Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-10-18 20:40 -0400 (Fri, 18 Oct 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4530 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4480 |
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 813/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GeneRegionScan 1.60.0 (landing page) Lasse Folkersen
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the GeneRegionScan package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GeneRegionScan.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: GeneRegionScan |
Version: 1.60.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GeneRegionScan.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeneRegionScan_1.60.0.tar.gz |
StartedAt: 2024-10-17 05:46:10 -0400 (Thu, 17 Oct 2024) |
EndedAt: 2024-10-17 05:52:12 -0400 (Thu, 17 Oct 2024) |
EllapsedTime: 361.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GeneRegionScan.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GeneRegionScan.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeneRegionScan_1.60.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/GeneRegionScan.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GeneRegionScan/DESCRIPTION’ ... OK * this is package ‘GeneRegionScan’ version ‘1.60.0’ * 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 ‘GeneRegionScan’ can be installed ... OK * checking installed package size ... NOTE installed size is 20.4Mb sub-directories of 1Mb or more: exec 19.7Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘Biobase’ ‘Biostrings’ A package should be listed in only one of these fields. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... NOTE 'library' or 'require' calls in package code: ‘AnnotationDbi’ ‘BSgenome’ ‘affy’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Package in Depends field not imported from: ‘methods’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE createFeatureData: no visible global function definition for ‘new’ exonStructure: no visible global function definition for ‘lines’ exonStructure: no visible global function definition for ‘points’ exonStructure: no visible global function definition for ‘text’ findSequenceInGenome: no visible global function definition for ‘seqnames’ findSequenceInGenome: no visible global function definition for ‘reverse’ findSequenceInGenome: no visible global function definition for ‘unmasked’ findSequenceInGenome: no visible global function definition for ‘startIndex’ getLocalMetaprobeIntensities: no visible global function definition for ‘read.table’ getLocalMetaprobeIntensities: no visible global function definition for ‘new’ getLocalProbeIntensities: no visible global function definition for ‘read.table’ getLocalProbeIntensities : get_probe_indices: no visible global function definition for ‘xy2indices’ getLocalProbeIntensities: no visible global function definition for ‘new’ getProbesetsFromRegionOfInterest: no visible global function definition for ‘revmap’ readFASTA_replacement: no visible global function definition for ‘read.DNAStringSet’ addSnpPdata,ExpressionSet: no visible global function definition for ‘sampleNames’ addSnpPdata,ExpressionSet: no visible global function definition for ‘pData’ addSnpPdata,ExpressionSet: no visible global function definition for ‘read.table’ addSnpPdata,ExpressionSet: no visible global function definition for ‘pData<-’ addSnpPdata,ExpressionSet: no visible global function definition for ‘notes’ addSnpPdata,ExpressionSet: no visible global function definition for ‘notes<-’ doProbeLinear,ExpressionSet: no visible global function definition for ‘pData’ doProbeLinear,ExpressionSet: no visible global function definition for ‘featureNames’ doProbeLinear,ExpressionSet: no visible global function definition for ‘lm’ doProbeTTest,ExpressionSet: no visible global function definition for ‘pData’ doProbeTTest,ExpressionSet: no visible global function definition for ‘featureNames’ doProbeTTest,ExpressionSet: no visible global function definition for ‘t.test’ doProbeTTest,ExpressionSet: no visible global function definition for ‘wilcox.test’ excludeDoubleMatchingProbes,ProbeLevelSet: no visible global function definition for ‘featureNames’ excludeDoubleMatchingProbes,ProbeLevelSet: no visible global function definition for ‘pData’ excludeDoubleMatchingProbes,ProbeLevelSet: no visible global function definition for ‘featureData’ excludeDoubleMatchingProbes,ProbeLevelSet: no visible global function definition for ‘pData<-’ excludeDoubleMatchingProbes,ProbeLevelSet: no visible global function definition for ‘featureData<-’ excludeDoubleMatchingProbes,ProbeLevelSet: no visible global function definition for ‘exprs<-’ excludeDoubleMatchingProbes,ProbeLevelSet: no visible global function definition for ‘notes’ excludeDoubleMatchingProbes,ProbeLevelSet: no visible global function definition for ‘notes<-’ findProbePositions,ExpressionSet: no visible global function definition for ‘pData’ findProbePositions,ExpressionSet: no visible global function definition for ‘featureData’ findProbePositions,ExpressionSet: no visible global function definition for ‘featureNames’ findProbePositions,ExpressionSet: no visible global function definition for ‘reverse’ findProbePositions,ExpressionSet: no visible global function definition for ‘startIndex’ geneRegionScan,ExpressionSet: no visible global function definition for ‘pdf’ geneRegionScan,ExpressionSet: no visible global function definition for ‘split.screen’ geneRegionScan,ExpressionSet: no visible global function definition for ‘screen’ geneRegionScan,ExpressionSet: no visible global function definition for ‘par’ geneRegionScan,ExpressionSet: no visible global function definition for ‘close.screen’ geneRegionScan,ExpressionSet: no visible global function definition for ‘dev.off’ getSequence,ProbeLevelSet: no visible global function definition for ‘pData’ getSequence,ProbeLevelSet: no visible global function definition for ‘featureData’ plotCoexpression,ExpressionSet: no visible global function definition for ‘pData’ plotCoexpression,ExpressionSet: no visible global function definition for ‘featureData’ plotCoexpression,ExpressionSet: no visible global function definition for ‘featureNames’ plotCoexpression,ExpressionSet: no visible binding for global variable ‘interval’ plotCoexpression,ExpressionSet: no visible global function definition for ‘frame’ plotCoexpression,ExpressionSet: no visible global function definition for ‘plot.window’ plotCoexpression,ExpressionSet: no visible global function definition for ‘lines’ plotCoexpression,ExpressionSet: no visible global function definition for ‘text’ plotCoexpression,ExpressionSet: no visible global function definition for ‘combn’ plotCoexpression,ExpressionSet : calculate_coexpression: no visible global function definition for ‘featureNames’ plotCoexpression,ExpressionSet : calculate_coexpression: no visible global function definition for ‘cor.test’ plotCoexpression,ExpressionSet: no visible global function definition for ‘points’ plotOnGene,ExpressionSet: no visible global function definition for ‘pData’ plotOnGene,ExpressionSet: no visible global function definition for ‘pData<-’ plotOnGene,ExpressionSet: no visible global function definition for ‘featureData’ plotOnGene,ExpressionSet: no visible global function definition for ‘featureNames’ plotOnGene,ExpressionSet: no visible binding for global variable ‘median’ plotOnGene,ExpressionSet: no visible binding for global variable ‘quantile’ plotOnGene,ExpressionSet: no visible global function definition for ‘plot.default’ plotOnGene,ExpressionSet: no visible global function definition for ‘mtext’ plotOnGene,ExpressionSet: no visible global function definition for ‘experimentData’ plotOnGene,ExpressionSet: no visible global function definition for ‘median’ plotOnGene,ExpressionSet: no visible global function definition for ‘quantile’ plotOnGene,ExpressionSet: no visible global function definition for ‘lines’ plotOnGene,ExpressionSet: no visible global function definition for ‘points’ plotStatistics,ExpressionSet: no