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BioC 3.3: CHECK report for canceR on moscato2

This page was generated on 2016-10-13 12:53:42 -0700 (Thu, 13 Oct 2016).

Package 144/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
canceR 1.4.0
Karim Mezhoud
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/canceR
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (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: 1.4.0
Command: rm -rf canceR.buildbin-libdir canceR.Rcheck && mkdir canceR.buildbin-libdir canceR.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=canceR.buildbin-libdir canceR_1.4.0.tar.gz >canceR.Rcheck\00install.out 2>&1 && cp canceR.Rcheck\00install.out canceR-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=canceR.buildbin-libdir --install="check:canceR-install.out" --force-multiarch --no-vignettes --timings canceR_1.4.0.tar.gz
StartedAt: 2016-10-13 01:40:38 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 01:51:48 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 669.7 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 && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=canceR.buildbin-libdir canceR_1.4.0.tar.gz >canceR.Rcheck\00install.out 2>&1 && cp canceR.Rcheck\00install.out canceR-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=canceR.buildbin-libdir --install="check:canceR-install.out" --force-multiarch --no-vignettes --timings canceR_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-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 '1.4.0'
* 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 38.4Mb
  sub-directories of 1Mb or more:
    data      7.1Mb
    doc      25.4Mb
    extdata   5.6Mb
* 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 'pdf'
GSEA: no visible global function definition for 'colors'
GSEA: no visible global function definition for 'savePlot'
GSEA: no visible global function definition for 'dev.cur'
GSEA: no visible global function definition for 'dev.off'
GSEA.Analyze.Sets: no visible global function definition for 'windows'
GSEA.Analyze.Sets: no visible global function definition for 'pdf'
GSEA.Analyze.Sets: no visible global function definition for 'savePlot'
GSEA.Analyze.Sets: no visible global function definition for 'dev.cur'
GSEA.Analyze.Sets: no visible global function definition for 'dev.off'
GSEA.HeatMapPlot2: no visible global function definition for 'rainbow'
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'
getGenProfs: no visible binding for global variable 'tl'
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'
plotModel : Save: no visible global function definition for
  'graphics.off'
plotModel : Save: no visible global function definition for 'jpeg'
plotModel : Save: no visible global function definition for 'dev.off'
plotModel : Save: no visible global function definition for 'png'
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 colors
  curselectCases dev.cur dev.off devSVG fname.CLS fname.GCT
  fname.MSigDB graphics.off jpeg lenght mSigDB_SubName myGlobalEnv pdf
  png rainbow savePlot tl ttCasesGenProfs ttMain windows x
Consider adding
  importFrom("grDevices", "colors", "dev.cur", "dev.off", "graphics.off",
             "jpeg", "pdf", "png", "rainbow", "savePlot", "windows")
to your NAMESPACE file.
* 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
  'E:/biocbld/bbs-3.3-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_1.4.0.zip
* DONE (canceR)

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

nameusersystemelapsed
ClinicalData0.030.000.03
GSEA.Analyze.Sets000
GSEA.ConsPlot000
GSEA.EnrichmentScore000
GSEA.EnrichmentScore2000
GSEA.Gct2Frame000
GSEA.Gct2Frame2000
GSEA.GeneRanking0.000.020.02
GSEA.HeatMapPlot000
GSEA.HeatMapPlot2000
GSEA.NormalizeCols0.250.000.25
GSEA.NormalizeRows000
GSEA000
GSEA.ReadClsFile0.230.000.23
GSEA.Res2Frame0.240.000.23
GSEA.Threshold0.250.000.25
GSEA.VarFilter0.230.000.24
GSEA.write.gct0.250.000.25
GeneExpMatrix0.060.000.06
Match_GeneList_MSigDB0.360.000.36
OLD.GSEA.EnrichmentScore0.220.000.22
Run.GSEA0.240.000.24
about0.000.000.06
canceR000
canceRHelp0.010.000.02
canceR_Vignette000
cbind.na000
dialogGeneClassifier0.060.000.06
dialogMetOption0.270.000.26
dialogMut0.30.00.3
dialogOptionCircos0.590.000.59
dialogOptionGSEAlm0.000.020.02
dialogOptionPhenoTest0.720.030.75
dialogPlotOption_SkinCor0.110.000.11
dialogSamplingGSEA0.340.010.36
dialogSelectFiles_GSEA0.260.000.26
dialogSpecificMut0.220.020.24
dialogSummary_GSEA0.270.000.26
dialoggetGeneListMSigDB000
displayInTable0.010.000.02
getCases0.660.221.73
getCasesGenProfs0.230.000.23
getCircos0.560.000.56
getClinicData_MultipleCases0.160.000.16
getClinicalDataMatrix0.140.030.17
getCor_ExpCNAMet0.620.000.62
getGCTCLSExample0.250.000.25
getGCT_CLSfiles0.240.000.24
getGSEAlm_Diseases0.220.010.23
getGSEAlm_Variables000
getGenProfs0.460.071.67
getGeneExpMatrix0.190.000.18
getGeneList000
getGeneListExample000
getGeneListFromMSigDB0.170.000.17
getGenesClassifier000
getGenesTree_MultipleCases0.160.000.16
getGenesTree_SingleCase0.280.000.28
getInTable0.020.000.02
getListProfData0.260.000.26
getMSigDB000
getMSigDBExample0.240.000.24
getMSigDBfile0.010.000.01
getMegaProfData0.190.000.19
getMetDataMultipleGenes0.250.000.25
getMutData0.250.000.25
getPhenoTest0.280.000.28
getProfilesDataMultipleGenes0.260.010.28
getProfilesDataSingleGene0.170.000.17
getSpecificMut0.220.020.24
getSummaryGSEA0.240.000.23
getSurvival000
getTextWin000
geteSet000
modalDialog0.150.000.15
myGlobalEnv000
plotModel0.100.000.09
plot_1Gene_2GenProfs0.060.000.07
plot_2Genes_1GenProf0.230.000.23
rbind.na0.020.000.02
setWorkspace0.150.000.15
testCheckedCaseGenProf0.180.000.17

