Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-04 11:37:52 -0500 (Mon, 04 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" | 4692 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.2 (2023-10-31 ucrt) -- "Eye Holes" | 4445 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" | 4466 |
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
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
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. |
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: 2024-03-03 23:32:00 -0500 (Sun, 03 Mar 2024) |
EndedAt: 2024-03-03 23:35:22 -0500 (Sun, 03 Mar 2024) |
EllapsedTime: 201.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: simplifyEnrichment.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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 ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/simplifyEnrichment.Rcheck’ * using R version 4.3.2 Patched (2023-11-01 r85457) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.3 (clang-1403.0.22.14.1) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * 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/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-x86_64/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 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-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 11.919 0.961 12.561
simplifyEnrichment.Rcheck/simplifyEnrichment-Ex.timings
name | user | system | elapsed | |
DO_similarity | 0.000 | 0.000 | 0.001 | |
GO_similarity | 0 | 0 | 0 | |
all_clustering_methods | 0 | 0 | 0 | |
anno_word_cloud | 2.069 | 0.071 | 2.154 | |
anno_word_cloud_from_GO | 0 | 0 | 0 | |
area_above_ecdf | 0.001 | 0.000 | 0.001 | |
binary_cut | 2.207 | 0.091 | 2.305 | |
cluster_by_MCL | 0.000 | 0.001 | 0.000 | |
cluster_by_apcluster | 0 | 0 | 0 | |
cluster_by_dynamicTreeCut | 0 | 0 | 0 | |
cluster_by_hdbscan | 0 | 0 | 0 | |
cluster_by_igraph | 0.000 | 0.000 | 0.001 | |
cluster_by_kmeans | 0.000 | 0.001 | 0.000 | |
cluster_by_mclust | 0 | 0 | 0 | |
cluster_by_pam | 0.000 | 0.000 | 0.001 | |
cluster_terms | 0 | 0 | 0 | |
cmp_make_clusters | 0.000 | 0.001 | 0.000 | |
cmp_make_plot | 0.001 | 0.000 | 0.001 | |
compare_clustering_methods | 0 | 0 | 0 | |
count_words | 0.482 | 0.020 | 0.503 | |
dend_node_apply | 0.005 | 0.000 | 0.005 | |
difference_score | 1.774 | 0.047 | 1.829 | |
edit_node | 0 | 0 | 0 | |
export_to_shiny_app | 0.000 | 0.001 | 0.000 | |
guess_ont | 0.000 | 0.000 | 0.001 | |
heightDetails.word_cloud | 0 | 0 | 0 | |
ht_clusters | 0.000 | 0.001 | 0.000 | |
keyword_enrichment_from_GO | 0.000 | 0.000 | 0.001 | |
partition_by_hclust | 0 | 0 | 0 | |
partition_by_kmeans | 0 | 0 | 0 | |
partition_by_kmeanspp | 0 | 0 | 0 | |
partition_by_pam | 0.000 | 0.001 | 0.001 | |
plot_binary_cut | 0 | 0 | 0 | |
random_DO | 0 | 0 | 0 | |
random_GO | 0.000 | 0.001 | 0.001 | |
register_clustering_methods | 0.001 | 0.000 | 0.001 | |
remove_clustering_methods | 0 | 0 | 0 | |
reset_clustering_methods | 0.000 | 0.001 | 0.001 | |
scale_fontsize | 0.000 | 0.001 | 0.000 | |
se_opt | 0.000 | 0.000 | 0.001 | |
select_cutoff | 0 | 0 | 0 | |
simplifyEnrichment | 0.000 | 0.001 | 0.000 | |
simplifyGO | 0.001 | 0.000 | 0.000 | |
simplifyGOFromMultipleLists | 0.000 | 0.000 | 0.001 | |
subset_enrichResult | 0 | 0 | 0 | |
term_similarity | 0 | 0 | 0 | |
term_similarity_from_KEGG | 0.000 | 0.001 | 0.000 | |
term_similarity_from_MSigDB | 0.001 | 0.000 | 0.001 | |
term_similarity_from_Reactome | 0 | 0 | 0 | |
term_similarity_from_enrichResult | 0.000 | 0.001 | 0.000 | |
term_similarity_from_gmt | 0 | 0 | 0 | |
widthDetails.word_cloud | 0.000 | 0.000 | 0.001 | |
word_cloud_grob | 0.148 | 0.006 | 0.156 | |