Karim Mezhoud
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/canceR |
| Branch: RELEASE_3_6 |
| Last Commit: b980fea |
| Last Changed Date: 2017-10-30 12:40:49 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:13:19 -0400 (Thu, 12 Apr 2018).
| Package 174/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| canceR 1.10.0 Karim Mezhoud
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: canceR |
| Version: 1.10.0 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings canceR_1.10.0.tar.gz |
| StartedAt: 2018-04-11 21:58:43 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 22:04:45 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 361.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: canceR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings canceR_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/canceR.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.10.0’
* 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 36.1Mb
sub-directories of 1Mb or more:
data 7.1Mb
doc 25.6Mb
extdata 3.0Mb
* 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)
* 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 ... 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: 5 NOTEs
See
‘/home/biocbuild/bbs-3.6-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/tests/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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
13.728 0.708 17.185
canceR.Rcheck/canceR-Ex.timings
| name | user | system | elapsed | |
| ClinicalData | 0.012 | 0.000 | 0.011 | |
| GSEA.Analyze.Sets | 0 | 0 | 0 | |
| GSEA.ConsPlot | 0.000 | 0.000 | 0.001 | |
| GSEA.EnrichmentScore | 0 | 0 | 0 | |
| GSEA.EnrichmentScore2 | 0.000 | 0.000 | 0.001 | |
| GSEA.Gct2Frame | 0.000 | 0.000 | 0.001 | |
| GSEA.Gct2Frame2 | 0 | 0 | 0 | |
| GSEA.GeneRanking | 0.000 | 0.000 | 0.001 | |
| GSEA.HeatMapPlot | 0.000 | 0.000 | 0.001 | |
| GSEA.HeatMapPlot2 | 0.000 | 0.000 | 0.001 | |
| GSEA.NormalizeCols | 0.212 | 0.004 | 0.222 | |
| GSEA.NormalizeRows | 0 | 0 | 0 | |
| GSEA | 0 | 0 | 0 | |
| GSEA.ReadClsFile | 0.16 | 0.00 | 0.16 | |
| GSEA.Res2Frame | 0.156 | 0.004 | 0.162 | |
| GSEA.Threshold | 0.164 | 0.000 | 0.160 | |
| GSEA.VarFilter | 0.196 | 0.004 | 0.199 | |
| GSEA.write.gct | 0.156 | 0.004 | 0.160 | |
| GeneExpMatrix | 0.02 | 0.00 | 0.02 | |
| Match_GeneList_MSigDB | 0.260 | 0.004 | 0.264 | |
| OLD.GSEA.EnrichmentScore | 0.160 | 0.004 | 0.163 | |
| Run.GSEA | 0.164 | 0.000 | 0.166 | |
| about | 0.016 | 0.000 | 0.020 | |
| canceR | 0 | 0 | 0 | |
| canceRHelp | 0.000 | 0.000 | 0.001 | |
| canceR_Vignette | 0.000 | 0.020 | 0.022 | |
| cbind.na | 0.004 | 0.000 | 0.005 | |
| dialogGeneClassifier | 0.052 | 0.008 | 0.060 | |
| dialogMetOption | 0.236 | 0.012 | 0.250 | |
| dialogMut | 0.176 | 0.000 | 0.176 | |
| dialogOptionCircos | 0.172 | 0.004 | 0.175 | |
| dialogOptionGSEAlm | 0.004 | 0.000 | 0.005 | |
| dialogOptionPhenoTest | 0.240 | 0.000 | 0.243 | |
| dialogPlotOption_SkinCor | 0.052 | 0.000 | 0.049 | |
| dialogSamplingGSEA | 0.172 | 0.000 | 0.172 | |
| dialogSelectFiles_GSEA | 0.240 | 0.000 | 0.238 | |
| dialogSpecificMut | 0.292 | 0.012 | 0.304 | |
| dialogSummary_GSEA | 0.264 | 0.012 | 0.277 | |
| dialoggetGeneListMSigDB | 0 | 0 | 0 | |
| displayInTable | 0.008 | 0.000 | 0.008 | |
| getCases | 0.272 | 0.016 | 0.864 | |
| getCasesGenProfs | 0.204 | 0.004 | 0.207 | |
| getCircos | 0.764 | 0.072 | 0.841 | |
| getClinicData_MultipleCases | 0.116 | 0.000 | 0.115 | |
| getClinicalDataMatrix | 0.116 | 0.000 | 0.115 | |
| getCor_ExpCNAMet | 0.152 | 0.004 | 0.157 | |
| getGCTCLSExample | 0.16 | 0.00 | 0.16 | |
| getGCT_CLSfiles | 0.188 | 0.000 | 0.187 | |
| getGSEAlm_Diseases | 0.160 | 0.008 | 0.169 | |
| getGSEAlm_Variables | 0.000 | 0.000 | 0.001 | |
| getGenProfs | 0.020 | 0.008 | 0.763 | |
| getGeneExpMatrix | 0.180 | 0.020 | 0.198 | |
| getGeneList | 0.000 | 0.000 | 0.001 | |
| getGeneListExample | 0 | 0 | 0 | |
| getGeneListFromMSigDB | 0.136 | 0.000 | 0.136 | |
| getGenesClassifier | 0 | 0 | 0 | |
| getGenesTree_MultipleCases | 0.144 | 0.000 | 0.145 | |
| getGenesTree_SingleCase | 0.180 | 0.008 | 0.190 | |
| getInTable | 0.004 | 0.000 | 0.006 | |
| getListProfData | 0.104 | 0.004 | 0.112 | |
| getMSigDB | 0 | 0 | 0 | |
| getMSigDBExample | 0.132 | 0.000 | 0.132 | |
| getMSigDBfile | 0.004 | 0.000 | 0.000 | |
| getMegaProfData | 0.144 | 0.004 | 0.151 | |
| getMetDataMultipleGenes | 0.200 | 0.004 | 0.204 | |
| getMutData | 0.160 | 0.008 | 0.167 | |
| getPhenoTest | 0.192 | 0.004 | 0.194 | |
| getProfilesDataMultipleGenes | 0.200 | 0.008 | 0.209 | |
| getProfilesDataSingleGene | 0.152 | 0.000 | 0.150 | |
| getSpecificMut | 0.196 | 0.008 | 0.204 | |
| getSummaryGSEA | 0.180 | 0.008 | 0.191 | |
| getSurvival | 0 | 0 | 0 | |
| getTextWin | 0.000 | 0.000 | 0.001 | |
| geteSet | 0 | 0 | 0 | |
| modalDialog | 0.128 | 0.000 | 0.130 | |
| myGlobalEnv | 0 | 0 | 0 | |
| plotModel | 0.048 | 0.004 | 0.053 | |
| plot_1Gene_2GenProfs | 0.052 | 0.000 | 0.052 | |
| plot_2Genes_1GenProf | 0.188 | 0.000 | 0.188 | |
| rbind.na | 0.004 | 0.000 | 0.002 | |
| setWorkspace | 0.12 | 0.00 | 0.12 | |
| testCheckedCaseGenProf | 0.108 | 0.004 | 0.116 | |