Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:01 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the crlmm package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/crlmm.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 412/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
crlmm 1.50.0 (landing page) Benilton S Carvalho
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: crlmm |
Version: 1.50.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:crlmm.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings crlmm_1.50.0.tar.gz |
StartedAt: 2021-10-14 21:42:12 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 21:59:03 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 1011.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: crlmm.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:crlmm.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings crlmm_1.50.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/crlmm.Rcheck' * using R version 4.1.1 (2021-08-10) * 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 '1.50.0' * 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 ... OK * checking installed package size ... NOTE installed size is 5.3Mb 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. Namespace in Imports field not imported from: '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-3.13-bioc/R/library/crlmm/libs/i386/crlmm.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) File 'C:/Users/biocbuild/bbs-3.13-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 (user + system) or elapsed time > 5s user system elapsed genotype 92.33 8.00 101.02 crlmm 77.23 3.19 81.23 snprma 25.45 1.07 26.53 celfile-utils 5.35 0.27 9.23 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed genotype 81.76 3.30 85.12 crlmm 67.63 1.83 69.45 snprma 17.59 1.05 18.64 * 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: 5 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/crlmm.Rcheck/00check.log' for details.
crlmm.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/crlmm_1.50.0.tar.gz && rm -rf crlmm.buildbin-libdir && mkdir crlmm.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=crlmm.buildbin-libdir crlmm_1.50.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL crlmm_1.50.0.zip && rm crlmm_1.50.0.tar.gz crlmm_1.50.0.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 0 3495k 0 13525 0 0 111k 0 0:00:31 --:--:-- 0:00:31 111k 87 3495k 87 3073k 0 0 2788k 0 0:00:01 0:00:01 --:--:-- 2788k 100 3495k 100 3495k 0 0 2953k 0 0:00:01 0:00:01 --:--:-- 2952k install for i386 * installing *source* package 'crlmm' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gtypeCaller.c -o gtypeCaller.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c trimmed.c -o trimmed.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utils.c -o utils.o C:/rtools40/mingw32/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-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/crlmm.buildbin-libdir/00LOCK-crlmm/00new/crlmm/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm' ** help *** installing help indices converting help for package 'crlmm' finding HTML links ... done ABpanel html 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 genotype html 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 No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm' ** testing if installed package can be loaded from final location No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm' ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'crlmm' ... ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gtypeCaller.c -o gtypeCaller.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c trimmed.c -o trimmed.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/preprocessCore/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utils.c -o utils.o C:/rtools40/mingw64/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-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/crlmm.buildbin-libdir/crlmm/libs/x64 ** testing if installed package can be loaded No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm' * MD5 sums packaged installation of 'crlmm' as crlmm_1.50.0.zip * DONE (crlmm) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'crlmm' successfully unpacked and MD5 sums checked
crlmm.Rcheck/tests_i386/crlmm_unit_tests.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 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 1.54.0 Loading required package: preprocessCore No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm' Welcome to crlmm version 1.50.0 [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 -- Thu Oct 14 21:54:48 2021 *********************************************** 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 81.45 3.29 84.71 |
crlmm.Rcheck/tests_x64/crlmm_unit_tests.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 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 1.54.0 Loading required package: preprocessCore No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm' Welcome to crlmm version 1.50.0 [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 -- Thu Oct 14 21:57:29 2021 *********************************************** 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 74.31 1.98 76.28 |
crlmm.Rcheck/tests_i386/doRUnit.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 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-3.13-bioc/meat/crlmm.Rcheck/tests_i386" $pathToUnitTests [1] "C:/Users/biocbuild/bbs-3.13-bioc/R/library/crlmm/unitTests" Loading required package: oligoClasses Welcome to oligoClasses version 1.54.0 Loading required package: preprocessCore No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm' Welcome to crlmm version 1.50.0 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 -- Thu Oct 14 21:56:12 2021 *********************************************** 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 80.23 3.17 83.39 |
crlmm.Rcheck/tests_x64/doRUnit.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 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-3.13-bioc/meat/crlmm.Rcheck/tests_x64" $pathToUnitTests [1] "C:/Users/biocbuild/bbs-3.13-bioc/R/library/crlmm/unitTests" Loading required package: oligoClasses Welcome to oligoClasses version 1.54.0 Loading required package: preprocessCore No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm' Welcome to crlmm version 1.50.0 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 -- Thu Oct 14 21:58:54 2021 *********************************************** 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 83.06 2.14 85.20 |
crlmm.Rcheck/examples_i386/crlmm-Ex.timings
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crlmm.Rcheck/examples_x64/crlmm-Ex.timings
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