Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 22/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
affxparser 1.77.0 (landing page) Kasper Daniel Hansen
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
To the developers/maintainers of the affxparser package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/affxparser.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: affxparser |
Version: 1.77.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:affxparser.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings affxparser_1.77.0.tar.gz |
StartedAt: 2024-06-09 23:33:34 -0400 (Sun, 09 Jun 2024) |
EndedAt: 2024-06-09 23:35:37 -0400 (Sun, 09 Jun 2024) |
EllapsedTime: 123.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: affxparser.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:affxparser.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings affxparser_1.77.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/affxparser.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘affxparser/DESCRIPTION’ ... OK * this is package ‘affxparser’ version ‘1.77.0’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘affxparser’ can be installed ... WARNING Found the following significant warnings: fusion/util/AffxConv.cpp:124:8: warning: self-comparison always evaluates to false [-Wtautological-compare] See ‘/Users/biocbuild/bbs-3.20-bioc/meat/affxparser.Rcheck/00install.out’ for details. * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... NOTE installed size is 8.9Mb sub-directories of 1Mb or more: libs 8.2Mb * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... NOTE checkRd: (-1) applyCdfGroups.Rd:37-46: Lost braces in \itemize; meant \describe ? checkRd: (-1) applyCdfGroups.Rd:47-59: Lost braces in \itemize; meant \describe ? * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... WARNING Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/affxparser/libs/affxparser.so’: Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++) Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++) Found ‘___stdoutp’, possibly from ‘stdout’ (C) Found ‘_exit’, possibly from ‘exit’ (C) Found ‘_printf’, possibly from ‘printf’ (C) Found ‘_rand’, possibly from ‘rand’ (C) Found ‘_sprintf’, possibly from ‘sprintf’ (C) Found ‘_srand’, possibly from ‘srand’ (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘convertCel.R’ Running ‘readCdfDataFrame.R’ Running ‘readCdfQc.R’ Running ‘readCdfUnitsWriteMap.R’ Running ‘readCdfUnits_etal.R’ Running ‘readCel.R’ Running ‘readCelIntensities.R’ Running ‘readCelRectangle.R’ Running ‘readCelUnits.R’ Running ‘readPgf.R’ Running ‘testWriteAndReadEmptyCdf.R’ Running ‘testWriteAndReadEmptyCel.R’ OK * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/affxparser.Rcheck/00check.log’ for details.
affxparser.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL affxparser ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘affxparser’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ rm -f fusion/calvin_files/data/src/CDFData.o fusion/calvin_files/data/src/CDFProbeGroupInformation.o fusion/calvin_files/data/src/CDFProbeInformation.o fusion/calvin_files/data/src/CDFProbeSetInformation.o fusion/calvin_files/data/src/CDFQCProbeInformation.o fusion/calvin_files/data/src/CDFQCProbeSetInformation.o fusion/calvin_files/data/src/CELData.o fusion/calvin_files/data/src/CHPBackgroundZone.o fusion/calvin_files/data/src/CHPData.o fusion/calvin_files/data/src/CHPExpressionEntry.o fusion/calvin_files/data/src/CHPMultiDataData.o fusion/calvin_files/data/src/CHPTilingData.o fusion/calvin_files/data/src/CHPQuantificationData.o fusion/calvin_files/data/src/CHPQuantificationDetectionData.o fusion/calvin_files/data/src/CHPGenotypeEntry.o fusion/calvin_files/data/src/CHPUniversalEntry.o fusion/calvin_files/data/src/ColumnInfo.o fusion/calvin_files/data/src/DataGroup.o fusion/calvin_files/data/src/DataGroupHeader.o fusion/calvin_files/data/src/DataSet.o fusion/calvin_files/data/src/DataSetHeader.o fusion/calvin_files/data/src/FileHeader.o fusion/calvin_files/data/src/GenericData.o fusion/calvin_files/data/src/GenericDataHeader.o fusion/calvin_files/exception/src/ExceptionBase.o fusion/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.o fusion/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.o fusion/calvin_files/fusion/src/FusionBPMAPData.o fusion/calvin_files/fusion/src/FusionCDFData.o fusion/calvin_files/fusion/src/FusionCDFQCProbeSetNames.o fusion/calvin_files/fusion/src/FusionCELData.o fusion/calvin_files/fusion/src/FusionCHPData.o fusion/calvin_files/fusion/src/FusionProbeSetResults.o fusion/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.o fusion/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.o fusion/calvin_files/fusion/src/FusionCHPLegacyData.o fusion/calvin_files/fusion/src/FusionCHPMultiDataAccessor.o fusion/calvin_files/fusion/src/FusionCHPMultiDataData.o fusion/calvin_files/fusion/src/FusionCHPTilingData.o fusion/calvin_files/fusion/src/FusionCHPGenericData.o fusion/calvin_files/fusion/src/FusionCHPQuantificationData.o fusion/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.o fusion/calvin_files/parameter/src/ParameterNameValueType.o fusion/calvin_files/parsers/src/CDFFileReader.o fusion/calvin_files/parsers/src/CelFileReader.o fusion/calvin_files/parsers/src/CHPFileReader.o fusion/calvin_files/parsers/src/CHPMultiDataFileReader.o fusion/calvin_files/parsers/src/CHPTilingFileReader.o fusion/calvin_files/parsers/src/CHPQuantificationFileReader.o fusion/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.o fusion/calvin_files/parsers/src/DataGroupHeaderReader.o fusion/calvin_files/parsers/src/DataGroupReader.o fusion/calvin_files/parsers/src/DataSetHeaderReader.o fusion/calvin_files/parsers/src/DataSetReader.o fusion/calvin_files/parsers/src/FileHeaderReader.o fusion/calvin_files/parsers/src/FileInput.o fusion/calvin_files/parsers/src/GenericDataHeaderReader.o fusion/calvin_files/parsers/src/GenericFileReader.o fusion/calvin_files/utils/src/AffymetrixGuid.o fusion/calvin_files/utils/src/DateTime.o fusion/calvin_files/utils/src/FileUtils.o fusion/calvin_files/utils/src/StringUtils.o fusion/calvin_files/utils/src/checksum.o fusion/file/BPMAPFileData.o fusion/file/BPMAPFileWriter.o fusion/file/CDFFileData.o fusion/file/CELFileData.o fusion/file/CHPFileData.o fusion/file/FileIO.o fusion/file/FileWriter.o fusion/file/TsvFile/ClfFile.o fusion/file/TsvFile/PgfFile.o fusion/file/TsvFile/TsvFile.o fusion/util/AffxByteArray.o fusion/util/AffxConv.o fusion/util/MsgStream.o fusion/util/Util.o fusion/util/Err.o fusion/util/Fs.o fusion/util/Verbose.o fusion/util/RowFile.o fusion/util/TableFile.o fusion/util/Convert.o R_affx_cel_parser.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 000.init.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CDFData.cpp -o fusion/calvin_files/data/src/CDFData.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CDFProbeGroupInformation.cpp -o fusion/calvin_files/data/src/CDFProbeGroupInformation.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CDFProbeInformation.cpp -o fusion/calvin_files/data/src/CDFProbeInformation.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CDFProbeSetInformation.cpp -o fusion/calvin_files/data/src/CDFProbeSetInformation.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CDFQCProbeInformation.cpp -o fusion/calvin_files/data/src/CDFQCProbeInformation.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CDFQCProbeSetInformation.cpp -o fusion/calvin_files/data/src/CDFQCProbeSetInformation.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CELData.cpp -o fusion/calvin_files/data/src/CELData.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CHPBackgroundZone.cpp -o fusion/calvin_files/data/src/CHPBackgroundZone.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CHPData.cpp -o fusion/calvin_files/data/src/CHPData.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CHPExpressionEntry.cpp -o fusion/calvin_files/data/src/CHPExpressionEntry.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CHPMultiDataData.cpp -o fusion/calvin_files/data/src/CHPMultiDataData.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CHPTilingData.cpp -o fusion/calvin_files/data/src/CHPTilingData.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CHPQuantificationData.cpp -o fusion/calvin_files/data/src/CHPQuantificationData.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CHPQuantificationDetectionData.cpp -o fusion/calvin_files/data/src/CHPQuantificationDetectionData.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CHPGenotypeEntry.cpp -o fusion/calvin_files/data/src/CHPGenotypeEntry.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CHPUniversalEntry.cpp -o fusion/calvin_files/data/src/CHPUniversalEntry.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/ColumnInfo.cpp -o fusion/calvin_files/data/src/ColumnInfo.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/DataGroup.cpp -o fusion/calvin_files/data/src/DataGroup.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/DataGroupHeader.cpp -o fusion/calvin_files/data/src/DataGroupHeader.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/DataSet.cpp -o fusion/calvin_files/data/src/DataSet.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/DataSetHeader.cpp -o fusion/calvin_files/data/src/DataSetHeader.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/FileHeader.cpp -o fusion/calvin_files/data/src/FileHeader.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/GenericData.cpp -o fusion/calvin_files/data/src/GenericData.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/GenericDataHeader.cpp -o fusion/calvin_files/data/src/GenericDataHeader.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/exception/src/ExceptionBase.cpp -o fusion/calvin_files/exception/src/ExceptionBase.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.cpp -o fusion/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.cpp -o fusion/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/fusion/src/FusionBPMAPData.cpp -o fusion/calvin_files/fusion/src/FusionBPMAPData.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/fusion/src/FusionCDFData.cpp -o fusion/calvin_files/fusion/src/FusionCDFData.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/fusion/src/FusionCDFQCProbeSetNames.cpp -o fusion/calvin_files/fusion/src/FusionCDFQCProbeSetNames.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/fusion/src/FusionCELData.cpp -o fusion/calvin_files/fusion/src/FusionCELData.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/fusion/src/FusionCHPData.cpp -o fusion/calvin_files/fusion/src/FusionCHPData.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/fusion/src/FusionProbeSetResults.cpp -o fusion/calvin_files/fusion/src/FusionProbeSetResults.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.cpp -o fusion/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.cpp -o fusion/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/fusion/src/FusionCHPLegacyData.cpp -o fusion/calvin_files/fusion/src/FusionCHPLegacyData.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/fusion/src/FusionCHPMultiDataAccessor.cpp -o fusion/calvin_files/fusion/src/FusionCHPMultiDataAccessor.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/fusion/src/FusionCHPMultiDataData.cpp -o fusion/calvin_files/fusion/src/FusionCHPMultiDataData.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/fusion/src/FusionCHPTilingData.cpp -o fusion/calvin_files/fusion/src/FusionCHPTilingData.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/fusion/src/FusionCHPGenericData.cpp -o fusion/calvin_files/fusion/src/FusionCHPGenericData.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/fusion/src/FusionCHPQuantificationData.cpp -o fusion/calvin_files/fusion/src/FusionCHPQuantificationData.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.cpp -o fusion/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/parameter/src/ParameterNameValueType.cpp -o fusion/calvin_files/parameter/src/ParameterNameValueType.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/parsers/src/CDFFileReader.cpp -o fusion/calvin_files/parsers/src/CDFFileReader.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/parsers/src/CelFileReader.cpp -o fusion/calvin_files/parsers/src/CelFileReader.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/parsers/src/CHPFileReader.cpp -o fusion/calvin_files/parsers/src/CHPFileReader.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/parsers/src/CHPMultiDataFileReader.cpp -o fusion/calvin_files/parsers/src/CHPMultiDataFileReader.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/parsers/src/CHPTilingFileReader.cpp -o fusion/calvin_files/parsers/src/CHPTilingFileReader.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/parsers/src/CHPQuantificationFileReader.cpp -o fusion/calvin_files/parsers/src/CHPQuantificationFileReader.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.cpp -o fusion/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/parsers/src/DataGroupHeaderReader.cpp -o fusion/calvin_files/parsers/src/DataGroupHeaderReader.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/parsers/src/DataGroupReader.cpp -o fusion/calvin_files/parsers/src/DataGroupReader.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/parsers/src/DataSetHeaderReader.cpp -o fusion/calvin_files/parsers/src/DataSetHeaderReader.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/parsers/src/DataSetReader.cpp -o fusion/calvin_files/parsers/src/DataSetReader.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/parsers/src/FileHeaderReader.cpp -o fusion/calvin_files/parsers/src/FileHeaderReader.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/parsers/src/FileInput.cpp -o fusion/calvin_files/parsers/src/FileInput.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/parsers/src/GenericDataHeaderReader.cpp -o fusion/calvin_files/parsers/src/GenericDataHeaderReader.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/parsers/src/GenericFileReader.cpp -o fusion/calvin_files/parsers/src/GenericFileReader.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/utils/src/AffymetrixGuid.cpp -o fusion/calvin_files/utils/src/AffymetrixGuid.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/utils/src/DateTime.cpp -o fusion/calvin_files/utils/src/DateTime.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/utils/src/FileUtils.cpp -o fusion/calvin_files/utils/src/FileUtils.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/utils/src/StringUtils.cpp -o fusion/calvin_files/utils/src/StringUtils.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/calvin_files/utils/src/checksum.cpp -o fusion/calvin_files/utils/src/checksum.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/file/BPMAPFileData.cpp -o fusion/file/BPMAPFileData.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/file/BPMAPFileWriter.cpp -o fusion/file/BPMAPFileWriter.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/file/CDFFileData.cpp -o fusion/file/CDFFileData.o fusion/file/CDFFileData.cpp:1040:7: warning: unused typedef 'TilingTypes' [-Wunused-local-typedef] } TilingTypes; ^ 1 warning generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/file/CELFileData.cpp -o fusion/file/CELFileData.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/file/CHPFileData.cpp -o fusion/file/CHPFileData.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/file/FileIO.cpp -o fusion/file/FileIO.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/file/FileWriter.cpp -o fusion/file/FileWriter.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/file/TsvFile/ClfFile.cpp -o fusion/file/TsvFile/ClfFile.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/file/TsvFile/PgfFile.cpp -o fusion/file/TsvFile/PgfFile.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/file/TsvFile/TsvFile.cpp -o fusion/file/TsvFile/TsvFile.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/util/AffxByteArray.cpp -o fusion/util/AffxByteArray.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/util/AffxConv.cpp -o fusion/util/AffxConv.o fusion/util/AffxConv.cpp:124:8: warning: self-comparison always evaluates to false [-Wtautological-compare] if (i != i) {return "nan";} ^ 1 warning generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/util/MsgStream.cpp -o fusion/util/MsgStream.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/util/Util.cpp -o fusion/util/Util.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/util/Err.cpp -o fusion/util/Err.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/util/Fs.cpp -o fusion/util/Fs.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/util/Verbose.cpp -o fusion/util/Verbose.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/util/RowFile.cpp -o fusion/util/RowFile.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/util/TableFile.cpp -o fusion/util/TableFile.o In file included from fusion/util/TableFile.cpp:28: fusion/util/TableFile.h:231:8: warning: private field 'm_Comment' is not used [-Wunused-private-field] char m_Comment; ///< Comment character for data. ^ 1 warning generated. clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c fusion/util/Convert.cpp -o fusion/util/Convert.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c R_affx_cel_parser.cpp -o R_affx_cel_parser.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c R_affx_cdf_parser.cpp -o R_affx_cdf_parser.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c R_affx_cdf_extras.cpp -o R_affx_cdf_extras.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c R_affx_bpmap_parser.cpp -o R_affx_bpmap_parser.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c R_affx_clf_pgf_parser.cpp -o R_affx_clf_pgf_parser.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -Wno-sign-compare -O0 -c R_affx_chp_parser.cpp -o R_affx_chp_parser.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c 000.init.c -o 000.init.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o affxparser.so fusion/calvin_files/data/src/CDFData.o fusion/calvin_files/data/src/CDFProbeGroupInformation.o fusion/calvin_files/data/src/CDFProbeInformation.o fusion/calvin_files/data/src/CDFProbeSetInformation.o fusion/calvin_files/data/src/CDFQCProbeInformation.o fusion/calvin_files/data/src/CDFQCProbeSetInformation.o fusion/calvin_files/data/src/CELData.o fusion/calvin_files/data/src/CHPBackgroundZone.o fusion/calvin_files/data/src/CHPData.o fusion/calvin_files/data/src/CHPExpressionEntry.o fusion/calvin_files/data/src/CHPMultiDataData.o fusion/calvin_files/data/src/CHPTilingData.o fusion/calvin_files/data/src/CHPQuantificationData.o fusion/calvin_files/data/src/CHPQuantificationDetectionData.o fusion/calvin_files/data/src/CHPGenotypeEntry.o fusion/calvin_files/data/src/CHPUniversalEntry.o fusion/calvin_files/data/src/ColumnInfo.o fusion/calvin_files/data/src/DataGroup.o fusion/calvin_files/data/src/DataGroupHeader.o fusion/calvin_files/data/src/DataSet.o fusion/calvin_files/data/src/DataSetHeader.o fusion/calvin_files/data/src/FileHeader.o fusion/calvin_files/data/src/GenericData.o fusion/calvin_files/data/src/GenericDataHeader.o fusion/calvin_files/exception/src/ExceptionBase.o fusion/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.o fusion/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.o fusion/calvin_files/fusion/src/FusionBPMAPData.o fusion/calvin_files/fusion/src/FusionCDFData.o fusion/calvin_files/fusion/src/FusionCDFQCProbeSetNames.o fusion/calvin_files/fusion/src/FusionCELData.o fusion/calvin_files/fusion/src/FusionCHPData.o fusion/calvin_files/fusion/src/FusionProbeSetResults.o fusion/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.o fusion/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.o fusion/calvin_files/fusion/src/FusionCHPLegacyData.o fusion/calvin_files/fusion/src/FusionCHPMultiDataAccessor.o fusion/calvin_files/fusion/src/FusionCHPMultiDataData.o fusion/calvin_files/fusion/src/FusionCHPTilingData.o fusion/calvin_files/fusion/src/FusionCHPGenericData.o fusion/calvin_files/fusion/src/FusionCHPQuantificationData.o fusion/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.o fusion/calvin_files/parameter/src/ParameterNameValueType.o fusion/calvin_files/parsers/src/CDFFileReader.o fusion/calvin_files/parsers/src/CelFileReader.o fusion/calvin_files/parsers/src/CHPFileReader.o fusion/calvin_files/parsers/src/CHPMultiDataFileReader.o fusion/calvin_files/parsers/src/CHPTilingFileReader.o fusion/calvin_files/parsers/src/CHPQuantificationFileReader.o fusion/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.o fusion/calvin_files/parsers/src/DataGroupHeaderReader.o fusion/calvin_files/parsers/src/DataGroupReader.o fusion/calvin_files/parsers/src/DataSetHeaderReader.o fusion/calvin_files/parsers/src/DataSetReader.o fusion/calvin_files/parsers/src/FileHeaderReader.o fusion/calvin_files/parsers/src/FileInput.o fusion/calvin_files/parsers/src/GenericDataHeaderReader.o fusion/calvin_files/parsers/src/GenericFileReader.o fusion/calvin_files/utils/src/AffymetrixGuid.o fusion/calvin_files/utils/src/DateTime.o fusion/calvin_files/utils/src/FileUtils.o fusion/calvin_files/utils/src/StringUtils.o fusion/calvin_files/utils/src/checksum.o fusion/file/BPMAPFileData.o fusion/file/BPMAPFileWriter.o fusion/file/CDFFileData.o fusion/file/CELFileData.o fusion/file/CHPFileData.o fusion/file/FileIO.o fusion/file/FileWriter.o fusion/file/TsvFile/ClfFile.o fusion/file/TsvFile/PgfFile.o fusion/file/TsvFile/TsvFile.o fusion/util/AffxByteArray.o fusion/util/AffxConv.o fusion/util/MsgStream.o fusion/util/Util.o fusion/util/Err.o fusion/util/Fs.o fusion/util/Verbose.o fusion/util/RowFile.o fusion/util/TableFile.o fusion/util/Convert.o R_affx_cel_parser.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 000.init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-affxparser/00new/affxparser/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (affxparser)
