Francesco Napolitano
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/gep2pep |
| Branch: RELEASE_3_9 |
| Last Commit: e083bac |
| Last Changed Date: 2019-05-02 11:54:09 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 13:01:25 -0400 (Wed, 16 Oct 2019).
| Package 671/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| gep2pep 1.4.0 Francesco Napolitano
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: gep2pep |
| Version: 1.4.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gep2pep.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gep2pep_1.4.0.tar.gz |
| StartedAt: 2019-10-16 03:13:59 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:17:00 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 180.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: gep2pep.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gep2pep.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gep2pep_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/gep2pep.Rcheck’ * using R version 3.6.1 (2019-07-05) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘gep2pep/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘gep2pep’ version ‘1.4.0’ * 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 ‘gep2pep’ can be installed ... OK * checking installed package size ... OK * 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 ... 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 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: OK
gep2pep.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL gep2pep ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘gep2pep’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** 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 (gep2pep)
gep2pep.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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(gep2pep)
>
> test_check("gep2pep")
Chunk 1 of 2, 521 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 666 bytes (current file size: 12.3 Kb)
Chunk 1 of 2, 540 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 692 bytes (current file size: 12.3 Kb)
Chunk 1 of 2, 550 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 686 bytes (current file size: 12.3 Kb)
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 154 | SKIPPED: 1 | WARNINGS: 9 | FAILED: 0 ]
>
> proc.time()
user system elapsed
19.203 1.931 21.220
gep2pep.Rcheck/gep2pep-Ex.timings
| name | user | system | elapsed | |
| CategorizedCollection | 0.272 | 0.031 | 0.314 | |
| CondSEA | 1.321 | 0.238 | 1.567 | |
| PathSEA | 1.014 | 0.127 | 1.144 | |
| addSingleGeneSets | 1.063 | 0.055 | 1.119 | |
| as.CategorizedCollection | 0.601 | 0.083 | 0.687 | |
| buildPEPs | 0.903 | 0.115 | 1.025 | |
| checkRepository | 0.333 | 0.054 | 0.389 | |
| clearCache | 1.085 | 0.143 | 1.247 | |
| createMergedRepository | 1.045 | 0.185 | 1.237 | |
| createRepository | 0.259 | 0.047 | 0.309 | |
| exportSEA | 0.860 | 0.106 | 0.969 | |
| gene2pathways | 0.297 | 0.053 | 0.354 | |
| getCollections | 0.262 | 0.049 | 0.314 | |
| getDetails | 0.856 | 0.117 | 0.977 | |
| getResults | 0.908 | 0.127 | 1.095 | |
| importFromRawMode | 0.930 | 0.130 | 1.064 | |
| importMSigDB.xml | 0.266 | 0.053 | 0.323 | |
| loadCollection | 0.294 | 0.057 | 0.370 | |
| loadESmatrix | 0.764 | 0.111 | 0.896 | |
| loadPVmatrix | 0.777 | 0.103 | 0.969 | |
| loadSampleGEP | 0.001 | 0.000 | 0.002 | |
| loadSamplePWS | 0.001 | 0.000 | 0.001 | |
| makeCollectionIDs | 0.064 | 0.000 | 0.065 | |
| openRepository | 0.236 | 0.044 | 0.308 | |
| setId2setName | 0.074 | 0.001 | 0.075 | |