Plots with transparent background in ggbio.

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Last seen 10.2 years ago

Can ggbio make a karyogram plot which has a transparent background? -- output of sessionInfo(): No info -- Sent via the guest posting facility at bioconductor.org.

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ADD COMMENT • link updated 11.2 years ago by Tengfei Yin ▴ 490 • written 11.2 years ago by Guest User ★ 13k

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Tengfei Yin ▴ 490

@tengfei-yin-6162

Last seen 10.2 years ago

Hi I am not sure what you mean "transparent background". Do you mean kayogram plot without cytoband? cheers Tengfei On Fri, Sep 27, 2013 at 1:38 AM, Costerwell Khyriem [guest] < guest@bioconductor.org> wrote: > > Can ggbio make a karyogram plot which has a transparent background? > > -- output of sessionInfo(): > > No info > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Tengfei Yin, PhD Seven Bridges Genomics sbgenomics.com 625 Mt. Auburn St. Suite #208 Cambridge, MA 02138 (617) 866-0446 [[alternative HTML version deleted]]

ADD COMMENT • link 11.2 years ago Tengfei Yin ▴ 490

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Hi guys, I tried to install affxparser in R3.0.1 in Cygwin x64, but got some errors. Makevars:4: recipe for target `fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.o' failed make: *** [fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.o] Error 1 ERROR: compilation failed for package affxparser * removing /usr/lib/R/site-library/affxparser Any suggestion? Thanks a lot for the help! Ying The following are the full text: > source("http://bioconductor.org/biocLite.R") Bioconductor version 2.12 (BiocInstaller 1.10.3), ?biocLite for help > biocLite("affxparser") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.12 (BiocInstaller 1.10.3), R version 3.0.1. Installing package(s) 'affxparser' trying URL 'http://bioconductor.org/packages/2.12/bioc/src/contrib/aff xparser_1.32.3.tar.gz' Content type 'application/x-gzip' length 803037 bytes (784 Kb) opened URL ================================================== downloaded 784 Kb * installing *source* package affxparser ... ** libs rm -f fusion_sdk/calvin_files/data/src/CDFData.o fusion_sdk/calvin_files/data/sr c/CDFProbeGroupInformation.o fusion_sdk/calvin_files/data/src/CDFProbeInformatio n.o fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.o fusion_sdk/calvin_ files/data/src/CDFQCProbeInformation.o fusion_sdk/calvin_files/data/src/CDFQCPro beSetInformation.o fusion_sdk/calvin_files/data/src/CELData.o fusion_sdk/calvin_ files/data/src/CHPBackgroundZone.o fusion_sdk/calvin_files/data/src/CHPData.o fu sion_sdk/calvin_files/data/src/CHPExpressionEntry.o fusion_sdk/calvin_files/data /src/CHPMultiDataData.o fusion_sdk/calvin_files/data/src/CHPTilingData.o fusion_ sdk/calvin_files/data/src/CHPQuantificationData.o fusion_sdk/calvin_files/data/s rc/CHPQuantificationDetectionData.o fusion_sdk/calvin_files/data/src/CHPGenotype Entry.o fusion_sdk/calvin_files/data/src/CHPUniversalEntry.o fusion_sdk/calvin_f iles/data/src/ColumnInfo.o fusion_sdk/calvin_files/data/src/DataGroup.o fusion_s dk/calvin_files/data/src/DataGroupHeader.o fusion_sdk/calvin_files/data/src/Data Set.o fusion_sdk/calvin_files/data/src/DataSetHeader.o fusion_sdk/calvin_files/d ata/src/FileHeader.o fusion_sdk/calvin_files/data/src/GenericData.o fusion_sdk/c alvin_files/data/src/GenericDataHeader.o fusion_sdk/calvin_files/exception/src/E xceptionBase.o fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAda pter.o fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataA dapter.o f usion_sdk/calvin_files/fusion/src/FusionBPMAPData.o fusion_sdk/calvin_files/fusi on/src/FusionCDFData.o fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNam es.o fusion_sdk/calvin_files/fusion/src/FusionCELData.o fusion_sdk/calvin_files/ fusion/src/FusionCHPData.o fusion_sdk/calvin_files/fusion/src/FusionProbeSetResu lts.o fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.o fusion _sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.o fusion_sdk/calvin_ files/fusion/src/FusionCHPLegacyData.o fusion_sdk/calvin_files/fusion/src/Fusion CHPMultiDataAccessor.o fusion_sdk/calvin_files/fusion/src/FusionCHPMultiDataData .o fusion_sdk/calvin_files/fusion/src/FusionCHPTilingData.o fusion_sdk/calvin_fi les/fusion/src/FusionCHPGenericData.o fusion_sdk/calvin_files/fusion/src/FusionC HPQuantificationData.o fusion_sdk/calvin_files/fusion/src/FusionCHPQuantificatio nDetectionData.o fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.o fusion_sdk/calvin_files/parsers/src/CDFFileReader.o fusion_sdk/calvin_files/pars ers/src/CelFileReader.o fusion_sdk/calvin_files/parsers/src/CHPFileReader.o fusi on_sdk/calvin_files/parsers/src/CHPMultiDataFileReader.o fusion_sdk/calvin_files /parsers/src/CHPTilingFileReader.o fusion_sdk/calvin_files/parsers/src/CHPQuanti ficationFileReader.o fusion_sdk/calvin_files/parsers/src/CHPQuantificationDetect ionFileReader.o fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.o