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This page was generated on 2024-04-18 11:32:19 -0400 (Thu, 18 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs | 
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 | 
| 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 1966/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| simplifyEnrichment 1.12.0  (landing page) Zuguang Gu 
 | kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | OK | OK |  | |||||||
| To the developers/maintainers of the simplifyEnrichment 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. | 
| Package: simplifyEnrichment | 
| Version: 1.12.0 | 
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:simplifyEnrichment.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings simplifyEnrichment_1.12.0.tar.gz | 
| StartedAt: 2024-04-18 04:08:39 -0400 (Thu, 18 Apr 2024) | 
| EndedAt: 2024-04-18 04:13:41 -0400 (Thu, 18 Apr 2024) | 
| EllapsedTime: 302.4 seconds | 
| RetCode: 0 | 
| Status: OK | 
| CheckDir: simplifyEnrichment.Rcheck | 
| Warnings: 0 | 
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:simplifyEnrichment.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings simplifyEnrichment_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/simplifyEnrichment.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘simplifyEnrichment/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘simplifyEnrichment’ version ‘1.12.0’
* 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 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/simplifyEnrichment.Rcheck/00check.log’
for details.
simplifyEnrichment.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL simplifyEnrichment ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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)
simplifyEnrichment.Rcheck/tests/test-all.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 
 12.891   0.580  14.299 
simplifyEnrichment.Rcheck/simplifyEnrichment-Ex.timings
| name | user | system | elapsed | |
| DO_similarity | 0.001 | 0.000 | 0.000 | |
| GO_similarity | 0 | 0 | 0 | |
| all_clustering_methods | 0.000 | 0.000 | 0.001 | |
| anno_word_cloud | 2.010 | 0.093 | 2.203 | |
| anno_word_cloud_from_GO | 0.000 | 0.000 | 0.001 | |
| area_above_ecdf | 0 | 0 | 0 | |
| binary_cut | 2.497 | 0.092 | 2.711 | |
| cluster_by_MCL | 0 | 0 | 0 | |
| cluster_by_apcluster | 0 | 0 | 0 | |
| cluster_by_dynamicTreeCut | 0 | 0 | 0 | |
| cluster_by_hdbscan | 0 | 0 | 0 | |
| cluster_by_igraph | 0 | 0 | 0 | |
| cluster_by_kmeans | 0.000 | 0.001 | 0.001 | |
| cluster_by_mclust | 0 | 0 | 0 | |
| cluster_by_pam | 0 | 0 | 0 | |
| cluster_terms | 0 | 0 | 0 | |
| cmp_make_clusters | 0 | 0 | 0 | |
| cmp_make_plot | 0.000 | 0.000 | 0.001 | |
| compare_clustering_methods | 0 | 0 | 0 | |
| count_words | 0.482 | 0.023 | 0.522 | |
| dend_node_apply | 0.006 | 0.000 | 0.007 | |
| difference_score | 1.902 | 0.043 | 2.038 | |
| edit_node | 0.001 | 0.000 | 0.000 | |
| export_to_shiny_app | 0 | 0 | 0 | |
| guess_ont | 0 | 0 | 0 | |
| heightDetails.word_cloud | 0 | 0 | 0 | |
| ht_clusters | 0.000 | 0.000 | 0.001 | |
| keyword_enrichment_from_GO | 0 | 0 | 0 | |
| partition_by_hclust | 0 | 0 | 0 | |
| partition_by_kmeans | 0.001 | 0.000 | 0.000 | |
| partition_by_kmeanspp | 0.000 | 0.000 | 0.001 | |
| partition_by_pam | 0.000 | 0.000 | 0.001 | |
| plot_binary_cut | 0 | 0 | 0 | |
| random_DO | 0.000 | 0.000 | 0.001 | |
| random_GO | 0.000 | 0.000 | 0.001 | |
| register_clustering_methods | 0.000 | 0.000 | 0.001 | |
| remove_clustering_methods | 0 | 0 | 0 | |
| reset_clustering_methods | 0.001 | 0.001 | 0.001 | |
| scale_fontsize | 0 | 0 | 0 | |
| se_opt | 0 | 0 | 0 | |
| select_cutoff | 0.000 | 0.000 | 0.001 | |
| simplifyEnrichment | 0 | 0 | 0 | |
| simplifyGO | 0 | 0 | 0 | |
| simplifyGOFromMultipleLists | 0 | 0 | 0 | |
| subset_enrichResult | 0 | 0 | 0 | |
| term_similarity | 0 | 0 | 0 | |
| term_similarity_from_KEGG | 0.001 | 0.000 | 0.001 | |
| term_similarity_from_MSigDB | 0 | 0 | 0 | |
| term_similarity_from_Reactome | 0 | 0 | 0 | |
| term_similarity_from_enrichResult | 0 | 0 | 0 | |
| term_similarity_from_gmt | 0.000 | 0.001 | 0.001 | |
| widthDetails.word_cloud | 0.000 | 0.001 | 0.000 | |
| word_cloud_grob | 0.123 | 0.006 | 0.134 | |