Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 11:57:04 -0400 (Tue, 09 Apr 2019).
Package 360/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
crlmm 1.41.0 Benilton S Carvalho
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: crlmm |
Version: 1.41.0 |
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:crlmm.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings crlmm_1.41.0.tar.gz |
StartedAt: 2019-04-09 02:04:46 -0400 (Tue, 09 Apr 2019) |
EndedAt: 2019-04-09 02:24:48 -0400 (Tue, 09 Apr 2019) |
EllapsedTime: 1201.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: crlmm.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:crlmm.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings crlmm_1.41.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/crlmm.Rcheck' * using R Under development (unstable) (2019-03-09 r76216) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'crlmm/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'crlmm' version '1.41.0' * 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 whether package 'crlmm' can be installed ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpCA4ORc/R.INSTALL1b786379812/crlmm/man/ABpanel.Rd:57: file link 'lpolygon' in package 'lattice' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpCA4ORc/R.INSTALL1b786379812/crlmm/man/genotype.Illumina.Rd:148: file link 'ocSamples' in package 'oligoClasses' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpCA4ORc/R.INSTALL1b786379812/crlmm/man/genotype.Rd:88: file link 'ocSamples' in package 'oligoClasses' does not exist and so has been treated as a topic See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/crlmm.Rcheck/00install.out' for details. * checking installed package size ... NOTE installed size is 5.1Mb sub-directories of 1Mb or more: R 1.2Mb data 2.7Mb * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE Versioned 'LinkingTo' value for 'preprocessCore' is only usable in R >= 3.0.2 * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... NOTE 'library' or 'require' call to 'RUnit' in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Namespaces in Imports field not imported from: 'SNPchip' 'splines' All declared Imports should be used. Unexported object imported by a ':::' call: 'Biobase:::assayDataEnvLock' See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .test: no visible global function definition for 'defineTestSuite' .test: no visible global function definition for 'runTestSuite' .test: no visible global function definition for 'printTextProtocol' calculateRBafCNSet : processByChromosome: no visible global function definition for 'position' genotypeInf: no visible binding for global variable 'anno' krlmm: no visible binding for global variable 'VGLMparameters' Undefined global functions or variables: VGLMparameters anno defineTestSuite position printTextProtocol runTestSuite * checking Rd files ... OK * 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... OK * checking include directives in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/crlmm/libs/i386/crlmm.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/crlmm/libs/x64/crlmm.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) 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. 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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed genotype 114.82 9.01 126.67 crlmm 89.70 3.22 94.45 snprma 25.19 1.01 26.20 celfile-utils 4.22 0.42 14.26 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed genotype 115.00 4.61 138.36 crlmm 81.75 2.03 83.80 snprma 22.53 1.05 23.59 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'crlmm_unit_tests.R' Running 'doRUnit.R' OK ** running tests for arch 'x64' ... Running 'crlmm_unit_tests.R' Running 'doRUnit.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 5 NOTEs See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/crlmm.Rcheck/00check.log' for details.
crlmm.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/crlmm_1.41.0.tar.gz && rm -rf crlmm.buildbin-libdir && mkdir crlmm.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=crlmm.buildbin-libdir crlmm_1.41.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL crlmm_1.41.0.zip && rm crlmm_1.41.0.tar.gz crlmm_1.41.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 3494k 100 3494k 0 0 15.4M 0 --:--:-- --:--:-- --:--:-- 15.8M install for i386 * installing *source* package 'crlmm' ... ** libs C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c gtypeCaller.c -o gtypeCaller.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c init.c -o init.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c trimmed.c -o trimmed.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c utils.c -o utils.o C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o crlmm.dll tmp.def gtypeCaller.o init.o trimmed.o utils.