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CHECK report for categoryCompare on tokay1

This page was generated on 2020-08-12 11:40:03 -0400 (Wed, 12 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE categoryCompare PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 229/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
categoryCompare 1.33.0
Robert M. Flight
Snapshot Date: 2020-08-11 14:50:16 -0400 (Tue, 11 Aug 2020)
URL: https://git.bioconductor.org/packages/categoryCompare
Branch: master
Last Commit: a7d8dcb
Last Changed Date: 2020-04-27 14:29:40 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: categoryCompare
Version: 1.33.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:categoryCompare.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings categoryCompare_1.33.0.tar.gz
StartedAt: 2020-08-12 00:49:21 -0400 (Wed, 12 Aug 2020)
EndedAt: 2020-08-12 00:53:31 -0400 (Wed, 12 Aug 2020)
EllapsedTime: 250.4 seconds
RetCode: 0
Status:  OK  
CheckDir: categoryCompare.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:categoryCompare.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings categoryCompare_1.33.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/categoryCompare.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'categoryCompare/DESCRIPTION' ... OK
* this is package 'categoryCompare' version '1.33.0'
* 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 'categoryCompare' 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
.ccCompareGO: no visible binding for global variable 'GOBPPARENTS'
.ccCompareGO: no visible binding for global variable 'GOMFPARENTS'
.ccCompareGO: no visible binding for global variable 'GOCCPARENTS'
.ccCompareGO: no visible binding for global variable 'GOTERM'
.ccCompareGO: no visible binding for global variable 'Term'
.ccCompareKEGG: no visible binding for global variable
  'KEGGPATHID2NAME'
.cytOutNodes: ... may be used in an incorrect context:
  exportImage(filename = fileName, type = "png", network = cwObj, ...)
.getDesc : <anonymous>: no visible global function definition for
  'Term'
show,HyperGResultCC: no visible global function definition for
  'description'
Undefined global functions or variables:
  GOBPPARENTS GOCCPARENTS GOMFPARENTS GOTERM KEGGPATHID2NAME Term
  description
* 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
** running examples for arch 'x64' ... OK
* 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-3.12-bioc/meat/categoryCompare.Rcheck/00check.log'
for details.



Installation output

categoryCompare.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/categoryCompare_1.33.0.tar.gz && rm -rf categoryCompare.buildbin-libdir && mkdir categoryCompare.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=categoryCompare.buildbin-libdir categoryCompare_1.33.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL categoryCompare_1.33.0.zip && rm categoryCompare_1.33.0.tar.gz categoryCompare_1.33.0.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 1769k  100 1769k    0     0  28.2M      0 --:--:-- --:--:-- --:--:-- 30.3M

install for i386

* installing *source* package 'categoryCompare' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Note: ... may be used in an incorrect context 
** help
*** installing help indices
  converting help for package 'categoryCompare'
    finding HTML links ... done
    GENccEnrichResult-class                 html  
    finding level-2 HTML links ... done

    HyperGParamsCC-class                    html  
    HyperGResultCC-class                    html  
    breakEdges-methods                      html  
    categoryCompare-package                 html  
    ccCompare                               html  
    ccCompareCollection-class               html  
    ccCompareGeneric-methods                html  
    ccCompareResult-class                   html  
    ccData                                  html  
    ccEnrich                                html  
    ccEnrichCollection-class                html  
    ccEnrichResult-class                    html  
    ccGeneList-class                        html  
    ccOptions-class                         html  
    ccOutCyt-methods                        html  
    ccSigList-class                         html  
    cwReload-methods                        html  
    cytOutData-methods                      html  
    cytOutNodes-methods                     html  
    fdr                                     html  
    getGeneSymbol                           html  
    graphType-methods                       html  
    hyperGTestCC                            html  
    listNames                               html  
    mergeLists-methods                      html  
    mergedData-class                        html  
    minCount                                html  
    minNodes                                html  
    pvalueType                              html  
    resetColors-methods                     html  
    show-methods                            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 'categoryCompare' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'categoryCompare' as categoryCompare_1.33.0.zip
* DONE (categoryCompare)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'categoryCompare' successfully unpacked and MD5 sums checked

Tests output


Example timings

categoryCompare.Rcheck/examples_i386/categoryCompare-Ex.timings

nameusersystemelapsed
GENccEnrichResult-class1.080.061.14
HyperGParamsCC-class000
HyperGResultCC-class000
breakEdges-methods0.920.010.93
ccCompare0.700.030.73
ccCompareCollection-class000
ccCompareResult-class000
ccData1.160.021.18
ccEnrich1.030.001.03
ccEnrichCollection-class1.800.061.86
ccEnrichResult-class3.400.033.43
ccGeneList-class0.690.020.71
ccOptions-class0.020.000.01
ccOutCyt-methods000
ccSigList-class000
cytOutData-methods000
cytOutNodes-methods000
hyperGTestCC1.160.031.19
mergeLists-methods1.190.011.20
mergedData-class1.070.021.09
minCount2.190.022.20
minNodes000
pvalueType2.330.042.38
show-methods000

categoryCompare.Rcheck/examples_x64/categoryCompare-Ex.timings

nameusersystemelapsed
GENccEnrichResult-class0.510.010.53
HyperGParamsCC-class0.000.020.02
HyperGResultCC-class000
breakEdges-methods0.600.010.61
ccCompare0.950.020.97
ccCompareCollection-class000
ccCompareResult-class000
ccData0.480.030.51
ccEnrich0.790.030.81
ccEnrichCollection-class1.370.031.41
ccEnrichResult-class2.980.053.03
ccGeneList-class1.110.001.11
ccOptions-class0.020.000.02
ccOutCyt-methods000
ccSigList-class000
cytOutData-methods000
cytOutNodes-methods000
hyperGTestCC101
mergeLists-methods0.890.020.91
mergedData-class0.710.000.72
minCount1.960.031.98
minNodes000
pvalueType2.190.012.20
show-methods000