Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-24 13:05:41 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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 simplifyEnrichment on nebbiolo2


To the developers/maintainers of the simplifyEnrichment package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1803/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
simplifyEnrichment 1.4.0  (landing page)
Zuguang Gu
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/simplifyEnrichment
git_branch: RELEASE_3_14
git_last_commit: 549d5f1
git_last_commit_date: 2021-10-26 13:00:10 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: simplifyEnrichment
Version: 1.4.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:simplifyEnrichment.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings simplifyEnrichment_1.4.0.tar.gz
StartedAt: 2022-01-23 09:43:07 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 09:45:34 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 146.2 seconds
RetCode: 0
Status:   OK  
CheckDir: simplifyEnrichment.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:simplifyEnrichment.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings simplifyEnrichment_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/simplifyEnrichment.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘simplifyEnrichment/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘simplifyEnrichment’ version ‘1.4.0’
* 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 ‘simplifyEnrichment’ 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 ... 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
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
ht_clusters 8.474   0.04   8.472
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.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: OK


Installation output

simplifyEnrichment.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL simplifyEnrichment
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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 version 4.1.2 (2021-11-01) -- "Bird Hippie"
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)
> suppressWarnings(suppressPackageStartupMessages(library(simplifyEnrichment)))
> 
> test_check("simplifyEnrichment")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 17 ]
> 
> proc.time()
   user  system elapsed 
  9.184   0.406   9.559 

Example timings

simplifyEnrichment.Rcheck/simplifyEnrichment-Ex.timings

nameusersystemelapsed
DO_similarity000
GO_similarity0.0000.0000.001
all_clustering_methods0.0010.0000.000
anno_word_cloud1.7590.0681.827
anno_word_cloud_from_GO000
binary_cut1.2850.0281.314
cluster_by_MCL000
cluster_by_apcluster000
cluster_by_dynamicTreeCut0.0000.0000.001
cluster_by_hdbscan000
cluster_by_igraph000
cluster_by_kmeans000
cluster_by_mclust000
cluster_terms000
cmp_make_clusters000
cmp_make_plot000
compare_clustering_methods000
count_word0.1180.0040.123
count_word_from_GO0.1070.0070.115
dend_node_apply0.0040.0000.004
difference_score1.3750.0281.403
edit_node000
export_to_shiny_app1.3360.0031.341
guess_ont000
heightDetails.word_cloud000
ht_clusters8.4740.0408.472
partition_by_hclust0.0000.0000.001
partition_by_kmeans0.0010.0000.000
partition_by_kmeanspp000
partition_by_pam000
plot_binary_cut000
random_DO000
random_GO000
register_clustering_methods0.0000.0000.001
remove_clustering_methods000
reset_clustering_methods0.0010.0000.000
scale_fontsize0.0000.0000.001
select_cutoff0.0010.0000.000
simplifyEnrichment000
simplifyGO000
simplifyGOFromMultipleLists000
subset_enrichResult000
term_similarity0.0010.0000.000
term_similarity_from_KEGG000
term_similarity_from_MSigDB000
term_similarity_from_Reactome000
term_similarity_from_enrichResult000
term_similarity_from_gmt000
widthDetails.word_cloud0.0000.0000.001
word_cloud_grob0.1010.0000.101