Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:46 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 460/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
crlmm 1.63.0 (landing page) Benilton S Carvalho
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the crlmm package: - 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 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: crlmm |
Version: 1.63.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:crlmm.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings crlmm_1.63.0.tar.gz |
StartedAt: 2024-08-27 03:53:26 -0000 (Tue, 27 Aug 2024) |
EndedAt: 2024-08-27 04:07:11 -0000 (Tue, 27 Aug 2024) |
EllapsedTime: 825.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: crlmm.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:crlmm.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings crlmm_1.63.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/crlmm.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘crlmm/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘crlmm’ version ‘1.63.0’ * 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 ‘crlmm’ can be installed ... OK * used C compiler: ‘gcc (GCC) 10.3.1’ * checking installed package size ... NOTE installed size is 5.0Mb 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 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 loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... NOTE No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’ It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. * 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) genotype.Illumina.Rd:127: Lost braces 127 | Ritchie ME, Carvalho BS, Hetrick KN, Tavar\'{e} S, Irizarry RA. | ^ checkRd: (-1) preprocessInf.Rd:55: Escaped LaTeX specials: \_ \_ checkRd: (-1) readGenCallOutput.Rd:39: Lost braces 39 | Ritchie ME, Carvalho BS, Hetrick KN, Tavar\'{e} S, Irizarry RA. | ^ 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) readIdatFiles.Rd:68: Lost braces 68 | Ritchie ME, Carvalho BS, Hetrick KN, Tavar\'{e} S, Irizarry RA. | ^ 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 is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed crlmm 124.508 0.915 125.649 genotype 98.393 1.055 99.645 snprma 23.654 0.287 23.991 * 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 ... 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, 6 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/crlmm.Rcheck/00check.log’ for details.
crlmm.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL crlmm ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘crlmm’ ... ** using staged installation ** libs using C compiler: ‘gcc (GCC) 10.3.1’ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/preprocessCore/include' -I/usr/local/include -fPIC -g -O2 -Wall -c gtypeCaller.c -o gtypeCaller.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/preprocessCore/include' -I/usr/local/include -fPIC -g -O2 -Wall -c init.c -o init.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/preprocessCore/include' -I/usr/local/include -fPIC -g -O2 -Wall -c trimmed.c -o trimmed.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/preprocessCore/include' -I/usr/local/include -fPIC -g -O2 -Wall -c utils.c -o utils.o gcc -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o crlmm.so gtypeCaller.o init.o trimmed.o utils.o -L/home/biocbuild/R/R-4.4.1/lib -lR installing to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-crlmm/00new/crlmm/libs ** 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’ ** checking absolute paths in shared objects and dynamic libraries ** 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 version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu 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 1.67.0 Loading required package: preprocessCore No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm' Welcome to crlmm version 1.63.0 [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 Aug 27 04:04:49 2024 *********************************************** 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 136.448 1.153 137.789
crlmm.Rcheck/tests/doRUnit.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu 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] "/home/biocbuild/bbs-3.20-bioc/meat/crlmm.Rcheck/tests" $pathToUnitTests [1] "/home/biocbuild/tmp/RtmpSQVzFc/RLIBS_3670b6614b0086/crlmm/unitTests" Loading required package: oligoClasses Welcome to oligoClasses version 1.67.0 Loading required package: preprocessCore No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm' Welcome to crlmm version 1.63.0 Executing test function test_crlmm ... Loading required package: genomewidesnp6Crlmm Annotation for genomewidesnp6Crlmm version 1.0.7 supports UCSC builds hg18 and hg19. Loading required package: hapmapsnp6 /-------------------------------------------\ | SAMPLE HAPMAP SNP 6.0 | |-------------------------------------------| | Data obtained from http://www.hapmap.org | | This package is meant to be used only for | | demonstration of BioConductor packages. | | Access http://www.hapmap.org for details. | |-------------------------------------------| | The contents of this package are provided | | in good faith and the maintainer does not | | warrant their accuracy. | \-------------------------------------------/ Loading annotations and mixture model parameters. Processing 3 files. | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% Loading annotations. Determining gender. Calling 906600 SNPs for recalibration... Done. Estimating recalibration parameters. Calling 906600 SNPs... Done. done successfully. Executing test function test_duplicates ... Error in crlmm(cels[c(1, 1, 2)]) : sample identifiers are not unique In addition: Warning messages: 1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: Marsaglia-Multicarry has poor statistical properties 2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry 3: In crlmmGT(res[["A"]], res[["B"]], res[["SNR"]], res[["mixtureParams"]], : Recalibration not possible. Possible cause: small sample size. done successfully. Executing test function test_dataExamples ... done successfully. ------------------- UNIT TEST SUMMARY --------------------- RUNIT TEST PROTOCOL -- Tue Aug 27 04:07:07 2024 *********************************************** Number of test functions: 3 Number of errors: 0 Number of failures: 0 1 Test Suite : crlmm unit testing - 3 test functions, 0 errors, 0 failures Warning messages: 1: In RNGkind(kind = testSuite$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 136.412 1.599 138.298
crlmm.Rcheck/crlmm-Ex.timings
name | user | system | elapsed | |
ListClassConstructors | 2.270 | 0.416 | 2.692 | |
PredictionRegion-class | 0.002 | 0.000 | 0.002 | |
batchStatisticAccessors | 0.245 | 0.012 | 0.258 | |
calculateRBaf | 1.150 | 0.562 | 1.717 | |
celfile-utils | 1.854 | 0.147 | 2.083 | |
cnSetExample | 1.202 | 0.028 | 1.232 | |
constructInf | 0 | 0 | 0 | |
copynumberAccessors | 0 | 0 | 0 | |
crlmm | 124.508 | 0.915 | 125.649 | |
genotype.Illumina | 0 | 0 | 0 | |
genotype | 98.393 | 1.055 | 99.645 | |
genotypeInf | 0 | 0 | 0 | |
genotypes | 0.011 | 0.000 | 0.011 | |
plotSNPs | 0 | 0 | 0 | |
posteriorProbability | 1.598 | 0.004 | 1.605 | |
predictionRegion | 0.389 | 0.000 | 0.390 | |
preprocessInf | 0.001 | 0.000 | 0.000 | |
readGenCallOutput | 0.000 | 0.000 | 0.001 | |
readIdatFiles | 0 | 0 | 0 | |
snprma | 23.654 | 0.287 | 23.991 | |
validCdfNames | 0.000 | 0.000 | 0.001 | |
xyplot | 0.502 | 0.023 | 0.526 | |