BioC 3.4: CHECK report for canceR on tokay1

Package: canceR

Version: 1.6.0

Command: rm -rf canceR.buildbin-libdir canceR.Rcheck && mkdir canceR.buildbin-libdir canceR.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=canceR.buildbin-libdir canceR_1.6.0.tar.gz >canceR.Rcheck\00install.out 2>&1 && cp canceR.Rcheck\00install.out canceR-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=canceR.buildbin-libdir --install="check:canceR-install.out" --force-multiarch --no-vignettes --timings canceR_1.6.0.tar.gz

StartedAt: 2017-04-14 21:18:30 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 21:26:17 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 466.8 seconds

RetCode: 0

Status:  OK

CheckDir: canceR.Rcheck

Warnings: 0

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### Running command:
###
###   rm -rf canceR.buildbin-libdir canceR.Rcheck && mkdir canceR.buildbin-libdir canceR.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=canceR.buildbin-libdir canceR_1.6.0.tar.gz >canceR.Rcheck\00install.out 2>&1 && cp canceR.Rcheck\00install.out canceR-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=canceR.buildbin-libdir --install="check:canceR-install.out" --force-multiarch --no-vignettes --timings canceR_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/canceR.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '1.6.0'
* 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 whether package 'canceR' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 35.8Mb
  sub-directories of 1Mb or more:
    data      7.1Mb
    doc      25.4Mb
    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
* 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: no visible global function definition for 'windows'
GSEA: no visible global function definition for 'savePlot'
GSEA.Analyze.Sets: no visible global function definition for 'windows'
GSEA.Analyze.Sets: no visible global function definition for 'savePlot'
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'
cbind.na: no visible global function definition for 'cbind2'
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 global function definition for 'new'
getGSEAlm_Diseases: no visible binding for global variable
  'mSigDB_SubName'
getGSEAlm_Variables: no visible global function definition for 'new'
getGSEAlm_Variables: no visible binding for global variable
  'GenesDetails'
getGeneExpMatrix: no visible binding for global variable 'ttMain'
getGenesClassifier: no visible global function definition for 'new'
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'
geteSet: no visible global function definition for 'new'
plotModel : Save: no visible global function definition for 'devSVG'
rbind.na: no visible global function definition for 'rbind2'
testCheckedCaseGenProf: no visible binding for global variable
  'ttCasesGenProfs'
Undefined global functions or variables:
  A CaseChoice CasesStudies Category Continu EventTime GenesDetails Li
  ListMetData ListMutData ListProfData MSigDB MSigDBFile age cbind2
  curselectCases devSVG fname.CLS fname.GCT fname.MSigDB lenght
  mSigDB_SubName myGlobalEnv new rbind2 savePlot ttCasesGenProfs ttMain
  windows x
Consider adding
  importFrom("grDevices", "savePlot", "windows")
  importFrom("methods", "cbind2", "new", "rbind2")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.4-bioc/meat/canceR.Rcheck/00check.log'
for details.

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_1.6.0.zip
* DONE (canceR)

name	user	system	elapsed
ClinicalData	0.01	0.00	0.02
GSEA.Analyze.Sets	0	0	0
GSEA.ConsPlot	0	0	0
GSEA.EnrichmentScore	0	0	0
GSEA.EnrichmentScore2	0	0	0
GSEA.Gct2Frame	0	0	0
GSEA.Gct2Frame2	0	0	0
GSEA.GeneRanking	0	0	0
GSEA.HeatMapPlot	0	0	0
GSEA.HeatMapPlot2	0	0	0
GSEA.NormalizeCols	0.20	0.00	0.21
GSEA.NormalizeRows	0	0	0
GSEA	0	0	0
GSEA.ReadClsFile	0.2	0.0	0.2
GSEA.Res2Frame	0.34	0.00	0.34
GSEA.Threshold	0.32	0.02	0.33
GSEA.VarFilter	0.34	0.00	0.34
GSEA.write.gct	0.33	0.00	0.32
GeneExpMatrix	0.03	0.02	0.05
Match_GeneList_MSigDB	0.36	0.00	0.36
OLD.GSEA.EnrichmentScore	0.36	0.00	0.36
Run.GSEA	0.35	0.00	0.34
about	0	0	0
canceR	0	0	0
canceRHelp	0	0	0
canceR_Vignette	0	0	0
cbind.na	0	0	0
dialogGeneClassifier	0.10	0.02	0.10
dialogMetOption	0.31	0.00	0.32
dialogMut	0.22	0.00	0.22
dialogOptionCircos	0.24	0.00	0.24
dialogOptionGSEAlm	0	0	0
dialogOptionPhenoTest	0.25	0.03	0.28
dialogPlotOption_SkinCor	0.07	0.00	0.07
dialogSamplingGSEA	0.2	0.0	0.2
dialogSelectFiles_GSEA	0.2	0.0	0.2
dialogSpecificMut	0.28	0.03	0.31
dialogSummary_GSEA	0.33	0.00	0.33
dialoggetGeneListMSigDB	0	0	0
displayInTable	0.00	0.02	0.01
getCases	0.45	0.20	0.89
getCasesGenProfs	0.69	0.00	0.69
getCircos	0.25	0.00	0.25
getClinicData_MultipleCases	0.82	0.00	0.81
getClinicalDataMatrix	0.2	0.0	0.2
getCor_ExpCNAMet	0.25	0.00	0.25
getGCTCLSExample	0.30	0.01	0.32
getGCT_CLSfiles	0.35	0.00	0.35
getGSEAlm_Diseases	0.24	0.00	0.24
getGSEAlm_Variables	0	0	0
getGenProfs	0.48	0.25	1.03
getGeneExpMatrix	0.24	0.00	0.23
getGeneList	0.01	0.00	0.02
getGeneListExample	0	0	0
getGeneListFromMSigDB	0.22	0.00	0.22
getGenesClassifier	0	0	0
getGenesTree_MultipleCases	0.17	0.02	0.19
getGenesTree_SingleCase	0.24	0.00	0.23
getInTable	0.03	0.00	0.03
getListProfData	0.14	0.02	0.16
getMSigDB	0	0	0
getMSigDBExample	0.14	0.00	0.14
getMSigDBfile	0	0	0
getMegaProfData	0.14	0.00	0.14
getMetDataMultipleGenes	0.20	0.01	0.22
getMutData	0.21	0.00	0.20
getPhenoTest	0.22	0.02	0.24
getProfilesDataMultipleGenes	0.23	0.00	0.23
getProfilesDataSingleGene	0.14	0.00	0.14
getSpecificMut	0.19	0.01	0.20
getSummaryGSEA	0.19	0.00	0.19
getSurvival	0	0	0
getTextWin	0	0	0
geteSet	0	0	0
modalDialog	0.14	0.00	0.14
myGlobalEnv	0	0	0
plotModel	0.06	0.00	0.07
plot_1Gene_2GenProfs	0.06	0.00	0.06
plot_2Genes_1GenProf	0.21	0.00	0.20
rbind.na	0	0	0
setWorkspace	0.14	0.00	0.14
testCheckedCaseGenProf	0.17	0.00	0.17

