BioC 3.4: CHECK report for canceR on moscato1
This page was generated on 2016-09-21 03:46:51 -0700 (Wed, 21 Sep 2016).
canceR 1.5.2
Karim Mezhoud
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/canceR | | Last Changed Rev: 120682 / Revision: 121152 | | Last Changed Date: 2016-09-02 07:18:27 -0700 (Fri, 02 Sep 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
Summary
| Package: canceR
|
| Version: 1.5.2
|
| Command: rm -rf canceR.buildbin-libdir canceR.Rcheck && mkdir canceR.buildbin-libdir canceR.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=canceR.buildbin-libdir canceR_1.5.2.tar.gz >canceR.Rcheck\00install.out 2>&1 && cp canceR.Rcheck\00install.out canceR-install.out && D:\biocbld\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_1.5.2.tar.gz
|
| StartedAt: 2016-09-20 05:07:10 -0700 (Tue, 20 Sep 2016)
|
| EndedAt: 2016-09-20 05:15:54 -0700 (Tue, 20 Sep 2016)
|
| EllapsedTime: 523.8 seconds
|
| RetCode: 0
|
| Status: OK
|
| CheckDir: canceR.Rcheck
|
| Warnings: 0
|
Command output
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###
### Running command:
###
### rm -rf canceR.buildbin-libdir canceR.Rcheck && mkdir canceR.buildbin-libdir canceR.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=canceR.buildbin-libdir canceR_1.5.2.tar.gz >canceR.Rcheck\00install.out 2>&1 && cp canceR.Rcheck\00install.out canceR-install.out && D:\biocbld\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_1.5.2.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/canceR.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.5.2'
* 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
'D:/biocbld/bbs-3.4-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_1.5.2.zip
* DONE (canceR)
canceR.Rcheck/examples_i386/canceR-Ex.timings:
| name | user | system | elapsed
|
| ClinicalData | 0.02 | 0.02 | 0.03 |
|
| GSEA.Analyze.Sets | 0 | 0 | 0 |
|
| GSEA.ConsPlot | 0.01 | 0.00 | 0.02 |
|
| 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 | 0.29 | 0.00 | 0.28 |
|
| GSEA.NormalizeRows | 0 | 0 | 0 |
|
| GSEA | 0 | 0 | 0 |
|
| GSEA.ReadClsFile | 0.23 | 0.00 | 0.23 |
|
| GSEA.Res2Frame | 0.53 | 0.01 | 0.55 |
|
| GSEA.Threshold | 0.23 | 0.00 | 0.23 |
|
| GSEA.VarFilter | 0.24 | 0.00 | 0.23 |
|
| GSEA.write.gct | 0.23 | 0.00 | 0.24 |
|
| GeneExpMatrix | 0.03 | 0.00 | 0.03 |
|
| Match_GeneList_MSigDB | 0.25 | 0.00 | 0.25 |
|
| OLD.GSEA.EnrichmentScore | 0.24 | 0.00 | 0.23 |
|
| Run.GSEA | 0.23 | 0.00 | 0.24 |
|
| about | 0.02 | 0.00 | 0.03 |
|
| canceR | 0 | 0 | 0 |
|
| canceRHelp | 0 | 0 | 0 |
|
| canceR_Vignette | 0 | 0 | 0 |
|
| cbind.na | 0 | 0 | 0 |
|
| dialogGeneClassifier | 0.06 | 0.00 | 0.07 |
|
| dialogMetOption | 0.33 | 0.00 | 0.32 |
