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This page was generated on 2024-02-20 13:15:08 -0500 (Tue, 20 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4657
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 1944/2244HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
simplifyEnrichment 1.13.1  (landing page)
Zuguang Gu
Snapshot Date: 2024-02-19 14:10:08 -0500 (Mon, 19 Feb 2024)
git_url: https://git.bioconductor.org/packages/simplifyEnrichment
git_branch: devel
git_last_commit: f347445
git_last_commit_date: 2023-11-06 09:46:53 -0500 (Mon, 06 Nov 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

CHECK results for simplifyEnrichment on nebbiolo1


To the developers/maintainers of the simplifyEnrichment package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/simplifyEnrichment.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: simplifyEnrichment
Version: 1.13.1
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:simplifyEnrichment.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings simplifyEnrichment_1.13.1.tar.gz
StartedAt: 2024-02-20 02:30:51 -0500 (Tue, 20 Feb 2024)
EndedAt: 2024-02-20 02:45:09 -0500 (Tue, 20 Feb 2024)
EllapsedTime: 857.5 seconds
RetCode: 0
Status:   OK  
CheckDir: simplifyEnrichment.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:simplifyEnrichment.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings simplifyEnrichment_1.13.1.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/simplifyEnrichment.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* 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 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘simplifyEnrichment/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘simplifyEnrichment’ version ‘1.13.1’
* 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 ‘simplifyEnrichment’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   5.9Mb
* 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 whether startup messages can be suppressed ... 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 ‘test-all.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/simplifyEnrichment.Rcheck/00check.log’
for details.



Installation output

simplifyEnrichment.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘simplifyEnrichment’ ...
** 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 (simplifyEnrichment)

Tests output

simplifyEnrichment.Rcheck/tests/test-all.Rout


R Under development (unstable) (2024-01-16 r85808) -- "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.

> library(testthat)
> suppressWarnings(suppressPackageStartupMessages(library(simplifyEnrichment)))
> 
> test_check("simplifyEnrichment")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 17 ]
> 
> proc.time()
   user  system elapsed 
 10.651   0.571  11.203 

Example timings

simplifyEnrichment.Rcheck/simplifyEnrichment-Ex.timings

nameusersystemelapsed
DO_similarity000
GO_similarity000
all_clustering_methods0.0000.0000.001
anno_word_cloud2.3560.1592.516
anno_word_cloud_from_GO000
area_above_ecdf0.0010.0000.001
binary_cut1.6150.0561.670
cluster_by_MCL000
cluster_by_apcluster000
cluster_by_dynamicTreeCut0.0010.0000.000
cluster_by_hdbscan000
cluster_by_igraph000
cluster_by_kmeans0.0000.0000.001
cluster_by_mclust000
cluster_by_pam000
cluster_terms000
cmp_make_clusters000
cmp_make_plot000
compare_clustering_methods000
count_words0.3680.0130.381
dend_node_apply0.0050.0000.005
difference_score1.6760.0511.728
edit_node000
export_to_shiny_app0.0000.0000.001
guess_ont000
heightDetails.word_cloud000
ht_clusters000
keyword_enrichment_from_GO000
partition_by_hclust0.0000.0000.001
partition_by_kmeans0.0000.0000.001
partition_by_kmeanspp000
partition_by_pam000
plot_binary_cut000
random_DO000
random_GO000
register_clustering_methods0.0000.0010.001
remove_clustering_methods000
reset_clustering_methods0.0000.0010.001
scale_fontsize0.0000.0010.000
se_opt000
select_cutoff0.0000.0000.001
simplifyEnrichment000
simplifyGO0.0000.0010.000
simplifyGOFromMultipleLists000
subset_enrichResult000
summarizeGO000
term_similarity000
term_similarity_from_KEGG0.0010.0000.000
term_similarity_from_MSigDB000
term_similarity_from_Reactome0.0000.0010.000
term_similarity_from_enrichResult000
term_similarity_from_gmt000
widthDetails.word_cloud0.0000.0010.000
word_cloud_grob0.1090.0010.110