Package: animalcules

Version: 1.2.1

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:animalcules.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings animalcules_1.2.1.tar.gz

StartedAt: 2020-04-15 06:32:19 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 06:37:59 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 340.4 seconds

RetCode: 0

Status:  OK

CheckDir: animalcules.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:animalcules.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings animalcules_1.2.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/animalcules.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘animalcules/DESCRIPTION’ ... OK
* this is package ‘animalcules’ version ‘1.2.1’
* 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 ... 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 or elapsed time > 5s
                        user system elapsed
find_biomarker         11.48  0.012  12.106
dimred_tsne             9.88  0.012   9.932
differential_abundance  9.40  0.084   9.569
* 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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/animalcules.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL animalcules
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 39 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 47.300   0.808  49.068 

name	user	system	elapsed
alpha_div_boxplot	0.840	0.012	0.906
alpha_div_test	0.004	0.000	0.006
counts_to_logcpm	0.004	0.000	0.003
counts_to_relabu	0.004	0.000	0.005
df_char_to_factor	0.004	0.000	0.001
differential_abundance	9.400	0.084	9.569
dimred_pca	0.220	0.016	0.239
dimred_pcoa	0.236	0.004	0.242
dimred_tsne	9.880	0.012	9.932
dimred_umap	0.856	0.008	0.867
diversities	0	0	0
diversities_help	0.000	0.000	0.001
diversity_beta_boxplot	0.356	0.000	0.368
diversity_beta_heatmap	0.324	0.012	0.339
diversity_beta_test	0.124	0.004	0.129
do_alpha_div_test	0.06	0.00	0.06
filter_categorize	0.904	0.028	0.599
filter_summary_bar_density	0.488	0.012	0.506
filter_summary_pie_box	0.280	0.008	0.296
find_biomarker	11.480	0.012	12.106
find_taxon_mat	0.344	0.008	0.985
find_taxonomy	0.108	0.004	0.696
find_taxonomy_300	0.124	0.000	0.748
gini_simpson	0	0	0
grep_tid	0	0	0
inverse_simpson	0	0	0
is_categorical	0	0	0
is_integer0	0	0	0
is_integer1	0	0	0
mae_pick_organisms	0.152	0.000	0.159
mae_pick_samples	0.160	0.000	0.165
pct2str	0.000	0.000	0.001
percent	0	0	0
relabu_barplot	1.632	0.012	1.653
relabu_boxplot	0.148	0.004	0.152
relabu_heatmap	0.204	0.004	0.207
run_animalcules	0	0	0
shannon	0	0	0
simpson_index	0	0	0
upsample_counts	0.020	0.000	0.044