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CHECK report for pathVar on tokay2

This page was generated on 2020-10-17 11:57:21 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE pathVar PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1275/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pathVar 1.18.0
Samuel Zimmerman
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/pathVar
Branch: RELEASE_3_11
Last Commit: 2d4dfad
Last Changed Date: 2020-04-27 14:51:53 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: pathVar
Version: 1.18.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pathVar.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings pathVar_1.18.0.tar.gz
StartedAt: 2020-10-17 06:46:04 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:52:50 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 405.7 seconds
RetCode: 0
Status:  OK  
CheckDir: pathVar.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pathVar.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings pathVar_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/pathVar.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pathVar/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pathVar' version '1.18.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
sigPway                            84.36   0.02   94.65
diagnosticsVarPlotsTwoSample       20.89   2.53   23.55
diagnosticsVarPlots                 9.72   0.74   10.47
pathVar-package                     6.64   0.10    6.74
plotAllTwoSampleDistributionCounts  6.11   0.07    7.08
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
sigPway                      72.62    0.0   72.64
diagnosticsVarPlots          33.39    3.5   36.90
diagnosticsVarPlotsTwoSample 19.41    2.3   21.70
* 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
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/pathVar.Rcheck/00check.log'
for details.



Installation output

pathVar.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/pathVar_1.18.0.tar.gz && rm -rf pathVar.buildbin-libdir && mkdir pathVar.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pathVar.buildbin-libdir pathVar_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL pathVar_1.18.0.zip && rm pathVar_1.18.0.tar.gz pathVar_1.18.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  900k  100  900k    0     0  2558k      0 --:--:-- --:--:-- --:--:-- 2610k

install for i386

* 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
  converting help for package 'pathVar'
    finding HTML links ... done
    bock                                    html  
    diagnosticsVarPlots                     html  
    diagnosticsVarPlotsTwoSample            html  
    geneDistributionSet-class               html  
    geneDistributionSet2-class              html  
    geneDistributionSet3-class              html  
    geneSet-class                           html  
    getGenes                                html  
    makeDBList                              html  
    pathVar-package                         html  
    pathVarOneSample                        html  
    pathVarTwoSamplesCont                   html  
    pathVarTwoSamplesDisc                   html  
    plotAllTwoSampleDistributionCounts      html  
    plotPway                                html  
    pways.kegg                              html  
    pways.reactome                          html  
    saveAsPDF                               html  
    sigPway                                 html  
    significantPathway-class                html  
    significantPathway2-class               html  
    significantPathway3-class               html  
** 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

install for x64

* installing *source* package 'pathVar' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pathVar' as pathVar_1.18.0.zip
* DONE (pathVar)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'pathVar' successfully unpacked and MD5 sums checked

Tests output


Example timings

pathVar.Rcheck/examples_i386/pathVar-Ex.timings

nameusersystemelapsed
bock0.010.000.02
diagnosticsVarPlots 9.72 0.7410.47
diagnosticsVarPlotsTwoSample20.89 2.5323.55
geneDistributionSet-class0.010.000.02
geneDistributionSet2-class000
geneDistributionSet3-class000
geneSet-class000
getGenes4.020.064.57
makeDBList000
pathVar-package6.640.106.74
pathVarOneSample4.110.044.16
pathVarTwoSamplesCont3.760.004.03
pathVarTwoSamplesDisc1.690.001.68
plotAllTwoSampleDistributionCounts6.110.077.08
plotPway4.700.034.74
pways.kegg000
pways.reactome0.020.000.01
saveAsPDF3.220.013.52
sigPway84.36 0.0294.65
significantPathway-class000
significantPathway2-class000
significantPathway3-class0.010.000.02

pathVar.Rcheck/examples_x64/pathVar-Ex.timings

nameusersystemelapsed
bock0.020.000.02
diagnosticsVarPlots33.39 3.5036.90
diagnosticsVarPlotsTwoSample19.41 2.3021.70
geneDistributionSet-class000
geneDistributionSet2-class000
geneDistributionSet3-class000
geneSet-class000
getGenes3.180.013.20
makeDBList000
pathVar-package4.610.024.62
pathVarOneSample3.830.003.83
pathVarTwoSamplesCont2.420.002.42
pathVarTwoSamplesDisc0.920.000.94
plotAllTwoSampleDistributionCounts3.250.004.11
plotPway3.740.043.78
pways.kegg000
pways.reactome000
saveAsPDF3.050.003.05
sigPway72.62 0.0072.64
significantPathway-class000
significantPathway2-class000
significantPathway3-class000