Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:28 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the animalcules package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 58/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
animalcules 1.8.1 (landing page) Yue Zhao
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: animalcules |
Version: 1.8.1 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:animalcules.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings animalcules_1.8.1.tar.gz |
StartedAt: 2021-10-14 16:12:45 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 16:18:57 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 372.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: animalcules.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:animalcules.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings animalcules_1.8.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/animalcules.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘animalcules/DESCRIPTION’ ... OK * this is package ‘animalcules’ version ‘1.8.1’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * 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 dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘reactable’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE alpha_div_boxplot: no visible binding for global variable ‘richness’ differential_abundance: no visible binding for global variable ‘padj’ differential_abundance: no visible binding for global variable ‘pValue’ differential_abundance: no visible binding for global variable ‘log2FoldChange’ diversities_help: no visible binding for global variable ‘x’ find_biomarker: no visible binding for global variable ‘rowname’ find_biomarker: no visible binding for global variable ‘importance’ find_biomarker: no visible binding for global variable ‘.’ find_biomarker: no visible binding for global variable ‘Overall’ find_biomarker: no visible binding for global variable ‘y’ find_biomarker: no visible binding for global variable ‘m’ find_biomarker: no visible binding for global variable ‘d’ relabu_barplot: no visible binding for global variable ‘.’ relabu_boxplot: no visible binding for global variable ‘.’ relabu_heatmap: no visible binding for global variable ‘.’ upsample_counts: no visible binding for global variable ‘.’ Undefined global functions or variables: . Overall d importance log2FoldChange m pValue padj richness rowname x y * 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed differential_abundance 10.342 0.107 10.456 dimred_tsne 9.300 0.252 9.562 find_biomarker 6.337 0.032 6.373 * 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 ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/animalcules.Rcheck/00check.log’ for details.
animalcules.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL animalcules ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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 5 | SKIP 0 | PASS 38 ] > > proc.time() user system elapsed 41.053 1.030 42.808
animalcules.Rcheck/animalcules-Ex.timings
name | user | system | elapsed | |
alpha_div_boxplot | 0.797 | 0.114 | 0.917 | |
alpha_div_test | 0.006 | 0.001 | 0.006 | |
counts_to_logcpm | 0.002 | 0.001 | 0.002 | |
counts_to_relabu | 0.003 | 0.001 | 0.004 | |
df_char_to_factor | 0.001 | 0.000 | 0.001 | |
differential_abundance | 10.342 | 0.107 | 10.456 | |
dimred_pca | 0.242 | 0.041 | 0.285 | |
dimred_pcoa | 0.185 | 0.042 | 0.231 | |
dimred_tsne | 9.300 | 0.252 | 9.562 | |
dimred_umap | 0.440 | 0.044 | 0.485 | |
diversities | 0 | 0 | 0 | |
diversities_help | 0.000 | 0.000 | 0.001 | |
diversity_beta_boxplot | 0.367 | 0.049 | 0.418 | |
diversity_beta_heatmap | 0.319 | 0.038 | 0.358 | |
diversity_beta_test | 0.158 | 0.003 | 0.161 | |
do_alpha_div_test | 0.059 | 0.001 | 0.059 | |
filter_categorize | 0.479 | 0.089 | 0.571 | |
filter_summary_bar_density | 0.457 | 0.038 | 0.538 | |
filter_summary_pie_box | 0.336 | 0.035 | 0.371 | |
find_biomarker | 6.337 | 0.032 | 6.373 | |
find_taxon_mat | 0.288 | 0.007 | 1.096 | |
find_taxonomy | 0.031 | 0.000 | 0.716 | |
find_taxonomy_300 | 0.041 | 0.000 | 0.623 | |
gini_simpson | 0.001 | 0.000 | 0.001 | |
grep_tid | 0.001 | 0.000 | 0.000 | |
inverse_simpson | 0 | 0 | 0 | |
is_categorical | 0 | 0 | 0 | |
is_integer0 | 0 | 0 | 0 | |
is_integer1 | 0.001 | 0.001 | 0.000 | |
mae_pick_organisms | 0.201 | 0.001 | 0.202 | |
mae_pick_samples | 0.239 | 0.001 | 0.240 | |
pct2str | 0 | 0 | 0 | |
percent | 0.001 | 0.000 | 0.000 | |
relabu_barplot | 1.280 | 0.041 | 1.322 | |
relabu_boxplot | 0.149 | 0.041 | 0.190 | |
relabu_heatmap | 0.183 | 0.036 | 0.219 | |
run_animalcules | 0 | 0 | 0 | |
shannon | 0 | 0 | 0 | |
simpson_index | 0.000 | 0.000 | 0.001 | |
upsample_counts | 0.021 | 0.001 | 0.021 | |