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BioC 3.2: CHECK report for canceR on oaxaca

This page was generated on 2016-04-23 10:28:59 -0700 (Sat, 23 Apr 2016).

Package 135/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
canceR 1.2.0
Karim Mezhoud
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/canceR
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: canceR
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings canceR_1.2.0.tar.gz
StartedAt: 2016-04-22 22:22:35 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 22:29:02 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 386.4 seconds
RetCode: 0
Status:  OK 
CheckDir: canceR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings canceR_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/canceR.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.2.0’
* 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 ... [36s/41s] OK
* checking installed package size ... NOTE
  installed size is 13.1Mb
  sub-directories of 1Mb or more:
    data      7.1Mb
    doc       2.6Mb
    extdata   2.9Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Formula’ ‘rpart’ ‘Biobase’
A package should be listed in only one of these fields.
* 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)
canceR : loadAllStudies: no visible binding for global variable ‘Li’
canceR : loadMatchStudies: no visible binding for global variable ‘A’
dialogOptionPhenoTest: no visible binding for global variable
  ‘EventTime’
dialogOptionPhenoTest: no visible binding for global variable
  ‘Category’
dialogOptionPhenoTest: no visible binding for global variable ‘Continu’
dialogOptionPhenoTest : loadCategorical: no visible binding for global
  variable ‘Category’
getClinicalDataMatrix: no visible binding for global variable ‘ttMain’
getCor_ExpCNAMet : getMatrices: no visible binding for global variable
  ‘x’
getGCTCLSExample: no visible binding for global variable ‘fname.GCT’
getGCTCLSExample: no visible binding for global variable ‘fname.CLS’
getGSEAlm_Diseases: no visible binding for global variable
  ‘mSigDB_SubName’
getGSEAlm_Variables: no visible binding for global variable
  ‘GenesDetails’
getGeneExpMatrix: no visible binding for global variable ‘ttMain’
getGenesClassifier: no visible binding for global variable
  ‘GenesDetails’
getGenesTree_MultipleCases: no visible binding for global variable
  ‘CaseChoice’
getListProfData: no visible binding for global variable ‘ListProfData’
getListProfData: no visible binding for global variable ‘ListMetData’
getListProfData: no visible binding for global variable ‘ListMutData’
getListProfData: no visible global function definition for ‘lenght’
getMSigDBExample : ifrm: no visible global function definition for
  ‘myGlobalEnv’
getMSigDBExample: no visible binding for global variable ‘MSigDB’
getMSigDBExample: no visible binding for global variable ‘MSigDBFile’
getMSigDBExample: no visible binding for global variable ‘fname.MSigDB’
getMegaProfData: no visible global function definition for ‘lenght’
getSurvival: no visible binding for global variable ‘age’
geteSet: no visible binding for global variable ‘CasesStudies’
geteSet: no visible binding for global variable ‘curselectCases’
plotModel : Save: no visible global function definition for ‘devSVG’
testCheckedCaseGenProf: no visible binding for global variable
  ‘ttCasesGenProfs’
* 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 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [16s/16s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘canceR_unit_tests.R’ [15s/25s]
 [15s/25s] OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/canceR.Rcheck/00check.log’
for details.


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)

canceR.Rcheck/canceR-Ex.timings:

nameusersystemelapsed
ClinicalData0.0010.0000.001
GSEA.Analyze.Sets000
GSEA.ConsPlot000
GSEA.EnrichmentScore0.0000.0000.001
GSEA.EnrichmentScore20.0000.0000.001
GSEA.Gct2Frame000
GSEA.Gct2Frame20.0010.0000.000
GSEA.GeneRanking0.0000.0000.001
GSEA.HeatMapPlot000
GSEA.HeatMapPlot20.0010.0000.001
GSEA.NormalizeCols0.0000.0000.001
GSEA.NormalizeRows0.0000.0000.001
GSEA000
GSEA.ReadClsFile0.0010.0000.001
GSEA.Res2Frame000
GSEA.Threshold0.0000.0000.001
GSEA.VarFilter0.0010.0000.000
GSEA.write.gct000
GeneExpMatrix0.0010.0000.000
Match_GeneList_MSigDB0.0010.0000.001
OLD.GSEA.EnrichmentScore0.0010.0000.001
Run.GSEA0.0010.0000.000
about000
canceR0.0010.0000.001
canceRHelp000
canceR_Vignette0.0010.0000.001
cbind.na0.0020.0000.002
dialogGeneClassifier0.3110.0200.331
dialogMetOption0.0000.0010.001
dialogMut0.0010.0000.001
dialogOptionCircos0.0010.0000.000
dialogOptionGSEAlm0.0010.0000.001
dialogOptionPhenoTest0.0010.0000.001
dialogPlotOption_SkinCor0.0010.0000.001
dialogSamplingGSEA0.0010.0000.001
dialogSelectFiles_GSEA0.2200.0130.234
dialogSpecificMut0.1730.0120.184
dialogSummary_GSEA0.0000.0000.001
dialoggetGeneListMSigDB0.0010.0000.000
displayInTable0.0010.0000.001
getCases0.0000.0010.001
getCasesGenProfs0.6080.0140.626
getCircos0.0000.0010.001
getClinicData_MultipleCases0.0010.0000.001
getClinicalDataMatrix0.0010.0000.001
getCor_ExpCNAMet000
getGCTCLSExample0.0000.0000.001
getGCT_CLSfiles0.0010.0000.001
getGSEAlm_Diseases000
getGSEAlm_Variables0.0010.0010.001
getGenProfs0.0010.0000.001
getGeneExpMatrix0.0010.0000.001
getGeneList0.0010.0000.000
getGeneListExample000
getGeneListFromMSigDB0.0010.0000.001
getGenesClassifier0.0010.0000.000
getGenesTree_MultipleCases0.0010.0000.000
getGenesTree_SingleCase0.0000.0000.001
getInTable0.0000.0010.000
getListProfData0.0000.0000.001
getMSigDB000
getMSigDBExample0.0000.0000.001
getMSigDBfile0.0010.0000.000
getMegaProfData0.0010.0000.001
getMetDataMultipleGenes0.0010.0010.001
getMutData0.0010.0000.001
getPhenoTest0.0010.0000.001
getProfilesDataMultipleGenes0.0010.0010.001
getProfilesDataSingleGene0.0010.0000.001
getSpecificMut0.0010.0000.001
getSummaryGSEA0.0000.0000.001
getSurvival0.0010.0000.000
getTextWin0.0010.0000.001
geteSet0.0010.0000.001
modalDialog0.0010.0000.001
myGlobalEnv0.0010.0000.000
plotModel0.0000.0000.001
plot_1Gene_2GenProfs000
plot_2Genes_1GenProf0.0000.0000.001
rbind.na0.0010.0000.001
setWorkspace0.0010.0000.001
testCheckedCaseGenProf0.0010.0000.001