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BioC 3.4: CHECK report for canceR on morelia

This page was generated on 2017-04-15 16:26:19 -0400 (Sat, 15 Apr 2017).

Package 156/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
canceR 1.6.0
Karim Mezhoud
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/canceR
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
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
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: canceR
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings canceR_1.6.0.tar.gz
StartedAt: 2017-04-14 23:29:35 -0700 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 23:35:38 -0700 (Fri, 14 Apr 2017)
EllapsedTime: 363.6 seconds
RetCode: 0
Status:  OK 
CheckDir: canceR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings canceR_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/canceR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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      25.3Mb
    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
* 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’
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 ttCasesGenProfs ttMain x
Consider adding
  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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/canceR.Rcheck/00check.log’
for details.


canceR.Rcheck/00install.out:

* 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’
* DONE (canceR)

canceR.Rcheck/canceR-Ex.timings:

nameusersystemelapsed
ClinicalData0.0100.0010.010
GSEA.Analyze.Sets0.0010.0010.000
GSEA.ConsPlot0.0010.0000.001
GSEA.EnrichmentScore0.0010.0000.000
GSEA.EnrichmentScore20.0000.0000.001
GSEA.Gct2Frame000
GSEA.Gct2Frame20.0010.0000.001
GSEA.GeneRanking0.0010.0000.001
GSEA.HeatMapPlot0.0010.0000.001
GSEA.HeatMapPlot20.0010.0000.001
GSEA.NormalizeCols0.1620.0080.170
GSEA.NormalizeRows0.0010.0000.000
GSEA0.0010.0000.001
GSEA.ReadClsFile0.2310.0090.240
GSEA.Res2Frame0.2220.0060.229
GSEA.Threshold0.1840.0070.191
GSEA.VarFilter0.1760.0080.183
GSEA.write.gct0.1560.0040.160
GeneExpMatrix0.0330.0010.034
Match_GeneList_MSigDB0.2290.0070.236
OLD.GSEA.EnrichmentScore0.2260.0080.232
Run.GSEA0.1860.0050.191
about0.0620.0500.156
canceR0.0010.0000.000
canceRHelp0.0010.0000.001
canceR_Vignette0.0020.0010.002
cbind.na0.0030.0000.002
dialogGeneClassifier0.0550.0040.060
dialogMetOption0.1870.0060.194
dialogMut0.1790.0050.184
dialogOptionCircos0.1650.0060.171
dialogOptionGSEAlm0.0060.0010.007
dialogOptionPhenoTest0.1870.0090.196
dialogPlotOption_SkinCor0.4710.0080.479
dialogSamplingGSEA0.1940.0060.200
dialogSelectFiles_GSEA0.2010.0070.208
dialogSpecificMut0.1940.0070.202
dialogSummary_GSEA0.2210.0060.228
dialoggetGeneListMSigDB0.0000.0000.001
displayInTable0.0070.0010.008
getCases0.0330.0202.508
getCasesGenProfs0.1300.0060.137
getCircos0.1790.0090.187
getClinicData_MultipleCases0.1190.0050.124
getClinicalDataMatrix0.1290.0060.135
getCor_ExpCNAMet0.1230.0050.129
getGCTCLSExample0.2250.0060.230
getGCT_CLSfiles0.1610.0050.167
getGSEAlm_Diseases0.2110.0070.218
getGSEAlm_Variables0.0010.0000.001
getGenProfs0.0340.0253.067
getGeneExpMatrix0.1170.0060.124
getGeneList0.0010.0000.001
getGeneListExample0.0000.0000.001
getGeneListFromMSigDB0.1140.0050.120
getGenesClassifier000
getGenesTree_MultipleCases0.1380.0070.144
getGenesTree_SingleCase0.2420.0070.250
getInTable0.4800.0010.483
getListProfData0.1690.0060.176
getMSigDB0.0000.0000.001
getMSigDBExample0.0990.0050.103
getMSigDBfile000
getMegaProfData0.1050.0050.109
getMetDataMultipleGenes0.2230.0060.230
getMutData0.2330.0070.240
getPhenoTest0.2360.0070.243
getProfilesDataMultipleGenes0.2250.0070.232
getProfilesDataSingleGene0.1170.0050.122
getSpecificMut0.1830.0070.190
getSummaryGSEA0.2180.0070.225
getSurvival0.0010.0000.001
getTextWin0.0010.0000.001
geteSet0.0000.0000.001
modalDialog0.1350.0060.141
myGlobalEnv0.0000.0000.001
plotModel0.0670.0040.072
plot_1Gene_2GenProfs0.0590.0040.064
plot_2Genes_1GenProf0.1740.0050.179
rbind.na0.0020.0000.003
setWorkspace0.1170.0050.121
testCheckedCaseGenProf0.1320.0050.138