visible global function definition for ‘pData’ plotStatistics,ExpressionSet: no visible global function definition for ‘mtext’ plotStatistics,ExpressionSet: no visible global function definition for ‘median’ plotStatistics,ExpressionSet: no visible global function definition for ‘quantile’ plotStatistics,ExpressionSet: no visible global function definition for ‘lines’ plotStatistics,ExpressionSet: no visible global function definition for ‘text’ translateSampleNames,ExpressionSet: no visible global function definition for ‘read.table’ translateSampleNames,ExpressionSet: no visible global function definition for ‘sampleNames’ translateSampleNames,ExpressionSet: no visible global function definition for ‘pData’ translateSampleNames,ExpressionSet: no visible global function definition for ‘pData<-’ translateSampleNames,ExpressionSet: no visible global function definition for ‘exprs<-’ Undefined global functions or variables: close.screen combn cor.test dev.off experimentData exprs<- featureData featureData<- featureNames frame interval lines lm median mtext new notes notes<- pData pData<- par pdf plot.default plot.window points quantile read.DNAStringSet read.table reverse revmap sampleNames screen seqnames split.screen startIndex t.test text unmasked wilcox.test xy2indices Consider adding importFrom("grDevices", "dev.off", "pdf") importFrom("graphics", "close.screen", "frame", "lines", "mtext", "par", "plot.default", "plot.window", "points", "screen", "split.screen", "text") importFrom("methods", "new") importFrom("stats", "cor.test", "lm", "median", "quantile", "t.test", "wilcox.test") importFrom("utils", "combn", "read.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE checkRd: (-1) geneRegionScan.rd:36: Escaped LaTeX specials: \_ checkRd: (-1) getLocalMetaprobeIntensities.rd:19: Escaped LaTeX specials: \_ checkRd: (-1) getMetaprobesetsFromRegionOfInterest.rd:18: Escaped LaTeX specials: \_ checkRd: (-1) getProbeLevelAnnotationForExonArrays.rd:16: Escaped LaTeX specials: \_ checkRd: (-1) getProbesetsFromMetaprobeset.rd:16: Escaped LaTeX specials: \_ checkRd: (-1) getProbesetsFromRegionOfInterest.rd:18: Escaped LaTeX specials: \_ checkRd: (-1) getProbesetsFromRegionOfInterest.rd:19: 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 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 geneRegionScan 64.713 0.609 77.139 plotCoexpression 43.005 0.287 49.743 plotOnGene 15.768 0.131 18.137 exonStructure 10.800 0.149 13.024 * 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: 5 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/GeneRegionScan.Rcheck/00check.log’ for details.
GeneRegionScan.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GeneRegionScan ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘GeneRegionScan’ ... ** using staged installation ** R ** data ** exec ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 * DONE (GeneRegionScan)
GeneRegionScan.Rcheck/GeneRegionScan-Ex.timings
name | user | system | elapsed | |
addSnpPdata | 0.000 | 0.001 | 0.002 | |
checkForFileInPath | 0.017 | 0.034 | 0.076 | |
doProbeLinear | 2.748 | 0.172 | 3.382 | |
doProbeTTest | 0.520 | 0.022 | 0.611 | |
exampleProbeLevelSet | 0.038 | 0.047 | 0.109 | |
excludeDoubleMatchingProbes | 0.000 | 0.000 | 0.001 | |
exonStructure | 10.800 | 0.149 | 13.024 | |
findProbePositions | 0.130 | 0.014 | 0.164 | |
findSequenceInGenome | 0.001 | 0.001 | 0.001 | |
geneRegionScan | 64.713 | 0.609 | 77.139 | |
getLocalMetaprobeIntensities | 0.000 | 0.001 | 0.001 | |
getLocalProbeIntensities | 0 | 0 | 0 | |
getMetaprobesetsFromRegionOfInterest | 0.001 | 0.000 | 0.003 | |
getProbeLevelAnnotationForExonArrays | 0 | 0 | 0 | |
getProbesetsFromMetaprobeset | 0.000 | 0.001 | 0.000 | |
getProbesetsFromRegionOfInterest | 0.000 | 0.001 | 0.001 | |
getSequence | 0.03 | 0.03 | 0.07 | |
getServerProbeIntensities | 0.000 | 0.001 | 0.001 | |
plotCoexpression | 43.005 | 0.287 | 49.743 | |
plotOnGene | 15.768 | 0.131 | 18.137 | |
readGeneInput | 0.002 | 0.001 | 0.003 | |
translateSampleNames | 0.064 | 0.006 | 0.076 | |