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/crlmm.buildbin-libdir/00LOCK-crlmm/00new/crlmm/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'crlmm' finding HTML links ... done ABpanel html Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpCA4ORc/R.INSTALL1b786379812/crlmm/man/ABpanel.Rd:57: file link 'lpolygon' in package 'lattice' does not exist and so has been treated as a topic AssayData-methods html finding level-2 HTML links ... done CNSet-methods html ListClassConstructors html PredictionRegion-class html batchStatisticAccessors html calculateRBaf html celfile-utils html cnSetExample html cnrmaAffy html constructAffyCNSet html constructInf html copynumberAccessors html crlmm-package html crlmm html crlmmCopynumber html genotype.Illumina html Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpCA4ORc/R.INSTALL1b786379812/crlmm/man/genotype.Illumina.Rd:148: file link 'ocSamples' in package 'oligoClasses' does not exist and so has been treated as a topic genotype html Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpCA4ORc/R.INSTALL1b786379812/crlmm/man/genotype.Rd:88: file link 'ocSamples' in package 'oligoClasses' does not exist and so has been treated as a topic genotypeAffy html genotypeInf html genotypes html plotSNPs html posteriorProbability html predictionRegion html preprocessInf html readGenCallOutput html readIdatFiles html snprma html snprmaAffy html validCdfNames html xyplot html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'crlmm' ... ** libs C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c gtypeCaller.c -o gtypeCaller.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c init.c -o init.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c trimmed.c -o trimmed.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/preprocessCore/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c utils.c -o utils.o C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o crlmm.dll tmp.def gtypeCaller.o init.o trimmed.o utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/crlmm.buildbin-libdir/crlmm/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'crlmm' as crlmm_1.41.0.zip * DONE (crlmm) * installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library' package 'crlmm' successfully unpacked and MD5 sums checked
crlmm.Rcheck/tests_i386/crlmm_unit_tests.Rout R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-bit) 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. > require("crlmm") || stop("unable to load crlmm package") Loading required package: crlmm Loading required package: oligoClasses Welcome to oligoClasses version 1.45.0 Loading required package: preprocessCore Welcome to crlmm version 1.41.0 [1] TRUE > crlmm:::.test() Loading required package: genomewidesnp6Crlmm Annotation for genomewidesnp6Crlmm version 1.0.7 supports UCSC builds hg18 and hg19. Loading required package: hapmapsnp6 /-------------------------------------------\ | SAMPLE HAPMAP SNP 6.0 | |-------------------------------------------| | Data obtained from http://www.hapmap.org | | This package is meant to be used only for | | demonstration of BioConductor packages. | | Access http://www.hapmap.org for details. | |-------------------------------------------| | The contents of this package are provided | | in good faith and the maintainer does not | | warrant their accuracy. | \-------------------------------------------/ Loading annotations and mixture model parameters. Processing 3 files. | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% Loading annotations. Determining gender. Calling 906600 SNPs for recalibration... Done. Estimating recalibration parameters. Calling 906600 SNPs... Done. Error in crlmm(cels[c(1, 1, 2)]) : sample identifiers are not unique In addition: Warning message: In crlmmGT(res[["A"]], res[["B"]], res[["SNR"]], res[["mixtureParams"]], : Recalibration not possible. Possible cause: small sample size. RUNIT TEST PROTOCOL -- Tue Apr 09 02:19:54 2019 *********************************************** Number of test functions: 3 Number of errors: 0 Number of failures: 0 1 Test Suite : crlmm RUnit Tests - 3 test functions, 0 errors, 0 failures Number of test functions: 3 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 81.85 3.00 84.89 |
