a(xsltutils.o) "_xmlFindCharEncodingHandler", referenced from: _xsltSaveResultToFilename in libxslt.a(xsltutils.o) _xsltSaveResultToFile in libxslt.a(xsltutils.o) _xsltSaveResultToFd in libxslt.a(xsltutils.o) _xsltSaveResultToString in libxslt.a(xsltutils.o) "_xmlFree", referenced from: _raptor_grddl_parse_chunk in libraptor2.a(raptor_grddl.o) _raptor_grddl_run_xpath_match in libraptor2.a(raptor_grddl.o) _raptor_sax2_start_element in libraptor2.a(raptor_sax2.o) _xsltFreeTransformContext in libxslt.a(transform.o) _xsltCopyTreeInternal in libxslt.a(transform.o) _xsltDocumentElem in libxslt.a(transform.o) _xsltShallowCopyAttr in libxslt.a(transform.o) ... "_xmlFreeDoc", referenced from: _raptor_grddl_parse_terminate in libraptor2.a(raptor_grddl.o) _raptor_grddl_parse_chunk in libraptor2.a(raptor_grddl.o) _raptor_libxml_endDocument in libraptor2.a(raptor_libxml.o) _raptor_libxml_free in libraptor2.a(raptor_libxml.o) _xsltFreeTransformContext in libxslt.a(transform.o) _xsltDocumentElem in libxslt.a(transform.o) _xsltApplyStylesheetInternal in libxslt.a(transform.o) ... "_xmlFreeDtd", referenced from: _xsltApplyStylesheetInternal in libxslt.a(transform.o) "_xmlFreeIDTable", referenced from: _xsltReleaseRVT in libxslt.a(variables.o) "_xmlFreeMutex", referenced from: _xsltCleanupGlobals in libxslt.a(extensions.o) "_xmlFreeNode", referenced from: _xsltProcessOneNode in libxslt.a(transform.o) _xsltApplyTemplates in libxslt.a(transform.o) _xsltApplyStripSpaces in libxslt.a(transform.o) _xsltParseTemplateContent in libxslt.a(xslt.o) _xsltPrecomputeStylesheet in libxslt.a(xslt.o) _xsltEvalTemplateString in libxslt.a(templates.o) "_xmlFreeNodeList", referenced from: _xsltAttrTemplateProcess in libxslt.a(templates.o) _xsltReleaseRVT in libxslt.a(variables.o) "_xmlFreeParserCtxt", referenced from: _raptor_grddl_parse_terminate in libraptor2.a(raptor_grddl.o) _raptor_grddl_parse_chunk in libraptor2.a(raptor_grddl.o) _raptor_libxml_free in libraptor2.a(raptor_libxml.o) _xsltDocDefaultLoaderFunc in libxslt.a(documents.o) "_xmlFreeRefTable", referenced from: _xsltReleaseRVT in libxslt.a(variables.o) "_xmlFreeURI", referenced from: _xsltCheckWrite in libxslt.a(security.o) _xsltCheckRead in libxslt.a(security.o) _xsltLoadStylesheetPI in libxslt.a(xslt.o) _xsltDocumentFunction in libxslt.a(functions.o) "_xmlGenericError", referenced from: _raptor_libxml_init in libraptor2.a(raptor_libxml.o) _xsltNewTransformContext in libxslt.a(transform.o) _xsltApplyXSLTTemplate in libxslt.a(transform.o) _xsltLocalVariablePush in libxslt.a(transform.o) _xsltAllocateExtraCtxt in libxslt.a(xslt.o) _xsltParseStylesheetProcess in libxslt.a(xslt.o) _xsltParseStylesheetExcludePrefix in libxslt.a(xslt.o) ... "_xmlGenericErrorContext", referenced from: _raptor_libxml_init in libraptor2.a(raptor_libxml.o) _xsltNewTransformContext in libxslt.a(transform.o) _xsltApplyXSLTTemplate in libxslt.a(transform.o) _xsltLocalVariablePush in libxslt.a(transform.o) _xsltAllocateExtraCtxt in libxslt.a(xslt.o) _xsltParseStylesheetProcess in libxslt.a(xslt.o) _xsltParseStylesheetExcludePrefix in libxslt.a(xslt.o) ... "_xmlGetCharEncodingName", referenced from: _xsltSaveResultTo in libxslt.a(xsltutils.o) "_xmlGetDocEntity", referenced from: _raptor_libxml_getEntity in libraptor2.a(raptor_libxml.o) _xsltUnparsedEntityURIFunction