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### Running command:
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### /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_1.58.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/GeneRegionScan.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneRegionScan/DESCRIPTION’ ... OK
* this is package ‘GeneRegionScan’ version ‘1.58.0’
* 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 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' 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 22.660 0.352 23.220
plotCoexpression 14.442 0.217 14.788
plotOnGene 6.500 0.086 6.621
* 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
‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/GeneRegionScan.Rcheck/00check.log’
for details.