affxparser.Rcheck/tests/convertCel.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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. 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. > if (require("AffymetrixDataTestFiles")) { + library("affxparser") + + ## rawData/ + pathR <- system.file(package="AffymetrixDataTestFiles", mustWork=TRUE) + pathR <- file.path(pathR, "rawData") + + ## File #1: Test3 + chipType <- "Test3" + path <- file.path(pathR, "FusionSDK_Test3", chipType, "2.Calvin") + filename <- list.files(path=path, pattern="[.]CEL$")[1] + pathname <- file.path(path, filename) + hdr <- readCelHeader(pathname) + str(hdr) + stopifnot(hdr$chiptype == chipType) + filename4 <- gsub(".CEL", ",v4.CEL", filename) + pathname4 <- convertCel(pathname, filename4, verbose=TRUE, .validate=TRUE) + print(pathname4) + hdr4 <- readCelHeader(pathname4) + str(hdr4) + stopifnot(hdr4$chiptype == hdr$chiptype) + + ## New chip type + newChipType <- sprintf("%s-custom", chipType) + filename4 <- gsub(".CEL", ",v4,custom.CEL", filename) + pathname4 <- convertCel(pathname, filename4, newChipType=newChipType, verbose=TRUE) + print(pathname4) + hdr4 <- readCelHeader(pathname4) + str(hdr4) + ## FIXME + ## stopifnot(hdr4$chiptype == newChipType) + + + ## File #2: FusionSDK_HG-U133A + chipType <- "HG-U133A" + path <- file.path(pathR, "FusionSDK_HG-U133A", chipType, "2.Calvin") + filename <- list.files(path=path, pattern="[.]CEL$")[1] + pathname <- file.path(path, filename) + hdr <- readCelHeader(pathname) + str(hdr) + stopifnot(hdr$chiptype == chipType) + filename4 <- gsub(".CEL", ",v4.CEL", filename) + pathname4 <- convertCel(pathname, filename4, verbose=TRUE, .validate=TRUE) + print(pathname4) + hdr4 <- readCelHeader(pathname4) + str(hdr4) + stopifnot(hdr4$chiptype == hdr$chiptype) + + ## New chip type + newChipType <- sprintf("%s-custom", chipType) + filename4 <- gsub(".CEL", ",v4,custom.CEL", filename) + pathname4 <- convertCel(pathname, filename4, newChipType=newChipType, verbose=TRUE) + print(pathname4) + hdr4 <- readCelHeader(pathname4) + str(hdr4) + stopifnot(hdr4$chiptype == newChipType) + + + ## File #3: FusionSDK_Focus + chipType <- "HG-Focus" + path <- file.path(pathR, "FusionSDK_HG-Focus", chipType, "2.Calvin") + filename <- list.files(path=path, pattern="[.]CEL$")[1] + pathname <- file.path(path, filename) + hdr <- readCelHeader(pathname) + str(hdr) + stopifnot(hdr$chiptype == chipType) + filename4 <- gsub(".CEL", ",v4.CEL", filename) + pathname4 <- convertCel(pathname, filename4, verbose=TRUE, .validate=TRUE) + print(pathname4) + hdr4 <- readCelHeader(pathname4) + str(hdr4) + stopifnot(hdr4$chiptype == hdr$chiptype) + + ## New chip type + newChipType <- sprintf("%s-custom", chipType) + filename4 <- gsub(".CEL", ",v4,custom.CEL", filename) + pathname4 <- convertCel(pathname, filename4, newChipType=newChipType, verbose=TRUE) + print(pathname4) + hdr4 <- readCelHeader(pathname4) + str(hdr4) + ## FIXME + ## stopifnot(hdr4$chiptype == newChipType) + } # if (require("AffymetrixDataTestFiles")) Loading required package: AffymetrixDataTestFiles List of 14 $ filename : chr "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/AffymetrixDataTestFiles/rawData/FusionSDK"| __truncated__ $ version : int 1 $ cols : int 126 $ rows : int 126 $ total : int 15876 $ algorithm : chr "Percentile" $ parameters : chr "Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004;GridULX:154.000000;GridULY:164.000000;GridURX:995"| __truncated__ $ chiptype : chr "Test3" $ header : chr "" $ datheader : chr "[12..40151] Fetal 3:CLS=1167 RWS=1167 XIN=3 YIN=3 VE=17 2.0 08/16/01 17:28:31 \024 \024 Test3.1sq"| __truncated__ $ librarypackage: chr "" $ cellmargin : int 2 $ noutliers : int 5 $ nmasked : int 0 Reading CEL file... Reading CEL file...done Creating empty CEL file... Creating empty CEL file...done Updating CEL file... Updating CEL file...done Validating CEL file... Comparing CELs... CEL 1: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/AffymetrixDataTestFiles/rawData/FusionSDK_Test3/Test3/2.Calvin/Test3-1-121502.CEL CEL 2: ./Test3-1-121502,v4.CEL Reading first... Reading first...done Reading second... Reading second...done Comparing CEL headers... Comparing CEL headers...done Comparing CEL data... Comparing CEL data...done Comparing CELs...done Validating CEL file...done [1] "./Test3-1-121502,v4.CEL" List of 14 $ filename : chr "./Test3-1-121502,v4.CEL" $ version : int 4 $ cols : int 126 $ rows : int 126 $ total : int 15876 $ algorithm : chr "Percentile" $ parameters : chr "Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004;GridULX:154.000000;GridULY:164.000000;GridURX:995"| __truncated__ $ chiptype : chr "Test3" $ header : chr "Cols=126\nRows=126\nTotalX=126\nTotalY=126\nOffsetX=0\nOffsetY=0\nGridCornerUL=154 164\nGridCornerUR=995 160\nG"| __truncated__ $ datheader : chr "[12..40151] Fetal 3:CLS=1167 RWS=1167 XIN=3 YIN=3 VE=17 2.0 08/16/01 17:28:31 \024 \024 Test3.1sq"| __truncated__ $ librarypackage: chr "" $ cellmargin : int 2 $ noutliers : int 5 $ nmasked : int 0 Reading CEL file... Reading CEL file...done Updating the chip type label from 'Test3' to 'Test3-custom'. Creating empty CEL file... Creating empty CEL file...done Updating CEL file... Updating CEL file...done [1] "./Test3-1-121502,v4,custom.CEL" List of 14 $ filename : chr "./Test3-1-121502,v4,custom.CEL" $ version : int 4 $ cols : int 126 $ rows : int 126 $ total : int 15876 $ algorithm : chr "Percentile" $ parameters : chr "Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004;GridULX:154.000000;GridULY:164.000000;GridURX:995"| __truncated__ $ chiptype : chr "Test3" $ header : chr "Cols=126\nRows=126\nTotalX=126\nTotalY=126\nOffsetX=0\nOffsetY=0\nGridCornerUL=154 164\nGridCornerUR=995 160\nG"| __truncated__ $ datheader : chr "[12..40151] Fetal 3:CLS=1167 RWS=1167 XIN=3 YIN=3 VE=17 2.0 08/16/01 17:28:31 \024 \024 Test3.1sq"| __truncated__ $ librarypackage: chr "" $ cellmargin : int 2 $ noutliers : int 5 $ nmasked : int 0 List of 14 $ filename : chr "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/AffymetrixDataTestFiles/rawData/FusionSDK"| __truncated__ $ version : int 4 $ cols : int 712 $ rows : int 712 $ total : int 506944 $ algorithm : chr "Percentile" $ parameters : chr "Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004;AlgVersion:6.0;FixedCellSize:FALSE;IgnoreOutliers"| __truncated__ $ chiptype : chr "HG-U133A" $ header : chr "Cols=712\nRows=712\nTotalX=712\nTotalY=712\nOffsetX=0\nOffsetY=0\nGridCornerUL=185 257\nGridCornerUR=5111 229\n"| __truncated__ $ datheader : chr "[46..48458] ethan1-1:CLS=5377 RWS=5377 XIN=2 YIN=2 VE=30 2.0 11/10/04 18:23:42 M10SIM M10 \024 \0"| __truncated__ $ librarypackage: chr "" $ cellmargin : int 2 $ noutliers : int 2085 $ nmasked : int 0 Reading CEL file... Reading CEL file...done Creating empty CEL file... Creating empty CEL file...done Updating CEL file... Updating CEL file...done Validating CEL file... Comparing CELs... CEL 1: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/AffymetrixDataTestFiles/rawData/FusionSDK_HG-U133A/HG-U133A/2.Calvin/ethan1-1.CEL CEL 2: ./ethan1-1,v4.CEL Reading first... Reading first...done Reading second... Reading second...done Comparing CEL headers... Comparing CEL headers...done Comparing CEL data... Comparing CEL data...done Comparing CELs...done Validating CEL file...done [1] "./ethan1-1,v4.CEL" List of 14 $ filename : chr "./ethan1-1,v4.CEL" $ version : int 4 $ cols : int 712 $ rows : int 712 $ total : int 506944 $ algorithm : chr "Percentile" $ parameters : chr "Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004;AlgVersion:6.0;FixedCellSize:FALSE;IgnoreOutliers"| __truncated__ $ chiptype : chr "HG-U133A" $ header : chr "Cols=712\nRows=712\nTotalX=712\nTotalY=712\nOffsetX=0\nOffsetY=0\nGridCornerUL=185 257\nGridCornerUR=5111 229\n"| __truncated__ $ datheader : chr "[46..48458] ethan1-1:CLS=5377 RWS=5377 XIN=2 YIN=2 VE=30 2.0 11/10/04 18:23:42 M10SIM M10 \024 \0"| __truncated__ $ librarypackage: chr "" $ cellmargin : int 2 $ noutliers : int 2085 $ nmasked : int 0 Reading CEL file... Reading CEL file...done Updating the chip type label from 'HG-U133A' to 'HG-U133A-custom'. Creating empty CEL file... Creating empty CEL file...done Updating CEL file... Updating CEL file...done [1] "./ethan1-1,v4,custom.CEL" List of 14 $ filename : chr "./ethan1-1,v4,custom.CEL" $ version : int 4 $ cols : int 712 $ rows : int 712 $ total : int 506944 $ algorithm : chr "Percentile" $ parameters : chr "Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004;AlgVersion:6.0;FixedCellSize:FALSE;IgnoreOutliers"| __truncated__ $ chiptype : chr "HG-U133A-custom" $ header : chr "Cols=712\nRows=712\nTotalX=712\nTotalY=712\nOffsetX=0\nOffsetY=0\nGridCornerUL=185 257\nGridCornerUR=5111 229\n"| __truncated__ $ datheader : chr "[46..48458] ethan1-1:CLS=5377 RWS=5377 XIN=2 YIN=2 VE=30 2.0 11/10/04 18:23:42 M10SIM M10 \024 \0"| __truncated__ $ librarypackage: chr "" $ cellmargin : int 2 $ noutliers : int 2085 $ nmasked : int 0 List of 14 $ filename : chr "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/AffymetrixDataTestFiles/rawData/FusionSDK"| __truncated__ $ version : int 1 $ cols : int 448 $ rows : int 448 $ total : int 200704 $ algorithm : chr "Percentile" $ parameters : chr "Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004;GridULX:62.000000;GridULY:117.000000;GridURX:2748"| __truncated__ $ chiptype : chr "HG-Focus" $ header : chr "" $ datheader : chr "[7..46138] B1:CLS=2920 RWS=2920 XIN=3 YIN=3 VE=17 2.0 05/15/02 11:07:10 \024 \024 HG-Focus.1sq \0"| __truncated__ $ librarypackage: chr "" $ cellmargin : int 2 $ noutliers : int 508 $ nmasked : int 0 Reading CEL file... Reading CEL file...done Creating empty CEL file... Creating empty CEL file...done Updating CEL file... Updating CEL file...done Validating CEL file... Comparing CELs... CEL 1: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/AffymetrixDataTestFiles/rawData/FusionSDK_HG-Focus/HG-Focus/2.Calvin/HG-Focus-1-121502.CEL CEL 2: ./HG-Focus-1-121502,v4.CEL Reading first... Reading first...done Reading second... Reading second...done Comparing CEL headers... Comparing CEL headers...done Comparing CEL data... Comparing CEL data...done Comparing CELs...done Validating CEL file...done [1] "./HG-Focus-1-121502,v4.CEL" List of 14 $ filename : chr "./HG-Focus-1-121502,v4.CEL" $ version : int 4 $ cols : int 448 $ rows : int 448 $ total : int 200704 $ algorithm : chr "Percentile" $ parameters : chr "Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004;GridULX:62.000000;GridULY:117.000000;GridURX:2748"| __truncated__ $ chiptype : chr "HG-Focus" $ header : chr "Cols=448\nRows=448\nTotalX=448\nTotalY=448\nOffsetX=0\nOffsetY=0\nGridCornerUL=62 117\nGridCornerUR=2748 119\nG"| __truncated__ $ datheader : chr "[7..46138] B1:CLS=2920 RWS=2920 XIN=3 YIN=3 VE=17 2.0 05/15/02 11:07:10 \024 \024 HG-Focus.1sq \0"| __truncated__ $ librarypackage: chr "" $ cellmargin : int 2 $ noutliers : int 508 $ nmasked : int 0 Reading CEL file... Reading CEL file...done Updating the chip type label from 'HG-Focus' to 'HG-Focus-custom'. Creating empty CEL file... Creating empty CEL file...done Updating CEL file... Updating CEL file...done [1] "./HG-Focus-1-121502,v4,custom.CEL" List of 14 $ filename : chr "./HG-Focus-1-121502,v4,custom.CEL" $ version : int 4 $ cols : int 448 $ rows : int 448 $ total : int 200704 $ algorithm : chr "Percentile" $ parameters : chr "Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004;GridULX:62.000000;GridULY:117.000000;GridURX:2748"| __truncated__ $ chiptype : chr "HG-Focus" $ header : chr "Cols=448\nRows=448\nTotalX=448\nTotalY=448\nOffsetX=0\nOffsetY=0\nGridCornerUL=62 117\nGridCornerUR=2748 119\nG"| __truncated__ $ datheader : chr "[7..46138] B1:CLS=2920 RWS=2920 XIN=3 YIN=3 VE=17 2.0 05/15/02 11:07:10 \024 \024 HG-Focus.1sq \0"| __truncated__ $ librarypackage: chr "" $ cellmargin : int 2 $ noutliers : int 508 $ nmasked : int 0 > > proc.time() user system elapsed 5.313 0.637 6.314
affxparser.Rcheck/tests/readCdfDataFrame.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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. 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. > if (require("AffymetrixDataTestFiles")) { + library("affxparser") + + pathR <- system.file(package="AffymetrixDataTestFiles") + pathA <- file.path(pathR, "annotationData", "chipTypes", "Test3") + + # Read CDF structure + cdf <- file.path(pathA, "1.XDA", "Test3.CDF") + hdr <- readCdfHeader(cdf) + Jall <- hdr$nunits + + # Various sets of indices to be read + idxsList <- list( + ## readNothing=integer(0L), # FIX ME + readAll=NULL, + readOne=10L, + readSome=11:20, + readDouble=as.double(11:20), + outOfRange=-1L, + outOfRange=0L, + outOfRange=1e9L + ) + + # Read full file + data <- readCdfDataFrame(cdf) + str(data) + stopifnot(length(unique(data$unitName)) == Jall) + + # Read different subsets of units + for (ii in seq_along(idxsList)) { + name <- names(idxsList)[ii] + message(sprintf("Testing readCdfDataFrame() with '%s' indices...", name)) + idxs <- idxsList[[ii]] + str(list(idxs=idxs)) + if (grepl("outOfRange", name)) { + res <- tryCatch(readCdfDataFrame(cdf, units=idxs), error=function(ex) ex) + str(res) + stopifnot(inherits(res, "error")) + } else { + data <- readCdfDataFrame(cdf, units=idxs) + str(data) + units <- if (is.null(idxs)) seq_len(Jall) else as.integer(idxs) + stopifnot(length(unique(data$unitName)) == length(units)) + stopifnot(identical(sort(unique(data$unit)), units)) + } + message(sprintf("Testing readCdfDataFrame() with '%s' indices...done", name)) + } # for (ii ...) + } # if (require("AffymetrixDataTestFiles")) Loading required package: AffymetrixDataTestFiles 'data.frame': 12708 obs. of 16 variables: $ unit : int 1 1 1 1 1 1 1 1 1 1 ... $ unitName : chr "Pae_16SrRNA_s_at" "Pae_16SrRNA_s_at" "Pae_16SrRNA_s_at" "Pae_16SrRNA_s_at" ... $ unitType : chr "expression" "expression" "expression" "expression" ... $ unitDirection : chr "antisense" "antisense" "antisense" "antisense" ... $ unitNbrOfAtoms : int 16 16 16 16 16 16 16 16 16 16 ... $ group : int 1 1 1 1 1 1 1 1 1 1 ... $ groupName : chr "Pae_16SrRNA_s_at" "Pae_16SrRNA_s_at" "Pae_16SrRNA_s_at" "Pae_16SrRNA_s_at" ... $ groupDirection : chr "antisense" "antisense" "antisense" "antisense" ... $ groupNbrOfAtoms: int 16 16 16 16 16 16 16 16 16 16 ... $ cell : int 10066 10192 2414 2540 5010 5136 6949 7075 14264 14390 ... $ x : int 111 111 19 19 95 95 18 18 25 25 ... $ y : int 79 80 19 20 39 40 55 56 113 114 ... $ pbase : chr "t" "a" "a" "t" ... $ tbase : chr "a" "a" "t" "t" ... $ indexPos : int 0 0 1 1 2 2 3 3 4 4 ... $ atom : int 0 0 1 1 2 2 3 3 4 4 ... Testing readCdfDataFrame() with 'readAll' indices... List of 1 $ idxs: NULL 'data.frame': 12708 obs. of 16 variables: $ unit : int 1 1 1 1 1 1 1 1 1 1 ... $ unitName : chr "Pae_16SrRNA_s_at" "Pae_16SrRNA_s_at" "Pae_16SrRNA_s_at" "Pae_16SrRNA_s_at" ... $ unitType : chr "expression" "expression" "expression" "expression" ... $ unitDirection : chr "antisense" "antisense" "antisense" "antisense" ... $ unitNbrOfAtoms : int 16 16 16 16 16 16 16 16 16 16 ... $ group : int 1 1 1 1 1 1 1 1 1 1 ... $ groupName : chr "Pae_16SrRNA_s_at" "Pae_16SrRNA_s_at" "Pae_16SrRNA_s_at" "Pae_16SrRNA_s_at" ... $ groupDirection : chr "antisense" "antisense" "antisense" "antisense" ... $ groupNbrOfAtoms: int 16 16 16 16 16 16 16 16 16 16 ... $ cell : int 10066 10192 2414 2540 5010 5136 6949 7075 14264 14390 ... $ x : int 111 111 19 19 95 95 18 18 25 25 ... $ y : int 79 80 19 20 39 40 55 56 113 114 ... $ pbase : chr "t" "a" "a" "t" ... $ tbase : chr "a" "a" "t" "t" ... $ indexPos : int 0 0 1 1 2 2 3 3 4 4 ... $ atom : int 0 0 1 1 2 2 3 3 4 4 ... Testing readCdfDataFrame() with 'readAll' indices...done Testing readCdfDataFrame() with 'readOne' indices... List of 1 $ idxs: int 10 'data.frame': 24 obs. of 16 variables: $ unit : int 10 10 10 10 10 10 10 10 10 10 ... $ unitName : chr "PA1178_oprH_st" "PA1178_oprH_st" "PA1178_oprH_st" "PA1178_oprH_st" ... $ unitType : chr "expression" "expression" "expression" "expression" ... $ unitDirection : chr "sense" "sense" "sense" "sense" ... $ unitNbrOfAtoms : int 12 12 12 12 12 12 12 12 12 12 ... $ group : int 1 1 1 1 1 1 1 1 1 1 ... $ groupName : chr "PA1178_oprH_st" "PA1178_oprH_st" "PA1178_oprH_st" "PA1178_oprH_st" ... $ groupDirection : chr "sense" "sense" "sense" "sense" ... $ groupNbrOfAtoms: int 12 12 12 12 12 12 12 12 12 12 ... $ cell : int 4196 4322 8522 8648 8259 8385 14038 14164 5498 5624 ... $ x : int 37 37 79 79 68 68 51 51 79 79 ... $ y : int 33 34 67 68 65 66 111 112 43 44 ... $ pbase : chr "t" "a" "c" "g" ... $ tbase : chr "a" "a" "g" "g" ... $ indexPos : int 0 0 1 1 2 2 3 3 4 4 ... $ atom : int 0 0 1 1 2 2 3 3 4 4 ... Testing readCdfDataFrame() with 'readOne' indices...done Testing readCdfDataFrame() with 'readSome' indices... List of 1 $ idxs: int [1:10] 11 12 13 14 15 16 17 18 19 20 'data.frame': 288 obs. of 16 variables: $ unit : int 11 11 11 11 11 11 11 11 11 11 ... $ unitName : chr "PA1816_dnaQ_st" "PA1816_dnaQ_st" "PA1816_dnaQ_st" "PA1816_dnaQ_st" ... $ unitType : chr "expression" "expression" "expression" "expression" ... $ unitDirection : chr "sense" "sense" "sense" "sense" ... $ unitNbrOfAtoms : int 12 12 12 12 12 12 12 12 12 12 ... $ group : int 1 1 1 1 1 1 1 1 1 1 ... $ groupName : chr "PA1816_dnaQ_st" "PA1816_dnaQ_st" "PA1816_dnaQ_st" "PA1816_dnaQ_st" ... $ groupDirection : chr "sense" "sense" "sense" "sense" ... $ groupNbrOfAtoms: int 12 12 12 12 12 12 12 12 12 12 ... $ cell : int 5686 5812 7218 7344 7014 7140 2256 2382 8310 8436 ... $ x : int 15 15 35 35 83 83 113 113 119 119 ... $ y : int 45 46 57 58 55 56 17 18 65 66 ... $ pbase : chr "t" "a" "t" "a" ... $ tbase : chr "a" "a" "a" "a" ... $ indexPos : int 0 0 1 1 2 2 3 3 4 4 ... $ atom : int 0 0 1 1 2 2 3 3 4 4 ... Testing readCdfDataFrame() with 'readSome' indices...done Testing readCdfDataFrame() with 'readDouble' indices... List of 1 $ idxs: num [1:10] 11 12 13 14 15 16 17 18 19 20 'data.frame': 288 obs. of 16 variables: $ unit : int 11 11 11 11 11 11 11 11 11 11 ... $ unitName : chr "PA1816_dnaQ_st" "PA1816_dnaQ_st" "PA1816_dnaQ_st" "PA1816_dnaQ_st" ... $ unitType : chr "expression" "expression" "expression" "expression" ... $ unitDirection : chr "sense" "sense" "sense" "sense" ... $ unitNbrOfAtoms : int 12 12 12 12 12 12 12 12 12 12 ... $ group : int 1 1 1 1 1 1 1 1 1 1 ... $ groupName : chr "PA1816_dnaQ_st" "PA1816_dnaQ_st" "PA1816_dnaQ_st" "PA1816_dnaQ_st" ... $ groupDirection : chr "sense" "sense" "sense" "sense" ... $ groupNbrOfAtoms: int 12 12 12 12 12 12 12 12 12 12 ... $ cell : int 5686 5812 7218 7344 7014 7140 2256 2382 8310 8436 ... $ x : int 15 15 35 35 83 83 113 113 119 119 ... $ y : int 45 46 57 58 55 56 17 18 65 66 ... $ pbase : chr "t" "a" "t" "a" ... $ tbase : chr "a" "a" "a" "a" ... $ indexPos : int 0 0 1 1 2 2 3 3 4 4 ... $ atom : int 0 0 1 1 2 2 3 3 4 4 ... Testing readCdfDataFrame() with 'readDouble' indices...done Testing readCdfDataFrame() with 'outOfRange' indices... List of 1 $ idxs: int -1 List of 2 $ message: chr "Argument 'units' contains non-positive indices." $ call : language readCdfDataFrame(cdf, units = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCdfDataFrame() with 'outOfRange' indices...done Testing readCdfDataFrame() with 'outOfRange' indices... List of 1 $ idxs: int 0 List of 2 $ message: chr "Argument 'units' contains non-positive indices." $ call : language readCdfDataFrame(cdf, units = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCdfDataFrame() with 'outOfRange' indices...done Testing readCdfDataFrame() with 'outOfRange' indices... List of 1 $ idxs: int 1000000000 List of 2 $ message: chr "Argument 'units' contains an element out of range [1,345]: 1000000000" $ call : language readCdf(filename, units = units, readXY = readXY, readBases = readBases, readIndexpos = readIndexpos, readAt| __truncated__ ... - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCdfDataFrame() with 'outOfRange' indices...done Warning messages: 1: In readCdfDataFrame(cdf) : Some of the fields were not read: expos 2: In readCdfDataFrame(cdf, units = idxs) : Some of the fields were not read: expos 3: In readCdfDataFrame(cdf, units = idxs) : Some of the fields were not read: expos 4: In readCdfDataFrame(cdf, units = idxs) : Some of the fields were not read: expos 5: In readCdfDataFrame(cdf, units = idxs) : Some of the fields were not read: expos > > proc.time() user system elapsed 5.247 0.216 5.815
