Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-10-16 11:35:23 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 787/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneRegionScan 1.56.0  (landing page)
Lasse Folkersen
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/GeneRegionScan
git_branch: RELEASE_3_17
git_last_commit: 3070615
git_last_commit_date: 2023-04-25 09:48:36 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for GeneRegionScan on nebbiolo1


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.

raw results


Summary

Package: GeneRegionScan
Version: 1.56.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GeneRegionScan.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings GeneRegionScan_1.56.0.tar.gz
StartedAt: 2023-10-15 21:32:14 -0400 (Sun, 15 Oct 2023)
EndedAt: 2023-10-15 21:35:03 -0400 (Sun, 15 Oct 2023)
EllapsedTime: 168.7 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneRegionScan.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GeneRegionScan.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings GeneRegionScan_1.56.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GeneRegionScan.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘GeneRegionScan/DESCRIPTION’ ... OK
* this is package ‘GeneRegionScan’ version ‘1.56.0’
* 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 11.2Mb
  sub-directories of 1Mb or more:
    exec  10.6Mb
* 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 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
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
geneRegionScan   22.416  0.104  22.521
plotCoexpression 14.654  0.056  14.709
plotOnGene        6.465  0.032   6.498
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘GeneRegionScan.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/GeneRegionScan.Rcheck/00check.log’
for details.



Installation output

GeneRegionScan.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL GeneRegionScan
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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)

Tests output


Example timings

GeneRegionScan.Rcheck/GeneRegionScan-Ex.timings

nameusersystemelapsed
addSnpPdata000
checkForFileInPath0.0110.0000.013
doProbeLinear0.9720.0521.025
doProbeTTest0.1550.0000.156
exampleProbeLevelSet0.0080.0240.033
excludeDoubleMatchingProbes000
exonStructure4.5080.0164.524
findProbePositions0.5180.0040.522
findSequenceInGenome0.0010.0000.000
geneRegionScan22.416 0.10422.521
getLocalMetaprobeIntensities0.0010.0000.000
getLocalProbeIntensities000
getMetaprobesetsFromRegionOfInterest0.0000.0000.001
getProbeLevelAnnotationForExonArrays000
getProbesetsFromMetaprobeset000
getProbesetsFromRegionOfInterest0.0000.0000.001
getSequence0.0180.0040.022
getServerProbeIntensities0.0010.0000.000
plotCoexpression14.654 0.05614.709
plotOnGene6.4650.0326.498
readGeneInput0.0010.0000.001
translateSampleNames0.0260.0040.031