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This page was generated on 2021-07-30 15:05:47 -0400 (Fri, 30 Jul 2021).

CHECK results for categoryCompare on tokay2

To the developers/maintainers of the categoryCompare package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/categoryCompare.git to
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raw results

Package 246/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
categoryCompare 1.36.0  (landing page)
Robert M. Flight
Snapshot Date: 2021-07-29 04:50:02 -0400 (Thu, 29 Jul 2021)
URL: https://git.bioconductor.org/packages/categoryCompare
Branch: RELEASE_3_13
Last Commit: 325b381
Last Changed Date: 2021-05-19 11:52:22 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: categoryCompare
Version: 1.36.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:categoryCompare.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings categoryCompare_1.36.0.tar.gz
StartedAt: 2021-07-29 20:58:06 -0400 (Thu, 29 Jul 2021)
EndedAt: 2021-07-29 21:02:53 -0400 (Thu, 29 Jul 2021)
EllapsedTime: 287.0 seconds
RetCode: 0
Status:   OK  
CheckDir: categoryCompare.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:categoryCompare.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings categoryCompare_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/categoryCompare.Rcheck'
* using R version 4.1.0 (2021-05-18)
* 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 '1.36.0'
* 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'
.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 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-3.13-bioc/meat/categoryCompare.Rcheck/00check.log'
for details.



Installation output

categoryCompare.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/categoryCompare_1.36.0.tar.gz && rm -rf categoryCompare.buildbin-libdir && mkdir categoryCompare.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=categoryCompare.buildbin-libdir categoryCompare_1.36.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL categoryCompare_1.36.0.zip && rm categoryCompare_1.36.0.tar.gz categoryCompare_1.36.0.zip
###
##############################################################################
##############################################################################


  % 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 1767k  100 1767k    0     0  4907k      0 --:--:-- --:--:-- --:--:-- 4922k

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  
REDIRECT:topic	 graphType<-,GENccEnrichResult-method -> GENccEnrichResult-class.html [ FAIL ]
    finding level-2 HTML links ... done