crlmm.Rcheck/tests_x64/crlmm_unit_tests.Rout R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) 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. > require("crlmm") || stop("unable to load crlmm package") Loading required package: crlmm Loading required package: oligoClasses Welcome to oligoClasses version 1.45.0 Loading required package: preprocessCore Welcome to crlmm version 1.41.0 [1] TRUE > crlmm:::.test() Loading required package: genomewidesnp6Crlmm Annotation for genomewidesnp6Crlmm version 1.0.7 supports UCSC builds hg18 and hg19. Loading required package: hapmapsnp6 /-------------------------------------------\ | SAMPLE HAPMAP SNP 6.0 | |-------------------------------------------| | Data obtained from http://www.hapmap.org | | This package is meant to be used only for | | demonstration of BioConductor packages. | | Access http://www.hapmap.org for details. | |-------------------------------------------| | The contents of this package are provided | | in good faith and the maintainer does not | | warrant their accuracy. | \-------------------------------------------/ Loading annotations and mixture model parameters. Processing 3 files. | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% Loading annotations. Determining gender. Calling 906600 SNPs for recalibration... Done. Estimating recalibration parameters. Calling 906600 SNPs... Done. Error in crlmm(cels[c(1, 1, 2)]) : sample identifiers are not unique In addition: Warning message: In crlmmGT(res[["A"]], res[["B"]], res[["SNR"]], res[["mixtureParams"]], : Recalibration not possible. Possible cause: small sample size. RUNIT TEST PROTOCOL -- Tue Apr 09 02:23:17 2019 *********************************************** Number of test functions: 3 Number of errors: 0 Number of failures: 0 1 Test Suite : crlmm RUnit Tests - 3 test functions, 0 errors, 0 failures Number of test functions: 3 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 100.01 2.64 103.34 |
crlmm.Rcheck/tests_i386/doRUnit.Rout R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-bit) 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. > ## from xmapcore package > if( require( "RUnit", quietly=TRUE ) ) { + pkg <- "crlmm" + + if( Sys.getenv( "RCMDCHECK" ) == "FALSE" ) { + path <- file.path( getwd(), "..", "inst", "unitTests" ) + } else { + path <- system.file( package=pkg, "unitTests" ) + } + + cat( "\nRunning unit tests\n" ) + print( list( pkg=pkg, getwd=getwd(), pathToUnitTests=path ) ) + library( package=pkg, character.only=TRUE ) + + ##xmap.clear.cache() + + ## do not fail on warnings (needed for crlmm() test) + options(warn=0) + + ## Get the pattern (if there is one?) + patt <- Sys.getenv( "RUNITFILEPATTERN" ) + if( is.null( patt ) || nchar( patt ) == 0 ) { + testSuite <- defineTestSuite(name=paste( pkg, "unit testing" ), + dirs=path, + testFileRegexp=paste( "^test.+", patt, "\\.[rR]$", sep="" )) + } else { + ##testSuite <- defineTestSuite( name=paste( pkg, "unit testing" ), testFileRegexp=paste( "^runit\\.", patt, "\\.[rR]$", sep="" ), dirs=path ) + testSuite <- defineTestSuite(name=paste( pkg, "unit testing" ), + testFileRegexp=paste( "^test.+", patt, "\\.[rR]$", sep="" ), + dirs=path ) + } + tests <- runTestSuite( testSuite ) + + pathReport <- file.path( path, "report" ) + + cat( "------------------- UNIT TEST SUMMARY ---------------------\n\n" ) + printTextProtocol( tests, showDetails=FALSE ) + printTextProtocol( tests, showDetails=FALSE, fileName=paste( pathReport, "Summary.txt", sep="" ) ) + printTextProtocol( tests, showDetails=TRUE, fileName=paste( pathReport, ".txt", sep="" ) ) + + printHTMLProtocol( tests, fileName=paste( pathReport, ".html", sep="" ) ) + + tmp <- getErrors( tests ) + if( tmp$nFail > 0 | tmp$nErr > 0 ){ + stop( paste( "\n\nunit testing failed (#test failures: ", tmp$nFail, ", #R errors: ", tmp$nErr, ")\n\n", sep="")) + } + } else { + warning( "cannot run unit tests -- package RUnit is not available" ) + } Running unit tests $pkg [1] "crlmm" $getwd [1] "C:/Users/biocbuild/bbs-3.9-bioc/meat/crlmm.Rcheck/tests_i386" $pathToUnitTests [1] "C:/Users/biocbuild/bbs-3.9-bioc/R/library/crlmm/unitTests" Loading required package: oligoClasses Welcome to oligoClasses version 1.45.0 Loading required package: preprocessCore Welcome to crlmm version 1.41.0 Executing test function test_crlmm ... Loading required package: genomewidesnp6Crlmm Annotation for genomewidesnp6Crlmm version 1.0.7 supports UCSC builds hg18 and hg19. Loading required package: hapmapsnp6 /-------------------------------------------\ | SAMPLE HAPMAP SNP 6.0 | |-------------------------------------------| | Data obtained from http://www.hapmap.org | | This package is meant to be used only for | | demonstration of BioConductor packages. | | Access http://www.hapmap.org for details. | |-------------------------------------------| | The contents of this package are provided | | in good faith and the maintainer does not | | warrant their accuracy. | \-------------------------------------------/ Loading annotations and mixture model parameters. Processing 3 files. | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% Loading annotations. Determining gender. Calling 906600 SNPs for recalibration... Done. Estimating recalibration parameters. Calling 906600 SNPs... Done. done successfully. Executing test function test_duplicates ... Error in crlmm(cels[c(1, 1, 2)]) : sample identifiers are not unique In addition: Warning message: In crlmmGT(res[["A"]], res[["B"]], res[["SNR"]], res[["mixtureParams"]], : Recalibration not possible. Possible cause: small sample size. done successfully. Executing test function test_dataExamples ... done successfully. ------------------- UNIT TEST SUMMARY --------------------- RUNIT TEST PROTOCOL -- Tue Apr 09 02:21:33 2019 *********************************************** Number of test functions: 3 Number of errors: 0 Number of failures: 0 1 Test Suite : crlmm unit testing - 3 test functions, 0 errors, 0 failures > > proc.time() user system elapsed 94.82 3.43 98.25 |