in libxslt.a(functions.o) "_xmlGetDtdAttrDesc", referenced from: _xsltGetCNsProp in libxslt.a(xsltutils.o) _xsltGetNsProp in libxslt.a(xsltutils.o) "_xmlGetID", referenced from: _xsltLoadStylesheetPI in libxslt.a(xslt.o) _xsltTestCompMatch in libxslt.a(pattern.o) "_xmlGetIntSubset", referenced from: _xsltApplyStylesheetInternal in libxslt.a(transform.o) "_xmlGetLineNo", referenced from: _xsltPrintErrorContext in libxslt.a(xsltutils.o) "_xmlGetNsList", referenced from: _xsltCopyTreeInternal in libxslt.a(transform.o) _xsltAddKey in libxslt.a(keys.o) _xsltCompilePatternInternal in libxslt.a(pattern.o) _xsltAttrTemplateValueProcessNode in libxslt.a(templates.o) _xsltCompileAttr in libxslt.a(attrvt.o) _xsltStylePreCompute in libxslt.a(preproc.o) "_xmlGetNsProp", referenced from: _xsltParseStylesheetOutput in libxslt.a(xslt.o) _xsltParseTemplateContent in libxslt.a(xslt.o) _xsltParseStylesheetProcess in libxslt.a(xslt.o) _xsltParseStylesheetExcludePrefix in libxslt.a(xslt.o) _xsltParseStylesheetExtPrefix in libxslt.a(xslt.o) _xsltMessage in libxslt.a(xsltutils.o) _xsltParseStylesheetAttributeSet in libxslt.a(attributes.o) ... "_xmlGetPredefinedEntity", referenced from: _raptor_libxml_getEntity in libraptor2.a(raptor_libxml.o) "_xmlGetProp", referenced from: _xsltGetCNsProp in libxslt.a(xsltutils.o) _xsltGetNsProp in libxslt.a(xsltutils.o) "_xmlHasNsProp", referenced from: _xsltAttributeInternal in libxslt.a(attributes.o) "_xmlHashAddEntry", referenced from: _xsltExtModuleRegisterDynamic in libxslt.a(extensions.o) _xsltStyleGetExtData in libxslt.a(extensions.o) _xsltGetExtData in libxslt.a(extensions.o) _xsltInitCtxtExt in libxslt.a(extensions.o) _xsltRegisterExtModuleFull in libxslt.a(extensions.o) _xsltInitCtxtKey in libxslt.a(keys.o) _xsltNamespaceAlias in libxslt.a(namespaces.o) ... "_xmlHashAddEntry2", referenced from: _xsltDocumentElem in libxslt.a(transform.o) _xsltRegisterExtFunction in libxslt.a(extensions.o) _xsltRegisterExtElement in libxslt.a(extensions.o) _xsltParseStylesheetOutput in libxslt.a(xslt.o) _xsltParseStylesheetProcess in libxslt.a(xslt.o) _xsltAddTemplate in libxslt.a(pattern.o) _xsltMergeSASCallback in libxslt.a(attributes.o) ... "_xmlHashAddEntry3", referenced from: _xsltAddTemplate in libxslt.a(pattern.o) "_xmlHashCreate", referenced from: _xsltDocumentElem in libxslt.a(transform.o) _xsltApplyStylesheetInternal in libxslt.a(transform.o) _xsltExtModuleRegisterDynamic in libxslt.a(extensions.o) _xsltStyleGetExtData in libxslt.a(extensions.o) _xsltRegisterExtFunction in libxslt.a(extensions.o) _xsltRegisterExtElement in libxslt.a(extensions.o) _xsltGetExtData in libxslt.a(extensions.o) ... "_xmlHashFree", referenced from: _xsltFreeCtxtExts in libxslt.a(extensions.o) _xsltShutdownCtxtExts in libxslt.a(extensions.o) _xsltShutdownExts in libxslt.a(extensions.o) _xsltCleanupGlobals in libxslt.a(extensions.o) _xsltFreeStylesheet in libxslt.a(xslt.o) _xsltFreeDocumentKeys in libxslt.a(keys.o) _xsltFreeTemplateHashes in libxslt.a(pattern.o) ... "_xmlHashLookup", referenced from: _xsltApplySequenceConstructor in libxslt.a(transform.o) _xsltRegisterExtPrefix in libxslt.a(extensions.o) _xsltExtModuleRegisterDynamic in libxslt.a(extensions.o) _xsltStyleGetExtData in libxslt.a(extensions.o) _xsltGetExtData in libxslt.a(extensions.o) _xsltInitCtxtExt