Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-02 09:00:25 -0500 (Mon, 02 Jan 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
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 |
To the developers/maintainers of the crlmm package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 435/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
crlmm 1.57.0 (landing page) Benilton S Carvalho
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ||||||||
Package: crlmm |
Version: 1.57.0 |
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:crlmm.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings crlmm_1.57.0.tar.gz |
StartedAt: 2022-12-28 22:53:22 -0500 (Wed, 28 Dec 2022) |
EndedAt: 2022-12-28 23:01:01 -0500 (Wed, 28 Dec 2022) |
EllapsedTime: 459.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: crlmm.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:crlmm.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings crlmm_1.57.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/crlmm.Rcheck' * using R Under development (unstable) (2022-12-25 r83502 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 10.4.0 GNU Fortran (GCC) 10.4.0 * running under: Windows Server x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'crlmm/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'crlmm' version '1.57.0' * 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 * used C compiler: 'gcc.exe (GCC) 12.2.0' * checking installed package size ... OK * 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 * 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 ... WARNING checkRd: (5) CNSet-methods.Rd:39-41: \item in \describe must have non-empty label checkRd: (5) CNSet-methods.Rd:65-67: \item in \describe must have non-empty label checkRd: (5) CNSet-methods.Rd:69-71: \item in \describe must have non-empty label checkRd: (-1) constructInf.Rd:35: Escaped LaTeX specials: \_ \_ checkRd: (-1) genotype.Illumina.Rd:48: Escaped LaTeX specials: \_ \_ checkRd: (-1) preprocessInf.Rd:55: Escaped LaTeX specials: \_ \_ checkRd: (-1) readIdatFiles.Rd:39: Escaped LaTeX specials: \_ \_ checkRd: (-1) readIdatFiles.Rd:55: Escaped LaTeX specials: \_ \_ checkRd: (-1) readIdatFiles.Rd:56: Escaped LaTeX specials: \_ checkRd: (-1) snprma.Rd:38: Escaped LaTeX specials: \_ \_ * 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 x64 is not available File 'F:/biocbuild/bbs-3.17-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 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 sizes of PDF files under 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed genotype 62.25 1.67 64.42 crlmm 56.95 0.92 58.91 snprma 14.17 0.49 14.66 * checking for unstated dependencies in 'tests' ... OK * checking tests ... 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, 4 NOTEs See 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/crlmm.Rcheck/00check.log' for details.
crlmm.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL crlmm ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'crlmm' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 12.2.0' gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/preprocessCore/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c gtypeCaller.c -o gtypeCaller.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/preprocessCore/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/preprocessCore/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c trimmed.c -o trimmed.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/preprocessCore/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utils.c -o utils.o gcc -shared -s -static-libgcc -o crlmm.dll tmp.def gtypeCaller.o init.o trimmed.o utils.o -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-crlmm/00new/crlmm/libs/x64 ** 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 ** 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 * DONE (crlmm)
crlmm.Rcheck/tests/crlmm_unit_tests.Rout
R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" Copyright (C) 2022 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 1.61.0 Loading required package: preprocessCore No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm' Welcome to crlmm version 1.57.0 [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 -- Wed Dec 28 22:59:41 2022 *********************************************** 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 65.90 1.17 67.07
crlmm.Rcheck/tests/doRUnit.Rout
R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" Copyright (C) 2022 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] "F:/biocbuild/bbs-3.17-bioc-rtools43/meat/crlmm.Rcheck/tests" $pathToUnitTests [1] "F:/biocbuild/bbs-3.17-bioc/R/library/crlmm/unitTests" Loading required package: oligoClasses Welcome to oligoClasses version 1.61.0 Loading required package: preprocessCore No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm' Welcome to crlmm version 1.57.0 Executing test function test_crlmm ... Loading required package: genomewidesnp6Crlmm Annotation for genomewidesnp6Crlmm version 1.0.7 supports UCSC builds hg18 and hg19. Loading required package: hapmapsnp6 /-------------------------------------------\ | SAMPLE HAPMAP SNP 6.0 | |-------------------------------------------| | Data obtained from http://www.hapmap.org | | This package is meant to be used only for | | demonstration of BioConductor packages. | | Access http://www.hapmap.org for details. | |-------------------------------------------| | The contents of this package are provided | | in good faith and the maintainer does not | | warrant their accuracy. | \-------------------------------------------/ Loading annotations and mixture model parameters. Processing 3 files. | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% Loading annotations. Determining gender. Calling 906600 SNPs for recalibration... Done. Estimating recalibration parameters. Calling 906600 SNPs... Done. done successfully. Executing test function test_duplicates ... Error in crlmm(cels[c(1, 1, 2)]) : sample identifiers are not unique In addition: Warning messages: 1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: Marsaglia-Multicarry has poor statistical properties 2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry 3: In crlmmGT(res[["A"]], res[["B"]], res[["SNR"]], res[["mixtureParams"]], : Recalibration not possible. Possible cause: small sample size. done successfully. Executing test function test_dataExamples ... done successfully. ------------------- UNIT TEST SUMMARY --------------------- RUNIT TEST PROTOCOL -- Wed Dec 28 23:00:48 2022 *********************************************** Number of test functions: 3 Number of errors: 0 Number of failures: 0 1 Test Suite : crlmm unit testing - 3 test functions, 0 errors, 0 failures Warning messages: 1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: Marsaglia-Multicarry has poor statistical properties 2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry 3: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: Marsaglia-Multicarry has poor statistical properties 4: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry > > proc.time() user system elapsed 65.60 1.32 66.87
crlmm.Rcheck/crlmm-Ex.timings
name | user | system | elapsed | |
ListClassConstructors | 1.17 | 0.04 | 1.22 | |
PredictionRegion-class | 0.02 | 0.00 | 0.01 | |
batchStatisticAccessors | 0.18 | 0.02 | 0.20 | |
calculateRBaf | 0.67 | 0.01 | 0.69 | |
celfile-utils | 1.16 | 0.16 | 2.69 | |
cnSetExample | 0.77 | 0.03 | 0.80 | |
constructInf | 0 | 0 | 0 | |
copynumberAccessors | 0.00 | 0.02 | 0.01 | |
crlmm | 56.95 | 0.92 | 58.91 | |
genotype.Illumina | 0 | 0 | 0 | |
genotype | 62.25 | 1.67 | 64.42 | |
genotypeInf | 0 | 0 | 0 | |
genotypes | 0 | 0 | 0 | |
plotSNPs | 0.00 | 0.02 | 0.02 | |
posteriorProbability | 0.97 | 0.12 | 1.09 | |
predictionRegion | 0.28 | 0.03 | 0.31 | |
preprocessInf | 0 | 0 | 0 | |
readGenCallOutput | 0 | 0 | 0 | |
readIdatFiles | 0 | 0 | 0 | |
snprma | 14.17 | 0.49 | 14.66 | |
validCdfNames | 0 | 0 | 0 | |
xyplot | 0.33 | 0.03 | 0.36 | |