affxparser compile error on mac
0
0
Entering edit mode
Mark Robinson ★ 1.1k
@mark-robinson-2171
Last seen 7.1 years ago
Hi all. Since the upgrade to R 2.5, I cannot get affxparser to compile on my mac. There is no compile error, it creates the shared object file affxparser.so), but cannot load it in the end. I've asked for a gcc compiler upgrade (out of my control) as a possible solution, currently have: target=powerpc-apple-darwin8 Thread model: posix gcc version 4.0.1 (Apple Computer, Inc. build 5367) Does anyone else have this problem? Downloaded source and binary from: http://www.bioconductor.org/packages/2.0/bioc/html/affxparser.html Few more details below. Thanks, Mark ------- I tried to install the binary, but doesn't seem to like being loaded: ------- > > library(affxparser) Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library '/Users/mrobinson/Library/R/2.5/ library/affxparser/libs/ppc/affxparser.so': dlopen(/Users/mrobinson/Library/R/2.5/library/affxparser/libs/ppc/ affxparser.so, 6): Symbol not found: __ZN20affymetrix_fusion_io13FusionCELData7GetStdvEi Referenced from: /Users/mrobinson/Library/R/2.5/library/affxparser/ libs/ppc/affxparser.so Expected in: dynamic lookup Error: package/namespace load failed for 'affxparser' > > > sessionInfo() R version 2.5.0 (2007-04-23) powerpc-apple-darwin8.9.1 locale: en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8 attached base packages: [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" "base" ------- Below is the compile output ... ------- R version 2.5.0 (2007-04-23) Copyright (C) 2007 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. (Using the menu ...) Warning in install.packages(file.choose(), , NULL, type = "source") : argument 'lib' is missing: using '/Users/mrobinson/Library/R/2.5/ library' WARNING: ignoring environment value of R_HOME * Installing *source* package 'affxparser' ... ** libs ** arch - i386 g++-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp- precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/ Frameworks/R.framework/Resources/include/i386 -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/ calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src - Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/ src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter - Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/ parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/ calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src - Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/ portability -D_USE_MEM_MAPPING_ -msse3 -fPIC -g -O2 -march=nocona - O0 -c fusion_sdk/calvin_files/data/src/CDFData.cpp -o fusion_sdk/ calvin_files/data/src/CDFData.o (..... edited) g++-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp- precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/ Frameworks/R.framework/Resources/include/ppc -imacros R_affx_constants.h -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/ calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src - Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/ src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter - Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/ parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/ calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src - Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/ portability -D_USE_MEM_MAPPING_ -I/usr/local/include -fPIC -g -O2 - O0 -c R_affx_bpmap_parser.cpp -o R_affx_bpmap_parser.o g++-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk - dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup - single_module -multiply_defined suppress -L/usr/local/lib -o affxparser.so fusion_sdk/calvin_files/data/src/CDFData.o fusion_sdk/ calvin_files/data/src/CDFProbeGroupInformation.o fusion_sdk/ calvin_files/data/src/CDFProbeInformation.o fusion_sdk/calvin_files/ data/src/CDFProbeSetInformation.o fusion_sdk/calvin_files/data/src/ CDFQCProbeInformation.o fusion_sdk/calvin_files/data/src/ CDFQCProbeSetInformation.o fusion_sdk/calvin_files/data/src/CELData.o fusion_sdk/calvin_files/data/src/DataGroup.o fusion_sdk/calvin_files/ data/src/DataGroupHeader.o fusion_sdk/calvin_files/data/src/DataSet.o fusion_sdk/calvin_files/data/src/DataSetHeader.o fusion_sdk/ calvin_files/data/src/FileHeader.o fusion_sdk/calvin_files/data/src/ GenericData.o fusion_sdk/calvin_files/data/src/GenericDataHeader.o fusion_sdk/calvin_files/exception/src/ExceptionBase.o fusion_sdk/ calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.o fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.o fusion_sdk/ calvin_files/fusion/src/FusionCDFData.o fusion_sdk/calvin_files/fusion/ src/FusionCDFQCProbeSetNames.o fusion_sdk/calvin_files/fusion/src/ FusionCELData.o fusion_sdk/calvin_files/fusion/src/GCOSAdapter/ GCOSCELDataAdapter.o fusion_sdk/calvin_files/parameter/src/ ParameterNameValueType.o fusion_sdk/calvin_files/parsers/src/ CDFFileReader.o fusion_sdk/calvin_files/parsers/src/CelFileReader.o fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.o fusion_sdk/ calvin_files/parsers/src/DataGroupReader.o fusion_sdk/calvin_files/ parsers/src/DataSetHeaderReader.o fusion_sdk/calvin_files/parsers/src/ DataSetReader.o fusion_sdk/calvin_files/parsers/src/FileHeaderReader.o fusion_sdk/calvin_files/parsers/src/FileInput.o fusion_sdk/ calvin_files/parsers/src/GenericDataHeaderReader.o fusion_sdk/ calvin_files/parsers/src/GenericFileReader.o fusion_sdk/calvin_files/ utils/src/AffymetrixGuid.o fusion_sdk/calvin_files/utils/src/ DateTime.o fusion_sdk/calvin_files/utils/src/FileUtils.o fusion_sdk/ calvin_files/utils/src/StringUtils.o fusion_sdk/calvin_files/utils/src/ checksum.o fusion_sdk/file/BPMAPFileData.o fusion_sdk/file/ BPMAPFileWriter.o fusion_sdk/file/CDFFileData.o fusion_sdk/file/ CELFileData.o fusion_sdk/file/FileIO.o fusion_sdk/file/FileWriter.o R_affx_cel_parser.o R_affx_cdf_parser.o R_affx_cdf_extras.o R_affx_bpmap_parser.o -F/Library/Frameworks/R.framework/.. - framework R ** R ** inst ** save image ** preparing package for lazy loading Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library '/Users/mrobinson/Library/R/2.5/library/ affxparser/libs/ppc/affxparser.so': dlopen(/Users/mrobinson/Library/R/2.5/library/affxparser/libs/ppc/ affxparser.so, 6): Symbol not found: __ZN20affymetrix_fusion_io13FusionCELData7GetStdvEi Referenced from: /Users/mrobinson/Library/R/2.5/library/affxparser/ libs/ppc/affxparser.so Expected in: dynamic lookup Execution halted ERROR: lazy loading failed for package 'affxparser' ** Removing '/Users/mrobinson/Library/R/2.5/library/affxparser'
affxparser affxparser • 684 views
ADD COMMENT

Login before adding your answer.

Traffic: 407 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6