in libxslt.a(extensions.o) _xsltRegisterExtModuleFull in libxslt.a(extensions.o) ... "_xmlHashLookup2", referenced from: _xsltCopyTextString in libxslt.a(transform.o) _xsltCopyText in libxslt.a(transform.o) _xsltApplyTemplates in libxslt.a(transform.o) _xsltExtModuleFunctionLookup in libxslt.a(extensions.o) _xsltPreComputeExtModuleElement in libxslt.a(extensions.o) _xsltExtElementLookup in libxslt.a(extensions.o) _xsltExtModuleElementLookup in libxslt.a(extensions.o) ... "_xmlHashLookup3", referenced from: _xsltAddTemplate in libxslt.a(pattern.o) _xsltGetTemplate in libxslt.a(pattern.o) "_xmlHashRemoveEntry", referenced from: _xsltUnregisterExtModule in libxslt.a(extensions.o) "_xmlHashRemoveEntry2", referenced from: _xsltUnregisterExtModuleFunction in libxslt.a(extensions.o) _xsltUnregisterExtModuleElement in libxslt.a(extensions.o) _xsltUnregisterExtModuleTopLevel in libxslt.a(extensions.o) "_xmlHashScan", referenced from: _xsltInitCtxtExts in libxslt.a(extensions.o) _xsltShutdownCtxtExts in libxslt.a(extensions.o) _xsltShutdownExts in libxslt.a(extensions.o) _xsltCleanupGlobals in libxslt.a(extensions.o) _xsltEvalGlobalVariables in libxslt.a(variables.o) _xsltFixImportedCompSteps in libxslt.a(imports.o) "_xmlHashScanFull", referenced from: _xsltDebugDumpExtensions in libxslt.a(extensions.o) _xsltResolveStylesheetAttributeSet in libxslt.a(attributes.o) "_xmlHashUpdateEntry", referenced from: _xsltParseStylesheetImportedDoc in libxslt.a(xslt.o) "_xmlHashUpdateEntry2", referenced from: _xsltRegisterExtModuleFunction in libxslt.a(extensions.o) _xsltRegisterExtModuleElement in libxslt.a(extensions.o) _xsltRegisterExtModuleTopLevel in libxslt.a(extensions.o) _xsltParseStylesheetAttributeSet in libxslt.a(attributes.o) _xsltMergeSASCallback in libxslt.a(attributes.o) "_xmlHashUpdateEntry3", referenced from: _xsltAddTemplate in libxslt.a(pattern.o) "_xmlInitParser", referenced from: _raptor_libxml_init in libraptor2.a(raptor_libxml.o) "_xmlIsBaseCharGroup", referenced from: _xsltScanNCName in libxslt.a(pattern.o) _xsltNumberFormatTokenize in libxslt.a(numbers.o) "_xmlIsBlankNode", referenced from: _xsltDocumentElem in libxslt.a(transform.o) _xsltApplyStylesheetInternal in libxslt.a(transform.o) "_xmlIsCombiningGroup", referenced from: _xsltScanNCName in libxslt.a(pattern.o) "_xmlIsDigitGroup", referenced from: _xsltScanNCName in libxslt.a(pattern.o) _xsltNumberFormatTokenize in libxslt.a(numbers.o) "_xmlIsExtenderGroup", referenced from: _xsltScanNCName in libxslt.a(pattern.o) "_xmlIsID", referenced from: _xsltAttributeInternal in libxslt.a(attributes.o) _xsltAttrListTemplateProcess in libxslt.a(templates.o) "_xmlLoadExternalEntity", referenced from: _raptor_libxml_resolveEntity in libraptor2.a(raptor_libxml.o) _xsltDocDefaultLoaderFunc in libxslt.a(documents.o) "_xmlMalloc", referenced from: _raptor_grddl_parse_chunk in libraptor2.a(raptor_grddl.o) _xsltNewTransformContext in libxslt.a(transform.o) _xsltApplyXSLTTemplate in libxslt.a(transform.o) _xsltLocalVariablePush in libxslt.a(transform.o) _xsltRegisterExtPrefix in libxslt.a(extensions.o) _xsltNewExtData in libxslt.a(extensions.o) _xsltRegisterExtModuleFull in libxslt.a(extensions.o) ... "_xmlModuleClose", referenced from: _xsltExtModuleRegisterDynamic in libxslt.a(extensions.o) _xsltHashScannerModuleFree in