Package: pathVar

Version: 1.16.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:pathVar.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings pathVar_1.16.0.tar.gz

StartedAt: 2020-04-15 03:22:43 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:26:00 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 197.5 seconds

RetCode: 0

Status:  OK

CheckDir: pathVar.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:pathVar.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings pathVar_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/pathVar.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pathVar/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pathVar’ version ‘1.16.0’
* 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 ‘pathVar’ 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
diagnosticsVarPlots: no visible binding for global variable ‘avg’
diagnosticsVarPlots: no visible binding for global variable ‘standDev’
diagnosticsVarPlots: no visible binding for global variable ‘medAbsDev’
diagnosticsVarPlots: no visible binding for global variable ‘cv’
diagnosticsVarPlotsTwoSample: no visible binding for global variable
  ‘avg’
diagnosticsVarPlotsTwoSample: no visible binding for global variable
  ‘standDev’
diagnosticsVarPlotsTwoSample: no visible binding for global variable
  ‘medAbsDev’
diagnosticsVarPlotsTwoSample: no visible binding for global variable
  ‘cv’
pathVarOneSample: no visible binding for global variable ‘APval’
pathVarOneSample: no visible binding for global variable
  ‘PercOfGenesInPway’
pathVarTwoSamplesCont: no visible binding for global variable ‘APval’
pathVarTwoSamplesCont: no visible binding for global variable
  ‘PercOfGenesInPway’
pathVarTwoSamplesDisc: no visible binding for global variable ‘APval’
pathVarTwoSamplesDisc: no visible binding for global variable
  ‘PercOfGenesInPway’
plotAllTwoSampleDistributionCounts: no visible binding for global
  variable ‘Cluster’
plotAllTwoSampleDistributionCounts: no visible binding for global
  variable ‘Number_of_genes’
plotOneSample: no visible binding for global variable ‘Cluster’
plotOneSample: no visible binding for global variable ‘Number_of_genes’
plotTwoSamplesCont: no visible binding for global variable ‘PwayName’
plotTwoSamplesCont: no visible binding for global variable
  ‘NumOfGenesFromDataSetInPathway’
plotTwoSamplesCont: no visible binding for global variable ‘value’
plotTwoSamplesCont: no visible binding for global variable
  ‘..density..’
plotTwoSamplesCont: no visible binding for global variable ‘group’
plotTwoSamplesDisc: no visible binding for global variable ‘Cluster’
plotTwoSamplesDisc: no visible binding for global variable
  ‘Number_of_genes’
sigOneSample: no visible binding for global variable ‘APval’
sigOneSample: no visible binding for global variable ‘PwayName’
sigTwoSamplesCont: no visible binding for global variable ‘APval’
sigTwoSamplesCont: no visible binding for global variable ‘PwayName’
sigTwoSamplesDisc: no visible binding for global variable ‘APval’
sigTwoSamplesDisc: no visible binding for global variable ‘PwayName’
Undefined global functions or variables:
  ..density.. APval Cluster NumOfGenesFromDataSetInPathway
  Number_of_genes PercOfGenesInPway PwayName avg cv group medAbsDev
  standDev value
* 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 ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
sigPway                      78.772  0.016  78.707
diagnosticsVarPlots          32.604  0.188  32.835
diagnosticsVarPlotsTwoSample 19.228  0.116  19.390
pathVar-package               5.368  0.024   5.086
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/pathVar.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL pathVar
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘pathVar’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (pathVar)

name	user	system	elapsed
bock	0.004	0.000	0.003
diagnosticsVarPlots	32.604	0.188	32.835
diagnosticsVarPlotsTwoSample	19.228	0.116	19.390
geneDistributionSet-class	0.008	0.000	0.005
geneDistributionSet2-class	0.000	0.000	0.003
geneDistributionSet3-class	0.000	0.000	0.003
geneSet-class	0.004	0.000	0.002
getGenes	3.576	0.004	3.438
makeDBList	0	0	0
pathVar-package	5.368	0.024	5.086
pathVarOneSample	3.700	0.004	3.459
pathVarTwoSamplesCont	2.980	0.004	2.745
pathVarTwoSamplesDisc	1.584	0.008	1.378
plotAllTwoSampleDistributionCounts	4.640	0.000	4.444
plotPway	3.932	0.032	3.424
pways.kegg	0.000	0.000	0.001
pways.reactome	0	0	0
saveAsPDF	4.336	0.012	3.606
sigPway	78.772	0.016	78.707
significantPathway-class	0.008	0.000	0.001
significantPathway2-class	0.000	0.000	0.001
significantPathway3-class	0.000	0.000	0.002