fusi on_sdk/calvin_files/parsers/src/DataGroupReader.o fusion_sdk/calvin_files/parser s/src/DataSetHeaderReader.o fusion_sdk/calvin_files/parsers/src/DataSetReader.o fusion_sdk/calvin_files/parsers/src/FileHeaderReader.o fusion_sdk/calvin_files/p arsers/src/FileInput.o fusion_sdk/calvin_files/parsers/src/GenericDataHeaderRead er.o fusion_sdk/calvin_files/parsers/src/GenericFileReader.o fusion_sdk/calvin_f iles/utils/src/AffymetrixGuid.o fusion_sdk/calvin_files/utils/src/DateTime.o fus ion_sdk/calvin_files/utils/src/FileUtils.o fusion_sdk/calvin_files/utils/src/Str ingUtils.o fusion_sdk/calvin_files/utils/src/checksum.o fusion_sdk/file/BPMAPFil eData.o fusion_sdk/file/BPMAPFileWriter.o fusion_sdk/file/CDFFileData.o fusion_s dk/file/CELFileData.o fusion_sdk/file/CHPFileData.o fusion_sdk/file/FileIO.o fus ion_sdk/file/FileWriter.o fusion_sdk/file/TsvFile/ClfFile.o fusion_sdk/file/TsvF ile/PgfFile.o fusion_sdk/file/TsvFile/TsvFile.o fusion_sdk/util/AffxByteArray.o fusion_sdk/util/AffxConv.o fusion_sdk/util/MsgStream.o fusion_sdk/util/Util.o fu sion_sdk/util/Err.o fusion_sdk/util/Fs.o fusion_sdk/util/Verbose.o fusion_sdk/ut il/RowFile.o fusion_sdk/util/TableFile.o fusion_sdk/util/Convert.o R_affx_cel_pa rser.o R_affx_cdf_parser.o R_affx_cdf_extras.o R_affx_bpmap_parser.o R_affx_clf_ pgf_parser.o R_affx_chp_parser.o g++ -I/usr/lib/R/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifus ion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_s dk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifu sion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/paramet er/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portabili ty/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/sr c -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvF ile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -ggdb -O2 -pipe -fdebug-prefix-map=/pub/devel/R/R-3.0.1-1/build=/usr/src/d ebug/R-3.0.1-1 -fdebug-prefix- map=/pub/devel/R/R-3.0.1-1/src/R-3.0.1=/usr/src/de bug/R-3.0.1-1 -O0 -c fusion_sdk/calvin_files/data/src/CDFData.cpp -o fusion_sdk /calvin_files/data/src/CDFData.o g++ -I/usr/lib/R/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifus ion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_s dk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifu sion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/paramet er/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portabili ty/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/sr c -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvF ile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -ggdb -O2 -pipe -fdebug-prefix-map=/pub/devel/R/R-3.0.1-1/build=/usr/src/d ebug/R-3.0.1-1 -fdebug-prefix- map=/pub/devel/R/R-3.0.1-1/src/R-3.0.1=/usr/src/de bug/R-3.0.1-1 -O0 -c fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation. cpp -o fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.o g++ -I/usr/lib/R/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifus ion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_s dk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifu sion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/paramet er/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portabili ty/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/sr c -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvF ile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -ggdb -O2 -pipe -fdebug-prefix-map=/pub/devel/R/R-3.0.1-1/build=/usr/src/d ebug/R-3.0.1-1 -fdebug-prefix- map=/pub/devel/R/R-3.0.1-1/src/R-3.0.1=/usr/src/de bug/R-3.0.1-1 -O0 -c fusion_sdk/calvin_files/data/src/CDFProbeInformation.cpp - o fusion_sdk/calvin_files/data/src/CDFProbeInformation.o g++ -I/usr/lib/R/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifus ion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_s dk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifu sion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/paramet er/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portabili ty/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/sr c -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvF ile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -ggdb -O2 -pipe -fdebug-prefix-map=/pub/devel/R/R-3.0.1-1/build=/usr/src/d ebug/R-3.0.1-1 -fdebug-prefix- map=/pub/devel/R/R-3.0.1-1/src/R-3.0.1=/usr/src/de bug/R-3.0.1-1 -O0 -c fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.cp p -o fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.o g++ -I/usr/lib/R/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifus ion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_s dk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifu sion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/paramet er/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portabili ty/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/sr c -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvF ile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -ggdb -O2 -pipe -fdebug-prefix-map=/pub/devel/R/R-3.0.1-1/build=/usr/src/d ebug/R-3.0.1-1 -fdebug-prefix- map=/pub/devel/R/R-3.0.1-1/src/R-3.0.1=/usr/src/de bug/R-3.0.1-1 -O0 -c fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.cpp -o fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.o g++ -I/usr/lib/R/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifus ion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_s dk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifu sion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/paramet er/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portabili ty/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/sr c -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvF ile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -ggdb -O2 -pipe -fdebug-prefix-map=/pub/devel/R/R-3.0.1-1/build=/usr/src/d ebug/R-3.0.1-1 -fdebug-prefix- map=/pub/devel/R/R-3.0.1-1/src/R-3.0.1=/usr/src/de bug/R-3.0.1-1 -O0 -c fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation. cpp -o fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.o g++ -I/usr/lib/R/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifus ion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_s dk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifu sion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/paramet er/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portabili ty/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/sr c -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvF ile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -ggdb -O2 -pipe -fdebug-prefix-map=/pub/devel/R/R-3.0.1-1/build=/usr/src/d ebug/R-3.0.1-1 -fdebug-prefix- map=/pub/devel/R/R-3.0.1-1/src/R-3.0.1=/usr/src/de bug/R-3.0.1-1 -O0 -c fusion_sdk/calvin_files/data/src/CELData.cpp -o fusion_sdk /calvin_files/data/src/CELData.o g++ -I/usr/lib/R/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifus ion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_s dk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifu sion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/paramet er/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portabili ty/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/sr c -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvF ile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -ggdb -O2 -pipe -fdebug-prefix-map=/pub/devel/R/R-3.0.1-1/build=/usr/src/d ebug/R-3.0.1-1 -fdebug-prefix- map=/pub/devel/R/R-3.0.1-1/src/R-3.0.1=/usr/src/de bug/R-3.0.1-1 -O0 -c fusion_sdk/calvin_files/data/src/CHPBackgroundZone.cpp -o fusion_sdk/calvin_files/data/src/CHPBackgroundZone.o g++ -I/usr/lib/R/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifus ion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_s dk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifu sion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/paramet er/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portabili ty/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/sr c -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvF ile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -ggdb -O2 -pipe -fdebug-prefix-map=/pub/devel/R/R-3.0.1-1/build=/usr/src/d ebug/R-3.0.1-1 -fdebug-prefix- map=/pub/devel/R/R-3.0.1-1/src/R-3.0.1=/usr/src/de bug/R-3.0.1-1 -O0 -c fusion_sdk/calvin_files/data/src/CHPData.cpp -o fusion_sdk /calvin_files/data/src/CHPData.o g++ -I/usr/lib/R/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifus ion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_s dk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifu sion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/paramet er/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portabili ty/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/sr c -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvF ile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -ggdb -O2 -pipe -fdebug-prefix-map=/pub/devel/R/R-3.0.1-1/build=/usr/src/d ebug/R-3.0.1-1 -fdebug-prefix- map=/pub/devel/R/R-3.0.1-1/src/R-3.0.1=/usr/src/de bug/R-3.0.1-1 -O0 -c fusion_sdk/calvin_files/data/src/CHPExpressionEntry.cpp -o fusion_sdk/calvin_files/data/src/CHPExpressionEntry.o g++ -I/usr/lib/R/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifus ion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_s dk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifu sion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/paramet er/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portabili ty/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/sr c -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvF ile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -ggdb -O2 -pipe -fdebug-prefix-map=/pub/devel/R/R-3.0.1-1/build=/usr/src/d ebug/R-3.0.1-1 -fdebug-prefix- map=/pub/devel/R/R-3.0.1-1/src/R-3.0.1=/usr/src/de bug/R-3.0.1-1 -O0 -c fusion_sdk/calvin_files/data/src/CHPMultiDataData.cpp -o f usion_sdk/calvin_files/data/src/CHPMultiDataData.o g++ -I/usr/lib/R/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifus ion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_s dk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifu sion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/paramet er/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portabili ty/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/sr c -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvF ile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -ggdb -O2 -pipe -fdebug-prefix-map=/pub/devel/R/R-3.0.1-1/build=/usr/src/d ebug/R-3.0.1-1 -fdebug-prefix- map=/pub/devel/R/R-3.0.1-1/src/R-3.0.1=/usr/src/de bug/R-3.0.1-1 -O0 -c fusion_sdk/calvin_files/data/src/CHPTilingData.cpp -o fusi on_sdk/calvin_files/data/src/CHPTilingData.o g++ -I/usr/lib/R/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifus ion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_s dk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifu sion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/paramet er/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portabili ty/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/sr c -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvF ile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -ggdb -O2 -pipe -fdebug-prefix-map=/pub/devel/R/R-3.0.1-1/build=/usr/src/d ebug/R-3.0.1-1 -fdebug-prefix- map=/pub/devel/R/R-3.0.1-1/src/R-3.0.1=/usr/src/de bug/R-3.0.1-1 -O0 -c fusion_sdk/calvin_files/data/src/CHPQuantificationData.cpp -o fusion_sdk/calvin_files/data/src/CHPQuantificationData.o g++ -I/usr/lib/R/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifus ion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_s dk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifu sion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/paramet er/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portabili ty/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/sr c -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvF ile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -ggdb -O2 -pipe -fdebug-prefix-map=/pub/devel/R/R-3.0.1-1/build=/usr/src/d ebug/R-3.0.1-1 -fdebug-prefix- map=/pub/devel/R/R-3.0.1-1/src/R-3.0.1=/usr/src/de bug/R-3.0.1-1 -O0 -c fusion_sdk/calvin_files/data/src/CHPQuantificationDetectio nData.cpp -o fusion_sdk/calvin_files/data/src/CHPQuantificationDetectionData.o g++ -I/usr/lib/R/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifus ion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_s dk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifu sion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/paramet er/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portabili ty/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/sr c -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvF ile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -ggdb -O2 -pipe -fdebug-prefix-map=/pub/devel/R/R-3.0.1-1/build=/usr/src/d ebug/R-3.0.1-1 -fdebug-prefix- map=/pub/devel/R/R-3.0.1-1/src/R-3.0.1=/usr/src/de bug/R-3.0.1-1 -O0 -c fusion_sdk/calvin_files/data/src/CHPGenotypeEntry.cpp -o f usion_sdk/calvin_files/data/src/CHPGenotypeEntry.o g++ -I/usr/lib/R/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifus ion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_s dk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifu sion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/paramet er/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portabili ty/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/sr c -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvF ile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -ggdb -O2 -pipe -fdebug-prefix-map=/pub/devel/R/R-3.0.1-1/build=/usr/src/d ebug/R-3.0.1-1 -fdebug-prefix- map=/pub/devel/R/R-3.0.1-1/src/R-3.0.1=/usr/src/de bug/R-3.0.1-1 -O0 -c fusion_sdk/calvin_files/data/src/CHPUniversalEntry.cpp -o fusion_sdk/calvin_files/data/src/CHPUniversalEntry.o g++ -I/usr/lib/R/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifus ion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_s dk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifu sion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/paramet er/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portabili ty/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/sr c -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvF ile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -ggdb -O2 -pipe -fdebug-prefix-map=/pub/devel/R/R-3.0.1-1/build=/usr/src/d ebug/R-3.0.1-1 -fdebug-prefix- map=/pub/devel/R/R-3.0.1-1/src/R-3.0.1=/usr/src/de bug/R-3.0.1-1 -O0 -c fusion_sdk/calvin_files/data/src/ColumnInfo.cpp -o fusion_ sdk/calvin_files/data/src/ColumnInfo.o g++ -I/usr/lib/R/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifus ion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_s dk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifu sion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/paramet er/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portabili ty/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/sr c -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvF ile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -ggdb -O2 -pipe -fdebug-prefix-map=/pub/devel/R/R-3.0.1-1/build=/usr/src/d ebug/R-3.0.1-1 -fdebug-prefix- map=/pub/devel/R/R-3.0.1-1/src/R-3.0.1=/usr/src/de bug/R-3.0.1-1 -O0 -c fusion_sdk/calvin_files/data/src/DataGroup.cpp -o fusion_s dk/calvin_files/data/src/DataGroup.o g++ -I/usr/lib/R/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifus ion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_s dk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifu sion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/paramet er/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portabili ty/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/sr c -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvF ile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -ggdb -O2 -pipe -fdebug-prefix-map=/pub/devel/R/R-3.0.1-1/build=/usr/src/d ebug/R-3.0.1-1 -fdebug-prefix- map=/pub/devel/R/R-3.0.1-1/src/R-3.0.1=/usr/src/de bug/R-3.0.1-1 -O0 -c fusion_sdk/calvin_files/data/src/DataGroupHeader.cpp -o fu sion_sdk/calvin_files/data/src/DataGroupHeader.o g++ -I/usr/lib/R/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifus ion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_s dk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifu sion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/paramet er/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portabili ty/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/sr c -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvF ile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -ggdb -O2 -pipe -fdebug-prefix-map=/pub/devel/R/R-3.0.1-1/build=/usr/src/d ebug/R-3.0.1-1 -fdebug-prefix- map=/pub/devel/R/R-3.0.1-1/src/R-3.0.1=/usr/src/de bug/R-3.0.1-1 -O0 -c fusion_sdk/calvin_files/data/src/DataSet.cpp -o fusion_sdk /calvin_files/data/src/DataSet.o g++ -I/usr/lib/R/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifus ion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_s dk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifu sion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/paramet er/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portabili ty/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/sr c -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvF ile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -ggdb -O2 -pipe -fdebug-prefix-map=/pub/devel/R/R-3.0.1-1/build=/usr/src/d ebug/R-3.0.1-1 -fdebug-prefix- map=/pub/devel/R/R-3.0.1-1/src/R-3.0.1=/usr/src/de bug/R-3.0.1-1 -O0 -c fusion_sdk/calvin_files/data/src/DataSetHeader.cpp -o fusi on_sdk/calvin_files/data/src/DataSetHeader.o g++ -I/usr/lib/R/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifus ion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_s dk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifu sion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/paramet er/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portabili ty/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/sr c -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvF ile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -ggdb -O2 -pipe -fdebug-prefix-map=/pub/devel/R/R-3.0.1-1/build=/usr/src/d ebug/R-3.0.1-1 -fdebug-prefix- map=/pub/devel/R/R-3.0.1-1/src/R-3.0.1=/usr/src/de bug/R-3.0.1-1 -O0 -c fusion_sdk/calvin_files/data/src/FileHeader.cpp -o fusion_ sdk/calvin_files/data/src/FileHeader.o g++ -I/usr/lib/R/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifus ion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_s dk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifu sion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/paramet er/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portabili ty/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/sr c -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvF ile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -ggdb -O2 -pipe -fdebug-prefix-map=/pub/devel/R/R-3.0.1-1/build=/usr/src/d ebug/R-3.0.1-1 -fdebug-prefix- map=/pub/devel/R/R-3.0.1-1/src/R-3.0.1=/usr/src/de bug/R-3.0.1-1 -O0 -c fusion_sdk/calvin_files/data/src/GenericData.cpp -o fusion _sdk/calvin_files/data/src/GenericData.o g++ -I/usr/lib/R/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifus ion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_s dk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifu sion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/paramet er/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portabili ty/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/sr c -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvF ile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -ggdb -O2 -pipe -fdebug-prefix-map=/pub/devel/R/R-3.0.1-1/build=/usr/src/d ebug/R-3.0.1-1 -fdebug-prefix- map=/pub/devel/R/R-3.0.1-1/src/R-3.0.1=/usr/src/de bug/R-3.0.1-1 -O0 -c fusion_sdk/calvin_files/data/src/GenericDataHeader.cpp -o fusion_sdk/calvin_files/data/src/GenericDataHeader.o g++ -I/usr/lib/R/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifus ion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_s dk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifu sion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/paramet er/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portabili ty/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/sr c -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvF ile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -ggdb -O2 -pipe -fdebug-prefix-map=/pub/devel/R/R-3.0.1-1/build=/usr/src/d ebug/R-3.0.1-1 -fdebug-prefix- map=/pub/devel/R/R-3.0.1-1/src/R-3.0.1=/usr/src/de bug/R-3.0.1-1 -O0 -c fusion_sdk/calvin_files/exception/src/ExceptionBase.cpp -o fusion_sdk/calvin_files/exception/src/ExceptionBase.o g++ -I/usr/lib/R/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifus ion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_s dk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifu sion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/paramet er/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portabili ty/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/sr c -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvF ile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -ggdb -O2 -pipe -fdebug-prefix-map=/pub/devel/R/R-3.0.1-1/build=/usr/src/d ebug/R-3.0.1-1 -fdebug-prefix- map=/pub/devel/R/R-3.0.1-1/src/R-3.0.1=/usr/src/de bug/R-3.0.1-1 -O0 -c fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCEL DataAdapter.cpp -o fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDat aAdapter.o g++ -I/usr/lib/R/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifus ion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_s dk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifu sion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/paramet er/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portabili ty/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/sr c -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvF ile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -ggdb -O2 -pipe -fdebug-prefix-map=/pub/devel/R/R-3.0.1-1/build=/usr/src/d ebug/R-3.0.1-1 -fdebug-prefix- map=/pub/devel/R/R-3.0.1-1/src/R-3.0.1=/usr/src/de bug/R-3.0.1-1 -O0 -c fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHP DataAdapter.cpp -o fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDat aAdapter.o g++ -I/usr/lib/R/include -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifus ion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_s dk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifu sion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/paramet er/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portabili ty/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/sr c -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvF ile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -ggdb -O2 -pipe -fdebug-prefix-map=/pub/devel/R/R-3.0.1-1/build=/usr/src/d ebug/R-3.0.1-1 -fdebug-prefix- map=/pub/devel/R/R-3.0.1-1/src/R-3.0.1=/usr/src/de bug/R-3.0.1-1 -O0 -c fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.o In file included from fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.h:27:0, from fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.cpp:21: fusion_sdk/file/BPMAPFileData.h:290:2: error: FILE does not name a type FILE *m_fp; ^ Makevars:4: recipe for target `fusion_sdk/calvin_files/fusion/src/FusionBPMAPDat a.o' failed make: *** [fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.o] Error 1 ERROR: compilation failed for package affxparser * removing /usr/lib/R/site-library/affxparser The downloaded source packages are in /tmp/RtmpKuZDMY/downloaded_packages Warning message: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package affxparser had non-zero exit status > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-unknown-cygwin (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.10.3 loaded via a namespace (and not attached): [1] tools_3.0.1 > traceback() No traceback available > > [[alternative HTML version deleted]]

ADD REPLY • link 11.2 years ago ying chen ▴ 340

0

Entering edit mode

I am not sure how well supported R is in general for this platform (R-admin says: Cygwin has not been tested for R 3.0.0 or later). It seems this error occurs because of file handling in this OS, related to memory mapping in affxparser. While Cygwin in general can be treated as a Unix OS it may be that for this particular case it needs to be treated like Windows, particular you could try setting _MSC_VER manually in src/Makevars. However, setting this also does other things so it may very well not work. You could try reading on on FILE handling in Cygwin vs. standard Unix. Given that this platform is not really supported by R, you're on your own. This could prove pretty hard to fix. Kasper [[alternative HTML version deleted]]

ADD REPLY • link 11.2 years ago Kasper Daniel Hansen ★ 6.5k

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