##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:pathVar.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings pathVar_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/pathVar.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘pathVar/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pathVar’ version ‘1.28.0’
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                     user system elapsed
sigPway                            88.467  0.763 113.748
diagnosticsVarPlots                32.435  0.515  33.733
diagnosticsVarPlotsTwoSample       16.126  0.252  16.379
plotAllTwoSampleDistributionCounts  6.021  0.036   6.058
pathVarTwoSamplesCont               4.137  0.068   6.212
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘pathVar.Rnw’ using ‘UTF-8’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/pathVar.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL pathVar
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-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)