GeneRegionScan 1.27.0
Lasse Folkersen
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GeneRegionScan | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
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### Running command:
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### rm -rf GeneRegionScan.buildbin-libdir GeneRegionScan.Rcheck && mkdir GeneRegionScan.buildbin-libdir GeneRegionScan.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneRegionScan.buildbin-libdir GeneRegionScan_1.27.0.tar.gz >GeneRegionScan.Rcheck\00install.out 2>&1 && cp GeneRegionScan.Rcheck\00install.out GeneRegionScan-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=GeneRegionScan.buildbin-libdir --install="check:GeneRegionScan-install.out" --force-multiarch --no-vignettes --timings GeneRegionScan_1.27.0.tar.gz
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/GeneRegionScan.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GeneRegionScan/DESCRIPTION' ... OK
* this is package 'GeneRegionScan' version '1.27.0'
* 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 '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
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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
plotOnGene,ExpressionSet: warning in plot.default(1, type = "n", xlab =
"bp", ylab = ylab, frame = FALSE, xlim = xlim, ylim = ylim, main =
paste("Expression of probes"), cex.main = 1): partial argument match
of 'frame' to 'frame.plot'
exonStructure: no visible global function definition for 'width'
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'
getLocalProbeIntensities : get_probe_indices: no visible global
function definition for 'xy2indices'
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
'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'
doProbeTTest,ExpressionSet: no visible global function definition for
'pData'
doProbeTTest,ExpressionSet: no visible global function definition for
'featureNames'
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 'elementLengths'
findProbePositions,ExpressionSet: no visible global function definition
for 'startIndex'
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 : calculate_coexpression: no visible
global function definition for 'featureNames'
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 global function definition for
'experimentData'
plotStatistics,ExpressionSet: no visible global function definition for
'pData'
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:
elementLengths experimentData exprs<- featureData featureData<-
featureNames interval notes notes<- pData pData<- read.DNAStringSet
reverse revmap sampleNames seqnames startIndex unmasked width
xy2indices
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [65s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
geneRegionScan 30.21 0.06 30.26
plotCoexpression 19.42 0.00 19.43
plotOnGene 6.52 0.02 6.53
** running examples for arch 'x64' ... [81s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
geneRegionScan 36.03 0.05 36.14
plotCoexpression 24.67 0.01 24.69
plotOnGene 8.72 0.02 8.73
exonStructure 6.17 0.03 6.20
* 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: 4 NOTEs
See
'c:/biocbld/bbs-3.3-bioc/meat/GeneRegionScan.Rcheck/00check.log'
for details.