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CHECK report for GeneRegionScan on tokay2

This page was generated on 2019-10-16 12:22:35 -0400 (Wed, 16 Oct 2019).

Package 637/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneRegionScan 1.40.0
Lasse Folkersen
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/GeneRegionScan
Branch: RELEASE_3_9
Last Commit: dcb8e17
Last Changed Date: 2019-05-02 11:53:11 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GeneRegionScan
Version: 1.40.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneRegionScan.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GeneRegionScan_1.40.0.tar.gz
StartedAt: 2019-10-16 03:55:53 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 03:59:59 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 246.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: GeneRegionScan.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneRegionScan.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GeneRegionScan_1.40.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GeneRegionScan.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.40.0'
* 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 ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpmk4M8M/R.INSTALL1028442ddd/GeneRegionScan/man/exonStructure.rd:21: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpmk4M8M/R.INSTALL1028442ddd/GeneRegionScan/man/genomic.Rd:13: file link 'readDNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpmk4M8M/R.INSTALL1028442ddd/GeneRegionScan/man/mrna.Rd:12: file link 'readDNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GeneRegionScan.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 20.5Mb
  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
* 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 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 ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
geneRegionScan   29.45   0.02   29.47
plotCoexpression 18.12   0.00   18.13
plotOnGene        7.47   0.00    7.47
exonStructure     5.08   0.00    5.08
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
geneRegionScan   26.89   0.01   26.91
plotCoexpression 16.85   0.03   16.87
plotOnGene        7.90   0.01    7.93
exonStructure     7.25   0.00    7.25
* 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
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/GeneRegionScan.Rcheck/00check.log'
for details.



Installation output

GeneRegionScan.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/GeneRegionScan_1.40.0.tar.gz && rm -rf GeneRegionScan.buildbin-libdir && mkdir GeneRegionScan.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GeneRegionScan.buildbin-libdir GeneRegionScan_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL GeneRegionScan_1.40.0.zip && rm GeneRegionScan_1.40.0.tar.gz GeneRegionScan_1.40.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 7397k  100 7397k    0     0  44.8M      0 --:--:-- --:--:-- --:--:-- 46.9M

install for i386

* installing *source* package 'GeneRegionScan' ...
** using staged installation
** R
** data
** exec
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GeneRegionScan'
    finding HTML links ... done
    Nondocumented-objects                   html  
    ProbeLevelSet-class                     html  
    addSnpPdata                             html  
    checkForFileInPath                      html  
    doProbeLinear                           html  
    doProbeTTest                            html  
    exampleProbeLevelSet                    html  
    excludeDoubleMatchingProbes             html  
    exonStructure                           html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpmk4M8M/R.INSTALL1028442ddd/GeneRegionScan/man/exonStructure.rd:21: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
    findProbePositions                      html  
    findSequenceInGenome                    html  
    geneRegionScan                          html  
    genomic                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpmk4M8M/R.INSTALL1028442ddd/GeneRegionScan/man/genomic.Rd:13: file link 'readDNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
    getLocalMetaprobeIntensities            html  
    getLocalProbeIntensities                html  
    getMetaprobesetsFromRegionOfInterest    html  
    getProbeLevelAnnotationForExonArrays    html  
    getProbesetsFromMetaprobeset            html  
    getProbesetsFromRegionOfInterest        html  
    getSequence                             html  
    getServerProbeIntensities               html  
    mrna                                    html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpmk4M8M/R.INSTALL1028442ddd/GeneRegionScan/man/mrna.Rd:12: file link 'readDNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
    plotCoexpression                        html  
    plotOnGene                              html  
    plotStatistics                          html  
    readGeneInput                           html  
    translateSampleNames                    html  
** 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

install for x64

* installing *source* package 'GeneRegionScan' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeneRegionScan' as GeneRegionScan_1.40.0.zip
* DONE (GeneRegionScan)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'GeneRegionScan' successfully unpacked and MD5 sums checked

Tests output


Example timings

GeneRegionScan.Rcheck/examples_i386/GeneRegionScan-Ex.timings

nameusersystemelapsed
addSnpPdata000
checkForFileInPath0.020.020.03
doProbeLinear1.060.121.19
doProbeTTest0.170.000.17
exampleProbeLevelSet0.030.000.03
excludeDoubleMatchingProbes000
exonStructure5.080.005.08
findProbePositions0.070.000.06
findSequenceInGenome000
geneRegionScan29.45 0.0229.47
getLocalMetaprobeIntensities000
getLocalProbeIntensities000
getMetaprobesetsFromRegionOfInterest000
getProbeLevelAnnotationForExonArrays000
getProbesetsFromMetaprobeset000
getProbesetsFromRegionOfInterest000
getSequence0.030.000.03
getServerProbeIntensities000
plotCoexpression18.12 0.0018.13
plotOnGene7.470.007.47
readGeneInput000
translateSampleNames0.070.000.06

GeneRegionScan.Rcheck/examples_x64/GeneRegionScan-Ex.timings

nameusersystemelapsed
addSnpPdata000
checkForFileInPath0.020.030.04
doProbeLinear1.280.041.32
doProbeTTest0.190.000.18
exampleProbeLevelSet0.000.030.03
excludeDoubleMatchingProbes000
exonStructure7.250.007.25
findProbePositions0.080.000.08
findSequenceInGenome000
geneRegionScan26.89 0.0126.91
getLocalMetaprobeIntensities000
getLocalProbeIntensities000
getMetaprobesetsFromRegionOfInterest000
getProbeLevelAnnotationForExonArrays000
getProbesetsFromMetaprobeset000
getProbesetsFromRegionOfInterest000
getSequence0.010.000.02
getServerProbeIntensities000
plotCoexpression16.85 0.0316.87
plotOnGene7.900.017.93
readGeneInput000
translateSampleNames0.030.000.03