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CHECK report for canceR on tokay1

This page was generated on 2020-08-07 12:05:51 -0400 (Fri, 07 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE canceR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 217/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
canceR 1.23.0
Karim Mezhoud
Snapshot Date: 2020-08-06 14:50:46 -0400 (Thu, 06 Aug 2020)
URL: https://git.bioconductor.org/packages/canceR
Branch: master
Last Commit: eaa1ca4
Last Changed Date: 2020-04-27 14:47:07 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
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: canceR
Version: 1.23.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:canceR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings canceR_1.23.0.tar.gz
StartedAt: 2020-08-07 02:04:11 -0400 (Fri, 07 Aug 2020)
EndedAt: 2020-08-07 02:09:45 -0400 (Fri, 07 Aug 2020)
EllapsedTime: 334.6 seconds
RetCode: 0
Status:  OK  
CheckDir: canceR.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:canceR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings canceR_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/canceR.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 'canceR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'canceR' version '1.23.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Files named as vignettes but with no recognized vignette engine:
   'inst/doc/canceR.Rnw'
(Is a VignetteBuilder field missing?)
* 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 'canceR' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   3.4Mb
* checking package 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 ... OK
* 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 installed files from 'inst/doc' ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'canceR.Rnw'
A 'vignettes' directory is required as from R 3.1.0
and these will not be indexed nor checked
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/canceR.Rcheck/00check.log'
for details.



Installation output

canceR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/canceR_1.23.0.tar.gz && rm -rf canceR.buildbin-libdir && mkdir canceR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=canceR.buildbin-libdir canceR_1.23.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL canceR_1.23.0.zip && rm canceR_1.23.0.tar.gz canceR_1.23.0.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
 82 28.3M   82 23.3M    0     0  70.9M      0 --:--:-- --:--:-- --:--:-- 71.6M
100 28.3M  100 28.3M    0     0  75.9M      0 --:--:-- --:--:-- --:--:-- 76.5M

install for i386

* installing *source* package 'canceR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'canceR'
    finding HTML links ... done
    GSEA.Analyze.Sets                       html  
    GSEA.ConsPlot                           html  
    GSEA.EnrichmentScore                    html  
    GSEA.EnrichmentScore2                   html  
    GSEA.Gct2Frame                          html  
    GSEA.Gct2Frame2                         html  
    GSEA.GeneRanking                        html  
    GSEA.HeatMapPlot                        html  
    GSEA.HeatMapPlot2                       html  
    GSEA.NormalizeCols                      html  
    GSEA.NormalizeRows                      html  
    GSEA                                    html  
    GSEA.ReadClsFile                        html  
    GSEA.Res2Frame                          html  
    GSEA.Threshold                          html  
    GSEA.VarFilter                          html  
    GSEA.write.gct                          html  
    Match_GeneList_MSigDB                   html  
    OLD.GSEA.EnrichmentScore                html  
    Run.GSEA                                html  
    about                                   html  
    canceR                                  html  
    canceRHelp                              html  
    canceR_Vignette                         html  
    cbind.na                                html  
    dialogGeneClassifier                    html  
    dialogMetOption                         html  
    dialogMut                               html  
    dialogOptionCircos                      html  
    dialogOptionGSEAlm                      html  
    dialogOptionPhenoTest                   html  
    dialogPlotOption_SkinCor                html  
    dialogSamplingGSEA                      html  
    dialogSelectFiles_GSEA                  html  
    dialogSpecificMut                       html  
    dialogSummary_GSEA                      html  
    dialoggetGeneListMSigDB                 html  
    displayInTable                          html  
    getCases                                html  
    getCasesGenProfs                        html  
    getCircos                               html  
    getClinicData_MultipleCases             html  
    getClinicalDataMatrix                   html  
    getCor_ExpCNAMet                        html  
    getGCTCLSExample                        html  
    getGCT_CLSfiles                         html  
    getGSEAlm_Diseases                      html  
    getGSEAlm_Variables                     html  
    getGenProfs                             html  
    getGeneExpMatrix                        html  
    getGeneList                             html  
    getGeneListExample                      html  
    getGeneListFromMSigDB                   html  
    getGenesClassifier                      html  
    getGenesTree_MultipleCases              html  
    getGenesTree_SingleCase                 html  
    getInTable                              html  
    getListProfData                         html  
    getMSigDB                               html  
    getMSigDBExample                        html  
    getMSigDBfile                           html  
    getMegaProfData                         html  
    getMetDataMultipleGenes                 html  
    getMutData                              html  
    getPhenoTest                            html  
    getProfilesDataMultipleGenes            html  
    getProfilesDataSingleGene               html  
    getSpecificMut                          html  
    getSummaryGSEA                          html  
    getSurvival                             html  
    getTextWin                              html  
    geteSet                                 html  
    modalDialog                             html  
    myGlobalEnv                             html  
    plotModel                               html  
    plot_1Gene_2GenProfs                    html  
    plot_2Genes_1GenProf                    html  
    rbind.na                                html  
    setWorkspace                            html  
    testCheckedCaseGenProf                  html  
** building package indices
** 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 'canceR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'canceR' as canceR_1.23.0.zip
* DONE (canceR)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'canceR' successfully unpacked and MD5 sums checked

