Package: pathVar

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pathVar.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pathVar_1.10.0.tar.gz

StartedAt: 2018-10-16 23:08:18 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 23:13:00 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 281.8 seconds

RetCode: 0

Status:  OK

CheckDir: pathVar.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pathVar.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pathVar_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/pathVar.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.10.0’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                     user system elapsed
sigPway                            90.757  3.102  94.792
diagnosticsVarPlots                50.248  0.447  51.217
diagnosticsVarPlotsTwoSample       31.152  0.308  31.794
plotAllTwoSampleDistributionCounts  9.374  1.220   9.302
saveAsPDF                           7.060  0.142   6.318
plotPway                            6.629  0.249   6.108
pathVar-package                     6.144  0.380   4.846
pathVarTwoSamplesCont               6.316  0.140   5.563
getGenes                            5.388  0.076   5.477
* 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
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/pathVar.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL pathVar
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘pathVar’ ...
** 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
* DONE (pathVar)

name	user	system	elapsed
bock	0.022	0.003	0.027
diagnosticsVarPlots	50.248	0.447	51.217
diagnosticsVarPlotsTwoSample	31.152	0.308	31.794
geneDistributionSet-class	0.007	0.000	0.007
geneDistributionSet2-class	0.004	0.000	0.004
geneDistributionSet3-class	0.004	0.001	0.004
geneSet-class	0.003	0.000	0.003
getGenes	5.388	0.076	5.477
makeDBList	0.009	0.000	0.001
pathVar-package	6.144	0.380	4.846
pathVarOneSample	3.474	0.034	3.513
pathVarTwoSamplesCont	6.316	0.140	5.563
pathVarTwoSamplesDisc	4.919	0.056	4.041
plotAllTwoSampleDistributionCounts	9.374	1.220	9.302
plotPway	6.629	0.249	6.108
pways.kegg	0.002	0.001	0.002
pways.reactome	0.002	0.001	0.002
saveAsPDF	7.060	0.142	6.318
sigPway	90.757	3.102	94.792
significantPathway-class	0.015	0.001	0.003
significantPathway2-class	0.010	0.002	0.002
significantPathway3-class	0.017	0.002	0.003