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BioC 3.2: CHECK report for canceR on moscato1

This page was generated on 2016-04-23 10:21:32 -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: rm -rf canceR.buildbin-libdir canceR.Rcheck && mkdir canceR.buildbin-libdir canceR.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=canceR.buildbin-libdir canceR_1.2.0.tar.gz >canceR.Rcheck\00install.out 2>&1 && cp canceR.Rcheck\00install.out canceR-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=canceR.buildbin-libdir --install="check:canceR-install.out" --force-multiarch --no-vignettes --timings canceR_1.2.0.tar.gz
StartedAt: 2016-04-23 00:14:30 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 00:25:26 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 656.0 seconds
RetCode: 0
Status:  OK  
CheckDir: canceR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf canceR.buildbin-libdir canceR.Rcheck && mkdir canceR.buildbin-libdir canceR.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=canceR.buildbin-libdir canceR_1.2.0.tar.gz >canceR.Rcheck\00install.out 2>&1 && cp canceR.Rcheck\00install.out canceR-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=canceR.buildbin-libdir --install="check:canceR-install.out" --force-multiarch --no-vignettes --timings canceR_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/canceR.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'canceR' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [15s] OK
** running examples for arch 'x64' ... [21s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'canceR_unit_tests.R' [22s]
 [23s] OK
** running tests for arch 'x64' ...
  Running 'canceR_unit_tests.R' [22s]
 [22s] OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  'D:/biocbld/bbs-3.2-bioc/meat/canceR.Rcheck/00check.log'
for details.


canceR.Rcheck/00install.out:


install for i386

* 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'

install for x64

* installing *source* package 'canceR' ...
** testing if installed package can be loaded
Warning: replacing previous import 'igraph::union' by 'GSEABase::union' when loading 'HTSanalyzeR'
* MD5 sums
packaged installation of 'canceR' as canceR_1.2.0.zip
* DONE (canceR)

canceR.Rcheck/examples_i386/canceR-Ex.timings:

nameusersystemelapsed
ClinicalData000
GSEA.Analyze.Sets000
GSEA.ConsPlot000
GSEA.EnrichmentScore000
GSEA.EnrichmentScore2000
GSEA.Gct2Frame000
GSEA.Gct2Frame2000
GSEA.GeneRanking000
GSEA.HeatMapPlot000
GSEA.HeatMapPlot20.020.000.01
GSEA.NormalizeCols000
GSEA.NormalizeRows000
GSEA000
GSEA.ReadClsFile000
GSEA.Res2Frame000
GSEA.Threshold000
GSEA.VarFilter000
GSEA.write.gct000
GeneExpMatrix000
Match_GeneList_MSigDB000
OLD.GSEA.EnrichmentScore000
Run.GSEA000
about000
canceR000
canceRHelp000
canceR_Vignette000
cbind.na0.020.000.02
dialogGeneClassifier0.370.000.37
dialogMetOption000
dialogMut000
dialogOptionCircos000
dialogOptionGSEAlm000
dialogOptionPhenoTest000
dialogPlotOption_SkinCor000
dialogSamplingGSEA000
dialogSelectFiles_GSEA0.390.020.41
dialogSpecificMut0.20.00.2
dialogSummary_GSEA000
dialoggetGeneListMSigDB000
displayInTable000
getCases000
getCasesGenProfs0.210.000.22
getCircos000
getClinicData_MultipleCases000
getClinicalDataMatrix000
getCor_ExpCNAMet000
getGCTCLSExample0.020.000.01
getGCT_CLSfiles000
getGSEAlm_Diseases000
getGSEAlm_Variables000
getGenProfs000
getGeneExpMatrix0.010.000.02
getGeneList000
getGeneListExample000
getGeneListFromMSigDB000
getGenesClassifier000
getGenesTree_MultipleCases000
getGenesTree_SingleCase000
getInTable000
getListProfData000
getMSigDB000
getMSigDBExample000
getMSigDBfile0.010.000.01
getMegaProfData000
getMetDataMultipleGenes000
getMutData000
getPhenoTest000
getProfilesDataMultipleGenes000
getProfilesDataSingleGene000
getSpecificMut000
getSummaryGSEA000
getSurvival000
getTextWin000
geteSet000
modalDialog000
myGlobalEnv000
plotModel000
plot_1Gene_2GenProfs000
plot_2Genes_1GenProf0.010.000.02
rbind.na000
setWorkspace000
testCheckedCaseGenProf000

canceR.Rcheck/examples_x64/canceR-Ex.timings:

nameusersystemelapsed
ClinicalData000
GSEA.Analyze.Sets000
GSEA.ConsPlot000
GSEA.EnrichmentScore000
GSEA.EnrichmentScore20.020.000.02
GSEA.Gct2Frame000
GSEA.Gct2Frame2000
GSEA.GeneRanking000
GSEA.HeatMapPlot000
GSEA.HeatMapPlot2000
GSEA.NormalizeCols000
GSEA.NormalizeRows000
GSEA000
GSEA.ReadClsFile0.000.020.01
GSEA.Res2Frame000
GSEA.Threshold000
GSEA.VarFilter000
GSEA.write.gct000
GeneExpMatrix000
Match_GeneList_MSigDB000
OLD.GSEA.EnrichmentScore000
Run.GSEA000
about000
canceR000
canceRHelp000
canceR_Vignette000
cbind.na000
dialogGeneClassifier0.260.000.27
dialogMetOption000
dialogMut000
dialogOptionCircos000
dialogOptionGSEAlm000
dialogOptionPhenoTest000
dialogPlotOption_SkinCor000
dialogSamplingGSEA000
dialogSelectFiles_GSEA0.230.000.24
dialogSpecificMut0.20.00.2
dialogSummary_GSEA000
dialoggetGeneListMSigDB0.020.000.01
displayInTable000
getCases000
getCasesGenProfs0.940.020.96
getCircos000
getClinicData_MultipleCases000
getClinicalDataMatrix000
getCor_ExpCNAMet000
getGCTCLSExample000
getGCT_CLSfiles000
getGSEAlm_Diseases0.020.000.02
getGSEAlm_Variables000
getGenProfs000
getGeneExpMatrix0.010.000.01
getGeneList000
getGeneListExample000
getGeneListFromMSigDB000
getGenesClassifier000
getGenesTree_MultipleCases000
getGenesTree_SingleCase000
getInTable000
getListProfData000
getMSigDB000
getMSigDBExample000
getMSigDBfile000
getMegaProfData000
getMetDataMultipleGenes000
getMutData000
getPhenoTest000
getProfilesDataMultipleGenes000
getProfilesDataSingleGene000
getSpecificMut000
getSummaryGSEA000
getSurvival000
getTextWin000
geteSet000
modalDialog000
myGlobalEnv000
plotModel000
plot_1Gene_2GenProfs000
plot_2Genes_1GenProf000
rbind.na000
setWorkspace000
testCheckedCaseGenProf000