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This page was generated on 2023-04-11 14:50:27 -0400 (Tue, 11 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
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 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 248/416HostnameOS / ArchINSTALLBUILDCHECK
msigdb 1.6.0  (landing page)
Dharmesh D. Bhuva
Snapshot Date: 2023-04-11 07:30:01 -0400 (Tue, 11 Apr 2023)
git_url: https://git.bioconductor.org/packages/msigdb
git_branch: RELEASE_3_16
git_last_commit: ae5f17d
git_last_commit_date: 2022-11-01 11:25:52 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published

Summary

Package: msigdb
Version: 1.6.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:msigdb.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings msigdb_1.6.0.tar.gz
StartedAt: 2023-04-11 12:04:31 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 12:30:58 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 1587.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: msigdb.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:msigdb.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings msigdb_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-data-experiment/meat/msigdb.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘msigdb/DESCRIPTION’ ... OK
* this is package ‘msigdb’ version ‘1.6.0’
* 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 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 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 ... 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
msigdb             210.885  2.476 214.342
getMsigOrganism    123.831  1.104 125.373
subsetCollection   119.033  1.180 120.658
getMsigIdType      118.200  0.927 119.682
getMsigdb          117.490  1.208 119.160
listSubCollections 116.939  1.128 118.515
listCollections    116.479  1.132 118.039
getIMEX             10.071  0.591  11.172
* 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 ...
  ‘msigdb.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.16-data-experiment/meat/msigdb.Rcheck/00check.log’
for details.



Installation output

msigdb.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL msigdb
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 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, aperm, 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(): 2022-10-31
see ?msigdb and browseVignettes('msigdb') for documentation
loading from cache
snapshotDate(): 2022-10-31
see ?msigdb and browseVignettes('msigdb') for documentation
loading from cache


[ FAIL 0 | WARN 0 | SKIP 0 | PASS 27 ]
> 
> proc.time()
   user  system elapsed 
244.723   3.308 249.442 

Example timings

msigdb.Rcheck/msigdb-Ex.timings

nameusersystemelapsed
getIMEX10.071 0.59111.172
getIMEXVersions0.0030.0000.002
getMsigIdType118.200 0.927119.682
getMsigOrganism123.831 1.104125.373
getMsigdb117.490 1.208119.160
getMsigdbVersions0.0020.0000.002
listCollections116.479 1.132118.039
listSubCollections116.939 1.128118.515
msigdb210.885 2.476214.342
subsetCollection119.033 1.180120.658