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This page was generated on 2024-12-07 15:24 -0500 (Sat, 07 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-11-14 r87333) -- "Unsuffered Consequences" 861
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Package 108/216HostnameOS / ArchINSTALLBUILDCHECK
GSEABase 1.69.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2024-12-07 12:00 -0500 (Sat, 07 Dec 2024)
git_url: https://git.bioconductor.org/packages/GSEABase
git_branch: devel
git_last_commit: 9f00f81
git_last_commit_date: 2024-10-29 09:27:57 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  


CHECK results for GSEABase on teran2

To the developers/maintainers of the GSEABase 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: GSEABase
Version: 1.69.0
Command: /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:GSEABase.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings GSEABase_1.69.0.tar.gz
StartedAt: 2024-12-07 14:29:40 -0500 (Sat, 07 Dec 2024)
EndedAt: 2024-12-07 14:31:49 -0500 (Sat, 07 Dec 2024)
EllapsedTime: 129.3 seconds
RetCode: 0
Status:   OK  
CheckDir: GSEABase.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:GSEABase.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings GSEABase_1.69.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/GSEABase.Rcheck’
* using R Under development (unstable) (2024-11-14 r87333)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘GSEABase/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GSEABase’ version ‘1.69.0’
* 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 ‘GSEABase’ 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 ... 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 ‘unitTests.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: OK


Installation output

GSEABase.Rcheck/00install.out

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###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL GSEABase
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’
* installing *source* package ‘GSEABase’ ...
** 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 (GSEABase)

Tests output

GSEABase.Rcheck/tests/unitTests.Rout


R Under development (unstable) (2024-11-14 r87333) -- "Unsuffered Consequences"
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.

> BiocGenerics:::testPackage("GSEABase")

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

Welcome to Bioconductor

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


Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname


Attaching package: 'graph'

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

    addNode




'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns


RUNIT TEST PROTOCOL -- Sat Dec  7 14:31:09 2024 
*********************************************** 
Number of test functions: 79 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GSEABase RUnit Tests - 79 test functions, 0 errors, 0 failures
Number of test functions: 79 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 11.908   0.745  12.651 

Example timings

GSEABase.Rcheck/GSEABase-Ex.timings

nameusersystemelapsed
CollectionType-class0.3190.0300.356
CollectionType-constructors0.0560.0020.060
GSEABase-package0.0440.0060.050
GeneColorSet-class0.0510.0010.052
GeneIdentifierType-class0.0390.0110.050
GeneIdentifierType-constructors0.0300.0070.037
GeneSet-class0.0520.0170.068
GeneSet-methods0.0290.0060.036
GeneSetCollection-class0.0030.0010.005
GeneSetCollection-methods1.9310.1712.103
OBOCollection-class0.0520.0020.053
getOBOCollection0.0170.0000.018
getObjects0.0080.0000.008
goSlim-methods0.2460.0110.265
incidence-methods0.0040.0010.004