libxslt.a(extensions.o) "_xmlModuleOpen", referenced from: _xsltExtModuleRegisterDynamic in libxslt.a(extensions.o) "_xmlModuleSymbol", referenced from: _xsltExtModuleRegisterDynamic in libxslt.a(extensions.o) "_xmlMutexLock", referenced from: _xsltRegisterExtPrefix in libxslt.a(extensions.o) _xsltExtModuleRegisterDynamic in libxslt.a(extensions.o) _xsltStyleGetExtData in libxslt.a(extensions.o) _xsltGetExtData in libxslt.a(extensions.o) _xsltRegisterExtModuleFull in libxslt.a(extensions.o) _xsltUnregisterExtModule in libxslt.a(extensions.o) _xsltRegisterExtModuleFunction in libxslt.a(extensions.o) ... "_xmlMutexUnlock", referenced from: _xsltRegisterExtPrefix in libxslt.a(extensions.o) _xsltExtModuleRegisterDynamic in libxslt.a(extensions.o) _xsltStyleGetExtData in libxslt.a(extensions.o) _xsltGetExtData in libxslt.a(extensions.o) _xsltRegisterExtModuleFull in libxslt.a(extensions.o) _xsltUnregisterExtModule in libxslt.a(extensions.o) _xsltRegisterExtModuleFunction in libxslt.a(extensions.o) ... "_xmlNewCDataBlock", referenced from: _xsltCopyTextString in libxslt.a(transform.o) _xsltCopyText in libxslt.a(transform.o) "_xmlNewChild", referenced from: _xsltGetProfileInformation in libxslt.a(xsltutils.o) "_xmlNewComment", referenced from: _xsltCopy in libxslt.a(transform.o) _xsltComment in libxslt.a(transform.o) _xsltExtElementTest in libxslt.a(extensions.o) "_xmlNewDoc", referenced from: _xsltDocumentElem in libxslt.a(transform.o) _xsltApplyStylesheetInternal in libxslt.a(transform.o) _xsltLoadStylesheetPI in libxslt.a(xslt.o) _xsltGetProfileInformation in libxslt.a(xsltutils.o) _xsltCreateRVT in libxslt.a(variables.o) "_xmlNewDocNode", referenced from: _xsltElement in libxslt.a(transform.o) _xsltGetProfileInformation in libxslt.a(xsltutils.o) _xsltEvalTemplateString in libxslt.a(templates.o) "_xmlNewDocNodeEatName", referenced from: _xsltElement in libxslt.a(transform.o) "_xmlNewDocPI", referenced from: _xsltCopy in libxslt.a(transform.o) _xsltProcessingInstruction in libxslt.a(transform.o) "_xmlNewDocProp", referenced from: _xsltAttrListTemplateProcess in libxslt.a(templates.o) "_xmlNewDocText", referenced from: _xsltText in libxslt.a(transform.o) "_xmlNewMutex", referenced from: _xsltRegisterTestModule in libxslt.a(extensions.o) _xsltInitGlobals in libxslt.a(extensions.o) "_xmlNewNs", referenced from: _xsltCopyTreeInternal in libxslt.a(transform.o) _xsltApplySequenceConstructor in libxslt.a(transform.o) _xsltShallowCopyNsNode in libxslt.a(transform.o) _xsltCopyNamespaceListInternal in libxslt.a(transform.o) _xsltLoadStylesheetPI in libxslt.a(xslt.o) _xsltGetSpecialNamespace in libxslt.a(namespaces.o) _xsltCopyNamespaceList in libxslt.a(namespaces.o) ... "_xmlNewNsProp", referenced from: _xsltCopyTreeInternal in libxslt.a(transform.o) _xsltAttrTemplateProcess in libxslt.a(templates.o) "_xmlNewParserCtxt", referenced from: _xsltDocDefaultLoaderFunc in libxslt.a(documents.o) "_xmlNewText", referenced from: _raptor_libxml_getEntity in libraptor2.a(raptor_libxml.o) _xsltAttributeInternal in libxslt.a(attributes.o) _xsltAttrTemplateProcess in libxslt.a(templates.o) _xsltAttrListTemplateProcess in libxslt.a(templates.o) "_xmlNewTextLen", referenced from: _xsltCopyTextString in libxslt.a(transform.o) _xsltCopyText in libxslt.a(transform.o) "_xmlNodeAddContent", referenced