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CHECK report for canceR on malbec1

This page was generated on 2018-04-12 13:13:19 -0400 (Thu, 12 Apr 2018).

Package 174/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
canceR 1.10.0
Karim Mezhoud
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/canceR
Branch: RELEASE_3_6
Last Commit: b980fea
Last Changed Date: 2017-10-30 12:40:49 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: canceR
Version: 1.10.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings canceR_1.10.0.tar.gz
StartedAt: 2018-04-11 21:58:43 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 22:04:45 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 361.4 seconds
RetCode: 0
Status:  OK 
CheckDir: canceR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings canceR_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/canceR.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (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 ‘1.10.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 36.1Mb
  sub-directories of 1Mb or more:
    data      7.1Mb
    doc      25.6Mb
    extdata   3.0Mb
* 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 loading without being on the library search path ... 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
GSEA.HeatMapPlot2: possible error in rainbow(100, s = 1, v = 0.75,
  start = 0, end = 0.75, gamma = 1.5): unused argument (gamma = 1.5)
* 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 installed files from ‘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: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/canceR.Rcheck/00check.log’
for details.



Installation output

canceR.Rcheck/00install.out

* installing *source* package ‘canceR’ ...
** R
** data
** inst
** preparing 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 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
 13.728   0.708  17.185 

Example timings

canceR.Rcheck/canceR-Ex.timings

nameusersystemelapsed
ClinicalData0.0120.0000.011
GSEA.Analyze.Sets000
GSEA.ConsPlot0.0000.0000.001
GSEA.EnrichmentScore000
GSEA.EnrichmentScore20.0000.0000.001
GSEA.Gct2Frame0.0000.0000.001
GSEA.Gct2Frame2000
GSEA.GeneRanking0.0000.0000.001
GSEA.HeatMapPlot0.0000.0000.001
GSEA.HeatMapPlot20.0000.0000.001
GSEA.NormalizeCols0.2120.0040.222
GSEA.NormalizeRows000
GSEA000
GSEA.ReadClsFile0.160.000.16
GSEA.Res2Frame0.1560.0040.162
GSEA.Threshold0.1640.0000.160
GSEA.VarFilter0.1960.0040.199
GSEA.write.gct0.1560.0040.160
GeneExpMatrix0.020.000.02
Match_GeneList_MSigDB0.2600.0040.264
OLD.GSEA.EnrichmentScore0.1600.0040.163
Run.GSEA0.1640.0000.166
about0.0160.0000.020
canceR000
canceRHelp0.0000.0000.001
canceR_Vignette0.0000.0200.022
cbind.na0.0040.0000.005
dialogGeneClassifier0.0520.0080.060
dialogMetOption0.2360.0120.250
dialogMut0.1760.0000.176
dialogOptionCircos0.1720.0040.175
dialogOptionGSEAlm0.0040.0000.005
dialogOptionPhenoTest0.2400.0000.243
dialogPlotOption_SkinCor0.0520.0000.049
dialogSamplingGSEA0.1720.0000.172
dialogSelectFiles_GSEA0.2400.0000.238
dialogSpecificMut0.2920.0120.304
dialogSummary_GSEA0.2640.0120.277
dialoggetGeneListMSigDB000
displayInTable0.0080.0000.008
getCases0.2720.0160.864
getCasesGenProfs0.2040.0040.207
getCircos0.7640.0720.841
getClinicData_MultipleCases0.1160.0000.115
getClinicalDataMatrix0.1160.0000.115
getCor_ExpCNAMet0.1520.0040.157
getGCTCLSExample0.160.000.16
getGCT_CLSfiles0.1880.0000.187
getGSEAlm_Diseases0.1600.0080.169
getGSEAlm_Variables0.0000.0000.001
getGenProfs0.0200.0080.763
getGeneExpMatrix0.1800.0200.198
getGeneList0.0000.0000.001
getGeneListExample000
getGeneListFromMSigDB0.1360.0000.136
getGenesClassifier000
getGenesTree_MultipleCases0.1440.0000.145
getGenesTree_SingleCase0.1800.0080.190
getInTable0.0040.0000.006
getListProfData0.1040.0040.112
getMSigDB000
getMSigDBExample0.1320.0000.132
getMSigDBfile0.0040.0000.000
getMegaProfData0.1440.0040.151
getMetDataMultipleGenes0.2000.0040.204
getMutData0.1600.0080.167
getPhenoTest0.1920.0040.194
getProfilesDataMultipleGenes0.2000.0080.209
getProfilesDataSingleGene0.1520.0000.150
getSpecificMut0.1960.0080.204
getSummaryGSEA0.1800.0080.191
getSurvival000
getTextWin0.0000.0000.001
geteSet000
modalDialog0.1280.0000.130
myGlobalEnv000
plotModel0.0480.0040.053
plot_1Gene_2GenProfs0.0520.0000.052
plot_2Genes_1GenProf0.1880.0000.188
rbind.na0.0040.0000.002
setWorkspace0.120.000.12
testCheckedCaseGenProf0.1080.0040.116