Package: animalcules

Version: 1.3.4

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_1.3.4.tar.gz

StartedAt: 2020-01-16 01:40:15 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 01:47:50 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 454.7 seconds

RetCode: 0

Status:  OK

CheckDir: animalcules.Rcheck

Warnings: 0

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### Running command:
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###   /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_1.3.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/animalcules.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘animalcules/DESCRIPTION’ ... OK
* this is package ‘animalcules’ version ‘1.3.4’
* 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: ‘biomformat’
  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         13.575  0.418  13.996
differential_abundance 11.558  0.080  11.639
dimred_tsne            11.053  0.582  11.637
* 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-3.11-bioc/meat/animalcules.Rcheck/00check.log’
for details.

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### Running command:
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###   /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)

R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 39 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 61.019   2.652  64.696 

name	user	system	elapsed
alpha_div_boxplot	1.155	0.117	1.434
alpha_div_test	0.006	0.000	0.006
counts_to_logcpm	0.002	0.000	0.003
counts_to_relabu	0.004	0.000	0.005
df_char_to_factor	0.001	0.000	0.001
differential_abundance	11.558	0.080	11.639
dimred_pca	0.289	0.048	0.338
dimred_pcoa	0.261	0.053	0.316
dimred_tsne	11.053	0.582	11.637
diversities	0.001	0.000	0.001
diversities_help	0.000	0.000	0.001
diversity_beta_boxplot	0.488	0.070	0.559
diversity_beta_heatmap	0.365	0.038	0.405
diversity_beta_test	0.158	0.009	0.167
do_alpha_div_test	0.134	0.010	0.144
filter_categorize	1.194	0.577	0.839
filter_summary_bar_density	0.681	0.046	0.729
filter_summary_pie_box	0.317	0.036	0.354
find_biomarker	13.575	0.418	13.996
find_taxon_mat	0.383	0.017	1.100
find_taxonomy	0.042	0.001	0.699
find_taxonomy_300	0.046	0.000	0.647
gini_simpson	0.000	0.000	0.001
grep_tid	0.001	0.001	0.001
inverse_simpson	0.000	0.000	0.001
is_categorical	0.001	0.001	0.000
is_integer0	0	0	0
is_integer1	0.000	0.000	0.001
mae_pick_organisms	0.247	0.001	0.247
mae_pick_samples	0.238	0.001	0.239
pct2str	0.000	0.000	0.001
percent	0.000	0.000	0.001
relabu_barplot	1.669	0.045	1.714
relabu_boxplot	0.175	0.036	0.213
relabu_heatmap	0.278	0.049	0.332
run_animalcules	0.000	0.000	0.001
shannon	0.000	0.000	0.001
simpson_index	0.001	0.001	0.001
upsample_counts	0.021	0.001	0.022