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This page was generated on 2025-09-30 15:01 -0400 (Tue, 30 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4831
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 259/432HostnameOS / ArchINSTALLBUILDCHECK
msigdb 1.16.0  (landing page)
Dharmesh D. Bhuva
Snapshot Date: 2025-09-30 07:30 -0400 (Tue, 30 Sep 2025)
git_url: https://git.bioconductor.org/packages/msigdb
git_branch: RELEASE_3_21
git_last_commit: d73d327
git_last_commit_date: 2025-04-15 10:16:57 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published


CHECK results for msigdb on nebbiolo1

To the developers/maintainers of the msigdb package:
- 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: msigdb
Version: 1.16.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:msigdb.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings msigdb_1.16.0.tar.gz
StartedAt: 2025-09-30 12:38:45 -0400 (Tue, 30 Sep 2025)
EndedAt: 2025-09-30 13:14:34 -0400 (Tue, 30 Sep 2025)
EllapsedTime: 2148.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: msigdb.Rcheck
Warnings: 1

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:msigdb.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings msigdb_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/msigdb.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘msigdb/DESCRIPTION’ ... OK
* this is package ‘msigdb’ 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 ‘msigdb’ 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 ... 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 ... WARNING
Undocumented arguments in Rd file 'listCollections.Rd'
  ‘gsc’

Undocumented arguments in Rd file 'listSubCollections.Rd'
  ‘gsc’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
msigdb             268.617  3.253 272.327
getMsigOrganism    169.611  1.595 171.446
subsetCollection   162.061  1.784 164.134
listCollections    159.930  2.346 162.649
getMsigdb          159.499  1.689 161.478
listSubCollections 158.984  1.747 160.962
getMsigIdType      157.889  1.457 159.573
getIMEX             11.447  0.654  12.337
* 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 WARNING
See
  ‘/home/biocbuild/bbs-3.21-data-experiment/meat/msigdb.Rcheck/00check.log’
for details.


Installation output

msigdb.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL msigdb
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘msigdb’ ...
** this is package ‘msigdb’ version ‘1.16.0’
** 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 (msigdb)

Tests output

msigdb.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 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(msigdb)
> 
> test_check("msigdb")
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: XML
Loading required package: graph

Attaching package: 'graph'

The following object is masked from 'package:XML':

    addNode

see ?msigdb and browseVignettes('msigdb') for documentation
loading from cache
see ?msigdb and browseVignettes('msigdb') for documentation
loading from cache


[ FAIL 0 | WARN 0 | SKIP 0 | PASS 27 ]
> 
> proc.time()
   user  system elapsed 
335.066   3.014 339.181 

Example timings

msigdb.Rcheck/msigdb-Ex.timings

nameusersystemelapsed
getIMEX11.447 0.65412.337
getIMEXVersions0.0020.0010.003
getMsigIdType157.889 1.457159.573
getMsigOrganism169.611 1.595171.446
getMsigdb159.499 1.689161.478
getMsigdbIDF1.5230.1682.178
getMsigdbVersions0.0030.0000.003
listCollections159.930 2.346162.649
listSubCollections158.984 1.747160.962
msigdb268.617 3.253272.327
subsetCollection162.061 1.784164.134