affxparser.Rcheck/tests/readCdfQc.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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. 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. > if (require("AffymetrixDataTestFiles")) { + library("affxparser") + + pathR <- system.file(package="AffymetrixDataTestFiles") + pathA <- file.path(pathR, "annotationData", "chipTypes", "Test3") + + # Read CDF structure + cdf <- file.path(pathA, "1.XDA", "Test3.CDF") + hdr <- readCdfHeader(cdf) + Jall <- hdr$nqcunits + + # Various sets of indices to be read + idxsList <- list( + ## readNothing=integer(0L), # FIX ME + readAll=NULL, + readOne=5L, + readSome=5:10, + readDouble=as.double(5:10), + outOfRange=-1L, + outOfRange=0L, + outOfRange=1e9L + ) + + # Read full file + data <- readCdfQc(cdf) + str(head(data)) + stopifnot(length(data) == Jall) + + # Read different subsets of units + for (ii in seq_along(idxsList)) { + name <- names(idxsList)[ii] + message(sprintf("Testing readCdfQc() with '%s' indices...", name)) + idxs <- idxsList[[ii]] + str(list(idxs=idxs)) + if (grepl("outOfRange", name)) { + res <- tryCatch(readCdfQc(cdf, units=idxs), error=function(ex) ex) + str(res) + stopifnot(inherits(res, "error")) + } else { + data <- readCdfQc(cdf, units=idxs) + str(head(data)) + J <- if (is.null(idxs)) Jall else length(idxs) + stopifnot(length(data) == J) + } + message(sprintf("Testing readCdfQc() with '%s' indices...done", name)) + } # for (ii ...) + } # if (require("AffymetrixDataTestFiles")) Loading required package: AffymetrixDataTestFiles List of 6 $ :List of 8 ..$ x : int [1:300] 77 77 77 77 77 78 78 78 78 78 ... ..$ y : int [1:300] 82 83 84 85 86 82 83 84 85 86 ... ..$ indices : int [1:300] 10410 10536 10662 10788 10914 10411 10537 10663 10789 10915 ... ..$ length : int [1:300] 20 20 20 20 1 20 20 20 20 1 ... ..$ pm : logi [1:300] FALSE TRUE FALSE FALSE FALSE FALSE ... ..$ background: logi [1:300] FALSE FALSE FALSE FALSE TRUE FALSE ... ..$ type : chr "geneExpNegative" ..$ ncells : int 300 $ :List of 8 ..$ x : int [1:300] 77 77 77 77 77 78 78 78 78 78 ... ..$ y : int [1:300] 80 79 78 77 81 80 79 78 77 81 ... ..$ indices : int [1:300] 10158 10032 9906 9780 10284 10159 10033 9907 9781 10285 ... ..$ length : int [1:300] 20 20 20 20 1 20 20 20 20 1 ... ..$ pm : logi [1:300] FALSE FALSE TRUE FALSE FALSE FALSE ... ..$ background: logi [1:300] FALSE FALSE FALSE FALSE TRUE FALSE ... ..$ type : chr "geneExpPositive" ..$ ncells : int 300 $ :List of 8 ..$ x : int [1:204] 120 118 116 114 112 110 108 106 104 102 ... ..$ y : int [1:204] 0 0 0 0 0 0 0 0 0 0 ... ..$ indices : int [1:204] 121 119 117 115 113 111 109 107 105 103 ... ..$ length : int [1:204] 25 25 25 25 25 25 25 25 25 25 ... ..$ pm : logi [1:204] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ background: logi [1:204] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ type : chr "crossHybeNegative" ..$ ncells : int 204 $ :List of 8 ..$ x : int [1:32] 1 124 122 3 124 122 2 123 125 0 ... ..$ y : int [1:32] 1 0 0 1 2 2 0 1 1 2 ... ..$ indices : int [1:32] 128 125 123 130 377 375 3 250 252 253 ... ..$ length : int [1:32] 25 25 25 25 25 25 25 25 25 25 ... ..$ pm : logi [1:32] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ background: logi [1:32] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ type : chr "checkerboardPositive" ..$ ncells : int 32 $ :List of 8 ..$ x : int [1:32] 0 125 123 2 3 124 3 1 122 124 ... ..$ y : int [1:32] 1 0 0 1 2 3 0 0 1 1 ... ..$ indices : int [1:32] 127 126 124 129 256 503 4 2 249 251 ... ..$ length : int [1:32] 25 25 25 25 25 25 25 25 25 25 ... ..$ pm : logi [1:32] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ background: logi [1:32] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ type : chr "checkerboardNegative" ..$ ncells : int 32 $ :List of 8 ..$ x : int [1:208] 119 117 115 113 111 109 107 105 103 101 ... ..$ y : int [1:208] 0 0 0 0 0 0 0 0 0 0 ... ..$ indices : int [1:208] 120 118 116 114 112 110 108 106 104 102 ... ..$ length : int [1:208] 25 25 25 25 25 25 25 25 25 25 ... ..$ pm : logi [1:208] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ background: logi [1:208] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ type : chr "crossHybePositive" ..$ ncells : int 208 Testing readCdfQc() with 'readAll' indices... List of 1 $ idxs: NULL List of 6 $ :List of 8 ..$ x : int [1:300] 77 77 77 77 77 78 78 78 78 78 ... ..$ y : int [1:300] 82 83 84 85 86 82 83 84 85 86 ... ..$ indices : int [1:300] 10410 10536 10662 10788 10914 10411 10537 10663 10789 10915 ... ..$ length : int [1:300] 20 20 20 20 1 20 20 20 20 1 ... ..$ pm : logi [1:300] FALSE TRUE FALSE FALSE FALSE FALSE ... ..$ background: logi [1:300] FALSE FALSE FALSE FALSE TRUE FALSE ... ..$ type : chr "geneExpNegative" ..$ ncells : int 300 $ :List of 8 ..$ x : int [1:300] 77 77 77 77 77 78 78 78 78 78 ... ..$ y : int [1:300] 80 79 78 77 81 80 79 78 77 81 ... ..$ indices : int [1:300] 10158 10032 9906 9780 10284 10159 10033 9907 9781 10285 ... ..$ length : int [1:300] 20 20 20 20 1 20 20 20 20 1 ... ..$ pm : logi [1:300] FALSE FALSE TRUE FALSE FALSE FALSE ... ..$ background: logi [1:300] FALSE FALSE FALSE FALSE TRUE FALSE ... ..$ type : chr "geneExpPositive" ..$ ncells : int 300 $ :List of 8 ..$ x : int [1:204] 120 118 116 114 112 110 108 106 104 102 ... ..$ y : int [1:204] 0 0 0 0 0 0 0 0 0 0 ... ..$ indices : int [1:204] 121 119 117 115 113 111 109 107 105 103 ... ..$ length : int [1:204] 25 25 25 25 25 25 25 25 25 25 ... ..$ pm : logi [1:204] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ background: logi [1:204] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ type : chr "crossHybeNegative" ..$ ncells : int 204 $ :List of 8 ..$ x : int [1:32] 1 124 122 3 124 122 2 123 125 0 ... ..$ y : int [1:32] 1 0 0 1 2 2 0 1 1 2 ... ..$ indices : int [1:32] 128 125 123 130 377 375 3 250 252 253 ... ..$ length : int [1:32] 25 25 25 25 25 25 25 25 25 25 ... ..$ pm : logi [1:32] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ background: logi [1:32] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ type : chr "checkerboardPositive" ..$ ncells : int 32 $ :List of 8 ..$ x : int [1:32] 0 125 123 2 3 124 3 1 122 124 ... ..$ y : int [1:32] 1 0 0 1 2 3 0 0 1 1 ... ..$ indices : int [1:32] 127 126 124 129 256 503 4 2 249 251 ... ..$ length : int [1:32] 25 25 25 25 25 25 25 25 25 25 ... ..$ pm : logi [1:32] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ background: logi [1:32] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ type : chr "checkerboardNegative" ..$ ncells : int 32 $ :List of 8 ..$ x : int [1:208] 119 117 115 113 111 109 107 105 103 101 ... ..$ y : int [1:208] 0 0 0 0 0 0 0 0 0 0 ... ..$ indices : int [1:208] 120 118 116 114 112 110 108 106 104 102 ... ..$ length : int [1:208] 25 25 25 25 25 25 25 25 25 25 ... ..$ pm : logi [1:208] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ background: logi [1:208] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ type : chr "crossHybePositive" ..$ ncells : int 208 Testing readCdfQc() with 'readAll' indices...done Testing readCdfQc() with 'readOne' indices... List of 1 $ idxs: int 5 List of 1 $ :List of 8 ..$ x : int [1:32] 0 125 123 2 3 124 3 1 122 124 ... ..$ y : int [1:32] 1 0 0 1 2 3 0 0 1 1 ... ..$ indices : int [1:32] 127 126 124 129 256 503 4 2 249 251 ... ..$ length : int [1:32] 25 25 25 25 25 25 25 25 25 25 ... ..$ pm : logi [1:32] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ background: logi [1:32] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ type : chr "checkerboardNegative" ..$ ncells : int 32 Testing readCdfQc() with 'readOne' indices...done Testing readCdfQc() with 'readSome' indices... List of 1 $ idxs: int [1:6] 5 6 7 8 9 10 List of 6 $ :List of 8 ..$ x : int [1:32] 0 125 123 2 3 124 3 1 122 124 ... ..$ y : int [1:32] 1 0 0 1 2 3 0 0 1 1 ... ..$ indices : int [1:32] 127 126 124 129 256 503 4 2 249 251 ... ..$ length : int [1:32] 25 25 25 25 25 25 25 25 25 25 ... ..$ pm : logi [1:32] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ background: logi [1:32] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ type : chr "checkerboardNegative" ..$ ncells : int 32 $ :List of 8 ..$ x : int [1:208] 119 117 115 113 111 109 107 105 103 101 ... ..$ y : int [1:208] 0 0 0 0 0 0 0 0 0 0 ... ..$ indices : int [1:208] 120 118 116 114 112 110 108 106 104 102 ... ..$ length : int [1:208] 25 25 25 25 25 25 25 25 25 25 ... ..$ pm : logi [1:208] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ background: logi [1:208] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ type : chr "crossHybePositive" ..$ ncells : int 208 $ :List of 8 ..$ x : int [1:24] 85 43 85 43 85 43 85 43 85 125 ... ..$ y : int [1:24] 0 1 1 2 2 0 125 125 124 36 ... ..$ indices : int [1:24] 86 170 212 296 338 44 15836 15794 15710 4662 ... ..$ length : int [1:24] 20 18 18 16 16 20 20 20 18 16 ... ..$ pm : logi [1:24] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ background: logi [1:24] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ type : chr "hybePositive" ..$ ncells : int 24 $ :List of 8 ..$ x : int [1:24] 83 41 41 83 41 83 83 41 0 83 ... ..$ y : int [1:24] 0 0 1 1 2 2 125 125 80 124 ... ..$ indices : int [1:24] 84 42 168 210 294 336 15834 15792 10081 15708 ... ..$ length : int [1:24] 20 20 18 18 16 16 20 20 20 18 ... ..$ pm : logi [1:24] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ background: logi [1:24] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ type : chr "hybeNegative" ..$ ncells : int 24 $ :List of 8 ..$ x : int [1:294] 12 16 18 19 20 21 22 24 25 26 ... ..$ y : int [1:294] 9 9 9 9 9 9 9 9 9 9 ... ..$ indices : int [1:294] 1147 1151 1153 1154 1155 1156 1157 1159 1160 1161 ... ..$ length : int [1:294] 25 25 25 25 25 25 25 25 25 25 ... ..$ pm : logi [1:294] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ background: logi [1:294] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ type : chr "textFeaturesPositive" ..$ ncells : int 294 $ :List of 8 ..$ x : int [1:161] 13 14 15 37 38 39 42 66 67 68 ... ..$ y : int [1:161] 9 9 9 9 9 9 9 9 9 9 ... ..$ indices : int [1:161] 1148 1149 1150 1172 1173 1174 1177 1201 1202 1203 ... ..$ length : int [1:161] 25 25 25 25 25 25 25 25 25 25 ... ..$ pm : logi [1:161] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ background: logi [1:161] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ type : chr "textFeaturesNegative" ..$ ncells : int 161 Testing readCdfQc() with 'readSome' indices...done Testing readCdfQc() with 'readDouble' indices... List of 1 $ idxs: num [1:6] 5 6 7 8 9 10 List of 6 $ :List of 8 ..$ x : int [1:32] 0 125 123 2 3 124 3 1 122 124 ... ..$ y : int [1:32] 1 0 0 1 2 3 0 0 1 1 ... ..$ indices : int [1:32] 127 126 124 129 256 503 4 2 249 251 ... ..$ length : int [1:32] 25 25 25 25 25 25 25 25 25 25 ... ..$ pm : logi [1:32] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ background: logi [1:32] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ type : chr "checkerboardNegative" ..$ ncells : int 32 $ :List of 8 ..$ x : int [1:208] 119 117 115 113 111 109 107 105 103 101 ... ..$ y : int [1:208] 0 0 0 0 0 0 0 0 0 0 ... ..$ indices : int [1:208] 120 118 116 114 112 110 108 106 104 102 ... ..$ length : int [1:208] 25 25 25 25 25 25 25 25 25 25 ... ..$ pm : logi [1:208] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ background: logi [1:208] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ type : chr "crossHybePositive" ..$ ncells : int 208 $ :List of 8 ..$ x : int [1:24] 85 43 85 43 85 43 85 43 85 125 ... ..$ y : int [1:24] 0 1 1 2 2 0 125 125 124 36 ... ..$ indices : int [1:24] 86 170 212 296 338 44 15836 15794 15710 4662 ... ..$ length : int [1:24] 20 18 18 16 16 20 20 20 18 16 ... ..$ pm : logi [1:24] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ background: logi [1:24] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ type : chr "hybePositive" ..$ ncells : int 24 $ :List of 8 ..$ x : int [1:24] 83 41 41 83 41 83 83 41 0 83 ... ..$ y : int [1:24] 0 0 1 1 2 2 125 125 80 124 ... ..$ indices : int [1:24] 84 42 168 210 294 336 15834 15792 10081 15708 ... ..$ length : int [1:24] 20 20 18 18 16 16 20 20 20 18 ... ..$ pm : logi [1:24] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ background: logi [1:24] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ type : chr "hybeNegative" ..$ ncells : int 24 $ :List of 8 ..$ x : int [1:294] 12 16 18 19 20 21 22 24 25 26 ... ..$ y : int [1:294] 9 9 9 9 9 9 9 9 9 9 ... ..$ indices : int [1:294] 1147 1151 1153 1154 1155 1156 1157 1159 1160 1161 ... ..$ length : int [1:294] 25 25 25 25 25 25 25 25 25 25 ... ..$ pm : logi [1:294] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ background: logi [1:294] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ type : chr "textFeaturesPositive" ..$ ncells : int 294 $ :List of 8 ..$ x : int [1:161] 13 14 15 37 38 39 42 66 67 68 ... ..$ y : int [1:161] 9 9 9 9 9 9 9 9 9 9 ... ..$ indices : int [1:161] 1148 1149 1150 1172 1173 1174 1177 1201 1202 1203 ... ..$ length : int [1:161] 25 25 25 25 25 25 25 25 25 25 ... ..$ pm : logi [1:161] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ background: logi [1:161] FALSE FALSE FALSE FALSE FALSE FALSE ... ..$ type : chr "textFeaturesNegative" ..$ ncells : int 161 Testing readCdfQc() with 'readDouble' indices...done Testing readCdfQc() with 'outOfRange' indices... List of 1 $ idxs: int -1 List of 2 $ message: chr "Argument 'units' contains an element out of range [1,13]: -1" $ call : language readCdfQc(cdf, units = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCdfQc() with 'outOfRange' indices...done Testing readCdfQc() with 'outOfRange' indices... List of 1 $ idxs: int 0 List of 2 $ message: chr "Argument 'units' contains an element out of range [1,13]: 0" $ call : language readCdfQc(cdf, units = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCdfQc() with 'outOfRange' indices...done Testing readCdfQc() with 'outOfRange' indices... List of 1 $ idxs: int 1000000000 List of 2 $ message: chr "Argument 'units' contains an element out of range [1,13]: 1000000000" $ call : language readCdfQc(cdf, units = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCdfQc() with 'outOfRange' indices...done > > proc.time() user system elapsed 0.825 0.179 1.030
affxparser.Rcheck/tests/readCdfUnits_etal.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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. 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. > if (require("AffymetrixDataTestFiles")) { + library("affxparser") + + pathR <- system.file(package="AffymetrixDataTestFiles") + pathA <- file.path(pathR, "annotationData", "chipTypes", "Test3") + + # Read CDF structure + cdf <- file.path(pathA, "1.XDA", "Test3.CDF") + hdr <- readCdfHeader(cdf) + Jall <- hdr$nunits + + # Various sets of indices to be read + idxsList <- list( + ## readNothing=integer(0L), # FIX ME + readAll=NULL, + readOne=10L, + readSome=11:20, + readDouble=as.double(11:20), + outOfRange=-1L, + outOfRange=0L, + outOfRange=1e9L + ) + + fcnNames <- c( + "readCdf", + "readCdfUnits", + "readCdfUnitNames", + "readCdfNbrOfCellsPerUnitGroup", + "readCdfGroupNames", + "readCdfCellIndices", + "readCdfIsPm" + ) + + # Read full file + for (fcnName in fcnNames) { + fcn <- get(fcnName, mode="function", envir=getNamespace("affxparser")) + data <- fcn(cdf) + str(head(data)) + stopifnot(length(data) == Jall) + } # for (fcn ...) + + for (fcnName in fcnNames) { + fcn <- get(fcnName, mode="function", envir=getNamespace("affxparser")) + + # Read different subsets of units + for (ii in seq_along(idxsList)) { + name <- names(idxsList)[ii] + message(sprintf("Testing %s() with '%s' indices...", fcnName, name)) + idxs <- idxsList[[ii]] + str(list(idxs=idxs)) + if (grepl("outOfRange", name)) { + res <- tryCatch(readCdfQc(cdf, units=idxs), error=function(ex) ex) + str(res) + stopifnot(inherits(res, "error")) + } else { + data <- fcn(cdf, units=idxs) + str(head(data)) + J <- if (is.null(idxs)) Jall else length(idxs) + stopifnot(length(data) == J) + } + message(sprintf("Testing %s() with '%s' indices...done", fcnName, name)) + } # for (ii ...) + } # for (fcn ...) + } # if (require("AffymetrixDataTestFiles")) Loading required package: AffymetrixDataTestFiles List of 6 $ Pae_16SrRNA_s_at:List of 7 ..$ groups :List of 1 .. ..$ Pae_16SrRNA_s_at:List of 9 .. .. ..$ x : int [1:32] 111 111 19 19 95 95 18 18 25 25 ... .. .. ..$ y : int [1:32] 79 80 19 20 39 40 55 56 113 114 ... .. .. ..$ pbase : chr [1:32] "t" "a" "a" "t" ... .. .. ..$ tbase : chr [1:32] "a" "a" "t" "t" ... .. .. ..$ atom : int [1:32] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ indexpos : int [1:32] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ groupdirection: chr "antisense" .. .. ..$ natoms : int 16 .. .. ..$ ncellsperatom : int 2 ..$ unittype : chr "expression" ..$ unitdirection: chr "antisense" ..$ natoms : int 16 ..$ ncells : int 32 ..$ ncellsperatom: int 2 ..$ unitnumber : int 1000 $ Pae_23SrRNA_s_at:List of 7 ..$ groups :List of 1 .. ..$ Pae_23SrRNA_s_at:List of 9 .. .. ..$ x : int [1:32] 124 124 56 56 1 1 85 85 62 62 ... .. .. ..$ y : int [1:32] 95 96 99 100 23 24 41 42 9 10 ... .. .. ..$ pbase : chr [1:32] "a" "t" "t" "a" ... .. .. ..$ tbase : chr [1:32] "t" "t" "a" "a" ... .. .. ..$ atom : int [1:32] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ indexpos : int [1:32] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ groupdirection: chr "antisense" .. .. ..$ natoms : int 16 .. .. ..$ ncellsperatom : int 2 ..$ unittype : chr "expression" ..$ unitdirection: chr "antisense" ..$ natoms : int 16 ..$ ncells : int 32 ..$ ncellsperatom: int 2 ..$ unitnumber : int 1001 $ PA1178_oprH_at :List of 7 ..$ groups :List of 1 .. ..$ PA1178_oprH_at:List of 9 .. .. ..$ x : int [1:24] 41 41 117 117 110 110 60 60 41 41 ... .. .. ..$ y : int [1:24] 49 50 45 46 41 42 75 76 47 48 ... .. .. ..$ pbase : chr [1:24] "a" "t" "g" "c" ... .. .. ..$ tbase : chr [1:24] "t" "t" "c" "c" ... .. .. ..$ atom : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ indexpos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ groupdirection: chr "antisense" .. .. ..$ natoms : int 12 .. .. ..$ ncellsperatom : int 2 ..$ unittype : chr "expression" ..$ unitdirection: chr "antisense" ..$ natoms : int 12 ..$ ncells : int 24 ..$ ncellsperatom: int 2 ..$ unitnumber : int 1002 $ PA1816_dnaQ_at :List of 7 ..$ groups :List of 1 .. ..$ PA1816_dnaQ_at:List of 9 .. .. ..$ x : int [1:24] 21 21 68 68 119 119 62 62 118 118 ... .. .. ..