|
| dialogMut | 0.24 | 0.00 | 0.24 |
|
| dialogOptionCircos | 0.51 | 0.00 | 0.51 |
|
| dialogOptionGSEAlm | 0 | 0 | 0 |
|
| dialogOptionPhenoTest | 0.25 | 0.00 | 0.25 |
|
| dialogPlotOption_SkinCor | 0.06 | 0.00 | 0.06 |
|
| dialogSamplingGSEA | 0.23 | 0.00 | 0.23 |
|
| dialogSelectFiles_GSEA | 0.22 | 0.00 | 0.22 |
|
| dialogSpecificMut | 0.25 | 0.00 | 0.25 |
|
| dialogSummary_GSEA | 0.22 | 0.00 | 0.22 |
|
| dialoggetGeneListMSigDB | 0 | 0 | 0 |
|
| displayInTable | 0 | 0 | 0 |
|
| getCases | 0.43 | 0.13 | 1.37 |
|
| getCasesGenProfs | 0.46 | 0.00 | 0.47 |
|
| getCircos | 0.19 | 0.00 | 0.18 |
|
| getClinicData_MultipleCases | 0.16 | 0.00 | 0.16 |
|
| getClinicalDataMatrix | 0.15 | 0.00 | 0.16 |
|
| getCor_ExpCNAMet | 0.21 | 0.00 | 0.20 |
|
| getGCTCLSExample | 0.21 | 0.01 | 0.23 |
|
| getGCT_CLSfiles | 0.24 | 0.00 | 0.24 |
|
| getGSEAlm_Diseases | 0.25 | 0.00 | 0.25 |
|
| getGSEAlm_Variables | 0 | 0 | 0 |
|
| getGenProfs | 0.34 | 0.14 | 1.60 |
|
| getGeneExpMatrix | 0.16 | 0.00 | 0.16 |
|
| getGeneList | 0 | 0 | 0 |
|
| getGeneListExample | 0 | 0 | 0 |
|
| getGeneListFromMSigDB | 0.16 | 0.00 | 0.15 |
|
| getGenesClassifier | 0 | 0 | 0 |
|
| getGenesTree_MultipleCases | 0.15 | 0.00 | 0.16 |
|
| getGenesTree_SingleCase | 0.25 | 0.00 | 0.25 |
|
| getInTable | 0.02 | 0.00 | 0.01 |
|
| getListProfData | 0.16 | 0.00 | 0.16 |
|
| getMSigDB | 0 | 0 | 0 |
|
| getMSigDBExample | 0.17 | 0.00 | 0.17 |
|
| getMSigDBfile | 0 | 0 | 0 |
|
| getMegaProfData | 0.15 | 0.00 | 0.16 |
|
| getMetDataMultipleGenes | 0.24 | 0.00 | 0.23 |
|
| getMutData | 0.23 | 0.00 | 0.23 |
|
| getPhenoTest | 0.23 | 0.00 | 0.24 |
|
| getProfilesDataMultipleGenes | 0.25 | 0.02 | 0.26 |
|
| getProfilesDataSingleGene | 0.16 | 0.00 | 0.16 |
|
| getSpecificMut | 0.22 | 0.02 | 0.23 |
|
| getSummaryGSEA | 0.22 | 0.00 | 0.22 |
|
| getSurvival | 0 | 0 | 0 |
|
| getTextWin | 0 | 0 | 0 |
|
| geteSet | 0 | 0 | 0 |
|
| modalDialog | 0.16 | 0.01 | 0.17 |
|
| myGlobalEnv | 0 | 0 | 0 |
|
| plotModel | 0.06 | 0.00 | 0.06 |
|
| plot_1Gene_2GenProfs | 0.06 | 0.00 | 0.06 |
|
| plot_2Genes_1GenProf | 0.22 | 0.00 | 0.22 |
|
| rbind.na | 0 | 0 | 0 |
|
| setWorkspace | 0.16 | 0.00 | 0.16 |
|
| testCheckedCaseGenProf | 0.17 | 0.00 | 0.17 |
|
canceR.Rcheck/examples_x64/canceR-Ex.timings:
| name | user | system | elapsed
|
| ClinicalData | 0.02 | 0.02 | 0.03 |
|
| 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 | 0.01 | 0.00 | 0.02 |
|
| GSEA.NormalizeCols | 0.17 | 0.01 | 0.19 |
|
| GSEA.NormalizeRows | 0 | 0 | 0 |
|
| GSEA | 0 | 0 | 0 |
|
| GSEA.ReadClsFile | 0.24 | 0.00 | 0.23 |
|
| GSEA.Res2Frame | 0.2 | 0.0 | 0.2 |
|
| GSEA.Threshold | 0.19 | 0.00 | 0.19 |
|
| GSEA.VarFilter | 0.63 | 0.02 | 0.64 |