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

nameusersystemelapsed
ClinicalData0.030.000.03
GSEA.Analyze.Sets000
GSEA.ConsPlot000
GSEA.EnrichmentScore000
GSEA.EnrichmentScore2000
GSEA.Gct2Frame000
GSEA.Gct2Frame2000
GSEA.GeneRanking0.020.000.01
GSEA.HeatMapPlot000
GSEA.HeatMapPlot2000
GSEA.NormalizeCols0.170.000.19
GSEA.NormalizeRows000
GSEA000
GSEA.ReadClsFile0.20.00.2
GSEA.Res2Frame0.20.00.2
GSEA.Threshold0.190.000.19
GSEA.VarFilter0.20.00.2
GSEA.write.gct0.20.00.2
GeneExpMatrix0.030.000.03
Match_GeneList_MSigDB0.270.000.27
OLD.GSEA.EnrichmentScore0.20.00.2
Run.GSEA0.190.000.19
about0.020.000.12
canceR000
canceRHelp000
canceR_Vignette000
cbind.na000
dialogGeneClassifier0.060.000.06
dialogMetOption0.210.000.21
dialogMut0.180.000.18
dialogOptionCircos0.230.000.23
dialogOptionGSEAlm0.000.010.02
dialogOptionPhenoTest0.810.020.82
dialogPlotOption_SkinCor0.070.000.07
dialogSamplingGSEA0.20.00.2
dialogSelectFiles_GSEA0.190.000.19
dialogSpecificMut0.180.020.20
dialogSummary_GSEA0.210.000.20
dialoggetGeneListMSigDB000
displayInTable000
getCases0.250.211.30
getCasesGenProfs0.140.020.15
getCircos0.640.000.64
getClinicData_MultipleCases0.230.000.24
getClinicalDataMatrix0.220.000.22
getCor_ExpCNAMet0.780.000.78
getGCTCLSExample0.280.000.28
getGCT_CLSfiles0.300.030.32
getGSEAlm_Diseases0.250.000.25
getGSEAlm_Variables000
getGenProfs0.310.111.55
getGeneExpMatrix0.170.000.17
getGeneList000
getGeneListExample000
getGeneListFromMSigDB0.190.000.19
getGenesClassifier000
getGenesTree_MultipleCases0.150.000.15
getGenesTree_SingleCase0.210.000.21
getInTable0.000.020.09
getListProfData0.140.000.14
getMSigDB000
getMSigDBExample0.140.000.14
getMSigDBfile000
getMegaProfData0.140.000.14
getMetDataMultipleGenes0.20.00.2
getMutData0.190.000.19
getPhenoTest0.210.000.22
getProfilesDataMultipleGenes0.240.000.23
getProfilesDataSingleGene0.140.000.14
getSpecificMut0.190.000.19
getSummaryGSEA0.210.000.22
getSurvival000
getTextWin000
geteSet000
modalDialog0.130.000.13
myGlobalEnv000
plotModel0.060.000.07
plot_1Gene_2GenProfs0.110.000.11
plot_2Genes_1GenProf0.340.000.34
rbind.na000
setWorkspace0.180.000.18
testCheckedCaseGenProf0.160.000.15