crlmm.Rcheck/tests_x64/doRUnit.Rout R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) 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. > ## from xmapcore package > if( require( "RUnit", quietly=TRUE ) ) { + pkg <- "crlmm" + + if( Sys.getenv( "RCMDCHECK" ) == "FALSE" ) { + path <- file.path( getwd(), "..", "inst", "unitTests" ) + } else { + path <- system.file( package=pkg, "unitTests" ) + } + + cat( "\nRunning unit tests\n" ) + print( list( pkg=pkg, getwd=getwd(), pathToUnitTests=path ) ) + library( package=pkg, character.only=TRUE ) + + ##xmap.clear.cache() + + ## do not fail on warnings (needed for crlmm() test) + options(warn=0) + + ## Get the pattern (if there is one?) + patt <- Sys.getenv( "RUNITFILEPATTERN" ) + if( is.null( patt ) || nchar( patt ) == 0 ) { + testSuite <- defineTestSuite(name=paste( pkg, "unit testing" ), + dirs=path, + testFileRegexp=paste( "^test.+", patt, "\\.[rR]$", sep="" )) + } else { + ##testSuite <- defineTestSuite( name=paste( pkg, "unit testing" ), testFileRegexp=paste( "^runit\\.", patt, "\\.[rR]$", sep="" ), dirs=path ) + testSuite <- defineTestSuite(name=paste( pkg, "unit testing" ), + testFileRegexp=paste( "^test.+", patt, "\\.[rR]$", sep="" ), + dirs=path ) + } + tests <- runTestSuite( testSuite ) + + pathReport <- file.path( path, "report" ) + + cat( "------------------- UNIT TEST SUMMARY ---------------------\n\n" ) + printTextProtocol( tests, showDetails=FALSE ) + printTextProtocol( tests, showDetails=FALSE, fileName=paste( pathReport, "Summary.txt", sep="" ) ) + printTextProtocol( tests, showDetails=TRUE, fileName=paste( pathReport, ".txt", sep="" ) ) + + printHTMLProtocol( tests, fileName=paste( pathReport, ".html", sep="" ) ) + + tmp <- getErrors( tests ) + if( tmp$nFail > 0 | tmp$nErr > 0 ){ + stop( paste( "\n\nunit testing failed (#test failures: ", tmp$nFail, ", #R errors: ", tmp$nErr, ")\n\n", sep="")) + } + } else { + warning( "cannot run unit tests -- package RUnit is not available" ) + } Running unit tests $pkg [1] "crlmm" $getwd [1] "C:/Users/biocbuild/bbs-3.9-bioc/meat/crlmm.Rcheck/tests_x64" $pathToUnitTests [1] "C:/Users/biocbuild/bbs-3.9-bioc/R/library/crlmm/unitTests" Loading required package: oligoClasses Welcome to oligoClasses version 1.45.0 Loading required package: preprocessCore Welcome to crlmm version 1.41.0 Executing test function test_crlmm ... Loading required package: genomewidesnp6Crlmm Annotation for genomewidesnp6Crlmm version 1.0.7 supports UCSC builds hg18 and hg19. Loading required package: hapmapsnp6 /-------------------------------------------\ | SAMPLE HAPMAP SNP 6.0 | |-------------------------------------------| | Data obtained from http://www.hapmap.org | | This package is meant to be used only for | | demonstration of BioConductor packages. | | Access http://www.hapmap.org for details. | |-------------------------------------------| | The contents of this package are provided | | in good faith and the maintainer does not | | warrant their accuracy. | \-------------------------------------------/ Loading annotations and mixture model parameters. Processing 3 files. | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% Loading annotations. Determining gender. Calling 906600 SNPs for recalibration... Done. Estimating recalibration parameters. Calling 906600 SNPs... Done. done successfully. Executing test function test_duplicates ... Error in crlmm(cels[c(1, 1, 2)]) : sample identifiers are not unique In addition: Warning message: In crlmmGT(res[["A"]], res[["B"]], res[["SNR"]], res[["mixtureParams"]], : Recalibration not possible. Possible cause: small sample size. done successfully. Executing test function test_dataExamples ... done successfully. ------------------- UNIT TEST SUMMARY --------------------- RUNIT TEST PROTOCOL -- Tue Apr 09 02:24:40 2019 *********************************************** Number of test functions: 3 Number of errors: 0 Number of failures: 0 1 Test Suite : crlmm unit testing - 3 test functions, 0 errors, 0 failures > > proc.time() user system elapsed 80.98 2.40 83.46 |
crlmm.Rcheck/examples_i386/crlmm-Ex.timings
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crlmm.Rcheck/examples_x64/crlmm-Ex.timings
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