BioC 3.3: CHECK report for pathVar on morelia

Package: pathVar

Version: 1.1.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pathVar_1.1.5.tar.gz

StartedAt: 2016-04-21 05:51:39 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 05:54:06 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 147.7 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 --no-vignettes --timings pathVar_1.1.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/pathVar.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘1.1.5’
* 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 ... [3s/3s] 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 ‘sd’
diagnosticsVarPlots : <anonymous>: no visible global function
  definition for ‘sd’
diagnosticsVarPlots: no visible binding for global variable ‘mad’
diagnosticsVarPlots: no visible binding for global variable ‘avg’
diagnosticsVarPlots: no visible binding for global variable ‘standDev’
diagnosticsVarPlots: no visible binding for global variable ‘loess’
diagnosticsVarPlots: no visible global function definition for ‘cor’
diagnosticsVarPlots: no visible binding for global variable ‘medAbsDev’
diagnosticsVarPlots: no visible binding for global variable ‘cv’
makeDBList: no visible global function definition for ‘read.table’
pathVarOneSample : <anonymous>: no visible global function definition
  for ‘sd’
pathVarOneSample : <anonymous>: no visible global function definition
  for ‘mad’
pathVarOneSample : <anonymous>: no visible global function definition
  for ‘pchisq’
pathVarOneSample: no visible global function definition for ‘p.adjust’
pathVarOneSample: no visible binding for global variable ‘APval’
pathVarOneSample: no visible binding for global variable
  ‘PercOfGenesInPway’
pathVarTwoSamplesCont : <anonymous>: no visible global function
  definition for ‘sd’
pathVarTwoSamplesCont : <anonymous>: no visible global function
  definition for ‘mad’
pathVarTwoSamplesCont: no visible global function definition for
  ‘p.adjust’
pathVarTwoSamplesCont: no visible binding for global variable ‘APval’
pathVarTwoSamplesCont: no visible binding for global variable
  ‘PercOfGenesInPway’
pathVarTwoSamplesDisc : <anonymous>: no visible global function
  definition for ‘sd’
pathVarTwoSamplesDisc : <anonymous>: no visible global function
  definition for ‘mad’
pathVarTwoSamplesDisc: no visible global function definition for
  ‘quantile’
pathVarTwoSamplesDisc : <anonymous>: no visible global function
  definition for ‘pchisq’
pathVarTwoSamplesDisc: no visible global function definition for
  ‘p.adjust’
pathVarTwoSamplesDisc: no visible binding for global variable ‘APval’
pathVarTwoSamplesDisc: no visible binding for global variable
  ‘PercOfGenesInPway’
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 global function definition for ‘na.omit’
plotTwoSamplesCont: no visible binding for global variable ‘value’
plotTwoSamplesCont: no visible binding for global variable
  ‘..density..’
plotTwoSamplesCont: no visible binding for global variable ‘group’
plotTwoSamplesCont: no visible global function definition for ‘plot’
plotTwoSamplesDisc: no visible binding for global variable ‘Cluster’
plotTwoSamplesDisc: no visible binding for global variable
  ‘Number_of_genes’
saveAsPDF: no visible global function definition for ‘pdf’
saveAsPDF: no visible global function definition for ‘dev.off’
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 cor cv dev.off group
  loess mad medAbsDev na.omit p.adjust pchisq pdf plot quantile
  read.table sd standDev value
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "plot")
  importFrom("stats", "cor", "loess", "mad", "na.omit", "p.adjust",
             "pchisq", "quantile", "sd")
  importFrom("utils", "read.table")
to your NAMESPACE file.
* 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 ... [118s/119s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
sigPway             63.725  3.483  67.283
diagnosticsVarPlots 34.077  0.232  34.321
* 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-3.3-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	0.017	0.002	0.019
diagnosticsVarPlots	34.077	0.232	34.321
geneDistributionSet-class	0.006	0.000	0.006
geneDistributionSet2-class	0.002	0.001	0.002
geneDistributionSet3-class	0.002	0.000	0.003
geneSet-class	0.002	0.000	0.001
getGenes	2.276	0.065	2.340
makeDBList	0.000	0.000	0.001
pathVar-package	2.471	0.040	2.612
pathVarOneSample	1.757	0.023	1.779
pathVarTwoSamplesCont	2.302	0.063	2.364
pathVarTwoSamplesDisc	1.309	0.006	1.333
plotPway	2.567	0.061	2.698
pways.kegg	0.001	0.000	0.002
pways.reactome	0.001	0.001	0.002
saveAsPDF	3.131	0.060	3.192
sigPway	63.725	3.483	67.283
significantPathway-class	0.001	0.000	0.001
significantPathway2-class	0.000	0.000	0.001
significantPathway3-class	0.001	0.001	0.001