Tests output

canceR.Rcheck/tests_i386/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(canceR)
Loading required package: tcltk
Loading required package: tcltk2
Loading required package: cgdsr
Please send questions to cbioportal@googlegroups.com

> 
> test_check("canceR")
getCancerStudies...  OK
getCaseLists (1/2) ...  OK
getCaseLists (2/2) ...  OK
getGeneticProfiles (1/2) ...  OK
getGeneticProfiles (2/2) ...  OK
getClinicalData (1/1) ...  OK
getProfileData (1/6) ...  OK
getProfileData (2/6) ...  OK
getProfileData (3/6) ...  OK
getProfileData (4/6) ...  OK
getProfileData (5/6) ...  OK
getProfileData (6/6) ...  OK
== testthat results  ===========================================================
[ OK: 0 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  10.28    1.12   12.84 

canceR.Rcheck/tests_x64/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(canceR)
Loading required package: tcltk
Loading required package: tcltk2
Loading required package: cgdsr
Please send questions to cbioportal@googlegroups.com

> 
> test_check("canceR")
getCancerStudies...  OK
getCaseLists (1/2) ...  OK
getCaseLists (2/2) ...  OK
getGeneticProfiles (1/2) ...  OK
getGeneticProfiles (2/2) ...  OK
getClinicalData (1/1) ...  OK
getProfileData (1/6) ...  OK
getProfileData (2/6) ...  OK
getProfileData (3/6) ...  OK
getProfileData (4/6) ...  OK
getProfileData (5/6) ...  OK
getProfileData (6/6) ...  OK
== testthat results  ===========================================================
[ OK: 0 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  13.39    0.81   14.76 