from: _xsltAddTextString in libxslt.a(transform.o) "_xmlNodeDumpOutput", referenced from: _xsltSaveResultTo in libxslt.a(xsltutils.o) "_xmlNodeGetBase", referenced from: _raptor_grddl_run_xpath_match in libraptor2.a(raptor_grddl.o) _xsltLoadStylesheetPI in libxslt.a(xslt.o) _xsltParseStylesheetImport in libxslt.a(imports.o) _xsltParseStylesheetInclude in libxslt.a(imports.o) _xsltDocumentFunction in libxslt.a(functions.o) "_xmlNodeGetContent", referenced from: _xsltEvalTemplateString in libxslt.a(templates.o) "_xmlNodeGetSpacePreserve", referenced from: _xsltPrecomputeStylesheet in libxslt.a(xslt.o) "_xmlNodeListGetString", referenced from: _xsltCopyTreeInternal in libxslt.a(transform.o) _xsltShallowCopyAttr in libxslt.a(transform.o) _xsltGetCNsProp in libxslt.a(xsltutils.o) _xsltGetNsProp in libxslt.a(xsltutils.o) "_xmlNodeSetContent", referenced from: _xsltParseTemplateContent in libxslt.a(xslt.o) _xsltPrecomputeStylesheet in libxslt.a(xslt.o) "_xmlOutputBufferClose", referenced from: _xsltSaveResultToFilename in libxslt.a(xsltutils.o) _xsltSaveResultToFile in libxslt.a(xsltutils.o) _xsltSaveResultToFd in libxslt.a(xsltutils.o) _xsltSaveResultToString in libxslt.a(xsltutils.o) "_xmlOutputBufferCreateFd", referenced from: _xsltSaveResultToFd in libxslt.a(xsltutils.o) "_xmlOutputBufferCreateFile", referenced from: _xsltSaveResultToFile in libxslt.a(xsltutils.o) "_xmlOutputBufferCreateFilename", referenced from: _xsltSaveResultToFilename in libxslt.a(xsltutils.o) "_xmlOutputBufferFlush", referenced from: _xsltSaveResultTo in libxslt.a(xsltutils.o) "_xmlOutputBufferWriteString", referenced from: _xsltSaveResultTo in libxslt.a(xsltutils.o) "_xmlParseChunk", referenced from: _raptor_grddl_parse_chunk in libraptor2.a(raptor_grddl.o) _raptor_grddl_uri_xml_parse_bytes in libraptor2.a(raptor_grddl.o) _raptor_sax2_parse_chunk in libraptor2.a(raptor_sax2.o) "_xmlParseCtxtExternalEntity", referenced from: _raptor_libxml_getEntity in libraptor2.a(raptor_libxml.o) "_xmlParseDocument", referenced from: _xsltDocDefaultLoaderFunc in libxslt.a(documents.o) "_xmlParseURI", referenced from: _xsltCheckWrite in libxslt.a(security.o) _xsltCheckRead in libxslt.a(security.o) _xsltLoadStylesheetPI in libxslt.a(xslt.o) _xsltDocumentFunction in libxslt.a(functions.o) "_xmlParserGetDirectory", referenced from: _xsltCheckWritePath in libxslt.a(security.o) _xsltDocDefaultLoaderFunc in libxslt.a(documents.o) "_xmlRealloc", referenced from: _xsltAddTextString in libxslt.a(transform.o) _xsltApplyXSLTTemplate in libxslt.a(transform.o) _xsltLocalVariablePush in libxslt.a(transform.o) _xsltAllocateExtraCtxt in libxslt.a(xslt.o) _xsltParseStylesheetProcess in libxslt.a(xslt.o) _xsltParseStylesheetExcludePrefix in libxslt.a(xslt.o) _xsltTransformError in libxslt.a(xsltutils.o) ... "_xmlSAX2EndDocument", referenced from: _raptor_libxml_endDocument in libraptor2.a(raptor_libxml.o) _raptor_libxml_free in libraptor2.a(raptor_libxml.o) "_xmlSAX2EntityDecl", referenced from: _raptor_libxml_entityDecl in libraptor2.a(raptor_libxml.o) "_xmlSAX2ExternalSubset", referenced from: _raptor_libxml_externalSubset in libraptor2.a(raptor_libxml.o) "_xmlSAX2GetParameterEntity", referenced from: _raptor_libxml_getParameterEntity in libraptor2.a(raptor_libxml.o) "_xmlSAX2HasExternalSubset", referenced from:

