Karim Mezhoud
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/canceR |
| Branch: master |
| Last Commit: d0e4002 |
| Last Changed Date: 2019-02-21 17:03:40 -0400 (Thu, 21 Feb 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:13:35 -0400 (Tue, 09 Apr 2019).
| Package 202/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| canceR 1.17.1 Karim Mezhoud
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: canceR |
| Version: 1.17.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:canceR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings canceR_1.17.1.tar.gz |
| StartedAt: 2019-04-09 00:22:00 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 00:36:34 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 873.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: canceR.Rcheck |
| Warnings: 1 |
##############################################################################
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:canceR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings canceR_1.17.1.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/canceR.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.17.1’
* package encoding: UTF-8
* 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 ... OK
* 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 10.7Mb
sub-directories of 1Mb or more:
data 7.1Mb
extdata 2.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 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 ‘savePlot’
GSEA: no visible global function definition for ‘dev.new’
GSEA.Analyze.Sets: no visible global function definition for ‘savePlot’
Undefined global functions or variables:
dev.new savePlot
Consider adding
importFrom("grDevices", "dev.new", "savePlot")
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 ... WARNING
‘data/datalist’ is a directory
Output for data("Circos", package = "canceR"):
/////////////////////////////////////////////////////////////////////////////
//------------------ Thanks for using HTSanalyzeR -------------------//
//------------please use function changes() to see new changes-------------//
//------------please report any bug to [email protected]//
/////////////////////////////////////////////////////////////////////////////
Warning message:
replacing previous import ‘igraph::union’ by ‘GSEABase::union’ when loading ‘HTSanalyzeR’
Output for data("brca_tcga73genes", package = "canceR"):
/////////////////////////////////////////////////////////////////////////////
//------------------ Thanks for using HTSanalyzeR -------------------//
//------------please use function changes() to see new changes-------------//
//------------please report any bug to [email protected]//
/////////////////////////////////////////////////////////////////////////////
Warning message:
replacing previous import ‘igraph::union’ by ‘GSEABase::union’ when loading ‘HTSanalyzeR’
Output for data("brca_tcgaClassifier223", package = "canceR"):
/////////////////////////////////////////////////////////////////////////////
//------------------ Thanks for using HTSanalyzeR -------------------//
//------------please use function changes() to see new changes-------------//
//------------please report any bug to [email protected]//
/////////////////////////////////////////////////////////////////////////////
Warning message:
replacing previous import ‘igraph::union’ by ‘GSEABase::union’ when loading ‘HTSanalyzeR’
Output for data("brca_tcgaGSEAlm1021", package = "canceR"):
/////////////////////////////////////////////////////////////////////////////
//------------------ Thanks for using HTSanalyzeR -------------------//
//------------please use function changes() to see new changes-------------//
//------------please report any bug to [email protected]//
/////////////////////////////////////////////////////////////////////////////
Warning message:
replacing previous import ‘igraph::union’ by ‘GSEABase::union’ when loading ‘HTSanalyzeR’
Output for data("gbm_tcgaPlotTwoGenProf", package = "canceR"):
/////////////////////////////////////////////////////////////////////////////
//------------------ Thanks for using HTSanalyzeR -------------------//
//------------please use function changes() to see new changes-------------//
//------------please report any bug to [email protected]//
/////////////////////////////////////////////////////////////////////////////
Warning message:
replacing previous import ‘igraph::union’ by ‘GSEABase::union’ when loading ‘HTSanalyzeR’
Output for data("prad_michPhenoTest1021", package = "canceR"):
/////////////////////////////////////////////////////////////////////////////
//------------------ Thanks for using HTSanalyzeR -------------------//
//------------please use function changes() to see new changes-------------//
//------------please report any bug to [email protected]//
/////////////////////////////////////////////////////////////////////////////
Warning message:
replacing previous import ‘igraph::union’ by ‘GSEABase::union’ when loading ‘HTSanalyzeR’
Output for data("ucec_tcga_pubGSEA1021", package = "canceR"):
/////////////////////////////////////////////////////////////////////////////
//------------------ Thanks for using HTSanalyzeR -------------------//
//------------please use function changes() to see new changes-------------//
//------------please report any bug to [email protected]//
/////////////////////////////////////////////////////////////////////////////
Warning message:
replacing previous import ‘igraph::union’ by ‘GSEABase::union’ when loading ‘HTSanalyzeR’
* 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 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: 1 WARNING, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/canceR.Rcheck/00check.log’
for details.
