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 11:41:31 -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: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:canceR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings canceR_1.17.1.tar.gz |
| StartedAt: 2019-04-08 23:11:39 -0400 (Mon, 08 Apr 2019) |
| EndedAt: 2019-04-08 23:20:32 -0400 (Mon, 08 Apr 2019) |
| EllapsedTime: 533.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: canceR.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:canceR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings canceR_1.17.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/canceR.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (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 10.8Mb
sub-directories of 1Mb or more:
data 7.1Mb
extdata 3.0Mb
* 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 xinwang2hms@gmail.com---------------//
/////////////////////////////////////////////////////////////////////////////
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 xinwang2hms@gmail.com---------------//
/////////////////////////////////////////////////////////////////////////////
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 xinwang2hms@gmail.com---------------//
/////////////////////////////////////////////////////////////////////////////
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 xinwang2hms@gmail.com---------------//
/////////////////////////////////////////////////////////////////////////////
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 xinwang2hms@gmail.com---------------//
/////////////////////////////////////////////////////////////////////////////
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 xinwang2hms@gmail.com---------------//
/////////////////////////////////////////////////////////////////////////////
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 xinwang2hms@gmail.com---------------//
/////////////////////////////////////////////////////////////////////////////
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 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
‘/home/biocbuild/bbs-3.9-bioc/meat/canceR.Rcheck/00check.log’
for details.
canceR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL canceR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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-pc-linux-gnu (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 cbioportal@googlegroups.com
/////////////////////////////////////////////////////////////////////////////
//------------------ Thanks for using HTSanalyzeR -------------------//
//------------please use function changes() to see new changes-------------//
//------------please report any bug to xinwang2hms@gmail.com---------------//
/////////////////////////////////////////////////////////////////////////////
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
16.695 1.248 20.113
canceR.Rcheck/canceR-Ex.timings
| name | user | system | elapsed | |
| ClinicalData | 0.007 | 0.000 | 0.008 | |
| 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 | 0 | 0 | |
| GSEA.NormalizeCols | 0.165 | 0.002 | 0.167 | |
| GSEA.NormalizeRows | 0.001 | 0.000 | 0.000 | |
| GSEA | 0 | 0 | 0 | |
| GSEA.ReadClsFile | 0.161 | 0.004 | 0.165 | |
| GSEA.Res2Frame | 0.193 | 0.000 | 0.194 | |
| GSEA.Threshold | 0.156 | 0.000 | 0.157 | |
| GSEA.VarFilter | 0.183 | 0.004 | 0.186 | |
| GSEA.write.gct | 0.287 | 0.000 | 0.287 | |
| GeneExpMatrix | 0.025 | 0.000 | 0.026 | |
| Match_GeneList_MSigDB | 0.305 | 0.000 | 0.305 | |
| OLD.GSEA.EnrichmentScore | 0.290 | 0.003 | 0.294 | |
| Run.GSEA | 0.156 | 0.008 | 0.164 | |
| about | 0 | 0 | 0 | |
| canceR | 0 | 0 | 0 | |
| canceRHelp | 0 | 0 | 0 | |
| canceR_Vignette | 0 | 0 | 0 | |
| cbind.na | 0 | 0 | 0 | |
| dialogGeneClassifier | 0.041 | 0.004 | 0.044 | |
| dialogMetOption | 0.149 | 0.004 | 0.153 | |
| dialogMut | 0.157 | 0.000 | 0.157 | |
| dialogOptionCircos | 0.176 | 0.000 | 0.176 | |
| dialogOptionGSEAlm | 0.004 | 0.000 | 0.004 | |
| dialogOptionPhenoTest | 0.211 | 0.008 | 0.219 | |
| dialogPlotOption_SkinCor | 0.079 | 0.004 | 0.082 | |
| dialogSamplingGSEA | 0.277 | 0.004 | 0.280 | |
| dialogSelectFiles_GSEA | 0.283 | 0.004 | 0.287 | |
| dialogSpecificMut | 0.274 | 0.008 | 0.282 | |
| dialogSummary_GSEA | 0.299 | 0.008 | 0.307 | |
| dialoggetGeneListMSigDB | 0 | 0 | 0 | |
| displayInTable | 0.005 | 0.000 | 0.006 | |
| getCases | 0.032 | 0.000 | 0.639 | |
| getCasesGenProfs | 0.199 | 0.000 | 0.204 | |
| getCircos | 0.214 | 0.000 | 0.218 | |
| getClinicData_MultipleCases | 0.171 | 0.000 | 0.172 | |
| getClinicalDataMatrix | 0.115 | 0.000 | 0.114 | |
| getCor_ExpCNAMet | 0.144 | 0.004 | 0.148 | |
| getGCTCLSExample | 0.210 | 0.012 | 0.222 | |
| getGCT_CLSfiles | 0.234 | 0.000 | 0.234 | |
| getGSEAlm_Diseases | 0.228 | 0.000 | 0.227 | |
| getGSEAlm_Variables | 0.000 | 0.000 | 0.001 | |
| getGenProfs | 0.011 | 0.018 | 0.916 | |
| getGeneExpMatrix | 0.197 | 0.001 | 0.198 | |
| getGeneList | 0 | 0 | 0 | |
| getGeneListExample | 0 | 0 | 0 | |
| getGeneListFromMSigDB | 0.192 | 0.008 | 0.201 | |
| getGenesClassifier | 0.001 | 0.000 | 0.000 | |
| getGenesTree_MultipleCases | 0.214 | 0.004 | 0.218 | |
| getGenesTree_SingleCase | 0.287 | 0.000 | 0.286 | |
| getInTable | 0.005 | 0.000 | 0.005 | |
| getListProfData | 0.186 | 0.004 | 0.190 | |
| getMSigDB | 0 | 0 | 0 | |
| getMSigDBExample | 0.183 | 0.004 | 0.187 | |
| getMSigDBfile | 0.000 | 0.000 | 0.001 | |
| getMegaProfData | 0.188 | 0.004 | 0.191 | |
| getMetDataMultipleGenes | 0.262 | 0.008 | 0.270 | |
| getMutData | 0.263 | 0.004 | 0.268 | |
| getPhenoTest | 0.274 | 0.008 | 0.283 | |
| getProfilesDataMultipleGenes | 0.302 | 0.008 | 0.310 | |
| getProfilesDataSingleGene | 0.195 | 0.000 | 0.195 | |
| getSpecificMut | 0.264 | 0.008 | 0.273 | |
| getSummaryGSEA | 0.267 | 0.003 | 0.270 | |
| getSurvival | 0 | 0 | 0 | |
| getTextWin | 0.000 | 0.000 | 0.001 | |
| geteSet | 0.000 | 0.000 | 0.001 | |
| modalDialog | 0.189 | 0.000 | 0.190 | |
| myGlobalEnv | 0 | 0 | 0 | |
| plotModel | 0.079 | 0.000 | 0.079 | |
| plot_1Gene_2GenProfs | 0.067 | 0.011 | 0.077 | |
| plot_2Genes_1GenProf | 0.278 | 0.007 | 0.286 | |
| rbind.na | 0.000 | 0.001 | 0.000 | |
| setWorkspace | 0.188 | 0.004 | 0.193 | |
| testCheckedCaseGenProf | 0.191 | 0.003 | 0.195 | |