On Jan 11, 2017, at 12:53 AM, Kiri Choi notifications@github.com wrote:

Allowing incomplete and non compliant Uris seems to fix it. The file 'SBOL1and2Test.rdf' still fails, which is not that surprising actually. We can talk about this tomorrow. Other files work okay.

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[cjmyers]

When I build the library I get some warnings:

[myers@jiaqi libSBOL]$ make [ 9%] Building CXX object source/CMakeFiles/sbol64.dir/sbolerror.cpp.o [ 18%] Building CXX object source/CMakeFiles/sbol64.dir/config.cpp.o /Users/myers/Downloads/libSBOL/source/config.cpp:12:16: warning: 'extern' variable has an initializer [-Wextern-initializer] extern Config& config = * new sbol::Config(); ///< Global configuratio... ^ 1 warning generated. [ 27%] Building CXX object source/CMakeFiles/sbol64.dir/validation.cpp.o [ 36%] Building CXX object source/CMakeFiles/sbol64.dir/properties.cpp.o [ 45%] Building CXX object source/CMakeFiles/sbol64.dir/object.cpp.o [ 54%] Building CXX object source/CMakeFiles/sbol64.dir/identified.cpp.o [ 63%] Building CXX object source/CMakeFiles/sbol64.dir/toplevel.cpp.o [ 72%] Building CXX object source/CMakeFiles/sbol64.dir/componentdefinition.cpp.o [ 81%] Building CXX object source/CMakeFiles/sbol64.dir/document.cpp.o [ 90%] Building CXX object source/CMakeFiles/sbol64.dir/assembly.cpp.o [100%] Linking CXX static library ../release/library/libsbol.a /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: ../release/library/libsbol.a(sbolerror.cpp.o) has no symbols /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: ../release/library/libsbol.a(identified.cpp.o) has no symbols /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: ../release/library/libsbol.a(toplevel.cpp.o) has no symbols /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: ../release/library/libsbol.a(componentdefinition.cpp.o) has no symbols /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: ../release/library/libsbol.a(sbolerror.cpp.o) has no symbols /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: ../release/library/libsbol.a(identified.cpp.o) has no symbols /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: ../release/library/libsbol.a(toplevel.cpp.o) has no symbols /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: ../release/library/libsbol.a(componentdefinition.cpp.o) has no symbols [100%] Built target sbol64