    HyperGParamsCC-class                    html  
REDIRECT:topic	 fdr<-,HyperGParamsCC-method -> HyperGParamsCC-class.html [ FAIL ]
    HyperGResultCC-class                    html  
REDIRECT:topic	 pvalueCutoff<-,HyperGResultCC-method -> HyperGResultCC-class.html [ FAIL ]
REDIRECT:topic	 pvalueType<-,HyperGResultCC-method -> HyperGResultCC-class.html [ FAIL ]
REDIRECT:topic	 minCount<-,HyperGResultCC-method -> HyperGResultCC-class.html [ FAIL ]
    breakEdges-methods                      html  
    categoryCompare-package                 html  
    ccCompare                               html  
    ccCompareCollection-class               html  
    ccCompareGeneric-methods                html  
    ccCompareResult-class                   html  
    ccData                                  html  
    ccEnrich                                html  
    ccEnrichCollection-class                html  
REDIRECT:topic	 pvalueCutoff<-,ccEnrichCollection-method -> ccEnrichCollection-class.html [ FAIL ]
REDIRECT:topic	 pvalueType<-,ccEnrichCollection-method -> ccEnrichCollection-class.html [ FAIL ]
REDIRECT:topic	 minCount<-,ccEnrichCollection-method -> ccEnrichCollection-class.html [ FAIL ]
REDIRECT:topic	 graphType<-,ccEnrichCollection-method -> ccEnrichCollection-class.html [ FAIL ]
    ccEnrichResult-class                    html  
REDIRECT:topic	 pvalueCutoff<-,ccEnrichResult-method -> ccEnrichResult-class.html [ FAIL ]
REDIRECT:topic	 pvalueType<-,ccEnrichResult-method -> ccEnrichResult-class.html [ FAIL ]
REDIRECT:topic	 minCount<-,ccEnrichResult-method -> ccEnrichResult-class.html [ FAIL ]
REDIRECT:topic	 graphType<-,ccEnrichResult-method -> ccEnrichResult-class.html [ FAIL ]
    ccGeneList-class                        html  
REDIRECT:topic	 fdr<-,ccGeneList-method -> ccGeneList-class.html [ FAIL ]
REDIRECT:topic	 pvalueCutoff<-,ccGeneList-method -> ccGeneList-class.html [ FAIL ]
REDIRECT:topic	 ccType<-,ccGeneList-method -> ccGeneList-class.html [ FAIL ]
REDIRECT:topic	 ccType<- -> ccGeneList-class.html [ FAIL ]
    ccOptions-class                         html  
REDIRECT:topic	 compareColors<-,ccOptions-method -> ccOptions-class.html [ FAIL ]
REDIRECT:topic	 compareNames<-,ccOptions-method -> ccOptions-class.html [ FAIL ]
REDIRECT:topic	 listNames<-,ccOptions-method -> ccOptions-class.html [ FAIL ]
REDIRECT:topic	 outType<-,ccOptions-method -> ccOptions-class.html [ FAIL ]
REDIRECT:topic	 compareColors<- -> ccOptions-class.html [ FAIL ]
REDIRECT:topic	 compareNames<- -> ccOptions-class.html [ FAIL ]
REDIRECT:topic	 outType<- -> ccOptions-class.html [ FAIL ]
    ccOutCyt-methods                        html  
    ccSigList-class                         html  
    cwReload-methods                        html  
    cytOutData-methods                      html  
    cytOutNodes-methods                     html  
    fdr                                     html  
REDIRECT:topic	 fdr<- -> fdr.html [ FAIL ]
    getGeneSymbol                           html  
    graphType-methods                       html  
REDIRECT:topic	 graphType<- -> graphType-methods.html [ FAIL ]
    hyperGTestCC                            html  
    listNames                               html  
    mergeLists-methods                      html  
    mergedData-class                        html  
    minCount                                html  
REDIRECT:topic	 minCount<- -> minCount.html [ FAIL ]
    minNodes                                html  
    pvalueType                              html  
REDIRECT:topic	 pvalueType<- -> pvalueType.html [ FAIL ]
    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_1.36.0.zip
* DONE (categoryCompare)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'categoryCompare' successfully unpacked and MD5 sums checked

Tests output


Example timings

categoryCompare.Rcheck/examples_i386/categoryCompare-Ex.timings

nameusersystemelapsed
GENccEnrichResult-class0.780.080.86
HyperGParamsCC-class000
HyperGResultCC-class000
breakEdges-methods0.690.000.69
ccCompare0.590.000.59
ccCompareCollection-class000
ccCompareResult-class000
ccData0.560.060.63
ccEnrich0.630.050.67
ccEnrichCollection-class1.970.062.03
ccEnrichResult-class2.530.052.58
ccGeneList-class0.650.000.65
ccOptions-class0.020.000.02
ccOutCyt-methods000
ccSigList-class000
cytOutData-methods000
cytOutNodes-methods000
hyperGTestCC1.090.011.12
mergeLists-methods0.940.040.97
mergedData-class0.750.000.75
minCount2.000.072.08
minNodes000
pvalueType2.340.072.40
show-methods000

categoryCompare.Rcheck/examples_x64/categoryCompare-Ex.timings

nameusersystemelapsed
GENccEnrichResult-class0.530.030.56
HyperGParamsCC-class000
HyperGResultCC-class000
breakEdges-methods0.580.020.59
ccCompare0.510.030.55
ccCompareCollection-class0.020.000.01
ccCompareResult-class000
ccData0.480.000.49
ccEnrich1.090.011.11
ccEnrichCollection-class1.710.101.79
ccEnrichResult-class3.090.033.13
ccGeneList-class0.530.000.53
ccOptions-class0.020.000.02
ccOutCyt-methods000
ccSigList-class000
cytOutData-methods000
cytOutNodes-methods000
hyperGTestCC1.170.011.67
mergeLists-methods0.860.020.87
mergedData-class0.660.010.67
minCount2.260.042.30
minNodes000
pvalueType2.990.013.00
show-methods000