$ y : int [1:24] 105 106 41 42 49 50 37 38 97 98 ... .. .. ..$ pbase : chr [1:24] "a" "t" "a" "t" ... .. .. ..$ tbase : chr [1:24] "t" "t" "t" "t" ... .. .. ..$ atom : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ indexpos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ groupdirection: chr "antisense" .. .. ..$ natoms : int 12 .. .. ..$ ncellsperatom : int 2 ..$ unittype : chr "expression" ..$ unitdirection: chr "antisense" ..$ natoms : int 12 ..$ ncells : int 24 ..$ ncellsperatom: int 2 ..$ unitnumber : int 1003 $ PA3183_zwf_at :List of 7 ..$ groups :List of 1 .. ..$ PA3183_zwf_at:List of 9 .. .. ..$ x : int [1:24] 104 104 106 106 79 79 53 53 77 77 ... .. .. ..$ y : int [1:24] 91 92 19 20 27 28 75 76 19 20 ... .. .. ..$ pbase : chr [1:24] "t" "a" "a" "t" ... .. .. ..$ tbase : chr [1:24] "a" "a" "t" "t" ... .. .. ..$ atom : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ indexpos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ groupdirection: chr "antisense" .. .. ..$ natoms : int 12 .. .. ..$ ncellsperatom : int 2 ..$ unittype : chr "expression" ..$ unitdirection: chr "antisense" ..$ natoms : int 12 ..$ ncells : int 24 ..$ ncellsperatom: int 2 ..$ unitnumber : int 1004 $ PA3640_dnaE_at :List of 7 ..$ groups :List of 1 .. ..$ PA3640_dnaE_at:List of 9 .. .. ..$ x : int [1:24] 113 113 81 81 10 10 110 110 119 119 ... .. .. ..$ y : int [1:24] 41 42 27 28 45 46 103 104 91 92 ... .. .. ..$ pbase : chr [1:24] "a" "t" "a" "t" ... .. .. ..$ tbase : chr [1:24] "t" "t" "t" "t" ... .. .. ..$ atom : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ indexpos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ groupdirection: chr "antisense" .. .. ..$ natoms : int 12 .. .. ..$ ncellsperatom : int 2 ..$ unittype : chr "expression" ..$ unitdirection: chr "antisense" ..$ natoms : int 12 ..$ ncells : int 24 ..$ ncellsperatom: int 2 ..$ unitnumber : int 1005 List of 6 $ Pae_16SrRNA_s_at:List of 3 ..$ type : int 1 ..$ direction: int 2 ..$ groups :List of 1 .. ..$ Pae_16SrRNA_s_at:List of 6 .. .. ..$ x : int [1:32] 111 111 19 19 95 95 18 18 25 25 ... .. .. ..$ y : int [1:32] 79 80 19 20 39 40 55 56 113 114 ... .. .. ..$ pbase : chr [1:32] "t" "a" "a" "t" ... .. .. ..$ tbase : chr [1:32] "a" "a" "t" "t" ... .. .. ..$ expos : int [1:32] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 2 $ Pae_23SrRNA_s_at:List of 3 ..$ type : int 1 ..$ direction: int 2 ..$ groups :List of 1 .. ..$ Pae_23SrRNA_s_at:List of 6 .. .. ..$ x : int [1:32] 124 124 56 56 1 1 85 85 62 62 ... .. .. ..$ y : int [1:32] 95 96 99 100 23 24 41 42 9 10 ... .. .. ..$ pbase : chr [1:32] "a" "t" "t" "a" ... .. .. ..$ tbase : chr [1:32] "t" "t" "a" "a" ... .. .. ..$ expos : int [1:32] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 2 $ PA1178_oprH_at :List of 3 ..$ type : int 1 ..$ direction: int 2 ..$ groups :List of 1 .. ..$ PA1178_oprH_at:List of 6 .. .. ..$ x : int [1:24] 41 41 117 117 110 110 60 60 41 41 ... .. .. ..$ y : int [1:24] 49 50 45 46 41 42 75 76 47 48 ... .. .. ..$ pbase : chr [1:24] "a" "t" "g" "c" ... .. .. ..$ tbase : chr [1:24] "t" "t" "c" "c" ... .. .. ..$ expos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 2 $ PA1816_dnaQ_at :List of 3 ..$ type : int 1 ..$ direction: int 2 ..$ groups :List of 1 .. ..$ PA1816_dnaQ_at:List of 6 .. .. ..$ x : int [1:24] 21 21 68 68 119 119 62 62 118 118 ... .. .. ..$ y : int [1:24] 105 106 41 42 49 50 37 38 97 98 ... .. .. ..$ pbase : chr [1:24] "a" "t" "a" "t" ... .. .. ..$ tbase : chr [1:24] "t" "t" "t" "t" ... .. .. ..$ expos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 2 $ PA3183_zwf_at :List of 3 ..$ type : int 1 ..$ direction: int 2 ..$ groups :List of 1 .. ..$ PA3183_zwf_at:List of 6 .. .. ..$ x : int [1:24] 104 104 106 106 79 79 53 53 77 77 ... .. .. ..$ y : int [1:24] 91 92 19 20 27 28 75 76 19 20 ... .. .. ..$ pbase : chr [1:24] "t" "a" "a" "t" ... .. .. ..$ tbase : chr [1:24] "a" "a" "t" "t" ... .. .. ..$ expos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 2 $ PA3640_dnaE_at :List of 3 ..$ type : int 1 ..$ direction: int 2 ..$ groups :List of 1 .. ..$ PA3640_dnaE_at:List of 6 .. .. ..$ x : int [1:24] 113 113 81 81 10 10 110 110 119 119 ... .. .. ..$ y : int [1:24] 41 42 27 28 45 46 103 104 91 92 ... .. .. ..$ pbase : chr [1:24] "a" "t" "a" "t" ... .. .. ..$ tbase : chr [1:24] "t" "t" "t" "t" ... .. .. ..$ expos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 2 chr [1:6] "Pae_16SrRNA_s_at" "Pae_23SrRNA_s_at" "PA1178_oprH_at" ... List of 6 $ Pae_16SrRNA_s_at: Named int 32 ..- attr(*, "names")= chr "Pae_16SrRNA_s_at" $ Pae_23SrRNA_s_at: Named int 32 ..- attr(*, "names")= chr "Pae_23SrRNA_s_at" $ PA1178_oprH_at : Named int 24 ..- attr(*, "names")= chr "PA1178_oprH_at" $ PA1816_dnaQ_at : Named int 24 ..- attr(*, "names")= chr "PA1816_dnaQ_at" $ PA3183_zwf_at : Named int 24 ..- attr(*, "names")= chr "PA3183_zwf_at" $ PA3640_dnaE_at : Named int 24 ..- attr(*, "names")= chr "PA3640_dnaE_at" List of 6 $ Pae_16SrRNA_s_at: chr "" $ Pae_23SrRNA_s_at: chr "" $ PA1178_oprH_at : chr "" $ PA1816_dnaQ_at : chr "" $ PA3183_zwf_at : chr "" $ PA3640_dnaE_at : chr "" List of 6 $ Pae_16SrRNA_s_at:List of 1 ..$ groups:List of 1 .. ..$ Pae_16SrRNA_s_at:List of 1 .. .. ..$ indices: int [1:32] 10066 10192 2414 2540 5010 5136 6949 7075 14264 14390 ... $ Pae_23SrRNA_s_at:List of 1 ..$ groups:List of 1 .. ..$ Pae_23SrRNA_s_at:List of 1 .. .. ..$ indices: int [1:32] 12095 12221 12531 12657 2900 3026 5252 5378 1197 1323 ... $ PA1178_oprH_at :List of 1 ..$ groups:List of 1 .. ..$ PA1178_oprH_at:List of 1 .. .. ..$ indices: int [1:24] 6216 6342 5788 5914 5277 5403 9511 9637 5964 6090 ... $ PA1816_dnaQ_at :List of 1 ..$ groups:List of 1 .. ..$ PA1816_dnaQ_at:List of 1 .. .. ..$ indices: int [1:24] 13252 13378 5235 5361 6294 6420 4725 4851 12341 12467 ... $ PA3183_zwf_at :List of 1 ..$ groups:List of 1 .. ..$ PA3183_zwf_at:List of 1 .. .. ..$ indices: int [1:24] 11571 11697 2501 2627 3482 3608 9504 9630 2472 2598 ... $ PA3640_dnaE_at :List of 1 ..$ groups:List of 1 .. ..$ PA3640_dnaE_at:List of 1 .. .. ..$ indices: int [1:24] 5280 5406 3484 3610 5681 5807 13089 13215 11586 11712 ... List of 6 $ Pae_16SrRNA_s_at:List of 1 ..$ Pae_16SrRNA_s_at: logi [1:32] TRUE FALSE TRUE FALSE TRUE FALSE ... $ Pae_23SrRNA_s_at:List of 1 ..$ Pae_23SrRNA_s_at: logi [1:32] TRUE FALSE TRUE FALSE TRUE FALSE ... $ PA1178_oprH_at :List of 1 ..$ PA1178_oprH_at: logi [1:24] TRUE FALSE TRUE FALSE TRUE FALSE ... $ PA1816_dnaQ_at :List of 1 ..$ PA1816_dnaQ_at: logi [1:24] TRUE FALSE TRUE FALSE TRUE FALSE ... $ PA3183_zwf_at :List of 1 ..$ PA3183_zwf_at: logi [1:24] TRUE FALSE TRUE FALSE TRUE FALSE ... $ PA3640_dnaE_at :List of 1 ..$ PA3640_dnaE_at: logi [1:24] TRUE FALSE TRUE FALSE TRUE FALSE ... Testing readCdf() with 'readAll' indices... List of 1 $ idxs: NULL List of 6 $ Pae_16SrRNA_s_at:List of 7 ..$ groups :List of 1 .. ..$ Pae_16SrRNA_s_at:List of 9 .. .. ..$ x : int [1:32] 111 111 19 19 95 95 18 18 25 25 ... .. .. ..$ y : int [1:32] 79 80 19 20 39 40 55 56 113 114 ... .. .. ..$ pbase : chr [1:32] "t" "a" "a" "t" ... .. .. ..$ tbase : chr [1:32] "a" "a" "t" "t" ... .. .. ..$ atom : int [1:32] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ indexpos : int [1:32] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ groupdirection: chr "antisense" .. .. ..$ natoms : int 16 .. .. ..$ ncellsperatom : int 2 ..$ unittype : chr "expression" ..$ unitdirection: chr "antisense" ..$ natoms : int 16 ..$ ncells : int 32 ..$ ncellsperatom: int 2 ..$ unitnumber : int 1000 $ Pae_23SrRNA_s_at:List of 7 ..$ groups :List of 1 .. ..$ Pae_23SrRNA_s_at:List of 9 .. .. ..$ x : int [1:32] 124 124 56 56 1 1 85 85 62 62 ... .. .. ..$ y : int [1:32] 95 96 99 100 23 24 41 42 9 10 ... .. .. ..$ pbase : chr [1:32] "a" "t" "t" "a" ... .. .. ..$ tbase : chr [1:32] "t" "t" "a" "a" ... .. .. ..$ atom : int [1:32] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ indexpos : int [1:32] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ groupdirection: chr "antisense" .. .. ..$ natoms : int 16 .. .. ..$ ncellsperatom : int 2 ..$ unittype : chr "expression" ..$ unitdirection: chr "antisense" ..$ natoms : int 16 ..$ ncells : int 32 ..$ ncellsperatom: int 2 ..$ unitnumber : int 1001 $ PA1178_oprH_at :List of 7 ..$ groups :List of 1 .. ..$ PA1178_oprH_at:List of 9 .. .. ..$ x : int [1:24] 41 41 117 117 110 110 60 60 41 41 ... .. .. ..$ y : int [1:24] 49 50 45 46 41 42 75 76 47 48 ... .. .. ..$ pbase : chr [1:24] "a" "t" "g" "c" ... .. .. ..$ tbase : chr [1:24] "t" "t" "c" "c" ... .. .. ..$ atom : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ indexpos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ groupdirection: chr "antisense" .. .. ..$ natoms : int 12 .. .. ..$ ncellsperatom : int 2 ..$ unittype : chr "expression" ..$ unitdirection: chr "antisense" ..$ natoms : int 12 ..$ ncells : int 24 ..$ ncellsperatom: int 2 ..$ unitnumber : int 1002 $ PA1816_dnaQ_at :List of 7 ..$ groups :List of 1 .. ..$ PA1816_dnaQ_at:List of 9 .. .. ..$ x : int [1:24] 21 21 68 68 119 119 62 62 118 118 ... .. .. ..$ y : int [1:24] 105 106 41 42 49 50 37 38 97 98 ... .. .. ..$ pbase : chr [1:24] "a" "t" "a" "t" ... .. .. ..$ tbase : chr [1:24] "t" "t" "t" "t" ... .. .. ..$ atom : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ indexpos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ groupdirection: chr "antisense" .. .. ..$ natoms : int 12 .. .. ..$ ncellsperatom : int 2 ..$ unittype : chr "expression" ..$ unitdirection: chr "antisense" ..$ natoms : int 12 ..$ ncells : int 24 ..$ ncellsperatom: int 2 ..$ unitnumber : int 1003 $ PA3183_zwf_at :List of 7 ..$ groups :List of 1 .. ..$ PA3183_zwf_at:List of 9 .. .. ..$ x : int [1:24] 104 104 106 106 79 79 53 53 77 77 ... .. .. ..$ y : int [1:24] 91 92 19 20 27 28 75 76 19 20 ... .. .. ..$ pbase : chr [1:24] "t" "a" "a" "t" ... .. .. ..$ tbase : chr [1:24] "a" "a" "t" "t" ... .. .. ..$ atom : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ indexpos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ groupdirection: chr "antisense" .. .. ..$ natoms : int 12 .. .. ..$ ncellsperatom : int 2 ..$ unittype : chr "expression" ..$ unitdirection: chr "antisense" ..$ natoms : int 12 ..$ ncells : int 24 ..$ ncellsperatom: int 2 ..$ unitnumber : int 1004 $ PA3640_dnaE_at :List of 7 ..$ groups :List of 1 .. ..$ PA3640_dnaE_at:List of 9 .. .. ..$ x : int [1:24] 113 113 81 81 10 10 110 110 119 119 ... .. .. ..$ y : int [1:24] 41 42 27 28 45 46 103 104 91 92 ... .. .. ..$ pbase : chr [1:24] "a" "t" "a" "t" ... .. .. ..$ tbase : chr [1:24] "t" "t" "t" "t" ... .. .. ..$ atom : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ indexpos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ groupdirection: chr "antisense" .. .. ..$ natoms : int 12 .. .. ..$ ncellsperatom : int 2 ..$ unittype : chr "expression" ..$ unitdirection: chr "antisense" ..$ natoms : int 12 ..$ ncells : int 24 ..$ ncellsperatom: int 2 ..$ unitnumber : int 1005 Testing readCdf() with 'readAll' indices...done Testing readCdf() with 'readOne' indices... List of 1 $ idxs: int 10 List of 1 $ PA1178_oprH_st:List of 7 ..$ groups :List of 1 .. ..$ PA1178_oprH_st:List of 9 .. .. ..$ x : int [1:24] 37 37 79 79 68 68 51 51 79 79 ... .. .. ..$ y : int [1:24] 33 34 67 68 65 66 111 112 43 44 ... .. .. ..$ pbase : chr [1:24] "t" "a" "c" "g" ... .. .. ..$ tbase : chr [1:24] "a" "a" "g" "g" ... .. .. ..$ atom : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ indexpos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ groupdirection: chr "sense" .. .. ..$ natoms : int 12 .. .. ..$ ncellsperatom : int 2 ..$ unittype : chr "expression" ..$ unitdirection: chr "sense" ..$ natoms : int 12 ..$ ncells : int 24 ..$ ncellsperatom: int 2 ..$ unitnumber : int 1052 Testing readCdf() with 'readOne' indices...done Testing readCdf() with 'readSome' indices... List of 1 $ idxs: int [1:10] 11 12 13 14 15 16 17 18 19 20 List of 6 $ PA1816_dnaQ_st :List of 7 ..$ groups :List of 1 .. ..$ PA1816_dnaQ_st:List of 9 .. .. ..$ x : int [1:24] 15 15 35 35 83 83 113 113 119 119 ... .. .. ..$ y : int [1:24] 45 46 57 58 55 56 17 18 65 66 ... .. .. ..$ pbase : chr [1:24] "t" "a" "t" "a" ... .. .. ..$ tbase : chr [1:24] "a" "a" "a" "a" ... .. .. ..$ atom : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ indexpos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ groupdirection: chr "sense" .. .. ..$ natoms : int 12 .. .. ..$ ncellsperatom : int 2 ..$ unittype : chr "expression" ..$ unitdirection: chr "sense" ..$ natoms : int 12 ..$ ncells : int 24 ..$ ncellsperatom: int 2 ..$ unitnumber : int 1053 $ PA3183_zwf_st :List of 7 ..$ groups :List of 1 .. ..$ PA3183_zwf_st:List of 9 .. .. ..$ x : int [1:24] 84 84 57 57 8 8 89 89 52 52 ... .. .. ..$ y : int [1:24] 101 102 113 114 27 28 17 18 107 108 ... .. .. ..$ pbase : chr [1:24] "a" "t" "t" "a" ... .. .. ..$ tbase : chr [1:24] "t" "t" "a" "a" ... .. .. ..$ atom : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ indexpos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ groupdirection: chr "sense" .. .. ..$ natoms : int 12 .. .. ..$ ncellsperatom : int 2 ..$ unittype : chr "expression" ..$ unitdirection: chr "sense" ..$ natoms : int 12 ..$ ncells : int 24 ..$ ncellsperatom: int 2 ..$ unitnumber : int 1054 $ PA3640_dnaE_st :List of 7 ..$ groups :List of 1 .. ..$ PA3640_dnaE_st:List of 9 .. .. ..$ x : int [1:24] 51 51 37 37 121 121 9 9 65 65 ... .. .. ..$ y : int [1:24] 75 76 25 26 23 24 23 24 57 58 ... .. .. ..$ pbase : chr [1:24] "t" "a" "t" "a" ... .. .. ..$ tbase : chr [1:24] "a" "a" "a" "a" ... .. .. ..$ atom : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ indexpos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ groupdirection: chr "sense" .. .. ..$ natoms : int 12 .. .. ..$ ncellsperatom : int 2 ..$ unittype : chr "expression" ..$ unitdirection: chr "sense" ..$ natoms : int 12 ..$ ncells : int 24 ..$ ncellsperatom: int 2 ..$ unitnumber : int 1055 $ PA4407_ftsZ_st :List of 7 ..$ groups :List of 1 .. ..$ PA4407_ftsZ_st:List of 9 .. .. ..$ x : int [1:24] 69 69 124 124 102 102 19 19 102 102 ... .. .. ..$ y : int [1:24] 87 88 97 98 35 36 101 102 11 12 ... .. .. ..$ pbase : chr [1:24] "g" "c" "t" "a" ... .. .. ..$ tbase : chr [1:24] "c" "c" "a" "a" ... .. .. ..$ atom : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ indexpos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ groupdirection: chr "sense" .. .. ..$ natoms : int 12 .. .. ..$ ncellsperatom : int 2 ..$ unittype : chr "expression" ..$ unitdirection: chr "sense" ..$ natoms : int 12 ..$ ncells : int 24 ..$ ncellsperatom: int 2 ..$ unitnumber : int 1056 $ AFFX-Athal-Actin_5_r_at:List of 7 ..$ groups :List of 1 .. ..$ AFFX-Athal-Actin_5_r_at:List of 9 .. .. ..$ x : int [1:32] 25 25 80 80 105 105 65 65 104 104 ... .. .. ..$ y : int [1:32] 51 52 23 24 75 76 87 88 73 74 ... .. .. ..$ pbase : chr [1:32] "c" "g" "c" "g" ... .. .. ..$ tbase : chr [1:32] "g" "g" "g" "g" ... .. .. ..$ atom : int [1:32] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ indexpos : int [1:32] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ groupdirection: chr "antisense" .. .. ..$ natoms : int 16 .. .. ..$ ncellsperatom : int 2 ..$ unittype : chr "expression" ..$ unitdirection: chr "antisense" ..$ natoms : int 16 ..$ ncells : int 32 ..$ ncellsperatom: int 2 ..$ unitnumber : int 1100 $ AFFX-Athal-Actin_M_at :List of 7 ..$ groups :List of 1 .. ..$ AFFX-Athal-Actin_M_at:List of 9 .. .. ..$ x : int [1:32] 28 28 8 8 7 7 21 21 41 41 ... .. .. ..$ y : int [1:32] 115 116 97 98 97 98 87 88 99 100 ... .. .. ..$ pbase : chr [1:32] "a" "t" "c" "g" ... .. .. ..$ tbase : chr [1:32] "t" "t" "g" "g" ... .. .. ..$ atom : int [1:32] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ indexpos : int [1:32] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ groupdirection: chr "antisense" .. .. ..$ natoms : int 16 .. .. ..$ ncellsperatom : int 2 ..$ unittype : chr "expression" ..$ unitdirection: chr "antisense" ..$ natoms : int 16 ..$ ncells : int 32 ..$ ncellsperatom: int 2 ..$ unitnumber : int 1101 Testing readCdf() with 'readSome' indices...done Testing readCdf() with 'readDouble' indices... List of 1 $ idxs: num [1:10] 11 12 13 14 15 16 17 18 19 20 List of 6 $ PA1816_dnaQ_st :List of 7 ..$ groups :List of 1 .. ..$ PA1816_dnaQ_st:List of 9 .. .. ..$ x : int [1:24] 15 15 35 35 83 83 113 113 119 119 ... .. .. ..$ y : int [1:24] 45 46 57 58 55 56 17 18 65 66 ... .. .. ..$ pbase : chr [1:24] "t" "a" "t" "a" ... .. .. ..$ tbase : chr [1:24] "a" "a" "a" "a" ... .. .. ..$ atom : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ indexpos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ groupdirection: chr "sense" .. .. ..$ natoms : int 12 .. .. ..$ ncellsperatom : int 2 ..$ unittype : chr "expression" ..$ unitdirection: chr "sense" ..$ natoms : int 12 ..$ ncells : int 24 ..$ ncellsperatom: int 2 ..$ unitnumber : int 1053 $ PA3183_zwf_st :List of 7 ..$ groups :List of 1 .. ..$ PA3183_zwf_st:List of 9 .. .. ..$ x : int [1:24] 84 84 57 57 8 8 89 89 52 52 ... .. .. ..$ y : int [1:24] 101 102 113 114 27 28 17 18 107 108 ... .. .. ..$ pbase : chr [1:24] "a" "t" "t" "a" ... .. .. ..$ tbase : chr [1:24] "t" "t" "a" "a" ... .. .. ..$ atom : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ indexpos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ groupdirection: chr "sense" .. .. ..$ natoms : int 12 .. .. ..$ ncellsperatom : int 2 ..$ unittype : chr "expression" ..$ unitdirection: chr "sense" ..$ natoms : int 12 ..$ ncells : int 24 ..$ ncellsperatom: int 2 ..$ unitnumber : int 1054 $ PA3640_dnaE_st :List of 7 ..$ groups :List of 1 .. ..$ PA3640_dnaE_st:List of 9 .. .. ..$ x : int [1:24] 51 51 37 37 121 121 9 9 65 65 ... .. .. ..$ y : int [1:24] 75 76 25 26 23 24 23 24 57 58 ... .. .. ..$ pbase : chr [1:24] "t" "a" "t" "a" ... .. .. ..$ tbase : chr [1:24] "a" "a" "a" "a" ... .. .. ..$ atom : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ indexpos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ groupdirection: chr "sense" .. .. ..$ natoms : int 12 .. .. ..$ ncellsperatom : int 2 ..$ unittype : chr "expression" ..$ unitdirection: chr "sense" ..$ natoms : int 12 ..$ ncells : int 24 ..$ ncellsperatom: int 2 ..$ unitnumber : int 1055 $ PA4407_ftsZ_st :List of 7 ..$ groups :List of 1 .. ..$ PA4407_ftsZ_st:List of 9 .. .. ..$ x : int [1:24] 69 69 124 124 102 102 19 19 102 102 ... .. .. ..$ y : int [1:24] 87 88 97 98 35 36 101 102 11 12 ... .. .. ..$ pbase : chr [1:24] "g" "c" "t" "a" ... .. .. ..$ tbase : chr [1:24] "c" "c" "a" "a" ... .. .. ..$ atom : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ indexpos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ groupdirection: chr "sense" .. .. ..$ natoms : int 12 .. .. ..$ ncellsperatom : int 2 ..$ unittype : chr "expression" ..$ unitdirection: chr "sense" ..$ natoms : int 12 ..$ ncells : int 24 ..$ ncellsperatom: int 2 ..$ unitnumber : int 1056 $ AFFX-Athal-Actin_5_r_at:List of 7 ..$ groups :List of 1 .. ..$ AFFX-Athal-Actin_5_r_at:List of 9 .. .. ..$ x : int [1:32] 25 25 80 80 105 105 65 65 104 104 ... .. .. ..$ y : int [1:32] 51 52 23 24 75 76 87 88 73 74 ... .. .. ..$ pbase : chr [1:32] "c" "g" "c" "g" ... .. .. ..$ tbase : chr [1:32] "g" "g" "g" "g" ... .. .. ..$ atom : int [1:32] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ indexpos : int [1:32] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ groupdirection: chr "antisense" .. .. ..$ natoms : int 16 .. .. ..$ ncellsperatom : int 2 ..$ unittype : chr "expression" ..$ unitdirection: chr "antisense" ..$ natoms : int 16 ..$ ncells : int 32 ..$ ncellsperatom: int 2 ..$ unitnumber : int 1100 $ AFFX-Athal-Actin_M_at :List of 7 ..$ groups :List of 1 .. ..$ AFFX-Athal-Actin_M_at:List of 9 .. .. ..$ x : int [1:32] 28 28 8 8 7 7 21 21 41 41 ... .. .. ..$ y : int [1:32] 115 116 97 98 97 98 87 88 99 100 ... .. .. ..$ pbase : chr [1:32] "a" "t" "c" "g" ... .. .. ..$ tbase : chr [1:32] "t" "t" "g" "g" ... .. .. ..$ atom : int [1:32] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ indexpos : int [1:32] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ groupdirection: chr "antisense" .. .. ..$ natoms : int 16 .. .. ..$ ncellsperatom : int 2 ..$ unittype : chr "expression" ..$ unitdirection: chr "antisense" ..$ natoms : int 16 ..$ ncells : int 32 ..$ ncellsperatom: int 2 ..