|
| GSEA.write.gct | 0.18 | 0.00 | 0.19 |
|
| GeneExpMatrix | 0.04 | 0.00 | 0.03 |
|
| Match_GeneList_MSigDB | 0.21 | 0.00 | 0.22 |
|
| OLD.GSEA.EnrichmentScore | 0.19 | 0.00 | 0.19 |
|
| Run.GSEA | 0.19 | 0.01 | 0.20 |
|
| about | 0.01 | 0.00 | 0.05 |
|
| canceR | 0 | 0 | 0 |
|
| canceRHelp | 0.02 | 0.00 | 0.01 |
|
| canceR_Vignette | 0 | 0 | 0 |
|
| cbind.na | 0 | 0 | 0 |
|
| dialogGeneClassifier | 0.06 | 0.00 | 0.07 |
|
| dialogMetOption | 0.19 | 0.00 | 0.18 |
|
| dialogMut | 0.19 | 0.00 | 0.19 |
|
| dialogOptionCircos | 0.15 | 0.02 | 0.17 |
|
| dialogOptionGSEAlm | 0 | 0 | 0 |
|
| dialogOptionPhenoTest | 0.23 | 0.01 | 0.25 |
|
| dialogPlotOption_SkinCor | 0.05 | 0.00 | 0.05 |
|
| dialogSamplingGSEA | 0.2 | 0.0 | 0.2 |
|
| dialogSelectFiles_GSEA | 0.19 | 0.00 | 0.19 |
|
| dialogSpecificMut | 0.2 | 0.0 | 0.2 |
|
| dialogSummary_GSEA | 0.20 | 0.00 | 0.21 |
|
| dialoggetGeneListMSigDB | 0 | 0 | 0 |
|
| displayInTable | 0 | 0 | 0 |
|
| getCases | 0.35 | 0.08 | 1.29 |
|
| getCasesGenProfs | 0.12 | 0.00 | 0.12 |
|
| getCircos | 0.61 | 0.00 | 0.61 |
|
| getClinicData_MultipleCases | 0.13 | 0.02 | 0.14 |
|
| getClinicalDataMatrix | 0.11 | 0.01 | 0.13 |
|
| getCor_ExpCNAMet | 0.16 | 0.00 | 0.16 |
|
| getGCTCLSExample | 0.2 | 0.0 | 0.2 |
|
| getGCT_CLSfiles | 0.17 | 0.02 | 0.19 |
|
| getGSEAlm_Diseases | 0.17 | 0.00 | 0.17 |
|
| getGSEAlm_Variables | 0 | 0 | 0 |
|
| getGenProfs | 0.33 | 0.06 | 1.54 |
|
| getGeneExpMatrix | 0.12 | 0.00 | 0.12 |
|
| getGeneList | 0 | 0 | 0 |
|
| getGeneListExample | 0 | 0 | 0 |
|
| getGeneListFromMSigDB | 0.14 | 0.00 | 0.14 |
|
| getGenesClassifier | 0 | 0 | 0 |
|
| getGenesTree_MultipleCases | 0.14 | 0.00 | 0.14 |
|
| getGenesTree_SingleCase | 0.20 | 0.00 | 0.21 |
|
| getInTable | 0.02 | 0.00 | 0.00 |
|
| getListProfData | 0.14 | 0.00 | 0.14 |
|
| getMSigDB | 0 | 0 | 0 |
|
| getMSigDBExample | 0.13 | 0.01 | 0.14 |
|
| getMSigDBfile | 0 | 0 | 0 |
|
| getMegaProfData | 0.13 | 0.00 | 0.12 |
|
| getMetDataMultipleGenes | 0.18 | 0.00 | 0.19 |
|
| getMutData | 0.19 | 0.00 | 0.18 |
|
| getPhenoTest | 0.21 | 0.00 | 0.22 |
|
| getProfilesDataMultipleGenes | 0.24 | 0.00 | 0.24 |
|
| getProfilesDataSingleGene | 0.12 | 0.00 | 0.12 |
|
| getSpecificMut | 0.19 | 0.00 | 0.18 |
|
| getSummaryGSEA | 0.18 | 0.00 | 0.19 |
|
| getSurvival | 0 | 0 | 0 |
|
| getTextWin | 0 | 0 | 0 |
|
| geteSet | 0 | 0 | 0 |
|
| modalDialog | 0.12 | 0.00 | 0.12 |
|
| myGlobalEnv | 0 | 0 | 0 |
|
| plotModel | 0.07 | 0.00 | 0.06 |
|
| plot_1Gene_2GenProfs | 0.04 | 0.00 | 0.05 |
|
| plot_2Genes_1GenProf | 0.19 | 0.00 | 0.17 |
|
| rbind.na | 0 | 0 | 0 |
|
| setWorkspace | 0.14 | 0.00 | 0.14 |
|
| testCheckedCaseGenProf | 0.14 | 0.00 | 0.14 |
|