Also, brew install had some warnings:

[myers@jiaqi ReadWriteTestlibSBOL]$ brew install raptor jsoncpp libxslt curl Warning: raptor-2.0.15 already installed Warning: jsoncpp-1.8.0 already installed Warning: libxslt is a keg-only and another version is linked to opt. Use brew install --force if you want to install this version Warning: curl is a keg-only and another version is linked to opt. Use brew install --force if you want to install this version [myers@jiaqi ReadWriteTestlibSBOL]$ brew install --force libxslt curl Warning: libxslt-1.1.29 already installed, it's just not linked. Warning: curl-7.52.1 already installed, it's just not linked.

On Jan 11, 2017, at 12:53 AM, Kiri Choi notifications@github.com wrote:

Allowing incomplete and non compliant Uris seems to fix it. The file 'SBOL1and2Test.rdf' still fails, which is not that surprising actually. We can talk about this tomorrow. Other files work okay.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/SynBioDex/libSBOL/issues/114#issuecomment-271745804, or mute the thread https://github.com/notifications/unsubscribe-auth/ADWD91wNDQoMaPgGwSFxntyfe6ywnL7Jks5rRCgbgaJpZM4LbNyq.

[cjmyers]

Meher: have you tried the new version? Have your errors gone away?

On Jan 10, 2017, at 11:51 PM, mehersam notifications@github.com wrote:

This actually looks like a read error. I found that I had to keep my files in the exact same location as the .cpp file.

Best,

Meher Samineni mehersam251@gmail.com 801-654-8841

On Tue, Jan 10, 2017 at 4:48 PM, cjmyers notifications@github.com wrote:

I forgot make install. After that in compiled, but I still get write error:

[myers@jiaqi ReadWriteTestlibSBOL]$ ./script.sh SBOL2/AnnotationOutput.rdf ./script.sh: line 3: 97379 Segmentation fault: 11 ./ReadWriteTestlibSBOL $f Out/$f Out/SBOL2/AnnotationOutput.rdf (No such file or directory) I/O exception. java.io.FileNotFoundException: Out/SBOL2/AnnotationOutput.rdf (No such file or directory) at java.io.FileInputStream.open(Native Method) at java.io.FileInputStream.(FileInputStream.java:146) at org.sbolstandard.core2.SBOLReader.read(SBOLReader.java:446) at org.sbolstandard.core2.SBOLReader.read(SBOLReader.java:379) at org.sbolstandard.core2.SBOLReader.read(SBOLReader.java:364) at org.sbolstandard.core2.SBOLValidate.validate(SBOLValidate.java:1568) at org.sbolstandard.core2.SBOLValidate.main(SBOLValidate.java:1816)

On Jan 10, 2017, at 10:52 PM, Kiri Choi notifications@github.com wrote:

Issue seems fixed on commit e003831 https://github.com/SynBioDex/ libSBOL/commit/e0038313afa2a1cc9992eb5a8689096f3bf253e4. Tested on Mac and Windows. There is a file called 'SBOL1and2Test.rdf' that fails, but this file also fails to be validated on online validator. In fact, multiple test files are actually invalid according to validator.

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[kirichoi]

@bbartley FYI, Python now has full roundtrip test implemented. (But only present in source not in pysbol2 github yet) There are several fail cases you might want to check.

[mehersam]

@cjmyers I haven't tried the new version yet. I'm downloading from source, since the binary installers haven't been updated. If there are any errors, I will report soon.

[cjmyers]

Fixed