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BioC 3.6: CHECK report for canceR on tokay1

This page was generated on 2017-08-16 13:34:11 -0400 (Wed, 16 Aug 2017).

Package 167/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
canceR 1.9.0
Karim Mezhoud
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/canceR
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: canceR
Version: 1.9.0
Command: rm -rf canceR.buildbin-libdir canceR.Rcheck && mkdir canceR.buildbin-libdir canceR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=canceR.buildbin-libdir canceR_1.9.0.tar.gz >canceR.Rcheck\00install.out 2>&1 && cp canceR.Rcheck\00install.out canceR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=canceR.buildbin-libdir --install="check:canceR-install.out" --force-multiarch --no-vignettes --timings canceR_1.9.0.tar.gz
StartedAt: 2017-08-15 22:09:09 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:17:47 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 518.2 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 && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=canceR.buildbin-libdir canceR_1.9.0.tar.gz >canceR.Rcheck\00install.out 2>&1 && cp canceR.Rcheck\00install.out canceR-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=canceR.buildbin-libdir --install="check:canceR-install.out" --force-multiarch --no-vignettes --timings canceR_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/canceR.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.9.0'
* 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)
Undefined global functions or variables:
  savePlot windows
Consider adding
  importFrom("grDevices", "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 ... NOTE
S3 methods shown with full name in documentation object 'cbind.na':
  'cbind.na'

S3 methods shown with full name in documentation object 'rbind.na':
  'rbind.na'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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: 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-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_1.9.0.zip
* DONE (canceR)

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

nameusersystemelapsed
ClinicalData0.010.000.01
GSEA.Analyze.Sets000
GSEA.ConsPlot000
GSEA.EnrichmentScore000
GSEA.EnrichmentScore2000
GSEA.Gct2Frame000
GSEA.Gct2Frame2000
GSEA.GeneRanking000
GSEA.HeatMapPlot000
GSEA.HeatMapPlot2000
GSEA.NormalizeCols0.200.020.22
GSEA.NormalizeRows000
GSEA000
GSEA.ReadClsFile0.190.000.19
GSEA.Res2Frame0.180.010.19
GSEA.Threshold0.260.020.28
GSEA.VarFilter0.190.010.20
GSEA.write.gct0.200.000.21
GeneExpMatrix0.020.000.01
Match_GeneList_MSigDB0.650.020.67
OLD.GSEA.EnrichmentScore0.210.000.21
Run.GSEA0.220.000.22
about0.010.000.02
canceR000
canceRHelp000
canceR_Vignette0.030.070.82
cbind.na000
dialogGeneClassifier0.070.000.07
dialogMetOption0.230.010.25
dialogMut0.200.020.22
dialogOptionCircos0.180.050.21
dialogOptionGSEAlm000
dialogOptionPhenoTest0.260.000.27
dialogPlotOption_SkinCor0.080.000.07
dialogSamplingGSEA0.190.020.21
dialogSelectFiles_GSEA0.20.00.2
dialogSpecificMut0.190.010.20
dialogSummary_GSEA0.200.000.21
dialoggetGeneListMSigDB000
displayInTable0.000.020.01
getCases0.310.120.71
getCasesGenProfs0.130.000.12
getCircos0.190.000.19
getClinicData_MultipleCases0.120.020.14
getClinicalDataMatrix0.130.010.14
getCor_ExpCNAMet0.620.020.64
getGCTCLSExample0.20.00.2
getGCT_CLSfiles0.190.020.21
getGSEAlm_Diseases0.20.00.2
getGSEAlm_Variables000
getGenProfs0.300.140.75
getGeneExpMatrix0.140.000.14
getGeneList000
getGeneListExample000
getGeneListFromMSigDB0.160.000.16
getGenesClassifier000
getGenesTree_MultipleCases0.150.000.15
getGenesTree_SingleCase0.250.000.25
getInTable0.000.010.02
getListProfData0.240.020.25
getMSigDB000
getMSigDBExample0.20.00.2
getMSigDBfile000
getMegaProfData0.140.000.14
getMetDataMultipleGenes0.210.000.20
getMutData0.200.000.21
getPhenoTest0.220.000.22
getProfilesDataMultipleGenes0.250.000.25
getProfilesDataSingleGene0.140.000.14
getSpecificMut0.210.000.21
getSummaryGSEA0.20.00.2
getSurvival000
getTextWin000
geteSet000
modalDialog0.140.000.15
myGlobalEnv000
plotModel0.060.000.06
plot_1Gene_2GenProfs0.060.000.06
plot_2Genes_1GenProf0.20.00.2
rbind.na000
setWorkspace0.140.000.14
testCheckedCaseGenProf0.140.000.14

