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CHECK report for animalcules on merida1

This page was generated on 2021-01-17 11:55:03 -0500 (Sun, 17 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE animalcules PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 58/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
animalcules 1.6.0
Yue Zhao
Snapshot Date: 2021-01-16 14:41:12 -0500 (Sat, 16 Jan 2021)
URL: https://git.bioconductor.org/packages/animalcules
Branch: RELEASE_3_12
Last Commit: a95d2e8
Last Changed Date: 2020-12-06 22:41:49 -0500 (Sun, 06 Dec 2020)
malbec1 Linux (Ubuntu 18.04.5 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: animalcules
Version: 1.6.0
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_1.6.0.tar.gz
StartedAt: 2021-01-16 23:10:53 -0500 (Sat, 16 Jan 2021)
EndedAt: 2021-01-16 23:17:23 -0500 (Sat, 16 Jan 2021)
EllapsedTime: 390.3 seconds
RetCode: 0
Status:  OK 
CheckDir: animalcules.Rcheck
Warnings: 0

Command output

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### 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_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/animalcules.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.6.0’
* 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 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
find_biomarker         10.878  0.083  10.975
dimred_tsne            10.315  0.194  10.540
differential_abundance  8.228  0.168   8.417
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/animalcules.Rcheck/00check.log’
for details.



Installation output

animalcules.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL animalcules
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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)

Tests output

animalcules.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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")
══ Warnings ════════════════════════════════════════════════════════════════════
── Warning (test-examples.R:148:5): dimred_tsne() is working ───────────────────
the condition has length > 1 and only the first element will be used
Backtrace:
 1. animalcules::dimred_tsne(...) test-examples.R:148:4
 2. tsne::tsne(scale(df), k = k, initial_dims = initial_dims, perplexity = perplexity)
 3. tsne:::.x2p(X, perplexity, 1e-05)

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 39 ]
> 
> proc.time()
   user  system elapsed 
 46.506   1.100  48.250 

Example timings

animalcules.Rcheck/animalcules-Ex.timings

nameusersystemelapsed
alpha_div_boxplot0.8400.0730.924
alpha_div_test0.0070.0010.008
counts_to_logcpm0.0020.0000.002
counts_to_relabu0.0030.0000.003
df_char_to_factor0.0010.0000.001
differential_abundance8.2280.1688.417
dimred_pca0.2310.0500.284
dimred_pcoa0.1670.0440.214
dimred_tsne10.315 0.19410.540
dimred_umap0.4880.0490.540
diversities0.0000.0010.001
diversities_help0.0010.0000.001
diversity_beta_boxplot0.3500.0430.395
diversity_beta_heatmap0.3010.0360.339
diversity_beta_test0.1270.0020.129
do_alpha_div_test0.0680.0020.069
filter_categorize0.4830.1010.590
filter_summary_bar_density0.4550.0380.494
filter_summary_pie_box0.2410.0320.274
find_biomarker10.878 0.08310.975
find_taxon_mat0.3030.0091.105
find_taxonomy0.0380.0010.735
find_taxonomy_3000.0340.0010.599
gini_simpson000
grep_tid0.0010.0000.000
inverse_simpson0.0000.0010.001
is_categorical0.0010.0000.000
is_integer00.0010.0000.001
is_integer10.0000.0010.001
mae_pick_organisms0.2340.0030.237
mae_pick_samples0.1990.0050.205
pct2str0.0000.0000.001
percent0.0000.0010.000
relabu_barplot1.5460.0551.604
relabu_boxplot0.1500.0370.187
relabu_heatmap0.1690.0360.208
run_animalcules000
shannon0.0000.0000.001
simpson_index0.0000.0010.000
upsample_counts0.0160.0010.017