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CHECK report for canceR on merida2

This page was generated on 2018-10-17 08:54:22 -0400 (Wed, 17 Oct 2018).

Package 182/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
canceR 1.14.0
Karim Mezhoud
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/canceR
Branch: RELEASE_3_7
Last Commit: dc44485
Last Changed Date: 2018-04-30 10:35:36 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: canceR
Version: 1.14.0
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_1.14.0.tar.gz
StartedAt: 2018-10-16 20:14:20 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 20:22:14 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 473.5 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_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/canceR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.14.0’
* 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 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 ... NOTE
Malformed Title field: should not end in a period.
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-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 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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) ...  OK
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 
 12.351   1.423  16.990 

Example timings

canceR.Rcheck/canceR-Ex.timings

nameusersystemelapsed
ClinicalData0.0080.0010.009
GSEA.Analyze.Sets0.0010.0000.001
GSEA.ConsPlot0.0010.0000.001
GSEA.EnrichmentScore0.0010.0000.002
GSEA.EnrichmentScore20.0010.0010.001
GSEA.Gct2Frame0.0010.0000.002
GSEA.Gct2Frame20.0010.0000.001
GSEA.GeneRanking0.0010.0000.001
GSEA.HeatMapPlot0.0010.0000.001
GSEA.HeatMapPlot20.0010.0000.001
GSEA.NormalizeCols0.1700.0070.178
GSEA.NormalizeRows0.0010.0000.001
GSEA0.0010.0010.001
GSEA.ReadClsFile0.1640.0050.170
GSEA.Res2Frame0.1600.0070.168
GSEA.Threshold0.1610.0050.166
GSEA.VarFilter0.7580.0050.762
GSEA.write.gct0.1570.0040.162
GeneExpMatrix0.0170.0010.019
Match_GeneList_MSigDB0.1710.0080.178
OLD.GSEA.EnrichmentScore0.1600.0060.166
Run.GSEA0.1540.0060.160
about0.0010.0000.001
canceR0.0010.0000.001
canceRHelp0.0010.0010.001
canceR_Vignette0.0000.0000.001
cbind.na0.0010.0000.001
dialogGeneClassifier0.0450.0040.050
dialogMetOption0.1590.0070.165
dialogMut0.1540.0060.161
dialogOptionCircos0.1370.0100.148
dialogOptionGSEAlm0.0040.0010.006
dialogOptionPhenoTest0.1870.0080.195
dialogPlotOption_SkinCor0.0440.0030.048
dialogSamplingGSEA0.1520.0040.156
dialogSelectFiles_GSEA0.1530.0040.157
dialogSpecificMut0.1550.0040.159
dialogSummary_GSEA0.1550.0040.159
dialoggetGeneListMSigDB0.0010.0000.001
displayInTable0.0040.0010.006
getCases0.0200.0111.778
getCasesGenProfs0.1090.0050.114
getCircos0.1320.0060.139
getClinicData_MultipleCases0.1090.0030.112
getClinicalDataMatrix0.1070.0010.108
getCor_ExpCNAMet0.1410.0080.149
getGCTCLSExample0.1570.0050.161
getGCT_CLSfiles0.1540.0020.155
getGSEAlm_Diseases0.1550.0020.156
getGSEAlm_Variables0.0010.0000.001
getGenProfs0.0170.0080.899
getGeneExpMatrix0.1070.0010.108
getGeneList0.0010.0000.002
getGeneListExample0.0010.0000.001
getGeneListFromMSigDB0.1100.0010.112
getGenesClassifier0.0010.0000.001
getGenesTree_MultipleCases0.1060.0000.108
getGenesTree_SingleCase0.1810.0060.188
getInTable0.0050.0010.006
getListProfData0.1120.0050.117
getMSigDB0.0010.0000.001
getMSigDBExample0.1120.0050.117
getMSigDBfile0.0010.0000.001
getMegaProfData0.1100.0040.114
getMetDataMultipleGenes0.1540.0040.158
getMutData0.1550.0040.159
getPhenoTest0.1970.0100.207
getProfilesDataMultipleGenes0.1670.0050.173
getProfilesDataSingleGene0.1100.0040.115
getSpecificMut0.1730.0040.178
getSummaryGSEA0.1540.0050.158
getSurvival0.0010.0000.001
getTextWin0.0000.0000.001
geteSet0.0010.0000.001
modalDialog0.1090.0040.115
myGlobalEnv0.0010.0000.001
plotModel0.0450.0040.048
plot_1Gene_2GenProfs0.0440.0030.048
plot_2Genes_1GenProf0.1520.0030.157
rbind.na0.0010.0000.001
setWorkspace0.1110.0040.116
testCheckedCaseGenProf0.1100.0050.115