| Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-04-17 11:35:46 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| 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 65/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| animalcules 1.18.3 (landing page) Jessica McClintock
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
| merida1 | 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 animalcules package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/animalcules.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: animalcules |
| Version: 1.18.3 |
| Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:animalcules.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings animalcules_1.18.3.tar.gz |
| StartedAt: 2024-04-15 20:01:11 -0400 (Mon, 15 Apr 2024) |
| EndedAt: 2024-04-15 20:06:14 -0400 (Mon, 15 Apr 2024) |
| EllapsedTime: 302.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: animalcules.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:animalcules.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings animalcules_1.18.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/animalcules.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘animalcules/DESCRIPTION’ ... OK
* this is package ‘animalcules’ version ‘1.18.3’
* package encoding: UTF-8
* 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 ‘animalcules’ 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 loading without being on the library search path ... 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 ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘animalcules.Rmd’ using ‘UTF-8’... OK
OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
animalcules.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL animalcules ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’ * installing *source* package ‘animalcules’ ... ** 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 (animalcules)
animalcules.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 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)
> library(animalcules)
>
> test_check("animalcules")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 38 ]
>
> proc.time()
user system elapsed
24.510 0.973 26.079
animalcules.Rcheck/animalcules-Ex.timings
| name | user | system | elapsed | |
| alpha_div_boxplot | 1.195 | 0.068 | 1.265 | |
| alpha_div_test | 0.003 | 0.000 | 0.003 | |
| counts_to_logcpm | 0.001 | 0.000 | 0.001 | |
| counts_to_relabu | 0.001 | 0.000 | 0.002 | |
| df_char_to_factor | 0 | 0 | 0 | |
| differential_abundance | 3.617 | 0.148 | 3.765 | |
| dimred_pca | 0.162 | 0.010 | 0.172 | |
| dimred_pcoa | 0.107 | 0.006 | 0.113 | |
| dimred_tsne | 4.508 | 0.084 | 4.592 | |
| dimred_umap | 0.358 | 0.008 | 0.366 | |
| diversities | 0 | 0 | 0 | |
| diversities_help | 0.000 | 0.000 | 0.001 | |
| diversity_beta_boxplot | 0.194 | 0.004 | 0.197 | |
| diversity_beta_heatmap | 0.202 | 0.004 | 0.206 | |
| diversity_beta_test | 0.168 | 0.004 | 0.172 | |
| do_alpha_div_test | 0.047 | 0.000 | 0.046 | |
| filter_categorize | 0.248 | 0.008 | 0.256 | |
| filter_summary_bar_density | 0.246 | 0.020 | 0.266 | |
| filter_summary_pie_box | 0.201 | 0.012 | 0.213 | |
| find_biomarker | 4.613 | 0.159 | 4.776 | |
| find_taxon_mat | 0.210 | 0.004 | 0.881 | |
| find_taxonomy | 0.021 | 0.000 | 0.566 | |
| find_taxonomy_300 | 0.022 | 0.000 | 0.544 | |
| gini_simpson | 0.001 | 0.000 | 0.000 | |
| grep_tid | 0 | 0 | 0 | |
| inverse_simpson | 0 | 0 | 0 | |
| is_categorical | 0 | 0 | 0 | |
| is_integer0 | 0 | 0 | 0 | |
| is_integer1 | 0.001 | 0.000 | 0.000 | |
| mae_pick_organisms | 0.105 | 0.000 | 0.106 | |
| mae_pick_samples | 0.127 | 0.012 | 0.140 | |
| pct2str | 0 | 0 | 0 | |
| percent | 0 | 0 | 0 | |
| relabu_barplot | 0.921 | 0.056 | 0.977 | |
| relabu_boxplot | 0.091 | 0.020 | 0.111 | |
| relabu_heatmap | 0.103 | 0.024 | 0.128 | |
| run_animalcules | 0 | 0 | 0 | |
| shannon | 0 | 0 | 0 | |
| simpson_index | 0 | 0 | 0 | |
| upsample_counts | 0.012 | 0.000 | 0.011 | |