Karim Mezhoud
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/canceR |
| git_branch: master |
| git_last_commit: 7d00feb |
| git_last_commit_date: 2021-10-26 12:19:06 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:06 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the canceR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/canceR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 238/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| canceR 1.29.0 (landing page) Karim Mezhoud
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: canceR |
| Version: 1.29.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:canceR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings canceR_1.29.0.tar.gz |
| StartedAt: 2022-03-17 18:38:06 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:41:17 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 191.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: canceR.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:canceR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings canceR_1.29.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/canceR.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.29.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Files named as vignettes but with no recognized vignette engine:
'inst/doc/canceR.Rnw'
(Is a VignetteBuilder field missing?)
* 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 whether package 'canceR' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.3Mb
sub-directories of 1Mb or more:
doc 3.4Mb
* checking package 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 ... OK
* 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 installed files from 'inst/doc' ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
'canceR.Rnw'
A 'vignettes' directory is required as from R 3.1.0
and these will not be indexed nor checked
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/canceR.Rcheck/00check.log'
for details.
canceR.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL canceR
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'canceR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'canceR'
finding HTML links ... done
GSEA.Analyze.Sets html
GSEA.ConsPlot html
GSEA.EnrichmentScore html
GSEA.EnrichmentScore2 html
GSEA.Gct2Frame html
GSEA.Gct2Frame2 html
GSEA.GeneRanking html
GSEA.HeatMapPlot html
GSEA.HeatMapPlot2 html
GSEA.NormalizeCols html
GSEA.NormalizeRows html
GSEA html
GSEA.ReadClsFile html
GSEA.Res2Frame html
GSEA.Threshold html
GSEA.VarFilter html
GSEA.write.gct html
Match_GeneList_MSigDB html
OLD.GSEA.EnrichmentScore html
Run.GSEA html
about html
canceR html
canceRHelp html
canceR_Vignette html
cbind.na html
dialogGeneClassifier html
dialogMetOption html
dialogMut html
dialogOptionCircos html
dialogOptionGSEAlm html
dialogOptionPhenoTest html
dialogPlotOption_SkinCor html
dialogSamplingGSEA html
dialogSelectFiles_GSEA html
dialogSpecificMut html
dialogSummary_GSEA html
dialoggetGeneListMSigDB html
displayInTable html
getCases html
getCasesGenProfs html
getCircos html
getClinicData_MultipleCases html
getClinicalDataMatrix html
getCor_ExpCNAMet html
getGCTCLSExample html
getGCT_CLSfiles html
getGSEAlm_Diseases html
getGSEAlm_Variables html
getGenProfs html
getGeneExpMatrix html
getGeneList html
getGeneListExample html
getGeneListFromMSigDB html
getGenesClassifier html
getGenesTree_MultipleCases html
getGenesTree_SingleCase html
getInTable html
getListProfData html
getMSigDB html
getMSigDBExample html
