| 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).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4724 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4459 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4473 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (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 1964/2264 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| simplifyEnrichment 1.11.0 (landing page) Zuguang Gu
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
| kjohnson1 | macOS 13.3.1 Ventura / arm64 | see weekly results here | ||||||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
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. |
| 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 |
##############################################################################
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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
###
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##############################################################################
* 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.
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)
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
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 | 0.000 | 0.000 | 0.001 | |
| anno_word_cloud | 2.397 | 0.108 | 2.511 | |
| anno_word_cloud_from_GO | 0 | 0 | 0 | |
| area_above_ecdf | 0 | 0 | 0 | |
| binary_cut | 3.110 | 0.096 | 3.211 | |
| cluster_by_MCL | 0 | 0 | 0 | |
| cluster_by_apcluster | 0 | 0 | 0 | |
| cluster_by_dynamicTreeCut | 0.000 | 0.000 | 0.001 | |
| cluster_by_hdbscan | 0 | 0 | 0 | |
| cluster_by_igraph | 0 | 0 | 0 | |
| cluster_by_kmeans | 0 | 0 | 0 | |
| 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 | 0 | 0 | |
| compare_clustering_methods | 0 | 0 | 0 | |
| count_words | 0.497 | 0.020 | 0.517 | |
| dend_node_apply | 0.007 | 0.000 | 0.007 | |
| difference_score | 2.582 | 0.052 | 2.638 | |
| edit_node | 0 | 0 | 0 | |
| export_to_shiny_app | 0.001 | 0.000 | 0.001 | |
| guess_ont | 0 | 0 | 0 | |
| heightDetails.word_cloud | 0 | 0 | 0 | |
| ht_clusters | 0 | 0 | 0 | |
| keyword_enrichment_from_GO | 0 | 0 | 0 | |
| partition_by_hclust | 0.001 | 0.000 | 0.000 | |
| partition_by_kmeans | 0 | 0 | 0 | |
| partition_by_kmeanspp | 0 | 0 | 0 | |
| partition_by_pam | 0 | 0 | 0 | |
| plot_binary_cut | 0 | 0 | 0 | |
| random_DO | 0.001 | 0.000 | 0.000 | |
| random_GO | 0 | 0 | 0 | |
| register_clustering_methods | 0 | 0 | 0 | |
| 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 | 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 | 0 | 0 | |
| term_similarity_from_MSigDB | 0 | 0 | 0 | |
| term_similarity_from_Reactome | 0 | 0 | 0 | |
| term_similarity_from_enrichResult | 0.000 | 0.000 | 0.001 | |
| term_similarity_from_gmt | 0 | 0 | 0 | |
| widthDetails.word_cloud | 0 | 0 | 0 | |
| word_cloud_grob | 0.164 | 0.002 | 0.166 | |