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CHECK report for canceR on merida1

This page was generated on 2019-04-16 11:58:24 -0400 (Tue, 16 Apr 2019).

Package 195/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
canceR 1.16.02
Karim Mezhoud
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/canceR
Branch: RELEASE_3_8
Last Commit: da04e10
Last Changed Date: 2019-04-04 15:56:48 -0400 (Thu, 04 Apr 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: canceR
Version: 1.16.02
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:canceR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings canceR_1.16.02.tar.gz
StartedAt: 2019-04-15 22:44:56 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 22:52:55 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 479.5 seconds
RetCode: 0
Status:  OK 
CheckDir: canceR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:canceR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings canceR_1.16.02.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/canceR.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘canceR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘canceR’ version ‘1.16.02’
* package encoding: UTF-8
* 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 ‘canceR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 10.7Mb
  sub-directories of 1Mb or more:
    data      7.1Mb
    extdata   2.9Mb
* 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 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 ... NOTE
S3 methods shown with full name in documentation object 'cbind.na':
  ‘cbind.na’

S3 methods shown with full name in documentation object 'rbind.na':
  ‘rbind.na’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/canceR.Rcheck/00check.log’
for details.



Installation output

canceR.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL canceR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘canceR’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘igraph::union’ by ‘GSEABase::union’ when loading ‘HTSanalyzeR’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘igraph::union’ by ‘GSEABase::union’ when loading ‘HTSanalyzeR’
* DONE (canceR)

Tests output

canceR.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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

/////////////////////////////////////////////////////////////////////////////

//------------------    Thanks for using HTSanalyzeR    -------------------//
 
//------------please use function changes() to see new changes-------------//

//------------please report any bug to xinwang2hms@gmail.com---------------//

/////////////////////////////////////////////////////////////////////////////
Warning message:
replacing previous import 'igraph::union' by 'GSEABase::union' when loading 'HTSanalyzeR' 
> 
> 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) ...  FAILED!
getProfileData (4/6) ...  OK
getProfileData (5/6) ...  OK
getProfileData (6/6) ...  OK
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 0 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 17.839   1.972  22.192 

Example timings

canceR.Rcheck/canceR-Ex.timings

nameusersystemelapsed
ClinicalData0.0090.0010.011
GSEA.Analyze.Sets0.0000.0000.001
GSEA.ConsPlot0.0010.0000.001
GSEA.EnrichmentScore000
GSEA.EnrichmentScore20.0000.0000.001
GSEA.Gct2Frame000
GSEA.Gct2Frame20.0000.0000.001
GSEA.GeneRanking000
GSEA.HeatMapPlot0.0000.0000.001
GSEA.HeatMapPlot2000
GSEA.NormalizeCols0.1840.0070.192
GSEA.NormalizeRows000
GSEA000
GSEA.ReadClsFile0.8120.0060.821
GSEA.Res2Frame0.2090.0050.214
GSEA.Threshold0.1650.0070.172
GSEA.VarFilter0.2130.0070.220
GSEA.write.gct0.1810.0060.189
GeneExpMatrix0.0270.0020.029
Match_GeneList_MSigDB0.2110.0090.222
OLD.GSEA.EnrichmentScore0.2130.0080.222
Run.GSEA0.1860.0080.196
about000
canceR000
canceRHelp0.0000.0000.001
canceR_Vignette000
cbind.na0.0010.0000.001
dialogGeneClassifier0.0620.0050.068
dialogMetOption0.2080.0070.217
dialogMut0.1910.0080.199
dialogOptionCircos0.2370.0140.253
dialogOptionGSEAlm0.0050.0010.006
dialogOptionPhenoTest0.2390.0110.254
dialogPlotOption_SkinCor0.0590.0040.064
dialogSamplingGSEA0.2240.0060.231
dialogSelectFiles_GSEA0.2230.0070.233
dialogSpecificMut0.1950.0060.203
dialogSummary_GSEA0.1920.0060.199
dialoggetGeneListMSigDB000
displayInTable0.0060.0010.007
getCases0.0250.0080.644
getCasesGenProfs0.1420.0060.148
getCircos0.1550.0070.163
getClinicData_MultipleCases0.1600.0050.167
getClinicalDataMatrix0.1520.0050.160
getCor_ExpCNAMet0.2060.0080.217
getGCTCLSExample0.2130.0060.220
getGCT_CLSfiles0.2300.0060.243
getGSEAlm_Diseases0.2090.0060.218
getGSEAlm_Variables0.0000.0000.001
getGenProfs0.0230.0090.833
getGeneExpMatrix0.1750.0070.182
getGeneList0.0010.0000.001
getGeneListExample0.0010.0000.000
getGeneListFromMSigDB0.1630.0060.172
getGenesClassifier0.0000.0010.000
getGenesTree_MultipleCases0.1680.0060.174
getGenesTree_SingleCase0.2360.0100.251
getInTable0.0060.0010.007
getListProfData0.1560.0060.163
getMSigDB000
getMSigDBExample0.1600.0070.169
getMSigDBfile0.0000.0000.001
getMegaProfData0.1650.0050.174
getMetDataMultipleGenes0.2090.0050.214
getMutData0.2110.0060.218
getPhenoTest0.2300.0070.237
getProfilesDataMultipleGenes0.2140.0070.222
getProfilesDataSingleGene0.1480.0050.152
getSpecificMut0.2660.0050.272
getSummaryGSEA0.1740.0030.178
getSurvival000
getTextWin000
geteSet0.0010.0000.001
modalDialog0.1620.0020.167
myGlobalEnv000
plotModel0.0600.0040.065
plot_1Gene_2GenProfs0.0560.0050.062
plot_2Genes_1GenProf0.2290.0050.235
rbind.na0.0000.0000.001
setWorkspace0.1640.0050.169
testCheckedCaseGenProf0.1300.0060.136