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

nameusersystemelapsed
ClinicalData0.020.000.02
GSEA.Analyze.Sets000
GSEA.ConsPlot000
GSEA.EnrichmentScore000
GSEA.EnrichmentScore2000
GSEA.Gct2Frame000
GSEA.Gct2Frame2000
GSEA.GeneRanking000
GSEA.HeatMapPlot000
GSEA.HeatMapPlot2000
GSEA.NormalizeCols0.170.000.17
GSEA.NormalizeRows000
GSEA000
GSEA.ReadClsFile0.160.020.17
GSEA.Res2Frame0.170.000.17
GSEA.Threshold0.150.010.18
GSEA.VarFilter0.240.020.25
GSEA.write.gct0.140.020.15
GeneExpMatrix0.010.000.01
Match_GeneList_MSigDB0.210.000.21
OLD.GSEA.EnrichmentScore0.150.000.15
Run.GSEA0.720.000.72
about0.000.000.97
canceR000
canceRHelp000
canceR_Vignette0.020.002.17
cbind.na000
dialogGeneClassifier0.050.000.05
dialogMetOption0.170.000.17
dialogMut0.160.010.17
dialogOptionCircos0.160.000.16
dialogOptionGSEAlm000
dialogOptionPhenoTest0.180.020.20
dialogPlotOption_SkinCor0.050.000.05
dialogSamplingGSEA0.140.030.17
dialogSelectFiles_GSEA0.150.000.15
dialogSpecificMut0.160.020.18
dialogSummary_GSEA0.150.000.15
dialoggetGeneListMSigDB000
displayInTable000
getCases0.300.120.65
getCasesGenProfs0.110.020.13
getCircos0.150.000.16
getClinicData_MultipleCases0.130.000.12
getClinicalDataMatrix0.120.000.13
getCor_ExpCNAMet0.170.000.17
getGCTCLSExample0.820.000.81
getGCT_CLSfiles0.170.000.17
getGSEAlm_Diseases0.170.000.17
getGSEAlm_Variables000
getGenProfs0.170.090.61
getGeneExpMatrix0.110.000.11
getGeneList000
getGeneListExample000
getGeneListFromMSigDB0.120.000.12
getGenesClassifier000
getGenesTree_MultipleCases0.130.000.13
getGenesTree_SingleCase0.20.00.2
getInTable000
getListProfData0.130.000.13
getMSigDB000
getMSigDBExample0.110.000.11
getMSigDBfile0.010.000.01
getMegaProfData0.090.000.10
getMetDataMultipleGenes0.160.010.17
getMutData0.170.000.17
getPhenoTest0.190.000.19
getProfilesDataMultipleGenes0.200.000.21
getProfilesDataSingleGene0.110.000.10
getSpecificMut0.170.000.18
getSummaryGSEA0.150.020.15
getSurvival000
getTextWin000
geteSet000
modalDialog0.130.000.12
myGlobalEnv000
plotModel0.040.010.07
plot_1Gene_2GenProfs0.050.000.04
plot_2Genes_1GenProf0.160.000.16
rbind.na000
setWorkspace0.100.020.11
testCheckedCaseGenProf0.120.000.13