$ unitnumber : int 1101 Testing readCdf() with 'readDouble' indices...done Testing readCdf() with 'outOfRange' indices... List of 1 $ idxs: int -1 List of 2 $ message: chr "Argument 'units' contains an element out of range [1,13]: -1" $ call : language readCdfQc(cdf, units = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCdf() with 'outOfRange' indices...done Testing readCdf() with 'outOfRange' indices... List of 1 $ idxs: int 0 List of 2 $ message: chr "Argument 'units' contains an element out of range [1,13]: 0" $ call : language readCdfQc(cdf, units = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCdf() with 'outOfRange' indices...done Testing readCdf() with 'outOfRange' indices... List of 1 $ idxs: int 1000000000 List of 2 $ message: chr "Argument 'units' contains an element out of range [1,13]: 1000000000" $ call : language readCdfQc(cdf, units = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCdf() with 'outOfRange' indices...done Testing readCdfUnits() with 'readAll' indices... List of 1 $ idxs: NULL List of 6 $ Pae_16SrRNA_s_at:List of 3 ..$ type : int 1 ..$ direction: int 2 ..$ groups :List of 1 .. ..$ Pae_16SrRNA_s_at:List of 6 .. .. ..$ x : int [1:32] 111 111 19 19 95 95 18 18 25 25 ... .. .. ..$ y : int [1:32] 79 80 19 20 39 40 55 56 113 114 ... .. .. ..$ pbase : chr [1:32] "t" "a" "a" "t" ... .. .. ..$ tbase : chr [1:32] "a" "a" "t" "t" ... .. .. ..$ expos : int [1:32] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 2 $ Pae_23SrRNA_s_at:List of 3 ..$ type : int 1 ..$ direction: int 2 ..$ groups :List of 1 .. ..$ Pae_23SrRNA_s_at:List of 6 .. .. ..$ x : int [1:32] 124 124 56 56 1 1 85 85 62 62 ... .. .. ..$ y : int [1:32] 95 96 99 100 23 24 41 42 9 10 ... .. .. ..$ pbase : chr [1:32] "a" "t" "t" "a" ... .. .. ..$ tbase : chr [1:32] "t" "t" "a" "a" ... .. .. ..$ expos : int [1:32] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 2 $ PA1178_oprH_at :List of 3 ..$ type : int 1 ..$ direction: int 2 ..$ groups :List of 1 .. ..$ PA1178_oprH_at:List of 6 .. .. ..$ x : int [1:24] 41 41 117 117 110 110 60 60 41 41 ... .. .. ..$ y : int [1:24] 49 50 45 46 41 42 75 76 47 48 ... .. .. ..$ pbase : chr [1:24] "a" "t" "g" "c" ... .. .. ..$ tbase : chr [1:24] "t" "t" "c" "c" ... .. .. ..$ expos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 2 $ PA1816_dnaQ_at :List of 3 ..$ type : int 1 ..$ direction: int 2 ..$ groups :List of 1 .. ..$ PA1816_dnaQ_at:List of 6 .. .. ..$ x : int [1:24] 21 21 68 68 119 119 62 62 118 118 ... .. .. ..$ y : int [1:24] 105 106 41 42 49 50 37 38 97 98 ... .. .. ..$ pbase : chr [1:24] "a" "t" "a" "t" ... .. .. ..$ tbase : chr [1:24] "t" "t" "t" "t" ... .. .. ..$ expos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 2 $ PA3183_zwf_at :List of 3 ..$ type : int 1 ..$ direction: int 2 ..$ groups :List of 1 .. ..$ PA3183_zwf_at:List of 6 .. .. ..$ x : int [1:24] 104 104 106 106 79 79 53 53 77 77 ... .. .. ..$ y : int [1:24] 91 92 19 20 27 28 75 76 19 20 ... .. .. ..$ pbase : chr [1:24] "t" "a" "a" "t" ... .. .. ..$ tbase : chr [1:24] "a" "a" "t" "t" ... .. .. ..$ expos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 2 $ PA3640_dnaE_at :List of 3 ..$ type : int 1 ..$ direction: int 2 ..$ groups :List of 1 .. ..$ PA3640_dnaE_at:List of 6 .. .. ..$ x : int [1:24] 113 113 81 81 10 10 110 110 119 119 ... .. .. ..$ y : int [1:24] 41 42 27 28 45 46 103 104 91 92 ... .. .. ..$ pbase : chr [1:24] "a" "t" "a" "t" ... .. .. ..$ tbase : chr [1:24] "t" "t" "t" "t" ... .. .. ..$ expos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 2 Testing readCdfUnits() with 'readAll' indices...done Testing readCdfUnits() with 'readOne' indices... List of 1 $ idxs: int 10 List of 1 $ PA1178_oprH_st:List of 3 ..$ type : int 1 ..$ direction: int 1 ..$ groups :List of 1 .. ..$ PA1178_oprH_st:List of 6 .. .. ..$ x : int [1:24] 37 37 79 79 68 68 51 51 79 79 ... .. .. ..$ y : int [1:24] 33 34 67 68 65 66 111 112 43 44 ... .. .. ..$ pbase : chr [1:24] "t" "a" "c" "g" ... .. .. ..$ tbase : chr [1:24] "a" "a" "g" "g" ... .. .. ..$ expos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 1 Testing readCdfUnits() with 'readOne' indices...done Testing readCdfUnits() with 'readSome' indices... List of 1 $ idxs: int [1:10] 11 12 13 14 15 16 17 18 19 20 List of 6 $ PA1816_dnaQ_st :List of 3 ..$ type : int 1 ..$ direction: int 1 ..$ groups :List of 1 .. ..$ PA1816_dnaQ_st:List of 6 .. .. ..$ x : int [1:24] 15 15 35 35 83 83 113 113 119 119 ... .. .. ..$ y : int [1:24] 45 46 57 58 55 56 17 18 65 66 ... .. .. ..$ pbase : chr [1:24] "t" "a" "t" "a" ... .. .. ..$ tbase : chr [1:24] "a" "a" "a" "a" ... .. .. ..$ expos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 1 $ PA3183_zwf_st :List of 3 ..$ type : int 1 ..$ direction: int 1 ..$ groups :List of 1 .. ..$ PA3183_zwf_st:List of 6 .. .. ..$ x : int [1:24] 84 84 57 57 8 8 89 89 52 52 ... .. .. ..$ y : int [1:24] 101 102 113 114 27 28 17 18 107 108 ... .. .. ..$ pbase : chr [1:24] "a" "t" "t" "a" ... .. .. ..$ tbase : chr [1:24] "t" "t" "a" "a" ... .. .. ..$ expos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 1 $ PA3640_dnaE_st :List of 3 ..$ type : int 1 ..$ direction: int 1 ..$ groups :List of 1 .. ..$ PA3640_dnaE_st:List of 6 .. .. ..$ x : int [1:24] 51 51 37 37 121 121 9 9 65 65 ... .. .. ..$ y : int [1:24] 75 76 25 26 23 24 23 24 57 58 ... .. .. ..$ pbase : chr [1:24] "t" "a" "t" "a" ... .. .. ..$ tbase : chr [1:24] "a" "a" "a" "a" ... .. .. ..$ expos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 1 $ PA4407_ftsZ_st :List of 3 ..$ type : int 1 ..$ direction: int 1 ..$ groups :List of 1 .. ..$ PA4407_ftsZ_st:List of 6 .. .. ..$ x : int [1:24] 69 69 124 124 102 102 19 19 102 102 ... .. .. ..$ y : int [1:24] 87 88 97 98 35 36 101 102 11 12 ... .. .. ..$ pbase : chr [1:24] "g" "c" "t" "a" ... .. .. ..$ tbase : chr [1:24] "c" "c" "a" "a" ... .. .. ..$ expos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 1 $ AFFX-Athal-Actin_5_r_at:List of 3 ..$ type : int 1 ..$ direction: int 2 ..$ groups :List of 1 .. ..$ AFFX-Athal-Actin_5_r_at:List of 6 .. .. ..$ x : int [1:32] 25 25 80 80 105 105 65 65 104 104 ... .. .. ..$ y : int [1:32] 51 52 23 24 75 76 87 88 73 74 ... .. .. ..$ pbase : chr [1:32] "c" "g" "c" "g" ... .. .. ..$ tbase : chr [1:32] "g" "g" "g" "g" ... .. .. ..$ expos : int [1:32] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 2 $ AFFX-Athal-Actin_M_at :List of 3 ..$ type : int 1 ..$ direction: int 2 ..$ groups :List of 1 .. ..$ AFFX-Athal-Actin_M_at:List of 6 .. .. ..$ x : int [1:32] 28 28 8 8 7 7 21 21 41 41 ... .. .. ..$ y : int [1:32] 115 116 97 98 97 98 87 88 99 100 ... .. .. ..$ pbase : chr [1:32] "a" "t" "c" "g" ... .. .. ..$ tbase : chr [1:32] "t" "t" "g" "g" ... .. .. ..$ expos : int [1:32] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 2 Testing readCdfUnits() with 'readSome' indices...done Testing readCdfUnits() with 'readDouble' indices... List of 1 $ idxs: num [1:10] 11 12 13 14 15 16 17 18 19 20 List of 6 $ PA1816_dnaQ_st :List of 3 ..$ type : int 1 ..$ direction: int 1 ..$ groups :List of 1 .. ..$ PA1816_dnaQ_st:List of 6 .. .. ..$ x : int [1:24] 15 15 35 35 83 83 113 113 119 119 ... .. .. ..$ y : int [1:24] 45 46 57 58 55 56 17 18 65 66 ... .. .. ..$ pbase : chr [1:24] "t" "a" "t" "a" ... .. .. ..$ tbase : chr [1:24] "a" "a" "a" "a" ... .. .. ..$ expos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 1 $ PA3183_zwf_st :List of 3 ..$ type : int 1 ..$ direction: int 1 ..$ groups :List of 1 .. ..$ PA3183_zwf_st:List of 6 .. .. ..$ x : int [1:24] 84 84 57 57 8 8 89 89 52 52 ... .. .. ..$ y : int [1:24] 101 102 113 114 27 28 17 18 107 108 ... .. .. ..$ pbase : chr [1:24] "a" "t" "t" "a" ... .. .. ..$ tbase : chr [1:24] "t" "t" "a" "a" ... .. .. ..$ expos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 1 $ PA3640_dnaE_st :List of 3 ..$ type : int 1 ..$ direction: int 1 ..$ groups :List of 1 .. ..$ PA3640_dnaE_st:List of 6 .. .. ..$ x : int [1:24] 51 51 37 37 121 121 9 9 65 65 ... .. .. ..$ y : int [1:24] 75 76 25 26 23 24 23 24 57 58 ... .. .. ..$ pbase : chr [1:24] "t" "a" "t" "a" ... .. .. ..$ tbase : chr [1:24] "a" "a" "a" "a" ... .. .. ..$ expos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 1 $ PA4407_ftsZ_st :List of 3 ..$ type : int 1 ..$ direction: int 1 ..$ groups :List of 1 .. ..$ PA4407_ftsZ_st:List of 6 .. .. ..$ x : int [1:24] 69 69 124 124 102 102 19 19 102 102 ... .. .. ..$ y : int [1:24] 87 88 97 98 35 36 101 102 11 12 ... .. .. ..$ pbase : chr [1:24] "g" "c" "t" "a" ... .. .. ..$ tbase : chr [1:24] "c" "c" "a" "a" ... .. .. ..$ expos : int [1:24] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 1 $ AFFX-Athal-Actin_5_r_at:List of 3 ..$ type : int 1 ..$ direction: int 2 ..$ groups :List of 1 .. ..$ AFFX-Athal-Actin_5_r_at:List of 6 .. .. ..$ x : int [1:32] 25 25 80 80 105 105 65 65 104 104 ... .. .. ..$ y : int [1:32] 51 52 23 24 75 76 87 88 73 74 ... .. .. ..$ pbase : chr [1:32] "c" "g" "c" "g" ... .. .. ..$ tbase : chr [1:32] "g" "g" "g" "g" ... .. .. ..$ expos : int [1:32] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 2 $ AFFX-Athal-Actin_M_at :List of 3 ..$ type : int 1 ..$ direction: int 2 ..$ groups :List of 1 .. ..$ AFFX-Athal-Actin_M_at:List of 6 .. .. ..$ x : int [1:32] 28 28 8 8 7 7 21 21 41 41 ... .. .. ..$ y : int [1:32] 115 116 97 98 97 98 87 88 99 100 ... .. .. ..$ pbase : chr [1:32] "a" "t" "c" "g" ... .. .. ..$ tbase : chr [1:32] "t" "t" "g" "g" ... .. .. ..$ expos : int [1:32] 0 0 1 1 2 2 3 3 4 4 ... .. .. ..$ direction: int 2 Testing readCdfUnits() with 'readDouble' indices...done Testing readCdfUnits() with 'outOfRange' indices... List of 1 $ idxs: int -1 List of 2 $ message: chr "Argument 'units' contains an element out of range [1,13]: -1" $ call : language readCdfQc(cdf, units = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCdfUnits() with 'outOfRange' indices...done Testing readCdfUnits() with 'outOfRange' indices... List of 1 $ idxs: int 0 List of 2 $ message: chr "Argument 'units' contains an element out of range [1,13]: 0" $ call : language readCdfQc(cdf, units = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCdfUnits() with 'outOfRange' indices...done Testing readCdfUnits() with 'outOfRange' indices... List of 1 $ idxs: int 1000000000 List of 2 $ message: chr "Argument 'units' contains an element out of range [1,13]: 1000000000" $ call : language readCdfQc(cdf, units = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCdfUnits() with 'outOfRange' indices...done Testing readCdfUnitNames() with 'readAll' indices... List of 1 $ idxs: NULL chr [1:6] "Pae_16SrRNA_s_at" "Pae_23SrRNA_s_at" "PA1178_oprH_at" ... Testing readCdfUnitNames() with 'readAll' indices...done Testing readCdfUnitNames() with 'readOne' indices... List of 1 $ idxs: int 10 chr "PA1178_oprH_st" Testing readCdfUnitNames() with 'readOne' indices...done Testing readCdfUnitNames() with 'readSome' indices... List of 1 $ idxs: int [1:10] 11 12 13 14 15 16 17 18 19 20 chr [1:6] "PA1816_dnaQ_st" "PA3183_zwf_st" "PA3640_dnaE_st" ... Testing readCdfUnitNames() with 'readSome' indices...done Testing readCdfUnitNames() with 'readDouble' indices... List of 1 $ idxs: num [1:10] 11 12 13 14 15 16 17 18 19 20 chr [1:6] "PA1816_dnaQ_st" "PA3183_zwf_st" "PA3640_dnaE_st" ... Testing readCdfUnitNames() with 'readDouble' indices...done Testing readCdfUnitNames() with 'outOfRange' indices... List of 1 $ idxs: int -1 List of 2 $ message: chr "Argument 'units' contains an element out of range [1,13]: -1" $ call : language readCdfQc(cdf, units = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCdfUnitNames() with 'outOfRange' indices...done Testing readCdfUnitNames() with 'outOfRange' indices... List of 1 $ idxs: int 0 List of 2 $ message: chr "Argument 'units' contains an element out of range [1,13]: 0" $ call : language readCdfQc(cdf, units = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCdfUnitNames() with 'outOfRange' indices...done Testing readCdfUnitNames() with 'outOfRange' indices... List of 1 $ idxs: int 1000000000 List of 2 $ message: chr "Argument 'units' contains an element out of range [1,13]: 1000000000" $ call : language readCdfQc(cdf, units = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCdfUnitNames() with 'outOfRange' indices...done Testing readCdfNbrOfCellsPerUnitGroup() with 'readAll' indices... List of 1 $ idxs: NULL List of 6 $ Pae_16SrRNA_s_at: Named int 32 ..- attr(*, "names")= chr "Pae_16SrRNA_s_at" $ Pae_23SrRNA_s_at: Named int 32 ..- attr(*, "names")= chr "Pae_23SrRNA_s_at" $ PA1178_oprH_at : Named int 24 ..- attr(*, "names")= chr "PA1178_oprH_at" $ PA1816_dnaQ_at : Named int 24 ..- attr(*, "names")= chr "PA1816_dnaQ_at" $ PA3183_zwf_at : Named int 24 ..- attr(*, "names")= chr "PA3183_zwf_at" $ PA3640_dnaE_at : Named int 24 ..- attr(*, "names")= chr "PA3640_dnaE_at" Testing readCdfNbrOfCellsPerUnitGroup() with 'readAll' indices...done Testing readCdfNbrOfCellsPerUnitGroup() with 'readOne' indices... List of 1 $ idxs: int 10 List of 1 $ PA1178_oprH_st: Named int 24 ..- attr(*, "names")= chr "PA1178_oprH_st" Testing readCdfNbrOfCellsPerUnitGroup() with 'readOne' indices...done Testing readCdfNbrOfCellsPerUnitGroup() with 'readSome' indices... List of 1 $ idxs: int [1:10] 11 12 13 14 15 16 17 18 19 20 List of 6 $ PA1816_dnaQ_st : Named int 24 ..- attr(*, "names")= chr "PA1816_dnaQ_st" $ PA3183_zwf_st : Named int 24 ..- attr(*, "names")= chr "PA3183_zwf_st" $ PA3640_dnaE_st : Named int 24 ..- attr(*, "names")= chr "PA3640_dnaE_st" $ PA4407_ftsZ_st : Named int 24 ..- attr(*, "names")= chr "PA4407_ftsZ_st" $ AFFX-Athal-Actin_5_r_at: Named int 32 ..- attr(*, "names")= chr "AFFX-Athal-Actin_5_r_at" $ AFFX-Athal-Actin_M_at : Named int 32 ..- attr(*, "names")= chr "AFFX-Athal-Actin_M_at" Testing readCdfNbrOfCellsPerUnitGroup() with 'readSome' indices...done Testing readCdfNbrOfCellsPerUnitGroup() with 'readDouble' indices... List of 1 $ idxs: num [1:10] 11 12 13 14 15 16 17 18 19 20 List of 6 $ PA1816_dnaQ_st : Named int 24 ..- attr(*, "names")= chr "PA1816_dnaQ_st" $ PA3183_zwf_st : Named int 24 ..- attr(*, "names")= chr "PA3183_zwf_st" $ PA3640_dnaE_st : Named int 24 ..- attr(*, "names")= chr "PA3640_dnaE_st" $ PA4407_ftsZ_st : Named int 24 ..- attr(*, "names")= chr "PA4407_ftsZ_st" $ AFFX-Athal-Actin_5_r_at: Named int 32 ..- attr(*, "names")= chr "AFFX-Athal-Actin_5_r_at" $ AFFX-Athal-Actin_M_at : Named int 32 ..- attr(*, "names")= chr "AFFX-Athal-Actin_M_at" Testing readCdfNbrOfCellsPerUnitGroup() with 'readDouble' indices...done Testing readCdfNbrOfCellsPerUnitGroup() with 'outOfRange' indices... List of 1 $ idxs: int -1 List of 2 $ message: chr "Argument 'units' contains an element out of range [1,13]: -1" $ call : language readCdfQc(cdf, units = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCdfNbrOfCellsPerUnitGroup() with 'outOfRange' indices...done Testing readCdfNbrOfCellsPerUnitGroup() with 'outOfRange' indices... List of 1 $ idxs: int 0 List of 2 $ message: chr "Argument 'units' contains an element out of range [1,13]: 0" $ call : language readCdfQc(cdf, units = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCdfNbrOfCellsPerUnitGroup() with 'outOfRange' indices...done Testing readCdfNbrOfCellsPerUnitGroup() with 'outOfRange' indices... List of 1 $ idxs: int 1000000000 List of 2 $ message: chr "Argument 'units' contains an element out of range [1,13]: 1000000000" $ call : language readCdfQc(cdf, units = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCdfNbrOfCellsPerUnitGroup() with 'outOfRange' indices...done Testing readCdfGroupNames() with 'readAll' indices... List of 1 $ idxs: NULL List of 6 $ Pae_16SrRNA_s_at: chr "" $ Pae_23SrRNA_s_at: chr "" $ PA1178_oprH_at : chr "" $ PA1816_dnaQ_at : chr "" $ PA3183_zwf_at : chr "" $ PA3640_dnaE_at : chr "" Testing readCdfGroupNames() with 'readAll' indices...done Testing readCdfGroupNames() with 'readOne' indices... List of 1 $ idxs: int 10 List of 1 $ PA1178_oprH_st: chr "" Testing readCdfGroupNames() with 'readOne' indices...done Testing readCdfGroupNames() with 'readSome' indices... List of 1 $ idxs: int [1:10] 11 12 13 14 15 16 17 18 19 20 List of 6 $ PA1816_dnaQ_st : chr "" $ PA3183_zwf_st : chr "" $ PA3640_dnaE_st : chr "" $ PA4407_ftsZ_st : chr "" $ AFFX-Athal-Actin_5_r_at: chr "" $ AFFX-Athal-Actin_M_at : chr "" Testing readCdfGroupNames() with 'readSome' indices...done Testing readCdfGroupNames() with 'readDouble' indices... List of 1 $ idxs: num [1:10] 11 12 13 14 15 16 17 18 19 20 List of 6 $ PA1816_dnaQ_st : chr "" $ PA3183_zwf_st : chr "" $ PA3640_dnaE_st : chr "" $ PA4407_ftsZ_st : chr "" $ AFFX-Athal-Actin_5_r_at: chr "" $ AFFX-Athal-Actin_M_at : chr "" Testing readCdfGroupNames() with 'readDouble' indices...done Testing readCdfGroupNames() with 'outOfRange' indices... List of 1 $ idxs: int -1 List of 2 $ message: chr "Argument 'units' contains an element out of range [1,13]: -1" $ call : language readCdfQc(cdf, units = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCdfGroupNames() with 'outOfRange' indices...done Testing readCdfGroupNames() with 'outOfRange' indices... List of 1 $ idxs: int 0 List of 2 $ message: chr "Argument 'units' contains an element out of range [1,13]: 0" $ call : language readCdfQc(cdf, units = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCdfGroupNames() with 'outOfRange' indices...done Testing readCdfGroupNames() with 'outOfRange' indices... List of 1 $ idxs: int 1000000000 List of 2 $ message: chr "Argument 'units' contains an element out of range [1,13]: 1000000000" $ call : language readCdfQc(cdf, units = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCdfGroupNames() with 'outOfRange' indices...done Testing readCdfCellIndices() with 'readAll' indices... List of 1 $ idxs: NULL List of 6 $ Pae_16SrRNA_s_at:List of 1 ..$ groups:List of 1 .. ..$ Pae_16SrRNA_s_at:List of 1 .. .. ..$ indices: int [1:32] 10066 10192 2414 2540 5010 5136 6949 7075 14264 14390 ... $ Pae_23SrRNA_s_at:List of 1 ..$ groups:List of 1 .. ..$ Pae_23SrRNA_s_at:List of 1 .. .. ..$ indices: int [1:32] 12095 12221 12531 12657 2900 3026 5252 5378 1197 1323 ... $ PA1178_oprH_at :List of 1 ..$ groups:List of 1 .. ..$ PA1178_oprH_at:List of 1 .. .. ..$ indices: int [1:24] 6216 6342 5788 5914 5277 5403 9511 9637 5964 6090 ... $ PA1816_dnaQ_at :List of 1 ..$ groups:List of 1 .. ..$ PA1816_dnaQ_at:List of 1 .. .. ..$ indices: int [1:24] 13252 13378 5235 5361 6294 6420 4725 4851 12341 12467 ... $ PA3183_zwf_at :List of 1 ..$ groups:List of 1 .. ..$ PA3183_zwf_at:List of 1 .. .. ..$ indices: int [1:24] 11571 11697 2501 2627 3482 3608 9504 9630 2472 2598 ... $ PA3640_dnaE_at :List of 1 ..$ groups:List of 1 .. ..$ PA3640_dnaE_at:List of 1 .. .. ..$ indices: int [1:24] 5280 5406 3484 3610 5681 5807 13089 13215 11586 11712 ... Testing readCdfCellIndices() with 'readAll' indices...done Testing readCdfCellIndices() with 'readOne' indices... List of 1 $ idxs: int 10 List of 1 $ PA1178_oprH_st:List of 1 ..$ groups:List of 1 .. ..$ PA1178_oprH_st:List of 1 .. .. ..$ indices: int [1:24] 4196 4322 8522 8648 8259 8385 14038 14164 5498 5624 ... Testing readCdfCellIndices() with 'readOne' indices...done Testing readCdfCellIndices() with 'readSome' indices... List of 1 $ idxs: int [1:10] 11 12 13 14 15 16 17 18 19 20 List of 6 $ PA1816_dnaQ_st :List of 1 ..$ groups:List of 1 .. ..$ PA1816_dnaQ_st:List of 1 .. .. ..$ indices: int [1:24] 5686 5812 7218 7344 7014 7140 2256 2382 8310 8436 ... $ PA3183_zwf_st :List of 1 ..$ groups:List of 1 .. ..$ PA3183_zwf_st:List of 1 .. .. ..$ indices: int [1:24] 12811 12937 14296 14422 3411 3537 2232 2358 13535 13661 ... $ PA3640_dnaE_st :List of 1 ..$ groups:List of 1 .. ..$ PA3640_dnaE_st:List of 1 .. .. ..$ indices: int [1:24] 9502 9628 3188 3314 3020 3146 2908 3034 7248 7374 ... $ PA4407_ftsZ_st :List of 1 ..$ groups:List of 1 .. ..$ PA4407_ftsZ_st:List of 1 .. .. ..$ indices: int [1:24] 11032 11158 12347 12473 4513 4639 12746 12872 1489 1615 ... $ AFFX-Athal-Actin_5_r_at:List of 1 ..$ groups:List of 1 .. ..$ AFFX-Athal-Actin_5_r_at:List of 1 .. .. ..$ indices: int [1:32] 6452 6578 2979 3105 9556 9682 11028 11154 9303 9429 ... $ AFFX-Athal-Actin_M_at :List of 1 ..$ groups:List of 1 .. ..$ AFFX-Athal-Actin_M_at:List of 1 .. .. ..