Example timings

canceR.Rcheck/examples_i386/canceR-Ex.timings

nameusersystemelapsed
GSEA.Analyze.Sets000
GSEA.ConsPlot000
GSEA.EnrichmentScore000
GSEA.EnrichmentScore2000
GSEA.Gct2Frame000
GSEA.Gct2Frame2000
GSEA.GeneRanking000
GSEA.HeatMapPlot000
GSEA.HeatMapPlot2000
GSEA.NormalizeCols000
GSEA.NormalizeRows000
GSEA000
GSEA.ReadClsFile000
GSEA.Res2Frame000
GSEA.Threshold000
GSEA.VarFilter000
GSEA.write.gct000
Match_GeneList_MSigDB000
OLD.GSEA.EnrichmentScore000
Run.GSEA000
about000
canceR000
canceRHelp000
canceR_Vignette000
cbind.na000
dialogGeneClassifier000
dialogMetOption000
dialogMut000
dialogOptionCircos000
dialogOptionGSEAlm000
dialogOptionPhenoTest000
dialogPlotOption_SkinCor000
dialogSamplingGSEA000
dialogSelectFiles_GSEA000
dialogSpecificMut000
dialogSummary_GSEA0.020.000.02
dialoggetGeneListMSigDB000
displayInTable000
getCases0.160.034.39
getCasesGenProfs000
getCircos000
getClinicData_MultipleCases000
getClinicalDataMatrix000
getCor_ExpCNAMet000
getGCTCLSExample000
getGCT_CLSfiles000
getGSEAlm_Diseases000
getGSEAlm_Variables000
getGenProfs0.090.000.20
getGeneList000
getGeneListExample000
getGeneListFromMSigDB000
getGenesClassifier000
getGenesTree_MultipleCases000
getGenesTree_SingleCase000
getInTable000
getListProfData000
getMSigDB000
getMSigDBExample000
getMSigDBfile000
getMegaProfData000
getMetDataMultipleGenes000
getMutData0.020.000.02
getPhenoTest000
getProfilesDataMultipleGenes000
getProfilesDataSingleGene000
getSpecificMut000
getSummaryGSEA000
getSurvival000
getTextWin0.000.010.01
geteSet000
modalDialog000
myGlobalEnv000
plotModel000
plot_1Gene_2GenProfs000
plot_2Genes_1GenProf000
rbind.na000
setWorkspace000
testCheckedCaseGenProf000

canceR.Rcheck/examples_x64/canceR-Ex.timings

nameusersystemelapsed
GSEA.Analyze.Sets000
GSEA.ConsPlot000
GSEA.EnrichmentScore000
GSEA.EnrichmentScore2000
GSEA.Gct2Frame000
GSEA.Gct2Frame2000
GSEA.GeneRanking000
GSEA.HeatMapPlot000
GSEA.HeatMapPlot2000
GSEA.NormalizeCols000
GSEA.NormalizeRows000
GSEA000
GSEA.ReadClsFile000
GSEA.Res2Frame000
GSEA.Threshold000
GSEA.VarFilter000
GSEA.write.gct000
Match_GeneList_MSigDB000
OLD.GSEA.EnrichmentScore000
Run.GSEA000
about000
canceR000
canceRHelp000
canceR_Vignette000
cbind.na000
dialogGeneClassifier000
dialogMetOption000
dialogMut000
dialogOptionCircos000
dialogOptionGSEAlm000
dialogOptionPhenoTest000
dialogPlotOption_SkinCor000
dialogSamplingGSEA000
dialogSelectFiles_GSEA000
dialogSpecificMut000
dialogSummary_GSEA000
dialoggetGeneListMSigDB000
displayInTable000
getCases0.070.000.17
getCasesGenProfs000
getCircos000
getClinicData_MultipleCases0.010.000.02
getClinicalDataMatrix000
getCor_ExpCNAMet000
getGCTCLSExample000
getGCT_CLSfiles000
getGSEAlm_Diseases000
getGSEAlm_Variables000
getGenProfs0.070.000.15
getGeneList000
getGeneListExample000
getGeneListFromMSigDB000
getGenesClassifier000
getGenesTree_MultipleCases000
getGenesTree_SingleCase000
getInTable000
getListProfData000
getMSigDB000
getMSigDBExample000
getMSigDBfile000
getMegaProfData000
getMetDataMultipleGenes000
getMutData000
getPhenoTest000
getProfilesDataMultipleGenes0.010.000.02
getProfilesDataSingleGene000
getSpecificMut000
getSummaryGSEA000
getSurvival000
getTextWin000
geteSet000
modalDialog000
myGlobalEnv000
plotModel000
plot_1Gene_2GenProfs000
plot_2Genes_1GenProf000
rbind.na000
setWorkspace000
testCheckedCaseGenProf000