BioC 3.4: CHECK report for pathVar on morelia

Package: pathVar

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pathVar_1.4.0.tar.gz

StartedAt: 2017-04-15 06:00:15 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 06:03:39 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 204.2 seconds

RetCode: 0

Status:  OK

CheckDir: pathVar.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pathVar_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/pathVar.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.4.0’
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                     user system elapsed
sigPway                            75.080  3.589  78.723
diagnosticsVarPlots                37.810  0.272  38.121
diagnosticsVarPlotsTwoSample       24.273  0.187  24.491
plotAllTwoSampleDistributionCounts  4.769  0.465   5.504
* 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-3.4-bioc/meat/pathVar.Rcheck/00check.log’
for details.

* installing *source* package ‘pathVar’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing 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	0.018	0.003	0.020
diagnosticsVarPlots	37.810	0.272	38.121
diagnosticsVarPlotsTwoSample	24.273	0.187	24.491
geneDistributionSet-class	0.005	0.000	0.005
geneDistributionSet2-class	0.004	0.000	0.004
geneDistributionSet3-class	0.004	0.000	0.005
geneSet-class	0.003	0.001	0.002
getGenes	3.323	0.072	3.397
makeDBList	0.001	0.001	0.001
pathVar-package	3.822	0.051	3.877
pathVarOneSample	2.758	0.022	2.784
pathVarTwoSamplesCont	3.470	0.065	3.537
pathVarTwoSamplesDisc	1.700	0.009	1.711
plotAllTwoSampleDistributionCounts	4.769	0.465	5.504
plotPway	3.624	0.079	3.706
pways.kegg	0.001	0.000	0.002
pways.reactome	0.001	0.001	0.003
saveAsPDF	4.040	0.074	4.119
sigPway	75.080	3.589	78.723
significantPathway-class	0.002	0.001	0.001
significantPathway2-class	0.001	0.000	0.001
significantPathway3-class	0.001	0.000	0.002