$ indices: int [1:32] 14519 14645 12231 12357 12230 12356 10984 11110 12516 12642 ... Testing readCdfCellIndices() with 'readSome' indices...done Testing readCdfCellIndices() with 'readDouble' indices... List of 1 $ idxs: num [1:10] 11 12 13 14 15 16 17 18 19 20 List of 6 $ PA1816_dnaQ_st :List of 1 ..$ groups:List of 1 .. ..$ PA1816_dnaQ_st:List of 1 .. .. ..$ indices: int [1:24] 5686 5812 7218 7344 7014 7140 2256 2382 8310 8436 ... $ PA3183_zwf_st :List of 1 ..$ groups:List of 1 .. ..$ PA3183_zwf_st:List of 1 .. .. ..$ indices: int [1:24] 12811 12937 14296 14422 3411 3537 2232 2358 13535 13661 ... $ PA3640_dnaE_st :List of 1 ..$ groups:List of 1 .. ..$ PA3640_dnaE_st:List of 1 .. .. ..$ indices: int [1:24] 9502 9628 3188 3314 3020 3146 2908 3034 7248 7374 ... $ PA4407_ftsZ_st :List of 1 ..$ groups:List of 1 .. ..$ PA4407_ftsZ_st:List of 1 .. .. ..$ indices: int [1:24] 11032 11158 12347 12473 4513 4639 12746 12872 1489 1615 ... $ AFFX-Athal-Actin_5_r_at:List of 1 ..$ groups:List of 1 .. ..$ AFFX-Athal-Actin_5_r_at:List of 1 .. .. ..$ indices: int [1:32] 6452 6578 2979 3105 9556 9682 11028 11154 9303 9429 ... $ AFFX-Athal-Actin_M_at :List of 1 ..$ groups:List of 1 .. ..$ AFFX-Athal-Actin_M_at:List of 1 .. .. ..$ indices: int [1:32] 14519 14645 12231 12357 12230 12356 10984 11110 12516 12642 ... Testing readCdfCellIndices() with 'readDouble' indices...done Testing readCdfCellIndices() with 'outOfRange' indices... List of 1 $ idxs: int -1 List of 2 $ message: chr "Argument 'units' contains an element out of range [1,13]: -1" $ call : language readCdfQc(cdf, units = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCdfCellIndices() with 'outOfRange' indices...done Testing readCdfCellIndices() with 'outOfRange' indices... List of 1 $ idxs: int 0 List of 2 $ message: chr "Argument 'units' contains an element out of range [1,13]: 0" $ call : language readCdfQc(cdf, units = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCdfCellIndices() with 'outOfRange' indices...done Testing readCdfCellIndices() with 'outOfRange' indices... List of 1 $ idxs: int 1000000000 List of 2 $ message: chr "Argument 'units' contains an element out of range [1,13]: 1000000000" $ call : language readCdfQc(cdf, units = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCdfCellIndices() with 'outOfRange' indices...done Testing readCdfIsPm() with 'readAll' indices... List of 1 $ idxs: NULL List of 6 $ Pae_16SrRNA_s_at:List of 1 ..$ Pae_16SrRNA_s_at: logi [1:32] TRUE FALSE TRUE FALSE TRUE FALSE ... $ Pae_23SrRNA_s_at:List of 1 ..$ Pae_23SrRNA_s_at: logi [1:32] TRUE FALSE TRUE FALSE TRUE FALSE ... $ PA1178_oprH_at :List of 1 ..$ PA1178_oprH_at: logi [1:24] TRUE FALSE TRUE FALSE TRUE FALSE ... $ PA1816_dnaQ_at :List of 1 ..$ PA1816_dnaQ_at: logi [1:24] TRUE FALSE TRUE FALSE TRUE FALSE ... $ PA3183_zwf_at :List of 1 ..$ PA3183_zwf_at: logi [1:24] TRUE FALSE TRUE FALSE TRUE FALSE ... $ PA3640_dnaE_at :List of 1 ..$ PA3640_dnaE_at: logi [1:24] TRUE FALSE TRUE FALSE TRUE FALSE ... Testing readCdfIsPm() with 'readAll' indices...done Testing readCdfIsPm() with 'readOne' indices... List of 1 $ idxs: int 10 List of 1 $ PA1178_oprH_st:List of 1 ..$ PA1178_oprH_st: logi [1:24] TRUE FALSE TRUE FALSE TRUE FALSE ... Testing readCdfIsPm() with 'readOne' indices...done Testing readCdfIsPm() with 'readSome' indices... List of 1 $ idxs: int [1:10] 11 12 13 14 15 16 17 18 19 20 List of 6 $ PA1816_dnaQ_st :List of 1 ..$ PA1816_dnaQ_st: logi [1:24] TRUE FALSE TRUE FALSE TRUE FALSE ... $ PA3183_zwf_st :List of 1 ..$ PA3183_zwf_st: logi [1:24] TRUE FALSE TRUE FALSE TRUE FALSE ... $ PA3640_dnaE_st :List of 1 ..$ PA3640_dnaE_st: logi [1:24] TRUE FALSE TRUE FALSE TRUE FALSE ... $ PA4407_ftsZ_st :List of 1 ..$ PA4407_ftsZ_st: logi [1:24] TRUE FALSE TRUE FALSE TRUE FALSE ... $ AFFX-Athal-Actin_5_r_at:List of 1 ..$ AFFX-Athal-Actin_5_r_at: logi [1:32] TRUE FALSE TRUE FALSE TRUE FALSE ... $ AFFX-Athal-Actin_M_at :List of 1 ..$ AFFX-Athal-Actin_M_at: logi [1:32] TRUE FALSE TRUE FALSE TRUE FALSE ... Testing readCdfIsPm() with 'readSome' indices...done Testing readCdfIsPm() with 'readDouble' indices... List of 1 $ idxs: num [1:10] 11 12 13 14 15 16 17 18 19 20 List of 6 $ PA1816_dnaQ_st :List of 1 ..$ PA1816_dnaQ_st: logi [1:24] TRUE FALSE TRUE FALSE TRUE FALSE ... $ PA3183_zwf_st :List of 1 ..$ PA3183_zwf_st: logi [1:24] TRUE FALSE TRUE FALSE TRUE FALSE ... $ PA3640_dnaE_st :List of 1 ..$ PA3640_dnaE_st: logi [1:24] TRUE FALSE TRUE FALSE TRUE FALSE ... $ PA4407_ftsZ_st :List of 1 ..$ PA4407_ftsZ_st: logi [1:24] TRUE FALSE TRUE FALSE TRUE FALSE ... $ AFFX-Athal-Actin_5_r_at:List of 1 ..$ AFFX-Athal-Actin_5_r_at: logi [1:32] TRUE FALSE TRUE FALSE TRUE FALSE ... $ AFFX-Athal-Actin_M_at :List of 1 ..$ AFFX-Athal-Actin_M_at: logi [1:32] TRUE FALSE TRUE FALSE TRUE FALSE ... Testing readCdfIsPm() with 'readDouble' indices...done Testing readCdfIsPm() with 'outOfRange' indices... List of 1 $ idxs: int -1 List of 2 $ message: chr "Argument 'units' contains an element out of range [1,13]: -1" $ call : language readCdfQc(cdf, units = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCdfIsPm() with 'outOfRange' indices...done Testing readCdfIsPm() with 'outOfRange' indices... List of 1 $ idxs: int 0 List of 2 $ message: chr "Argument 'units' contains an element out of range [1,13]: 0" $ call : language readCdfQc(cdf, units = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCdfIsPm() with 'outOfRange' indices...done Testing readCdfIsPm() with 'outOfRange' indices... List of 1 $ idxs: int 1000000000 List of 2 $ message: chr "Argument 'units' contains an element out of range [1,13]: 1000000000" $ call : language readCdfQc(cdf, units = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCdfIsPm() with 'outOfRange' indices...done > > proc.time() user system elapsed 2.119 0.445 2.756
affxparser.Rcheck/tests/readCdfUnitsWriteMap.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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. 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. > if (require("AffymetrixDataTestFiles")) { + library("affxparser") + + pathR <- system.file(package="AffymetrixDataTestFiles") + pathA <- file.path(pathR, "annotationData", "chipTypes", "Test3") + + # Read CDF structure + cdf <- file.path(pathA, "1.XDA", "Test3.CDF") + hdr <- readCdfHeader(cdf) + Jall <- hdr$nunits + + # Various sets of indices to be read + idxsList <- list( + ## readNothing=integer(0L), # FIX ME + readAll=NULL, + readOne=10L, + readSome=11:20, + readDouble=as.double(11:20), + outOfRange=-1L, + outOfRange=0L, + outOfRange=1e9L + ) + + # Read full file + data <- readCdfUnitsWriteMap(cdf) + str(data) + Jall <- length(data) + + # Read different subsets of units + for (ii in seq_along(idxsList)) { + name <- names(idxsList)[ii] + message(sprintf("Testing readCdfUnitsWriteMap() with '%s' indices...", name)) + idxs <- idxsList[[ii]] + str(list(idxs=idxs)) + if (grepl("outOfRange", name)) { + res <- tryCatch(readCdfUnitsWriteMap(cdf, units=idxs), error=function(ex) ex) + str(res) + stopifnot(inherits(res, "error")) + } else { + data <- readCdfUnitsWriteMap(cdf, units=idxs) + str(data) + stopifnot(length(data) == Jall) + } + message(sprintf("Testing readCdfUnitsWriteMap() with '%s' indices...done", name)) + } # for (ii ...) + } # if (require("AffymetrixDataTestFiles")) Loading required package: AffymetrixDataTestFiles int [1:15876] 10066 10192 2414 2540 5010 5136 6949 7075 14264 14390 ... Testing readCdfUnitsWriteMap() with 'readAll' indices... List of 1 $ idxs: NULL int [1:15876] 10066 10192 2414 2540 5010 5136 6949 7075 14264 14390 ... Testing readCdfUnitsWriteMap() with 'readAll' indices...done Testing readCdfUnitsWriteMap() with 'readOne' indices... List of 1 $ idxs: int 10 int [1:15876] 4196 4322 8522 8648 8259 8385 14038 14164 5498 5624 ... Testing readCdfUnitsWriteMap() with 'readOne' indices...done Testing readCdfUnitsWriteMap() with 'readSome' indices... List of 1 $ idxs: int [1:10] 11 12 13 14 15 16 17 18 19 20 int [1:15876] 5686 5812 7218 7344 7014 7140 2256 2382 8310 8436 ... Testing readCdfUnitsWriteMap() with 'readSome' indices...done Testing readCdfUnitsWriteMap() with 'readDouble' indices... List of 1 $ idxs: num [1:10] 11 12 13 14 15 16 17 18 19 20 int [1:15876] 5686 5812 7218 7344 7014 7140 2256 2382 8310 8436 ... Testing readCdfUnitsWriteMap() with 'readDouble' indices...done Testing readCdfUnitsWriteMap() with 'outOfRange' indices... List of 1 $ idxs: int -1 List of 2 $ message: chr "Argument 'units' contains non-positive indices: -1" $ call : language readCdfUnitsWriteMap(cdf, units = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCdfUnitsWriteMap() with 'outOfRange' indices...done Testing readCdfUnitsWriteMap() with 'outOfRange' indices... List of 1 $ idxs: int 0 List of 2 $ message: chr "Argument 'units' contains non-positive indices: 0" $ call : language readCdfUnitsWriteMap(cdf, units = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCdfUnitsWriteMap() with 'outOfRange' indices...done Testing readCdfUnitsWriteMap() with 'outOfRange' indices... List of 1 $ idxs: int 1000000000 List of 2 $ message: chr "Argument 'units' contains indices out of range [1,345]: 1e+09" $ call : language readCdfUnitsWriteMap(cdf, units = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCdfUnitsWriteMap() with 'outOfRange' indices...done > > proc.time() user system elapsed 0.590 0.165 0.744
affxparser.Rcheck/tests/readCel.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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. 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. > if (require("AffymetrixDataTestFiles")) { + library("affxparser") + + pathR <- system.file(package="AffymetrixDataTestFiles") + pathD <- file.path(pathR, "rawData", "FusionSDK_Test3", "Test3") + + # Find all CEL files + cels <- list.files(path=pathD, pattern="[.]CEL$", + recursive=TRUE, full.names=TRUE) + + # Various sets of indices to be read + idxsList <- list( + # readNothing=integer(0L), # FIX ME + readAll=NULL, + readOne=10L, + readSome=11:20, + readDouble=as.double(11:20), + outOfRange=-1L, + outOfRange=0L, + outOfRange=1e9L + ) + + for (kk in seq_along(cels)) { + cel <- cels[kk] + + # Read full file + data <- readCel(cel) + str(data) + Jall <- data$header$total + stopifnot(length(data$intensities) == Jall) + + # Read different subsets of cells + for (ii in seq_along(idxsList)) { + name <- names(idxsList)[ii] + message(sprintf("Testing readCel() with '%s' indices...", name)) + idxs <- idxsList[[ii]] + str(list(idxs=idxs)) + if (grepl("outOfRange", name)) { + res <- tryCatch(readCel(cel, indices=idxs), error=function(ex) ex) + str(res) + stopifnot(inherits(res, "error")) + } else { + data <- readCel(cel, indices=idxs) + str(data) + J <- if (is.null(idxs)) Jall else length(idxs) + stopifnot(length(data$intensities) == J) + } + message(sprintf("Testing readCel() with '%s' indices...done", name)) + } # for (ii ...) + } # for (kk ...) + } # if (require("AffymetrixDataTestFiles")) Loading required package: AffymetrixDataTestFiles List of 4 $ header :List of 14 ..$ filename : chr "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/AffymetrixDataTestFiles/rawData/FusionSDK"| __truncated__ ..$ version : int 1 ..$ cols : int 126 ..$ rows : int 126 ..$ total : int 15876 ..$ algorithm : chr "Percentile" ..$ parameters : chr "Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004;GridULX:154.000000;GridULY:164.000000;GridURX:995"| __truncated__ ..$ chiptype : chr "Test3" ..$ header : chr "" ..$ datheader : chr "[12..40151] Fetal 3:CLS=1167 RWS=1167 XIN=3 YIN=3 VE=17 2.0 08/16/01 17:28:31 \024 \024 Test3.1sq"| __truncated__ ..$ librarypackage: chr "" ..$ cellmargin : int 2 ..$ noutliers : int 5 ..$ nmasked : int 0 $ intensities: num [1:15876] 190 11263 164 11272 181 ... $ outliers : int [1:5] 1585 9833 10307 14227 14426 $ masked : NULL Testing readCel() with 'readAll' indices... List of 1 $ idxs: NULL List of 4 $ header :List of 14 ..$ filename : chr "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/AffymetrixDataTestFiles/rawData/FusionSDK"| __truncated__ ..$ version : int 1 ..$ cols : int 126 ..$ rows : int 126 ..$ total : int 15876 ..$ algorithm : chr "Percentile" ..$ parameters : chr "Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004;GridULX:154.000000;GridULY:164.000000;GridURX:995"| __truncated__ ..$ chiptype : chr "Test3" ..$ header : chr "" ..$ datheader : chr "[12..40151] Fetal 3:CLS=1167 RWS=1167 XIN=3 YIN=3 VE=17 2.0 08/16/01 17:28:31 \024 \024 Test3.1sq"| __truncated__ ..$ librarypackage: chr "" ..$ cellmargin : int 2 ..$ noutliers : int 5 ..$ nmasked : int 0 $ intensities: num [1:15876] 190 11263 164 11272 181 ... $ outliers : int [1:5] 1585 9833 10307 14227 14426 $ masked : NULL Testing readCel() with 'readAll' indices...done Testing readCel() with 'readOne' indices... List of 1 $ idxs: int 10 List of 4 $ header :List of 14 ..$ filename : chr "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/AffymetrixDataTestFiles/rawData/FusionSDK"| __truncated__ ..$ version : int 1 ..$ cols : int 126 ..$ rows : int 126 ..$ total : int 15876 ..$ algorithm : chr "Percentile" ..$ parameters : chr "Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004;GridULX:154.000000;GridULY:164.000000;GridURX:995"| __truncated__ ..$ chiptype : chr "Test3" ..$ header : chr "" ..$ datheader : chr "[12..40151] Fetal 3:CLS=1167 RWS=1167 XIN=3 YIN=3 VE=17 2.0 08/16/01 17:28:31 \024 \024 Test3.1sq"| __truncated__ ..$ librarypackage: chr "" ..$ cellmargin : int 2 ..$ noutliers : int 5 ..$ nmasked : int 0 $ intensities: num 143 $ outliers : NULL $ masked : NULL Testing readCel() with 'readOne' indices...done Testing readCel() with 'readSome' indices... List of 1 $ idxs: int [1:10] 11 12 13 14 15 16 17 18 19 20 List of 4 $ header :List of 14 ..$ filename : chr "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/AffymetrixDataTestFiles/rawData/FusionSDK"| __truncated__ ..$ version : int 1 ..$ cols : int 126 ..$ rows : int 126 ..$ total : int 15876 ..$ algorithm : chr "Percentile" ..$ parameters : chr "Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004;GridULX:154.000000;GridULY:164.000000;GridURX:995"| __truncated__ ..$ chiptype : chr "Test3" ..$ header : chr "" ..$ datheader : chr "[12..40151] Fetal 3:CLS=1167 RWS=1167 XIN=3 YIN=3 VE=17 2.0 08/16/01 17:28:31 \024 \024 Test3.1sq"| __truncated__ ..$ librarypackage: chr "" ..$ cellmargin : int 2 ..$ noutliers : int 5 ..$ nmasked : int 0 $ intensities: num [1:10] 11053 161 11466 152 11210 ... $ outliers : NULL $ masked : NULL Testing readCel() with 'readSome' indices...done Testing readCel() with 'readDouble' indices... List of 1 $ idxs: num [1:10] 11 12 13 14 15 16 17 18 19 20 List of 4 $ header :List of 14 ..$ filename : chr "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/AffymetrixDataTestFiles/rawData/FusionSDK"| __truncated__ ..$ version : int 1 ..$ cols : int 126 ..$ rows : int 126 ..$ total : int 15876 ..$ algorithm : chr "Percentile" ..$ parameters : chr "Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004;GridULX:154.000000;GridULY:164.000000;GridURX:995"| __truncated__ ..$ chiptype : chr "Test3" ..$ header : chr "" ..$ datheader : chr "[12..40151] Fetal 3:CLS=1167 RWS=1167 XIN=3 YIN=3 VE=17 2.0 08/16/01 17:28:31 \024 \024 Test3.1sq"| __truncated__ ..$ librarypackage: chr "" ..$ cellmargin : int 2 ..$ noutliers : int 5 ..$ nmasked : int 0 $ intensities: num [1:10] 11053 161 11466 152 11210 ... $ outliers : NULL $ masked : NULL Testing readCel() with 'readDouble' indices...done Testing readCel() with 'outOfRange' indices... List of 1 $ idxs: int -1 List of 2 $ message: chr "Argument 'indices' is out of range [1,15876]." $ call : language readCel(cel, indices = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCel() with 'outOfRange' indices...done Testing readCel() with 'outOfRange' indices... List of 1 $ idxs: int 0 List of 2 $ message: chr "Argument 'indices' is out of range [1,15876]." $ call : language readCel(cel, indices = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCel() with 'outOfRange' indices...done Testing readCel() with 'outOfRange' indices... List of 1 $ idxs: int 1000000000 List of 2 $ message: chr "Argument 'indices' is out of range [1,15876]." $ call : language readCel(cel, indices = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCel() with 'outOfRange' indices...done List of 4 $ header :List of 14 ..$ filename : chr "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/AffymetrixDataTestFiles/rawData/FusionSDK"| __truncated__ ..$ version : int 1 ..$ cols : int 126 ..$ rows : int 126 ..$ total : int 15876 ..$ algorithm : chr "Percentile" ..$ parameters : chr "Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004;GridULX:154.000000;GridULY:164.000000;GridURX:995"| __truncated__ ..$ chiptype : chr "Test3" ..$ header : chr "" ..$ datheader : chr "[6..38103] Fetal 5:CLS=1167 RWS=1167 XIN=3 YIN=3 VE=17 2.0 08/16/01 17:32:06 \024 \024 Test3.1sq "| __truncated__ ..$ librarypackage: chr "" ..$ cellmargin : int 2 ..$ noutliers : int 45 ..$ nmasked : int 0 $ intensities: num [1:15876] 164 11900.8 152 11748 80.3 ... $ outliers : int [1:45] 213 512 809 1344 1372 1603 1687 1690 1953 2204 ... $ masked : NULL Testing readCel() with 'readAll' indices... List of 1 $ idxs: NULL List of 4 $ header :List of 14 ..$ filename : chr "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/AffymetrixDataTestFiles/rawData/FusionSDK"| __truncated__ ..$ version : int 1 ..$ cols : int 126 ..$ rows : int 126 ..$ total : int 15876 ..$ algorithm : chr "Percentile" ..$ parameters : chr "Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004;GridULX:154.000000;GridULY:164.000000;GridURX:995"| __truncated__ ..$ chiptype : chr "Test3" ..$ header : chr "" ..$ datheader : chr "[6..38103] Fetal 5:CLS=1167 RWS=1167 XIN=3 YIN=3 VE=17 2.0 08/16/01 17:32:06 \024 \024 Test3.1sq "| __truncated__ ..$ librarypackage: chr "" ..$ cellmargin : int 2 ..$ noutliers : int 45 ..$ nmasked : int 0 $ intensities: num [1:15876] 164 11900.8 152 11748 80.3 ... $ outliers : int [1:45] 213 512 809 1344 1372 1603 1687 1690 1953 2204 ... $ masked : NULL Testing readCel() with 'readAll' indices...done Testing readCel() with 'readOne' indices... List of 1 $ idxs: int 10 List of 4 $ header :List of 14 ..$ filename : chr "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/AffymetrixDataTestFiles/rawData/FusionSDK"| __truncated__ ..$ version : int 1 ..$ cols : int 126 ..$ rows : int 126 ..$ total : int 15876 ..$ algorithm : chr "Percentile" ..$ parameters : chr "Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004;GridULX:154.000000;GridULY:164.000000;GridURX:995"| __truncated__ ..$ chiptype : chr "Test3" ..$ header : chr "" ..$ datheader : chr "[6..38103] Fetal 5:CLS=1167 RWS=1167 XIN=3 YIN=3 VE=17 2.0 08/16/01 17:32:06 \024 \024 Test3.1sq "| __truncated__ ..$ librarypackage: chr "" ..$ cellmargin : int 2 ..$ noutliers : int 45 ..$ nmasked : int 0 $ intensities: num 136 $ outliers : NULL $ masked : NULL Testing readCel() with 'readOne' indices...done Testing readCel() with 'readSome' indices... List of 1 $ idxs: int [1:10] 11 12 13 14 15 16 17 18 19 20 List of 4 $ header :List of 14 ..$ filename : chr "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/AffymetrixDataTestFiles/rawData/FusionSDK"| __truncated__ ..$ version : int 1 ..$ cols : int 126 ..$ rows : int 126 ..$ total : int 15876 ..$ algorithm : chr "Percentile" ..$ parameters : chr "Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004;GridULX:154.000000;GridULY:164.000000;GridURX:995"| __truncated__ ..$ chiptype : chr "Test3" ..$ header : chr "" ..$ datheader : chr "[6..38103] Fetal 5:CLS=1167 RWS=1167 XIN=3 YIN=3 VE=17 2.0 08/16/01 17:32:06 \024 \024 Test3.1sq "| __truncated__ ..$ librarypackage: chr "" ..$ cellmargin : int 2 ..$ noutliers : int 45 ..$ nmasked : int 0 $ intensities: num [1:10] 9044 121 10406 180 11062 ... $ outliers : NULL $ masked : NULL Testing readCel() with 'readSome' indices...done Testing readCel() with 'readDouble' indices... List of 1 $ idxs: num [1:10] 11 12 13 14 15 16 17 18 19 20 List of 4 $ header :List of 14 ..$ filename : chr "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/AffymetrixDataTestFiles/rawData/FusionSDK"| __truncated__ ..$ version : int 1 ..$ cols : int 126 ..$ rows : int 126 ..$ total : int 15876 ..$ algorithm : chr "Percentile" ..