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BioC 3.5: CHECK report for canceR on malbec2

This page was generated on 2017-08-16 13:16:27 -0400 (Wed, 16 Aug 2017).

Package 166/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
canceR 1.8.0
Karim Mezhoud
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/canceR
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: canceR
Version: 1.8.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings canceR_1.8.0.tar.gz
StartedAt: 2017-08-15 21:41:03 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 21:47:08 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 365.0 seconds
RetCode: 0
Status:  OK 
CheckDir: canceR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings canceR_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/canceR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.8.0’
* 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-3.5-bioc/meat/canceR.Rcheck/00check.log’
for details.


canceR.Rcheck/00install.out:

* installing *source* package ‘canceR’ ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "RSQLite" for requests: dbGetQuery
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
No methods found in "RSQLite" for requests: dbGetQuery
Warning: replacing previous import ‘igraph::union’ by ‘GSEABase::union’ when loading ‘HTSanalyzeR’
* DONE (canceR)

canceR.Rcheck/canceR-Ex.timings:

nameusersystemelapsed
ClinicalData0.0080.0000.008
GSEA.Analyze.Sets000
GSEA.ConsPlot0.0040.0000.000
GSEA.EnrichmentScore0.0000.0000.001
GSEA.EnrichmentScore2000
GSEA.Gct2Frame0.0040.0000.000
GSEA.Gct2Frame2000
GSEA.GeneRanking0.0000.0000.001
GSEA.HeatMapPlot0.0000.0000.001
GSEA.HeatMapPlot2000
GSEA.NormalizeCols0.1520.0040.157
GSEA.NormalizeRows0.0040.0000.000
GSEA0.0000.0000.001
GSEA.ReadClsFile0.1600.0000.159
GSEA.Res2Frame0.1560.0040.158
GSEA.Threshold0.1520.0040.158
GSEA.VarFilter0.1600.0000.161
GSEA.write.gct0.1720.0040.175
GeneExpMatrix0.0200.0000.021
Match_GeneList_MSigDB0.1840.0040.186
OLD.GSEA.EnrichmentScore0.1640.0000.163
Run.GSEA0.1520.0080.160
about0.0120.0040.036
canceR0.0000.0000.001
canceRHelp0.0040.0000.002
canceR_Vignette0.0000.0200.021
cbind.na0.0040.0000.004
dialogGeneClassifier0.0720.0000.075
dialogMetOption0.1760.0000.179
dialogMut0.1640.0040.169
dialogOptionCircos0.1560.0040.160
dialogOptionGSEAlm0.0040.0000.006
dialogOptionPhenoTest0.1760.0000.176
dialogPlotOption_SkinCor0.0400.0040.046
dialogSamplingGSEA0.1840.0000.183
dialogSelectFiles_GSEA0.1640.0040.168
dialogSpecificMut0.1960.0000.196
dialogSummary_GSEA0.160.000.16
dialoggetGeneListMSigDB0.0000.0000.001
displayInTable0.0080.0000.005
getCases0.1520.0080.773
getCasesGenProfs0.1840.0040.190
getCircos0.2320.0000.232
getClinicData_MultipleCases0.1960.0000.195
getClinicalDataMatrix0.1120.0000.113
getCor_ExpCNAMet0.1520.0040.159
getGCTCLSExample0.160.000.16
getGCT_CLSfiles0.1600.0000.161
getGSEAlm_Diseases0.1600.0000.161
getGSEAlm_Variables0.0000.0000.001
getGenProfs0.0120.0120.836
getGeneExpMatrix0.1800.0120.196
getGeneList000
getGeneListExample0.0000.0000.001
getGeneListFromMSigDB0.1160.0000.114
getGenesClassifier0.0000.0000.001
getGenesTree_MultipleCases0.1160.0000.116
getGenesTree_SingleCase0.2000.0000.198
getInTable0.0040.0000.006
getListProfData0.1160.0000.114
getMSigDB0.0000.0000.001
getMSigDBExample0.1120.0000.111
getMSigDBfile0.0000.0000.001
getMegaProfData0.1160.0000.115
getMetDataMultipleGenes0.1640.0000.162
getMutData0.1600.0000.161
getPhenoTest0.1840.0120.195
getProfilesDataMultipleGenes0.2680.0000.266
getProfilesDataSingleGene0.1160.0080.122
getSpecificMut0.1600.0000.158
getSummaryGSEA0.1680.0000.169
getSurvival0.0040.0000.000
getTextWin000
geteSet000
modalDialog0.1160.0000.115
myGlobalEnv0.0000.0000.001
plotModel0.0440.0000.048
plot_1Gene_2GenProfs0.0440.0040.047
plot_2Genes_1GenProf0.2840.0040.290
rbind.na0.0040.0000.004
setWorkspace0.1680.0000.170
testCheckedCaseGenProf0.1200.0000.116