Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:20:19 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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

CHECK results for gep2pep on nebbiolo1


To the developers/maintainers of the gep2pep package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gep2pep.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 793/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gep2pep 1.16.0  (landing page)
Francesco Napolitano
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/gep2pep
git_branch: RELEASE_3_15
git_last_commit: 9661693
git_last_commit_date: 2022-04-26 11:45:30 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: gep2pep
Version: 1.16.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:gep2pep.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings gep2pep_1.16.0.tar.gz
StartedAt: 2022-10-18 19:55:25 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 19:57:50 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 144.4 seconds
RetCode: 0
Status:   OK  
CheckDir: gep2pep.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:gep2pep.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings gep2pep_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/gep2pep.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (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 ‘1.16.0’
* 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


Installation output

gep2pep.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL gep2pep
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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)

Tests output

gep2pep.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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(gep2pep)
> 
> test_check("gep2pep")
Chunk 1 of 2, 519 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 665 bytes (current file size: 16.3 Kb)
Chunk 1 of 2, 540 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 692 bytes (current file size: 16.3 Kb)
Chunk 1 of 2, 549 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 684 bytes (current file size: 16.3 Kb)
[ FAIL 0 | WARN 2273 | SKIP 1 | PASS 154 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)

[ FAIL 0 | WARN 2273 | SKIP 1 | PASS 154 ]
> 
> proc.time()
   user  system elapsed 
 28.014   1.394  29.408 

Example timings

gep2pep.Rcheck/gep2pep-Ex.timings

nameusersystemelapsed
CategorizedCollection0.3470.0000.348
CondSEA1.6750.1561.832
PathSEA1.0030.1961.200
addSingleGeneSets0.4390.0690.507
as.CategorizedCollection0.2910.0480.338
buildPEPs1.3690.1241.494
checkRepository0.1700.0200.191
clearCache0.9900.0401.031
createMergedRepository0.9120.0400.952
createRepository0.1530.0120.164
exportSEA0.8710.0720.942
gene2pathways0.1570.0120.170
getCollections0.1410.0150.156
getDetails0.8700.0530.923
getResults0.8240.0300.854
importFromRawMode0.8730.0470.920
importMSigDB.xml0.1390.0240.195
loadCollection0.1450.0190.167
loadESmatrix0.6930.0800.773
loadPVmatrix0.6950.0210.714
loadSampleGEP0.0010.0000.001
loadSamplePWS0.0010.0000.001
makeCollectionIDs0.0310.0000.031
openRepository0.1160.0240.139
setId2setName0.0290.0030.032