$ parameters : chr "Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004;GridULX:154.000000;GridULY:164.000000;GridURX:995"| __truncated__ ..$ chiptype : chr "Test3" ..$ header : chr "" ..$ datheader : chr "[6..38103] Fetal 5:CLS=1167 RWS=1167 XIN=3 YIN=3 VE=17 2.0 08/16/01 17:32:06 \024 \024 Test3.1sq "| __truncated__ ..$ librarypackage: chr "" ..$ cellmargin : int 2 ..$ noutliers : int 45 ..$ nmasked : int 0 $ intensities: num [1:10] 9044 121 10406 180 11062 ... $ outliers : NULL $ masked : NULL Testing readCel() with 'readDouble' indices...done Testing readCel() with 'outOfRange' indices... List of 1 $ idxs: int -1 List of 2 $ message: chr "Argument 'indices' is out of range [1,15876]." $ call : language readCel(cel, indices = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCel() with 'outOfRange' indices...done Testing readCel() with 'outOfRange' indices... List of 1 $ idxs: int 0 List of 2 $ message: chr "Argument 'indices' is out of range [1,15876]." $ call : language readCel(cel, indices = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCel() with 'outOfRange' indices...done Testing readCel() with 'outOfRange' indices... List of 1 $ idxs: int 1000000000 List of 2 $ message: chr "Argument 'indices' is out of range [1,15876]." $ call : language readCel(cel, indices = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCel() with 'outOfRange' indices...done List of 4 $ header :List of 14 ..$ filename : chr "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/AffymetrixDataTestFiles/rawData/FusionSDK"| __truncated__ ..$ version : int 3 ..$ cols : int 126 ..$ rows : int 126 ..$ total : int 15876 ..$ algorithm : chr "Percentile" ..$ parameters : chr "Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004" ..$ chiptype : chr "Test3" ..$ header : chr "Cols=126\nRows=126\nTotalX=126\nTotalY=126\nOffsetX=0\nOffsetY=0\nGridCornerUL=154 164\nGridCornerUR=995 160\nG"| __truncated__ ..$ datheader : chr "[12..40151] Fetal 3:CLS=1167 RWS=1167 XIN=3 YIN=3 VE=17 2.0 08/16/01 17:28:31 \024 \024 Test3.1sq"| __truncated__ ..$ librarypackage: chr "" ..$ cellmargin : int 2 ..$ noutliers : int 5 ..$ nmasked : int 0 $ intensities: num [1:15876] 190 11263 164 11272 181 ... $ outliers : int [1:5] 1585 9833 10307 14227 14426 $ masked : NULL Testing readCel() with 'readAll' indices... List of 1 $ idxs: NULL List of 4 $ header :List of 14 ..$ filename : chr "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/AffymetrixDataTestFiles/rawData/FusionSDK"| __truncated__ ..$ version : int 3 ..$ cols : int 126 ..$ rows : int 126 ..$ total : int 15876 ..$ algorithm : chr "Percentile" ..$ parameters : chr "Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004" ..$ chiptype : chr "Test3" ..$ header : chr "Cols=126\nRows=126\nTotalX=126\nTotalY=126\nOffsetX=0\nOffsetY=0\nGridCornerUL=154 164\nGridCornerUR=995 160\nG"| __truncated__ ..$ datheader : chr "[12..40151] Fetal 3:CLS=1167 RWS=1167 XIN=3 YIN=3 VE=17 2.0 08/16/01 17:28:31 \024 \024 Test3.1sq"| __truncated__ ..$ librarypackage: chr "" ..$ cellmargin : int 2 ..$ noutliers : int 5 ..$ nmasked : int 0 $ intensities: num [1:15876] 190 11263 164 11272 181 ... $ outliers : int [1:5] 1585 9833 10307 14227 14426 $ masked : NULL Testing readCel() with 'readAll' indices...done Testing readCel() with 'readOne' indices... List of 1 $ idxs: int 10 List of 4 $ header :List of 14 ..$ filename : chr "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/AffymetrixDataTestFiles/rawData/FusionSDK"| __truncated__ ..$ version : int 3 ..$ cols : int 126 ..$ rows : int 126 ..$ total : int 15876 ..$ algorithm : chr "Percentile" ..$ parameters : chr "Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004" ..$ chiptype : chr "Test3" ..$ header : chr "Cols=126\nRows=126\nTotalX=126\nTotalY=126\nOffsetX=0\nOffsetY=0\nGridCornerUL=154 164\nGridCornerUR=995 160\nG"| __truncated__ ..$ datheader : chr "[12..40151] Fetal 3:CLS=1167 RWS=1167 XIN=3 YIN=3 VE=17 2.0 08/16/01 17:28:31 \024 \024 Test3.1sq"| __truncated__ ..$ librarypackage: chr "" ..$ cellmargin : int 2 ..$ noutliers : int 5 ..$ nmasked : int 0 $ intensities: num 143 $ outliers : NULL $ masked : NULL Testing readCel() with 'readOne' indices...done Testing readCel() with 'readSome' indices... List of 1 $ idxs: int [1:10] 11 12 13 14 15 16 17 18 19 20 List of 4 $ header :List of 14 ..$ filename : chr "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/AffymetrixDataTestFiles/rawData/FusionSDK"| __truncated__ ..$ version : int 3 ..$ cols : int 126 ..$ rows : int 126 ..$ total : int 15876 ..$ algorithm : chr "Percentile" ..$ parameters : chr "Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004" ..$ chiptype : chr "Test3" ..$ header : chr "Cols=126\nRows=126\nTotalX=126\nTotalY=126\nOffsetX=0\nOffsetY=0\nGridCornerUL=154 164\nGridCornerUR=995 160\nG"| __truncated__ ..$ datheader : chr "[12..40151] Fetal 3:CLS=1167 RWS=1167 XIN=3 YIN=3 VE=17 2.0 08/16/01 17:28:31 \024 \024 Test3.1sq"| __truncated__ ..$ librarypackage: chr "" ..$ cellmargin : int 2 ..$ noutliers : int 5 ..$ nmasked : int 0 $ intensities: num [1:10] 11053 161 11466 152 11210 ... $ outliers : NULL $ masked : NULL Testing readCel() with 'readSome' indices...done Testing readCel() with 'readDouble' indices... List of 1 $ idxs: num [1:10] 11 12 13 14 15 16 17 18 19 20 List of 4 $ header :List of 14 ..$ filename : chr "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/AffymetrixDataTestFiles/rawData/FusionSDK"| __truncated__ ..$ version : int 3 ..$ cols : int 126 ..$ rows : int 126 ..$ total : int 15876 ..$ algorithm : chr "Percentile" ..$ parameters : chr "Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004" ..$ chiptype : chr "Test3" ..$ header : chr "Cols=126\nRows=126\nTotalX=126\nTotalY=126\nOffsetX=0\nOffsetY=0\nGridCornerUL=154 164\nGridCornerUR=995 160\nG"| __truncated__ ..$ datheader : chr "[12..40151] Fetal 3:CLS=1167 RWS=1167 XIN=3 YIN=3 VE=17 2.0 08/16/01 17:28:31 \024 \024 Test3.1sq"| __truncated__ ..$ librarypackage: chr "" ..$ cellmargin : int 2 ..$ noutliers : int 5 ..$ nmasked : int 0 $ intensities: num [1:10] 11053 161 11466 152 11210 ... $ outliers : NULL $ masked : NULL Testing readCel() with 'readDouble' indices...done Testing readCel() with 'outOfRange' indices... List of 1 $ idxs: int -1 List of 2 $ message: chr "Argument 'indices' is out of range [1,15876]." $ call : language readCel(cel, indices = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCel() with 'outOfRange' indices...done Testing readCel() with 'outOfRange' indices... List of 1 $ idxs: int 0 List of 2 $ message: chr "Argument 'indices' is out of range [1,15876]." $ call : language readCel(cel, indices = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCel() with 'outOfRange' indices...done Testing readCel() with 'outOfRange' indices... List of 1 $ idxs: int 1000000000 List of 2 $ message: chr "Argument 'indices' is out of range [1,15876]." $ call : language readCel(cel, indices = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCel() with 'outOfRange' indices...done List of 4 $ header :List of 14 ..$ filename : chr "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/AffymetrixDataTestFiles/rawData/FusionSDK"| __truncated__ ..$ version : int 3 ..$ cols : int 126 ..$ rows : int 126 ..$ total : int 15876 ..$ algorithm : chr "Percentile" ..$ parameters : chr "Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004" ..$ chiptype : chr "Test3" ..$ header : chr "Cols=126\nRows=126\nTotalX=126\nTotalY=126\nOffsetX=0\nOffsetY=0\nGridCornerUL=154 164\nGridCornerUR=995 165\nG"| __truncated__ ..$ datheader : chr "[6..38103] Fetal 5:CLS=1167 RWS=1167 XIN=3 YIN=3 VE=17 2.0 08/16/01 17:32:06 \024 \024 Test3.1sq "| __truncated__ ..$ librarypackage: chr "" ..$ cellmargin : int 2 ..$ noutliers : int 45 ..$ nmasked : int 0 $ intensities: num [1:15876] 164 11900.8 152 11748 80.3 ... $ outliers : int [1:45] 213 512 809 1344 1372 1603 1687 1690 1953 2204 ... $ masked : NULL Testing readCel() with 'readAll' indices... List of 1 $ idxs: NULL List of 4 $ header :List of 14 ..$ filename : chr "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/AffymetrixDataTestFiles/rawData/FusionSDK"| __truncated__ ..$ version : int 3 ..$ cols : int 126 ..$ rows : int 126 ..$ total : int 15876 ..$ algorithm : chr "Percentile" ..$ parameters : chr "Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004" ..$ chiptype : chr "Test3" ..$ header : chr "Cols=126\nRows=126\nTotalX=126\nTotalY=126\nOffsetX=0\nOffsetY=0\nGridCornerUL=154 164\nGridCornerUR=995 165\nG"| __truncated__ ..$ datheader : chr "[6..38103] Fetal 5:CLS=1167 RWS=1167 XIN=3 YIN=3 VE=17 2.0 08/16/01 17:32:06 \024 \024 Test3.1sq "| __truncated__ ..$ librarypackage: chr "" ..$ cellmargin : int 2 ..$ noutliers : int 45 ..$ nmasked : int 0 $ intensities: num [1:15876] 164 11900.8 152 11748 80.3 ... $ outliers : int [1:45] 213 512 809 1344 1372 1603 1687 1690 1953 2204 ... $ masked : NULL Testing readCel() with 'readAll' indices...done Testing readCel() with 'readOne' indices... List of 1 $ idxs: int 10 List of 4 $ header :List of 14 ..$ filename : chr "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/AffymetrixDataTestFiles/rawData/FusionSDK"| __truncated__ ..$ version : int 3 ..$ cols : int 126 ..$ rows : int 126 ..$ total : int 15876 ..$ algorithm : chr "Percentile" ..$ parameters : chr "Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004" ..$ chiptype : chr "Test3" ..$ header : chr "Cols=126\nRows=126\nTotalX=126\nTotalY=126\nOffsetX=0\nOffsetY=0\nGridCornerUL=154 164\nGridCornerUR=995 165\nG"| __truncated__ ..$ datheader : chr "[6..38103] Fetal 5:CLS=1167 RWS=1167 XIN=3 YIN=3 VE=17 2.0 08/16/01 17:32:06 \024 \024 Test3.1sq "| __truncated__ ..$ librarypackage: chr "" ..$ cellmargin : int 2 ..$ noutliers : int 45 ..$ nmasked : int 0 $ intensities: num 136 $ outliers : NULL $ masked : NULL Testing readCel() with 'readOne' indices...done Testing readCel() with 'readSome' indices... List of 1 $ idxs: int [1:10] 11 12 13 14 15 16 17 18 19 20 List of 4 $ header :List of 14 ..$ filename : chr "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/AffymetrixDataTestFiles/rawData/FusionSDK"| __truncated__ ..$ version : int 3 ..$ cols : int 126 ..$ rows : int 126 ..$ total : int 15876 ..$ algorithm : chr "Percentile" ..$ parameters : chr "Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004" ..$ chiptype : chr "Test3" ..$ header : chr "Cols=126\nRows=126\nTotalX=126\nTotalY=126\nOffsetX=0\nOffsetY=0\nGridCornerUL=154 164\nGridCornerUR=995 165\nG"| __truncated__ ..$ datheader : chr "[6..38103] Fetal 5:CLS=1167 RWS=1167 XIN=3 YIN=3 VE=17 2.0 08/16/01 17:32:06 \024 \024 Test3.1sq "| __truncated__ ..$ librarypackage: chr "" ..$ cellmargin : int 2 ..$ noutliers : int 45 ..$ nmasked : int 0 $ intensities: num [1:10] 9044 121 10406 180 11062 ... $ outliers : NULL $ masked : NULL Testing readCel() with 'readSome' indices...done Testing readCel() with 'readDouble' indices... List of 1 $ idxs: num [1:10] 11 12 13 14 15 16 17 18 19 20 List of 4 $ header :List of 14 ..$ filename : chr "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/AffymetrixDataTestFiles/rawData/FusionSDK"| __truncated__ ..$ version : int 3 ..$ cols : int 126 ..$ rows : int 126 ..$ total : int 15876 ..$ algorithm : chr "Percentile" ..$ parameters : chr "Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004" ..$ chiptype : chr "Test3" ..$ header : chr "Cols=126\nRows=126\nTotalX=126\nTotalY=126\nOffsetX=0\nOffsetY=0\nGridCornerUL=154 164\nGridCornerUR=995 165\nG"| __truncated__ ..$ datheader : chr "[6..38103] Fetal 5:CLS=1167 RWS=1167 XIN=3 YIN=3 VE=17 2.0 08/16/01 17:32:06 \024 \024 Test3.1sq "| __truncated__ ..$ librarypackage: chr "" ..$ cellmargin : int 2 ..$ noutliers : int 45 ..$ nmasked : int 0 $ intensities: num [1:10] 9044 121 10406 180 11062 ... $ outliers : NULL $ masked : NULL Testing readCel() with 'readDouble' indices...done Testing readCel() with 'outOfRange' indices... List of 1 $ idxs: int -1 List of 2 $ message: chr "Argument 'indices' is out of range [1,15876]." $ call : language readCel(cel, indices = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCel() with 'outOfRange' indices...done Testing readCel() with 'outOfRange' indices... List of 1 $ idxs: int 0 List of 2 $ message: chr "Argument 'indices' is out of range [1,15876]." $ call : language readCel(cel, indices = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCel() with 'outOfRange' indices...done Testing readCel() with 'outOfRange' indices... List of 1 $ idxs: int 1000000000 List of 2 $ message: chr "Argument 'indices' is out of range [1,15876]." $ call : language readCel(cel, indices = idxs) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCel() with 'outOfRange' indices...done > > proc.time() user system elapsed 2.159 0.296 2.684
affxparser.Rcheck/tests/readCelIntensities.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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. 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. > if (require("AffymetrixDataTestFiles")) { + library("affxparser") + + pathR <- system.file(package="AffymetrixDataTestFiles") + pathD <- file.path(pathR, "rawData", "FusionSDK_Test3", "Test3") + + # Find all CEL files + path <- file.path(pathD, "2.Calvin") + cels <- list.files(path=path, pattern="[.]CEL$", full.names=TRUE) + + hdr <- readCelHeader(cels[1L]) + I <- length(cels) + Jall <- hdr$total + + # Read full file + data <- readCelIntensities(cels) + str(data) + stopifnot(all(dim(data) == c(Jall,I))) + + # Various sets of indices to be read + idxsList <- list( + # readNothing=integer(0L), # FIX ME + readAll=NULL, + readOne=10L, + readSome=11:20, + readDouble=as.double(11:20), + outOfRange=-1L, + outOfRange=0L, + outOfRange=1e9L + ) + + # Read different subsets of cells + for (ii in seq_along(idxsList)) { + name <- names(idxsList)[ii] + message(sprintf("Testing readCelIntensities() with '%s' indices...", name)) + idxs <- idxsList[[ii]] + str(list(idxs=idxs)) + if (grepl("outOfRange", name)) { + res <- tryCatch(readCelIntensities(cels, indices=idxs), error=function(ex) ex) + str(res) + stopifnot(inherits(res, "error")) + } else { + data <- readCelIntensities(cels, indices=idxs) + str(data) + J <- if (is.null(idxs)) Jall else length(idxs) + stopifnot(all(dim(data) == c(J,I))) + } + message(sprintf("Testing readCelIntensities() with '%s' indices...done", name)) + } # for (ii ...) + } # if (require("AffymetrixDataTestFiles")) Loading required package: AffymetrixDataTestFiles num [1:15876, 1:2] 190 11263 164 11272 181 ... - attr(*, "dimnames")=List of 2 ..$ : NULL ..$ : chr [1:2] "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/AffymetrixDataTestFiles/rawData/FusionSDK"| __truncated__ "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/AffymetrixDataTestFiles/rawData/FusionSDK"| __truncated__ Testing readCelIntensities() with 'readAll' indices... List of 1 $ idxs: NULL num [1:15876, 1:2] 190 11263 164 11272 181 ... - attr(*, "dimnames")=List of 2 ..$ : NULL ..$ : chr [1:2] "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/AffymetrixDataTestFiles/rawData/FusionSDK"| __truncated__ "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/AffymetrixDataTestFiles/rawData/FusionSDK"| __truncated__ Testing readCelIntensities() with 'readAll' indices...done Testing readCelIntensities() with 'readOne' indices... List of 1 $ idxs: int 10 num [1, 1:2] 143 136 - attr(*, "dimnames")=List of 2 ..$ : NULL ..$ : chr [1:2] "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/AffymetrixDataTestFiles/rawData/FusionSDK"| __truncated__ "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/AffymetrixDataTestFiles/rawData/FusionSDK"| __truncated__ Testing readCelIntensities() with 'readOne' indices...done Testing readCelIntensities() with 'readSome' indices... List of 1 $ idxs: int [1:10] 11 12 13 14 15 16 17 18 19 20 num [1:10, 1:2] 11053 161 11466 152 11210 ... - attr(*, "dimnames")=List of 2 ..$ : NULL ..$ : chr [1:2] "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/AffymetrixDataTestFiles/rawData/FusionSDK"| __truncated__ "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/AffymetrixDataTestFiles/rawData/FusionSDK"| __truncated__ Testing readCelIntensities() with 'readSome' indices...done Testing readCelIntensities() with 'readDouble' indices... List of 1 $ idxs: num [1:10] 11 12 13 14 15 16 17 18 19 20 num [1:10, 1:2] 11053 161 11466 152 11210 ... - attr(*, "dimnames")=List of 2 ..$ : NULL ..$ : chr [1:2] "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/AffymetrixDataTestFiles/rawData/FusionSDK"| __truncated__ "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/AffymetrixDataTestFiles/rawData/FusionSDK"| __truncated__ Testing readCelIntensities() with 'readDouble' indices...done Testing readCelIntensities() with 'outOfRange' indices... List of 1 $ idxs: int -1 List of 2 $ message: chr "Argument 'indices' is out of range [1,15876]." $ call : language readCel(filename = filenames[i], indices = indices, readIntensities = TRUE, readHeader = FALSE, readStdvs = | __truncated__ ... - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCelIntensities() with 'outOfRange' indices...done Testing readCelIntensities() with 'outOfRange' indices... List of 1 $ idxs: int 0 List of 2 $ message: chr "Argument 'indices' is out of range [1,15876]." $ call : language readCel(filename = filenames[i], indices = indices, readIntensities = TRUE, readHeader = FALSE, readStdvs = | __truncated__ ... - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCelIntensities() with 'outOfRange' indices...done Testing readCelIntensities() with 'outOfRange' indices... List of 1 $ idxs: int 1000000000 List of 2 $ message: chr "Argument 'indices' is out of range [1,15876]." $ call : language readCel(filename = filenames[i], indices = indices, readIntensities = TRUE, readHeader = FALSE, readStdvs = | __truncated__ ... - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCelIntensities() with 'outOfRange' indices...done > > proc.time() user system elapsed 0.718 0.178 0.902
affxparser.Rcheck/tests/readCelRectangle.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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. 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. > if (require("AffymetrixDataTestFiles")) { + library("affxparser") + + rotate270 <- function(x, ...) { + x <- t(x) + nc <- ncol(x) + if (nc < 2) return(x) + x[,nc:1,drop=FALSE] + } + + # Search for some available CEL files + pathR <- system.file(package="AffymetrixDataTestFiles") + pathD <- file.path(pathR, "rawData", "FusionSDK_HG-Focus", "HG-Focus") + cel <- file.path(pathD, "2.Calvin", "HG-Focus-1-121502.CEL") + + # Read CEL intensities in the upper left corner + range <- c(0,250) + data <- readCelRectangle(cel, xrange=range, yrange=range) + + # Displaying image + z <- rotate270(data$intensities) + sub <- sprintf("Chip type: %s", data$header$chiptype) + image(z, col=gray.colors(256), axes=FALSE, main=basename(cel), sub=sub) + text(x=0, y=1, labels="(0,0)", adj=c(0,-0.7), cex=0.8, xpd=TRUE) + text(x=1, y=0, labels="(250,250)", adj=c(1,1.2), cex=0.8, xpd=TRUE) + + # Read 1x1 rectangle + range <- c(0,0) + data <- readCelRectangle(cel, xrange=range, yrange=range) + print(data$intensities) + stopifnot(all(dim(data$intensities) == c(1,1))) + } Loading required package: AffymetrixDataTestFiles [,1] [1,] 83.3 > > > > proc.time() user system elapsed 0.974 0.174 1.199