canceR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL canceR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘canceR’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare 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 from temporary location Warning: replacing previous import ‘igraph::union’ by ‘GSEABase::union’ when loading ‘HTSanalyzeR’ ** testing if installed package can be loaded from final location Warning: replacing previous import ‘igraph::union’ by ‘GSEABase::union’ when loading ‘HTSanalyzeR’ ** testing if installed package keeps a record of temporary installation path * DONE (canceR)
canceR.Rcheck/tests/testthat.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin15.6.0 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(canceR) Loading required package: tcltk Loading required package: tcltk2 Loading required package: cgdsr Please send questions to [email protected] ///////////////////////////////////////////////////////////////////////////// //------------------ Thanks for using HTSanalyzeR -------------------// //------------please use function changes() to see new changes-------------// //------------please report any bug to [email protected]// ///////////////////////////////////////////////////////////////////////////// Warning message: replacing previous import 'igraph::union' by 'GSEABase::union' when loading 'HTSanalyzeR' > > test_check("canceR") getCancerStudies... OK getCaseLists (1/2) ... OK getCaseLists (2/2) ... OK getGeneticProfiles (1/2) ... OK getGeneticProfiles (2/2) ... OK getClinicalData (1/1) ... OK getProfileData (1/6) ... OK getProfileData (2/6) ... OK getProfileData (3/6) ... OK getProfileData (4/6) ... OK getProfileData (5/6) ... OK getProfileData (6/6) ... OK ══ testthat results ═══════════════════════════════════════════════════════════ OK: 0 SKIPPED: 1 FAILED: 0 > > proc.time() user system elapsed 23.747 4.933 30.978
canceR.Rcheck/canceR-Ex.timings
| name | user | system | elapsed | |
| ClinicalData | 0.011 | 0.004 | 0.016 | |
| GSEA.Analyze.Sets | 0 | 0 | 0 | |
| GSEA.ConsPlot | 0.000 | 0.000 | 0.001 | |
| GSEA.EnrichmentScore | 0.000 | 0.001 | 0.000 | |
| GSEA.EnrichmentScore2 | 0.001 | 0.000 | 0.000 | |
| GSEA.Gct2Frame | 0 | 0 | 0 | |
| GSEA.Gct2Frame2 | 0.001 | 0.000 | 0.001 | |
| GSEA.GeneRanking | 0.000 | 0.001 | 0.001 | |
| GSEA.HeatMapPlot | 0 | 0 | 0 | |
| GSEA.HeatMapPlot2 | 0.000 | 0.000 | 0.001 | |
| GSEA.NormalizeCols | 0.281 | 0.024 | 0.304 | |
| GSEA.NormalizeRows | 0 | 0 | 0 | |
| GSEA | 0.001 | 0.000 | 0.001 | |
| GSEA.ReadClsFile | 0.267 | 0.018 | 0.286 | |
| GSEA.Res2Frame | 0.221 | 0.021 | 0.242 | |
| GSEA.Threshold | 0.257 | 0.013 | 0.270 | |
| GSEA.VarFilter | 0.268 | 0.011 | 0.278 | |
| GSEA.write.gct | 0.265 | 0.011 | 0.276 | |
| GeneExpMatrix | 0.032 | 0.004 | 0.037 | |
| Match_GeneList_MSigDB | 0.239 | 0.020 | 0.260 | |