name	user	system	elapsed
ClinicalData	0.00	0.01	0.01
GSEA.Analyze.Sets	0	0	0
GSEA.ConsPlot	0	0	0
GSEA.EnrichmentScore	0	0	0
GSEA.EnrichmentScore2	0	0	0
GSEA.Gct2Frame	0	0	0
GSEA.Gct2Frame2	0	0	0
GSEA.GeneRanking	0	0	0
GSEA.HeatMapPlot	0	0	0
GSEA.HeatMapPlot2	0	0	0
GSEA.NormalizeCols	0.16	0.02	0.17
GSEA.NormalizeRows	0	0	0
GSEA	0	0	0
GSEA.ReadClsFile	0.15	0.01	0.17
GSEA.Res2Frame	0.18	0.00	0.17
GSEA.Threshold	0.17	0.00	0.17
GSEA.VarFilter	0.17	0.00	0.18
GSEA.write.gct	0.16	0.02	0.17
GeneExpMatrix	0.01	0.00	0.01
Match_GeneList_MSigDB	0.19	0.00	0.19
OLD.GSEA.EnrichmentScore	0.16	0.01	0.17
Run.GSEA	0.18	0.00	0.19
about	0.00	0.00	0.11
canceR	0	0	0
canceRHelp	0	0	0
canceR_Vignette	0	0	0
cbind.na	0	0	0
dialogGeneClassifier	0.05	0.00	0.04
dialogMetOption	0.17	0.00	0.17
dialogMut	0.15	0.00	0.16
dialogOptionCircos	0.75	0.00	0.75
dialogOptionGSEAlm	0	0	0
dialogOptionPhenoTest	0.21	0.00	0.20
dialogPlotOption_SkinCor	0.04	0.00	0.05
dialogSamplingGSEA	0.14	0.02	0.16
dialogSelectFiles_GSEA	0.16	0.00	0.16
dialogSpecificMut	0.17	0.00	0.17
dialogSummary_GSEA	0.17	0.00	0.17
dialoggetGeneListMSigDB	0	0	0
displayInTable	0.02	0.00	0.02
getCases	0.28	0.08	0.58
getCasesGenProfs	0.12	0.00	0.12
getCircos	0.14	0.01	0.16
getClinicData_MultipleCases	0.11	0.02	0.12
getClinicalDataMatrix	0.13	0.00	0.13
getCor_ExpCNAMet	0.12	0.01	0.14
getGCTCLSExample	0.19	0.00	0.19
getGCT_CLSfiles	0.16	0.02	0.17
getGSEAlm_Diseases	0.15	0.00	0.15
getGSEAlm_Variables	0	0	0
getGenProfs	0.14	0.20	0.64
getGeneExpMatrix	0.13	0.00	0.13
getGeneList	0	0	0
getGeneListExample	0	0	0
getGeneListFromMSigDB	0.12	0.00	0.12
getGenesClassifier	0	0	0
getGenesTree_MultipleCases	0.13	0.00	0.13
getGenesTree_SingleCase	0.15	0.03	0.19
getInTable	0.02	0.00	0.01
getListProfData	0.12	0.00	0.13
getMSigDB	0	0	0
getMSigDBExample	0.13	0.00	0.12
getMSigDBfile	0	0	0
getMegaProfData	0.12	0.00	0.12
getMetDataMultipleGenes	0.18	0.00	0.17
getMutData	0.18	0.00	0.19
getPhenoTest	0.21	0.00	0.21
getProfilesDataMultipleGenes	0.2	0.0	0.2
getProfilesDataSingleGene	0.12	0.00	0.12
getSpecificMut	0.18	0.00	0.18
getSummaryGSEA	0.17	0.00	0.17
getSurvival	0	0	0
getTextWin	0	0	0
geteSet	0	0	0
modalDialog	0.12	0.00	0.12
myGlobalEnv	0	0	0
plotModel	0.05	0.00	0.05
plot_1Gene_2GenProfs	0.06	0.00	0.06
plot_2Genes_1GenProf	0.17	0.00	0.17
rbind.na	0	0	0
setWorkspace	0.11	0.02	0.13
testCheckedCaseGenProf	0.13	0.00	0.12