affxparser.Rcheck/tests/readCelUnits.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > if (require("AffymetrixDataTestFiles")) { + library("affxparser") + + pathR <- system.file(package="AffymetrixDataTestFiles") + pathA <- file.path(pathR, "annotationData", "chipTypes", "Test3") + pathD <- file.path(pathR, "rawData", "FusionSDK_Test3", "Test3") + + # Read CDF structure + cdf <- file.path(pathA, "1.XDA", "Test3.CDF") + hdr <- readCdfHeader(cdf) + Jall <- hdr$nunits + + # Find all CEL files + cels <- list.files(path=pathD, pattern="[.]CEL$", + recursive=TRUE, full.names=TRUE) + + # Various sets of indices to be read + idxsList <- list( + ## readNothing=integer(0L), # FIX ME + readAll=NULL, + readOne=10L, + readSome=11:20, + readDouble=as.double(11:20), + outOfRange=-1L, + outOfRange=0L, + outOfRange=1e9L + ) + + # Read full file + data <- readCelUnits(cels, cdf=cdf) + str(head(data)) + stopifnot(length(data) == Jall) + + # Read different subsets of units + for (ii in seq_along(idxsList)) { + name <- names(idxsList)[ii] + message(sprintf("Testing readCelUnits() with '%s' indices...", name)) + idxs <- idxsList[[ii]] + str(list(idxs=idxs)) + if (grepl("outOfRange", name)) { + res <- tryCatch(readCelUnits(cels, units=idxs, cdf=cdf), error=function(ex) ex) + str(res) + stopifnot(inherits(res, "error")) + } else { + data <- readCelUnits(cels, units=idxs, cdf=cdf) + str(head(data)) + J <- if (is.null(idxs)) Jall else length(idxs) + stopifnot(length(data) == J) + } + message(sprintf("Testing readCelUnits() with '%s' indices...done", name)) + } # for (ii ...) + } # if (require("AffymetrixDataTestFiles")) Loading required package: AffymetrixDataTestFiles List of 6 $ Pae_16SrRNA_s_at:List of 1 ..$ Pae_16SrRNA_s_at:List of 1 .. ..$ intensities: num [1:32, 1:4] 181 132 134 159 107 ... $ Pae_23SrRNA_s_at:List of 1 ..$ Pae_23SrRNA_s_at:List of 1 .. ..$ intensities: num [1:32, 1:4] 122 135 93 108 154 ... $ PA1178_oprH_at :List of 1 ..$ PA1178_oprH_at:List of 1 .. ..$ intensities: num [1:24, 1:4] 97 108 126 214 157 ... $ PA1816_dnaQ_at :List of 1 ..$ PA1816_dnaQ_at:List of 1 .. ..$ intensities: num [1:24, 1:4] 117 112 126 132 142 ... $ PA3183_zwf_at :List of 1 ..$ PA3183_zwf_at:List of 1 .. ..$ intensities: num [1:24, 1:4] 264 163 238 466 248 ... $ PA3640_dnaE_at :List of 1 ..$ PA3640_dnaE_at:List of 1 .. ..$ intensities: num [1:24, 1:4] 98 88.5 412 1025 362.3 ... Testing readCelUnits() with 'readAll' indices... List of 1 $ idxs: NULL List of 6 $ Pae_16SrRNA_s_at:List of 1 ..$ Pae_16SrRNA_s_at:List of 1 .. ..$ intensities: num [1:32, 1:4] 181 132 134 159 107 ... $ Pae_23SrRNA_s_at:List of 1 ..$ Pae_23SrRNA_s_at:List of 1 .. ..$ intensities: num [1:32, 1:4] 122 135 93 108 154 ... $ PA1178_oprH_at :List of 1 ..$ PA1178_oprH_at:List of 1 .. ..$ intensities: num [1:24, 1:4] 97 108 126 214 157 ... $ PA1816_dnaQ_at :List of 1 ..$ PA1816_dnaQ_at:List of 1 .. ..$ intensities: num [1:24, 1:4] 117 112 126 132 142 ... $ PA3183_zwf_at :List of 1 ..$ PA3183_zwf_at:List of 1 .. ..$ intensities: num [1:24, 1:4] 264 163 238 466 248 ... $ PA3640_dnaE_at :List of 1 ..$ PA3640_dnaE_at:List of 1 .. ..$ intensities: num [1:24, 1:4] 98 88.5 412 1025 362.3 ... Testing readCelUnits() with 'readAll' indices...done Testing readCelUnits() with 'readOne' indices... List of 1 $ idxs: int 10 List of 1 $ PA1178_oprH_st:List of 1 ..$ PA1178_oprH_st:List of 1 .. ..$ intensities: num [1:24, 1:4] 114 119 142 139 170 ... Testing readCelUnits() with 'readOne' indices...done Testing readCelUnits() with 'readSome' indices... List of 1 $ idxs: int [1:10] 11 12 13 14 15 16 17 18 19 20 List of 6 $ PA1816_dnaQ_st :List of 1 ..$ PA1816_dnaQ_st:List of 1 .. ..$ intensities: num [1:24, 1:4] 114 109 121 114 138 ... $ PA3183_zwf_st :List of 1 ..$ PA3183_zwf_st:List of 1 .. ..$ intensities: num [1:24, 1:4] 143 221 124 137 184 ... $ PA3640_dnaE_st :List of 1 ..$ PA3640_dnaE_st:List of 1 .. ..$ intensities: num [1:24, 1:4] 141 134 181 180 246 ... $ PA4407_ftsZ_st :List of 1 ..$ PA4407_ftsZ_st:List of 1 .. ..$ intensities: num [1:24, 1:4] 180 222 135 129 240 ... $ AFFX-Athal-Actin_5_r_at:List of 1 ..$ AFFX-Athal-Actin_5_r_at:List of 1 .. ..$ intensities: num [1:32, 1:4] 274 170 266 227 314 ... $ AFFX-Athal-Actin_M_at :List of 1 ..$ AFFX-Athal-Actin_M_at:List of 1 .. ..$ intensities: num [1:32, 1:4] 112 178 131 112 144 ... Testing readCelUnits() with 'readSome' indices...done Testing readCelUnits() with 'readDouble' indices... List of 1 $ idxs: num [1:10] 11 12 13 14 15 16 17 18 19 20 List of 6 $ PA1816_dnaQ_st :List of 1 ..$ PA1816_dnaQ_st:List of 1 .. ..$ intensities: num [1:24, 1:4] 114 109 121 114 138 ... $ PA3183_zwf_st :List of 1 ..$ PA3183_zwf_st:List of 1 .. ..$ intensities: num [1:24, 1:4] 143 221 124 137 184 ... $ PA3640_dnaE_st :List of 1 ..$ PA3640_dnaE_st:List of 1 .. ..$ intensities: num [1:24, 1:4] 141 134 181 180 246 ... $ PA4407_ftsZ_st :List of 1 ..$ PA4407_ftsZ_st:List of 1 .. ..$ intensities: num [1:24, 1:4] 180 222 135 129 240 ... $ AFFX-Athal-Actin_5_r_at:List of 1 ..$ AFFX-Athal-Actin_5_r_at:List of 1 .. ..$ intensities: num [1:32, 1:4] 274 170 266 227 314 ... $ AFFX-Athal-Actin_M_at :List of 1 ..$ AFFX-Athal-Actin_M_at:List of 1 .. ..$ intensities: num [1:32, 1:4] 112 178 131 112 144 ... Testing readCelUnits() with 'readDouble' indices...done Testing readCelUnits() with 'outOfRange' indices... List of 1 $ idxs: int -1 List of 2 $ message: chr "Argument 'units' contains non-positive indices." $ call : language readCelUnits(cels, units = idxs, cdf = cdf) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCelUnits() with 'outOfRange' indices...done Testing readCelUnits() with 'outOfRange' indices... List of 1 $ idxs: int 0 List of 2 $ message: chr "Argument 'units' contains non-positive indices." $ call : language readCelUnits(cels, units = idxs, cdf = cdf) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCelUnits() with 'outOfRange' indices...done Testing readCelUnits() with 'outOfRange' indices... List of 1 $ idxs: int 1000000000 List of 2 $ message: chr "Argument 'units' contains an element out of range: 1000000000" $ call : language readCdfCellIndices(cdfFile, units = units, stratifyBy = stratifyBy, verbose = FALSE) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readCelUnits() with 'outOfRange' indices...done > > proc.time() user system elapsed 1.127 0.218 1.396
affxparser.Rcheck/tests/readPgf.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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. 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. > if (require("AffymetrixDataTestFiles") && packageVersion("AffymetrixDataTestFiles") >= "0.4.0") { + library("affxparser") + + pathR <- system.file(package="AffymetrixDataTestFiles") + pathA <- file.path(pathR, "annotationData", "chipTypes", "HuGene-1_0-st-v1") + + # Read PGF structure + pgf <- file.path(pathA, "HuGene-1_0-st-v1.r4,10_probesets.pgf") + + # NOTE: Hard-coded + Jall <- 10L + + # Various sets of indices to be read + idxsList <- list( + ## readNothing=integer(0L), # FIX ME + readAll=NULL, + readOne=5L, + readSome=1:5, + readDouble=as.double(1:5), + outOfRange=-1L, + outOfRange=0L, + outOfRange=1e9L + ) + + data <- readPgf(pgf) + str(head(data)) + stopifnot(identical(data$header$chip_type, "HuGene-1_0-st-v1")) + stopifnot(length(data$probesetName) == Jall) + + # Read different subsets of units + for (ii in seq_along(idxsList)) { + name <- names(idxsList)[ii] + message(sprintf("Testing readPgf() with '%s' indices...", name)) + idxs <- idxsList[[ii]] + str(list(idxs=idxs)) + if (grepl("outOfRange", name)) { + res <- tryCatch(readPgf(pgf, indices=idxs), error=function(ex) ex) + str(res) + stopifnot(inherits(res, "error")) + } else { + data <- readPgf(pgf, indices=idxs) + str(head(data)) + stopifnot(identical(data$header$chip_type, "HuGene-1_0-st-v1")) + J <- if (is.null(idxs)) Jall else length(idxs) + stopifnot(length(data$probesetName) == J) + } + message(sprintf("Testing readPgf() with '%s' indices...done", name)) + } # for (ii ...) + + + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + # Validate correctness of subsets + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + subsetPgf <- function(data, indices=NULL, ...) { + if (is.null(indices)) return(data) + + # Atoms + offsets <- data$probesetStartAtom + natoms <- diff(c(offsets, length(data0$atomStartProbe)+1L)) + offsets <- offsets[indices] + natoms <- natoms[indices] + # Identify atoms to keep + keep <- logical(length(data$atomStartProbe)) + for (kk in seq_along(offsets)) { + keep[seq(from=offsets[kk], by=1L, length=natoms[kk])] <- TRUE; + } + + for (ff in c("probeSequence", "probeId", "probeGcCount", "atomExonPosition", "atomId", "probeInterrogationPosition", "probeLength", "probeType")) { + data[[ff]] <- data[[ff]][keep] + } + + data$atomStartProbe <- seq_len(sum(natoms)) + data$probesetStartAtom <- c(1L, cumsum(natoms))[length(indices)] + + # Probesets + for (ff in c("probesetName", "probesetId", "probesetType")) { + data[[ff]] <- data[[ff]][indices] + } + + data + } # subsetPgf() + + data0 <- readPgf(pgf) + Jall <- length(data0$probesetId) + + for (kk in 1:10) { + n <- sample(Jall, size=1L) + idxs <- sort(sample(1:Jall, size=n, replace=FALSE)) + data <- readPgf(pgf, indices=idxs) + dataS <- subsetPgf(data0, indices=idxs) + for (ff in c("probesetStartAtom", "atomExonPosition")) + data[[ff]] <- dataS[[ff]] <- NULL + stopifnot(all.equal(data, dataS)) + } + } # if (require("AffymetrixDataTestFiles")) Loading required package: AffymetrixDataTestFiles List of 6 $ probeSequence : chr [1:40] "AAGCTTAGTAGACTATAAATATGAC" "GCTTAGTAGACTATAAATATGACTT" "GTAGACTATAAATATGACTTACTCA" "ACTATAAATATGACTTACTCAATGA" ... $ probesetName : chr [1:10] "" "" "" "" ... $ probesetStartAtom: int [1:10] 1 5 9 13 17 21 25 29 33 37 $ probeId : int [1:40] 116371 943979 493089 907039 1033309 653512 690769 997409 379979 469846 ... $ probesetId : int [1:10] 7892501 7892502 7892503 7892504 7892505 7892506 7892507 7892508 7892509 7892510 $ probesetType : chr [1:10] "normgene->exon" "normgene->intron" "normgene->intron" "normgene->intron" ... Testing readPgf() with 'readAll' indices... List of 1 $ idxs: NULL List of 6 $ probeSequence : chr [1:40] "AAGCTTAGTAGACTATAAATATGAC" "GCTTAGTAGACTATAAATATGACTT" "GTAGACTATAAATATGACTTACTCA" "ACTATAAATATGACTTACTCAATGA" ... $ probesetName : chr [1:10] "" "" "" "" ... $ probesetStartAtom: int [1:10] 1 5 9 13 17 21 25 29 33 37 $ probeId : int [1:40] 116371 943979 493089 907039 1033309 653512 690769 997409 379979 469846 ... $ probesetId : int [1:10] 7892501 7892502 7892503 7892504 7892505 7892506 7892507 7892508 7892509 7892510 $ probesetType : chr [1:10] "normgene->exon" "normgene->intron" "normgene->intron" "normgene->intron" ... Testing readPgf() with 'readAll' indices...done Testing readPgf() with 'readOne' indices... List of 1 $ idxs: int 5 List of 6 $ probeSequence : chr [1:4] "AGATGTGTATAGAGGGTTTAACTTA" "TGTGTATAGAGGGTTTAACTTAAAT" "GTGTATAGAGGGTTTAACTTAAATA" "GATGTGTATAGAGGGTTTAACTTAA" $ probesetName : chr "" $ probesetStartAtom: int 1 $ probeId : int [1:4] 611456 834021 857576 980218 $ probesetId : int 7892505 $ probesetType : chr "normgene->intron" Testing readPgf() with 'readOne' indices...done Testing readPgf() with 'readSome' indices... List of 1 $ idxs: int [1:5] 1 2 3 4 5 List of 6 $ probeSequence : chr [1:20] "AAGCTTAGTAGACTATAAATATGAC" "GCTTAGTAGACTATAAATATGACTT" "GTAGACTATAAATATGACTTACTCA" "ACTATAAATATGACTTACTCAATGA" ... $ probesetName : chr [1:5] "" "" "" "" ... $ probesetStartAtom: int [1:5] 1 5 9 13 17 $ probeId : int [1:20] 116371 943979 493089 907039 1033309 653512 690769 997409 379979 469846 ... $ probesetId : int [1:5] 7892501 7892502 7892503 7892504 7892505 $ probesetType : chr [1:5] "normgene->exon" "normgene->intron" "normgene->intron" "normgene->intron" ... Testing readPgf() with 'readSome' indices...done Testing readPgf() with 'readDouble' indices... List of 1 $ idxs: num [1:5] 1 2 3 4 5 List of 6 $ probeSequence : chr [1:20] "AAGCTTAGTAGACTATAAATATGAC" "GCTTAGTAGACTATAAATATGACTT" "GTAGACTATAAATATGACTTACTCA" "ACTATAAATATGACTTACTCAATGA" ... $ probesetName : chr [1:5] "" "" "" "" ... $ probesetStartAtom: int [1:5] 1 5 9 13 17 $ probeId : int [1:20] 116371 943979 493089 907039 1033309 653512 690769 997409 379979 469846 ... $ probesetId : int [1:5] 7892501 7892502 7892503 7892504 7892505 $ probesetType : chr [1:5] "normgene->exon" "normgene->intron" "normgene->intron" "normgene->intron" ... Testing readPgf() with 'readDouble' indices...done Testing readPgf() with 'outOfRange' indices... List of 1 $ idxs: int -1 List of 2 $ message: chr "Argument 'indices' contains a non-positive element" $ call : language readPgfEnv(file, readBody = TRUE, indices = indices) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readPgf() with 'outOfRange' indices...done Testing readPgf() with 'outOfRange' indices... List of 1 $ idxs: int 0 List of 2 $ message: chr "Argument 'indices' contains a non-positive element" $ call : language readPgfEnv(file, readBody = TRUE, indices = indices) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readPgf() with 'outOfRange' indices...done Testing readPgf() with 'outOfRange' indices... List of 1 $ idxs: int 1000000000 List of 2 $ message: chr "Argument 'indices' contains an element out of range [1,10]: 1000000000" $ call : language readPgfEnv(file, readBody = TRUE, indices = indices) - attr(*, "class")= chr [1:3] "simpleError" "error" "condition" Testing readPgf() with 'outOfRange' indices...done > > proc.time() user system elapsed 0.768 0.198 1.029
affxparser.Rcheck/tests/testWriteAndReadEmptyCdf.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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. 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. > systemR <- function(command="", ..., verbose=FALSE) { + # Locate the R executable + Rbin <- file.path(R.home("bin"), "R") + cmd <- sprintf('%s %s', shQuote(Rbin), command) + if (verbose) cat("Command: ", cmd, "\n", sep="") + system(cmd, ...) + } # systemR() > > > ## Explicitly append 'affxparser' to library path > ## Needed for covr::coverage() > pd <- packageDescription("affxparser") > libpath <- dirname(dirname(dirname(attr(pd, "file")))) > cmd <- sprintf(' -e ".libPaths(\'%s\'); affxparser:::.testWriteAndReadEmptyCdf()"', libpath) > out <- systemR(cmd, intern=TRUE, wait=TRUE, verbose=TRUE) Command: '/Library/Frameworks/R.framework/Resources/bin/R' -e ".libPaths('/private/tmp/RtmpJTrVs4/RLIBS_8b25149d3a1'); affxparser:::.testWriteAndReadEmptyCdf()" > cat(out, sep="\n") R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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. 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. > .libPaths('/private/tmp/RtmpJTrVs4/RLIBS_8b25149d3a1'); affxparser:::.testWriteAndReadEmptyCdf() Pathname: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/affxparser/testscripts/writeAndReadEmptyCdf.R > library("affxparser") > hdr <- list(chiptype = "Empty2x3", nrows = 2, ncols = 3, + nunits = 0, nqcunits = 0, refseq = "") > units <- qcUnits <- list() > pathname <- file.path(tempdir(), "Empty2x3.cdf") > str(pathname) chr "/tmp/RtmpjH3Zbs/Empty2x3.cdf" > writeCdf(pathname, cdfheader = hdr, cdf = units, cdfqc = qcUnits, + overwrite = TRUE) > hdr2 <- readCdfHeader(pathname) > str(hdr2) List of 12 $ ncols : int 3 $ nrows : int 2 $ nunits : int 0 $ nqcunits : int 0 $ refseq : chr "" $ chiptype : chr "Empty2x3" $ filename : chr "/tmp/RtmpjH3Zbs/Empty2x3.cdf" $ rows : int 2 $ cols : int 3 $ probesets : int 0 $ qcprobesets: int 0 $ reference : chr "" > units2 <- readCdfUnits(pathname) > str(units2) Named list() COMPLETE > > > res <- any(regexpr("COMPLETE", out) != -1) > cat("Test result: ", res, "\n", sep="") Test result: TRUE > if (!res) { + stop("affxparser:::.testWriteAndReadEmptyCdf() failed.") + } > > ############################################################################ > # HISTORY: > # 2012-05-22 > # o ROBUSTNESS: Now launching R without assuming it is on the search path, > # cf. R-devel thread 'Best way to locate R executable from within R?' > # on May 22, 2012. > # 2012-05-18 > # o Added because of the OSX build bug, cf. > # https://groups.google.com/d/topic/aroma-affymetrix/lEfDanThLEA/discussion > # o Created. > ############################################################################ > > proc.time() user system elapsed 0.806 0.268 1.093
affxparser.Rcheck/tests/testWriteAndReadEmptyCel.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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. 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. > systemR <- function(command="", ..., verbose=FALSE) { + # Locate the R executable + Rbin <- file.path(R.home("bin"), "R") + cmd <- sprintf('%s %s', shQuote(Rbin), command) + if (verbose) cat("Command: ", cmd, "\n", sep="") + system(cmd, ...) + } # systemR() > > > ## Explicitly append 'affxparser' to library path > ## Needed for covr::coverage() > pd <- packageDescription("affxparser") > libpath <- dirname(dirname(dirname(attr(pd, "file")))) > cmd <- sprintf(' -e ".libPaths(\'%s\'); affxparser:::.testWriteAndReadEmptyCel()"', libpath) > out <- systemR(cmd, intern=TRUE, wait=TRUE, verbose=TRUE) Command: '/Library/Frameworks/R.framework/Resources/bin/R' -e ".libPaths('/private/tmp/RtmpJTrVs4/RLIBS_8b25149d3a1'); affxparser:::.testWriteAndReadEmptyCel()" > cat(out, sep="\n") R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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. 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. > .libPaths('/private/tmp/RtmpJTrVs4/RLIBS_8b25149d3a1'); affxparser:::.testWriteAndReadEmptyCel() Pathname: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/affxparser/testscripts/writeAndReadEmptyCel.R > library("affxparser") > hdr <- list(version = 4, chiptype = "Empty2x3", rows = 2, + cols = 3, algorithm = "Percentile\nAlgorithm", parameters = "Percentile:75;CellMarg ..." ... [TRUNCATED] > hdr$header <- sprintf("Cols=%d\nRows=%d\nTotalX=%d\nTotalY=%d\nOffsetX=0\nOffsetY=0\nGridCornerUL=223 141\nGridCornerUR=3590 166\nGridCornerLR=3565 ..." ... [TRUNCATED] > pathname <- file.path(tempdir(), "Empty2x3.cel") > str(pathname) chr "/tmp/RtmpW3yODB/Empty2x3.cel" > createCel(pathname, header = hdr, overwrite = TRUE) > hdr2 <- readCelHeader(pathname) > str(hdr2) List of 14 $ filename : chr "/tmp/RtmpW3yODB/Empty2x3.cel" $ version : int 4 $ cols : int 3 $ rows : int 2 $ total : int 6 $ algorithm : chr "Percentile\nAlgorithm" $ parameters : chr "Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004;AlgVersion:6.0;FixedCellSize:TRUE;FullFeatureWidt"| __truncated__ $ chiptype : chr "Empty2x3" $ header : chr "Cols=3\nRows=2\nTotalX=3\nTotalY=2\nOffsetX=0\nOffsetY=0\nGridCornerUL=223 141\nGridCornerUR=3590 166\nGridCorn"| __truncated__ $ datheader : chr "[13..25244] 050523MJA_SNP10K-2.0_KJ05:CLS=3666 RWS=3666 XIN=1 YIN=1 VE=30 2.0 09/26/12 10:01:02 50102"| __truncated__ $ librarypackage: chr "" $ cellmargin : int 2 $ noutliers : int 0 $ nmasked : int 0 > data2 <- readCel(pathname) > str(data2) List of 4 $ header :List of 14 ..$ filename : chr "/tmp/RtmpW3yODB/Empty2x3.cel" ..$ version : int 4 ..$ cols : int 3 ..$ rows : int 2 ..$ total : int 6 ..$ algorithm : chr "Percentile\nAlgorithm" ..$ parameters : chr "Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004;AlgVersion:6.0;FixedCellSize:TRUE;FullFeatureWidt"| __truncated__ ..$ chiptype : chr "Empty2x3" ..$ header : chr "Cols=3\nRows=2\nTotalX=3\nTotalY=2\nOffsetX=0\nOffsetY=0\nGridCornerUL=223 141\nGridCornerUR=3590 166\nGridCorn"| __truncated__ ..$ datheader : chr "[13..25244] 050523MJA_SNP10K-2.0_KJ05:CLS=3666 RWS=3666 XIN=1 YIN=1 VE=30 2.0 09/26/12 10:01:02 50102"| __truncated__ ..$ librarypackage: chr "" ..$ cellmargin : int 2 ..$ noutliers : int 0 ..$ nmasked : int 0 $ intensities: num [1:6] 0 0 0 0 0 0 $ outliers : NULL $ masked : NULL COMPLETE > > > res <- any(regexpr("COMPLETE", out) != -1) > cat("Test result: ", res, "\n", sep="") Test result: TRUE > if (!res) { + stop("affxparser:::.testWriteAndReadEmptyCel() failed.") + } > > ############################################################################ > # HISTORY: > # 2012-09-26 > # o Created from tests/testWriteAndReadEmptyCdf.R. > ############################################################################ > > proc.time() user system elapsed 0.856 0.278 1.217
affxparser.Rcheck/affxparser-Ex.timings
name | user | system | elapsed | |
applyCdfGroups | 0.176 | 0.169 | 0.440 | |
convertCdf | 1.956 | 0.054 | 2.186 | |
convertCel | 0.239 | 0.027 | 0.293 | |
createCel | 0.463 | 0.040 | 0.569 | |
findCdf | 0.122 | 0.018 | 0.152 | |
invertMap | 0.710 | 0.062 | 0.853 | |
readCdfDataFrame | 1.305 | 0.086 | 1.524 | |
readCdfHeader | 0.019 | 0.005 | 0.027 | |
readCdfNbrOfCellsPerUnitGroup | 0.915 | 0.433 | 1.575 | |
readCdfUnitNames | 0 | 0 | 0 | |
readCdfUnits | 2.460 | 0.150 | 2.871 | |
readCdfUnitsWriteMap | 0.949 | 0.066 | 1.108 | |
readCel | 0.021 | 0.001 | 0.024 | |
readCelHeader | 0.001 | 0.001 | 0.002 | |
readCelIntensities | 0.000 | 0.001 | 0.001 | |
readCelRectangle | 0.472 | 0.047 | 0.568 | |
readCelUnits | 0.037 | 0.007 | 0.045 | |
readChp | 0.034 | 0.007 | 0.044 | |
updateCel | 1.299 | 0.309 | 1.847 | |
updateCelUnits | 2.395 | 0.440 | 3.129 | |