Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-06-14 14:37 -0400 (Fri, 14 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
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

Package 853/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gep2pep 1.24.0  (landing page)
Francesco Napolitano
Snapshot Date: 2024-06-12 14:00 -0400 (Wed, 12 Jun 2024)
git_url: https://git.bioconductor.org/packages/gep2pep
git_branch: RELEASE_3_19
git_last_commit: c397d7e
git_last_commit_date: 2024-04-30 11:02:39 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 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


CHECK results for gep2pep on nebbiolo1

To the developers/maintainers of the gep2pep package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: gep2pep
Version: 1.24.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:gep2pep.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings gep2pep_1.24.0.tar.gz
StartedAt: 2024-06-12 23:33:05 -0400 (Wed, 12 Jun 2024)
EndedAt: 2024-06-12 23:35:30 -0400 (Wed, 12 Jun 2024)
EllapsedTime: 145.3 seconds
RetCode: 0
Status:   OK  
CheckDir: gep2pep.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:gep2pep.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings gep2pep_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/gep2pep.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘gep2pep/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gep2pep’ version ‘1.24.0’
* 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 code 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) as.CategorizedCollection.Rd:27: Lost braces; missing escapes or markup?
    27 |     in the collection to {CategorizedCollection}. If
       |                          ^
checkRd: (-1) gep2pep-package.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gep2pep-package.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gep2pep-package.Rd:55-56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gep2pep-package.Rd:58-61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gep2pep-package.Rd:63-65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gep2pep-package.Rd:67-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gep2pep-package.Rd:71-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loadESmatrix.Rd:19: Lost braces
    19 |     reports the ES for the pathway \code{i}, condition{j}. If
       |                                                       ^
checkRd: (-1) loadPVmatrix.Rd:19: Lost braces
    19 |     reports the PV for the pathway \code{i}, condition{j}. If
       |                                                       ^
* 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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/gep2pep.Rcheck/00check.log’
for details.


Installation output

gep2pep.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL gep2pep
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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, 520 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, 691 bytes (current file size: 16.3 Kb)
Chunk 1 of 2, 549 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 685 bytes (current file size: 16.3 Kb)
[ FAIL 0 | WARN 2270 | SKIP 1 | PASS 154 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_rawMode.R:216:1'

[ FAIL 0 | WARN 2270 | SKIP 1 | PASS 154 ]
> 
> proc.time()
   user  system elapsed 
 26.264   1.503  27.771 

Example timings

gep2pep.Rcheck/gep2pep-Ex.timings

nameusersystemelapsed
CategorizedCollection0.0900.0000.089
CondSEA0.7570.0210.779
PathSEA0.9980.2961.331
addSingleGeneSets0.4840.0520.760
as.CategorizedCollection0.2700.0670.337
buildPEPs0.4460.0800.526
checkRepository0.1560.0280.185
clearCache0.5860.0960.682
createMergedRepository0.5610.0320.594
createRepository0.130.020.15
exportSEA0.4430.0360.480
gene2pathways0.1550.0000.155
getCollections0.1150.0320.147
getDetails0.4480.0480.497
getResults0.4570.0240.482
importFromRawMode0.5120.0170.528
importMSigDB.xml0.1370.0070.143
loadCollection0.1550.0080.163
loadESmatrix0.4030.0430.447
loadPVmatrix0.3650.0320.397
loadSampleGEP0.0010.0000.001
loadSamplePWS0.0010.0000.001
makeCollectionIDs0.0330.0000.033
openRepository0.1300.0080.137
setId2setName0.0330.0000.033