getMSigDBfile html
getMegaProfData html
getMetDataMultipleGenes html
getMutData html
getPhenoTest html
getProfilesDataMultipleGenes html
getProfilesDataSingleGene html
getSpecificMut html
getSummaryGSEA html
getSurvival html
getTextWin html
geteSet html
modalDialog html
myGlobalEnv html
plotModel html
plot_1Gene_2GenProfs html
plot_2Genes_1GenProf html
rbind.na html
setWorkspace html
testCheckedCaseGenProf html
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (canceR)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'InTAD' is missing or broken
done
canceR.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
>
> 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
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 0 ]
== Skipped tests ===============================================================
* empty test (1)
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 0 ]
>
> proc.time()
user system elapsed
8.01 0.54 9.60
canceR.Rcheck/canceR-Ex.timings
| name | user | system | elapsed | |
| 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 | 0 | 0 | |
| GSEA.NormalizeRows | 0 | 0 | 0 | |
| GSEA | 0 | 0 | 0 | |
| GSEA.ReadClsFile | 0 | 0 | 0 | |
| GSEA.Res2Frame | 0 | 0 | 0 | |
| GSEA.Threshold | 0 | 0 | 0 | |
| GSEA.VarFilter | 0 | 0 | 0 | |
| GSEA.write.gct | 0 | 0 | 0 | |
| Match_GeneList_MSigDB | 0 | 0 | 0 | |
| OLD.GSEA.EnrichmentScore | 0 | 0 | 0 | |
| Run.GSEA | 0 | 0 | 0 | |
| about | 0 | 0 | 0 | |
| canceR | 0 | 0 | 0 | |
| canceRHelp | 0 | 0 | 0 | |
| canceR_Vignette | 0 | 0 | 0 | |
| cbind.na | 0 | 0 | 0 | |
| dialogGeneClassifier | 0 | 0 | 0 | |
| dialogMetOption | 0 | 0 | 0 | |
| dialogMut | 0 | 0 | 0 | |
| dialogOptionCircos | 0 | 0 | 0 | |
| dialogOptionGSEAlm | 0 | 0 | 0 | |
| dialogOptionPhenoTest | 0 | 0 | 0 | |
| dialogPlotOption_SkinCor | 0 | 0 | 0 | |
| dialogSamplingGSEA | 0 | 0 | 0 | |
| dialogSelectFiles_GSEA | 0 | 0 | 0 | |
| dialogSpecificMut | 0 | 0 | 0 | |
| dialogSummary_GSEA | 0.01 | 0.00 | 0.02 | |
| dialoggetGeneListMSigDB | 0 | 0 | 0 | |
| displayInTable | 0 | 0 | 0 | |
| getCases | 0.13 | 0.00 | 0.31 | |
| getCasesGenProfs | 0 | 0 | 0 | |
| getCircos | 0 | 0 | 0 | |
| getClinicData_MultipleCases | 0 | 0 | 0 | |
| getClinicalDataMatrix | 0 | 0 | 0 | |
| getCor_ExpCNAMet | 0 | 0 | 0 | |
| getGCTCLSExample | 0 | 0 | 0 | |
| getGCT_CLSfiles | 0.01 | 0.00 | 0.02 | |
| getGSEAlm_Diseases | 0 | 0 | 0 | |
| getGSEAlm_Variables | 0 | 0 | 0 | |
| getGenProfs | 0.05 | 0.00 | 0.23 | |
| getGeneList | 0 | 0 | 0 | |
| getGeneListExample | 0 | 0 | 0 | |
| getGeneListFromMSigDB | 0 | 0 | 0 | |
| getGenesClassifier | 0 | 0 | 0 | |
| getGenesTree_MultipleCases | 0 | 0 | 0 | |
| getGenesTree_SingleCase | 0 | 0 | 0 | |
| getInTable | 0 | 0 | 0 | |
| getListProfData | 0 | 0 | 0 | |
| getMSigDB | 0 | 0 | 0 | |
| getMSigDBExample | 0 | 0 | 0 | |
| getMSigDBfile | 0 | 0 | 0 | |
| getMegaProfData | 0 | 0 | 0 | |
| getMetDataMultipleGenes | 0 | 0 | 0 | |
| getMutData | 0 | 0 | 0 | |
| getPhenoTest | 0 | 0 | 0 | |
| getProfilesDataMultipleGenes | 0 | 0 | 0 | |
| getProfilesDataSingleGene | 0 | 0 | 0 | |
| getSpecificMut | 0.00 | 0.02 | 0.01 | |
| getSummaryGSEA | 0 | 0 | 0 | |
| getSurvival | 0 | 0 | 0 | |
| getTextWin | 0 | 0 | 0 | |
| geteSet | 0 | 0 | 0 | |
| modalDialog | 0 | 0 | 0 | |
| myGlobalEnv | 0 | 0 | 0 | |
| plotModel | 0 | 0 | 0 | |
| plot_1Gene_2GenProfs | 0 | 0 | 0 | |
| plot_2Genes_1GenProf | 0 | 0 | 0 | |
| rbind.na | 0 | 0 | 0 | |
| setWorkspace | 0 | 0 | 0 | |
| testCheckedCaseGenProf | 0 | 0 | 0 | |