Package: pathVar

Version: 1.10.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:pathVar.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings pathVar_1.10.0.tar.gz

StartedAt: 2018-10-16 02:34:43 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 02:37:18 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 155.2 seconds

RetCode: 0

Status:  OK

CheckDir: pathVar.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:pathVar.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings pathVar_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/pathVar.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.10.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
sigPway                      53.764  0.004  53.792
diagnosticsVarPlots          28.928  0.160  29.106
diagnosticsVarPlotsTwoSample 17.076  0.100  17.185
* 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-3.7-bioc/meat/pathVar.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL pathVar
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/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	0.012	0.000	0.012
diagnosticsVarPlots	28.928	0.160	29.106
diagnosticsVarPlotsTwoSample	17.076	0.100	17.185
geneDistributionSet-class	0.004	0.000	0.004
geneDistributionSet2-class	0.004	0.000	0.001
geneDistributionSet3-class	0.000	0.000	0.002
geneSet-class	0.004	0.000	0.001
getGenes	3.100	0.000	3.088
makeDBList	0	0	0
pathVar-package	3.896	0.008	3.888
pathVarOneSample	3.088	0.020	3.097
pathVarTwoSamplesCont	2.944	0.000	2.940
pathVarTwoSamplesDisc	2.224	0.000	2.212
plotAllTwoSampleDistributionCounts	4.652	0.008	4.640
plotPway	3.284	0.000	3.271
pways.kegg	0.004	0.000	0.001
pways.reactome	0.000	0.000	0.001
saveAsPDF	3.736	0.000	3.724
sigPway	53.764	0.004	53.792
significantPathway-class	0.000	0.000	0.002
significantPathway2-class	0.000	0.000	0.002
significantPathway3-class	0.004	0.000	0.003