| OLD.GSEA.EnrichmentScore | 0.232 | 0.014 | 0.247 | |
| Run.GSEA | 0.244 | 0.015 | 0.259 | |
| about | 0.000 | 0.000 | 0.001 | |
| canceR | 0.000 | 0.000 | 0.001 | |
| canceRHelp | 0.000 | 0.000 | 0.001 | |
| canceR_Vignette | 0.001 | 0.000 | 0.000 | |
| cbind.na | 0.000 | 0.000 | 0.001 | |
| dialogGeneClassifier | 0.079 | 0.010 | 0.090 | |
| dialogMetOption | 0.222 | 0.014 | 0.235 | |
| dialogMut | 0.248 | 0.015 | 0.263 | |
| dialogOptionCircos | 0.243 | 0.031 | 0.275 | |
| dialogOptionGSEAlm | 0.006 | 0.003 | 0.010 | |
| dialogOptionPhenoTest | 0.258 | 0.025 | 0.282 | |
| dialogPlotOption_SkinCor | 0.058 | 0.008 | 0.065 | |
| dialogSamplingGSEA | 0.242 | 0.012 | 0.253 | |
| dialogSelectFiles_GSEA | 0.219 | 0.012 | 0.230 | |
| dialogSpecificMut | 0.223 | 0.007 | 0.230 | |
| dialogSummary_GSEA | 0.268 | 0.010 | 0.279 | |
| dialoggetGeneListMSigDB | 0 | 0 | 0 | |
| displayInTable | 0.007 | 0.003 | 0.010 | |
| getCases | 0.030 | 0.017 | 0.912 | |
| getCasesGenProfs | 0.216 | 0.011 | 0.227 | |
| getCircos | 0.207 | 0.014 | 0.221 | |
| getClinicData_MultipleCases | 0.196 | 0.011 | 0.207 | |
| getClinicalDataMatrix | 0.190 | 0.009 | 0.199 | |
| getCor_ExpCNAMet | 0.233 | 0.022 | 0.256 | |
| getGCTCLSExample | 0.161 | 0.008 | 0.168 | |
| getGCT_CLSfiles | 0.187 | 0.013 | 0.200 | |
| getGSEAlm_Diseases | 0.247 | 0.011 | 0.259 | |
| getGSEAlm_Variables | 0.000 | 0.000 | 0.001 | |
| getGenProfs | 0.026 | 0.017 | 0.818 | |
| getGeneExpMatrix | 0.184 | 0.011 | 0.195 | |
| getGeneList | 0.000 | 0.001 | 0.001 | |
| getGeneListExample | 0.001 | 0.000 | 0.000 | |
| getGeneListFromMSigDB | 0.182 | 0.006 | 0.217 | |
| getGenesClassifier | 0.001 | 0.000 | 0.000 | |
| getGenesTree_MultipleCases | 0.178 | 0.008 | 0.186 | |
| getGenesTree_SingleCase | 0.243 | 0.017 | 0.259 | |
| getInTable | 0.005 | 0.003 | 0.007 | |
| getListProfData | 0.113 | 0.008 | 0.121 | |
| getMSigDB | 0.000 | 0.000 | 0.001 | |
| getMSigDBExample | 0.112 | 0.006 | 0.119 | |
| getMSigDBfile | 0.000 | 0.000 | 0.001 | |
| getMegaProfData | 0.114 | 0.008 | 0.121 | |
| getMetDataMultipleGenes | 0.159 | 0.006 | 0.166 | |
| getMutData | 0.290 | 0.012 | 0.303 | |
| getPhenoTest | 0.268 | 0.019 | 0.287 | |
| getProfilesDataMultipleGenes | 0.221 | 0.015 | 0.237 | |
| getProfilesDataSingleGene | 0.139 | 0.007 | 0.145 | |
| getSpecificMut | 0.281 | 0.008 | 0.289 | |
| getSummaryGSEA | 0.204 | 0.009 | 0.214 | |
| getSurvival | 0.001 | 0.000 | 0.000 | |
| getTextWin | 0.000 | 0.000 | 0.001 | |
| geteSet | 0 | 0 | 0 | |
| modalDialog | 0.179 | 0.010 | 0.190 | |
| myGlobalEnv | 0.001 | 0.000 | 0.000 | |
| plotModel | 0.072 | 0.005 | 0.077 | |
| plot_1Gene_2GenProfs | 0.075 | 0.006 | 0.081 | |
| plot_2Genes_1GenProf | 0.253 | 0.009 | 0.263 | |
| rbind.na | 0.001 | 0.000 | 0.000 | |
| setWorkspace | 0.196 | 0.008 | 0.205 | |
| testCheckedCaseGenProf | 0.115 | 0.008 | 0.122 | |