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This page was generated on 2021-10-23 15:51:47 -0400 (Sat, 23 Oct 2021).

CHECK results for msigdb on nebbiolo2

To the developers/maintainers of the msigdb package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 243/408HostnameOS / ArchINSTALLBUILDCHECK
msigdb 1.1.5  (landing page)
Dharmesh D. Bhuva
Snapshot Date: 2021-10-23 09:30:01 -0400 (Sat, 23 Oct 2021)
git_url: https://git.bioconductor.org/packages/msigdb
git_branch: master
git_last_commit: 57f15b7
git_last_commit_date: 2021-10-12 16:25:19 -0400 (Tue, 12 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published

Summary

Package: msigdb
Version: 1.1.5
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:msigdb.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings msigdb_1.1.5.tar.gz
StartedAt: 2021-10-23 12:31:14 -0400 (Sat, 23 Oct 2021)
EndedAt: 2021-10-23 12:33:50 -0400 (Sat, 23 Oct 2021)
EllapsedTime: 156.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: msigdb.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:msigdb.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings msigdb_1.1.5.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-data-experiment/meat/msigdb.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘msigdb/DESCRIPTION’ ... OK
* this is package ‘msigdb’ version ‘1.1.5’
* 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 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 ... NOTE
getMsigdbIDF: no visible global function definition for
  ‘checkMsigdbVersion’
Undefined global functions or variables:
  checkMsigdbVersion
* 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 documentation object 'listCollections'
  ‘gsc’

Undocumented arguments in documentation object 'listSubCollections'
  ‘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
getMsigOrganism    18.501  0.416  19.359
getIMEX            12.455  0.559  13.639
msigdb             11.724  0.160  12.629
subsetCollection    8.663  0.084   9.168
getMsigIdType       8.028  0.176   8.630
listCollections     7.444  0.059   7.888
listSubCollections  7.087  0.079   7.592
getMsigdb           6.274  0.193   6.814
* 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: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.14-data-experiment/meat/msigdb.Rcheck/00check.log’
for details.



Installation output

msigdb.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL msigdb
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘msigdb’ ...
** 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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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(msigdb)
> 
> test_check("msigdb")
Loading required package: BiocGenerics

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, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, 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 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

snapshotDate(): 2021-10-18
see ?msigdb and browseVignettes('msigdb') for documentation
loading from cache
snapshotDate(): 2021-10-18
see ?msigdb and browseVignettes('msigdb') for documentation
loading from cache


[ FAIL 0 | WARN 0 | SKIP 0 | PASS 27 ]
> 
> proc.time()
   user  system elapsed 
 33.038   1.349  35.792 

Example timings

msigdb.Rcheck/msigdb-Ex.timings

nameusersystemelapsed
getIMEX12.455 0.55913.639
getIMEXVersions0.0020.0000.002
getMsigIdType8.0280.1768.630
getMsigOrganism18.501 0.41619.359
getMsigdb6.2740.1936.814
getMsigdbVersions0.0020.0000.002
listCollections7.4440.0597.888
listSubCollections7.0870.0797.592
msigdb11.724 0.16012.629
subsetCollection8.6630.0849.168