Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2023-10-24 11:41:32 -0400 (Tue, 24 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4724
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4459
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4473
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 4461
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 1964/2264HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
simplifyEnrichment 1.11.0  (landing page)
Zuguang Gu
Snapshot Date: 2023-10-23 14:05:08 -0400 (Mon, 23 Oct 2023)
git_url: https://git.bioconductor.org/packages/simplifyEnrichment
git_branch: devel
git_last_commit: 317cfca
git_last_commit_date: 2023-04-25 11:18:39 -0400 (Tue, 25 Apr 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.6.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.3.1 Ventura / arm64see weekly results here
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for simplifyEnrichment on kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: simplifyEnrichment
Version: 1.11.0
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:simplifyEnrichment.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings simplifyEnrichment_1.11.0.tar.gz
StartedAt: 2023-10-24 13:07:34 -0000 (Tue, 24 Oct 2023)
EndedAt: 2023-10-24 13:29:05 -0000 (Tue, 24 Oct 2023)
EllapsedTime: 1291.0 seconds
RetCode: 0
Status:   OK  
CheckDir: simplifyEnrichment.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:simplifyEnrichment.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings simplifyEnrichment_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/simplifyEnrichment.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘simplifyEnrichment/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘simplifyEnrichment’ version ‘1.11.0’
* 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 ... NOTE
  installed size is  6.5Mb
  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 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘interactive.Rmd’ using ‘UTF-8’... OK
  ‘simplifyEnrichment.Rmd’ using ‘UTF-8’... OK
  ‘word_cloud_anno.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/simplifyEnrichment.Rcheck/00check.log’
for details.



Installation output

simplifyEnrichment.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL simplifyEnrichment
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/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 version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 
 15.058   0.481  15.553 

Example timings

simplifyEnrichment.Rcheck/simplifyEnrichment-Ex.timings

nameusersystemelapsed
DO_similarity0.0000.0000.001
GO_similarity000
all_clustering_methods0.0000.0000.001
anno_word_cloud2.3970.1082.511
anno_word_cloud_from_GO000
area_above_ecdf000
binary_cut3.1100.0963.211
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_by_pam000
cluster_terms000
cmp_make_clusters000
cmp_make_plot000
compare_clustering_methods000
count_words0.4970.0200.517
dend_node_apply0.0070.0000.007
difference_score2.5820.0522.638
edit_node000
export_to_shiny_app0.0010.0000.001
guess_ont000
heightDetails.word_cloud000
ht_clusters000
keyword_enrichment_from_GO000
partition_by_hclust0.0010.0000.000
partition_by_kmeans000
partition_by_kmeanspp000
partition_by_pam000
plot_binary_cut000
random_DO0.0010.0000.000
random_GO000
register_clustering_methods000
remove_clustering_methods000
reset_clustering_methods0.0000.0010.001
scale_fontsize0.0000.0010.000
se_opt0.0000.0000.001
select_cutoff000
simplifyEnrichment000
simplifyGO000
simplifyGOFromMultipleLists000
subset_enrichResult000
term_similarity000
term_similarity_from_KEGG000
term_similarity_from_MSigDB000
term_similarity_from_Reactome000
term_similarity_from_enrichResult0.0000.0000.001
term_similarity_from_gmt000
widthDetails.word_cloud000
word_cloud_grob0.1640.0020.166