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CHECK report for pathRender on celaya2

This page was generated on 2020-01-16 13:29:58 -0500 (Thu, 16 Jan 2020).

Package 1226/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pathRender 1.55.0
Vince Carey
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/pathRender
Branch: master
Last Commit: b7a64ae
Last Changed Date: 2019-10-29 13:34:40 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: pathRender
Version: 1.55.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pathRender.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pathRender_1.55.0.tar.gz
StartedAt: 2020-01-16 07:16:58 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 07:19:26 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 147.1 seconds
RetCode: 0
Status:  OK 
CheckDir: pathRender.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pathRender.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pathRender_1.55.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/pathRender.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pathRender/DESCRIPTION’ ... OK
* this is package ‘pathRender’ version ‘1.55.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'graph', 'Rgraphviz', 'RColorBrewer', 'cMAP', 'AnnotationDbi',
  'stats4'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘pathRender’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
graphcMAP: no visible binding for global variable ‘cMAPKEGGPATHWAY’
graphcMAP: no visible binding for global variable ‘cMAPCARTAPATHWAY’
graphcMAP: no visible binding for global variable ‘cMAPKEGGINTERACTION’
graphcMAP: no visible binding for global variable ‘cMAPKEGGMOLECULE’
graphcMAP: no visible binding for global variable
  ‘cMAPCARTAINTERACTION’
graphcMAP: no visible binding for global variable ‘cMAPCARTAMOLECULE’
plotExGraph: no visible global function definition for
  ‘colorRampPalette’
plotExGraph: no visible global function definition for ‘exprs’
quantizeByRow : <anonymous>: no visible global function definition for
  ‘quantile’
quantizeByRow: no visible global function definition for ‘featureNames’
quantizeByRow: no visible global function definition for ‘exprs<-’
quantizeByRow: no visible global function definition for ‘exprs’
quantizeByRow: no visible global function definition for
  ‘featureNames<-’
reduceES: no visible global function definition for ‘na.omit’
reduceES: no visible global function definition for ‘featureData<-’
reduceES: no visible global function definition for ‘exprs’
reduceES: no visible global function definition for ‘phenoData’
rendercMAPPathway: no visible binding for global variable
  ‘cMAPKEGGPATHWAY’
rendercMAPPathway: no visible binding for global variable
  ‘cMAPCARTAPATHWAY’
rendercMAPPathway: no visible binding for global variable
  ‘cMAPKEGGINTERACTION’
rendercMAPPathway: no visible binding for global variable
  ‘cMAPKEGGMOLECULE’
rendercMAPPathway: no visible binding for global variable
  ‘cMAPCARTAINTERACTION’
rendercMAPPathway: no visible binding for global variable
  ‘cMAPCARTAMOLECULE’
plot,coloredGraph-ANY: no visible global function definition for
  ‘palette’
Undefined global functions or variables:
  cMAPCARTAINTERACTION cMAPCARTAMOLECULE cMAPCARTAPATHWAY
  cMAPKEGGINTERACTION cMAPKEGGMOLECULE cMAPKEGGPATHWAY colorRampPalette
  exprs exprs<- featureData<- featureNames featureNames<- na.omit
  palette phenoData quantile
Consider adding
  importFrom("grDevices", "colorRampPalette", "palette")
  importFrom("stats", "na.omit", "quantile")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/pathRender.Rcheck/00check.log’
for details.



Installation output

pathRender.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL pathRender
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘pathRender’ ...
** using staged installation
** R
** 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 (pathRender)

Tests output


Example timings

pathRender.Rcheck/pathRender-Ex.timings

nameusersystemelapsed
colorNodes0.2970.0540.354
coloredGraph-class0.1730.0050.179
graphcMAP0.5340.0560.594
plotExGraph2.9510.2303.261
pwayGraph-class0.1250.0230.148
reduceES1.9470.0962.044
rendercMAP0.7240.0540.781