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This page was generated on 2021-12-06 13:05:49 -0500 (Mon, 06 Dec 2021).

CHECK results for animalcules on machv2

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.

raw results

Package 56/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
animalcules 1.10.0  (landing page)
Yue Zhao
Snapshot Date: 2021-12-05 01:55:05 -0500 (Sun, 05 Dec 2021)
git_url: https://git.bioconductor.org/packages/animalcules
git_branch: RELEASE_3_14
git_last_commit: 4c16173
git_last_commit_date: 2021-10-26 12:51:53 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: animalcules
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:animalcules.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings animalcules_1.10.0.tar.gz
StartedAt: 2021-12-05 11:42:14 -0500 (Sun, 05 Dec 2021)
EndedAt: 2021-12-05 11:49:24 -0500 (Sun, 05 Dec 2021)
EllapsedTime: 430.1 seconds
RetCode: 0
Status:   OK  
CheckDir: animalcules.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:animalcules.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings animalcules_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/animalcules.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.10.0’
* 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 ... OK
* 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 12.695  0.147  12.862
dimred_tsne            11.028  0.152  11.196
find_biomarker          7.983  0.070   8.064
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/animalcules.Rcheck/00check.log’
for details.



Installation output

animalcules.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL animalcules
###
##############################################################################
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* 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)

Tests output

animalcules.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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 
 54.644   1.204  56.529 

Example timings

animalcules.Rcheck/animalcules-Ex.timings

nameusersystemelapsed
alpha_div_boxplot0.8200.1270.956
alpha_div_test0.0060.0010.006
counts_to_logcpm0.0020.0000.003
counts_to_relabu0.0040.0000.004
df_char_to_factor0.0010.0000.002
differential_abundance12.695 0.14712.862
dimred_pca0.3360.0670.404
dimred_pcoa0.1580.0410.200
dimred_tsne11.028 0.15211.196
dimred_umap0.5130.0390.553
diversities0.0000.0010.000
diversities_help000
diversity_beta_boxplot0.3030.0400.344
diversity_beta_heatmap0.2990.0410.341
diversity_beta_test0.1230.0020.124
do_alpha_div_test0.0690.0020.070
filter_categorize0.3820.0790.463
filter_summary_bar_density0.4640.0460.511
filter_summary_pie_box0.2500.0390.290
find_biomarker7.9830.0708.064
find_taxon_mat0.3100.0081.008
find_taxonomy0.0320.0000.749
find_taxonomy_3000.0360.0000.579
gini_simpson0.0010.0010.001
grep_tid0.0010.0000.000
inverse_simpson000
is_categorical0.0000.0010.000
is_integer00.0000.0000.001
is_integer10.0000.0000.001
mae_pick_organisms0.2060.0010.208
mae_pick_samples0.0980.0000.098
pct2str0.0000.0000.001
percent0.0000.0010.000
relabu_barplot1.6100.0601.674
relabu_boxplot0.1710.0380.210
relabu_heatmap0.1960.0370.233
run_animalcules000
shannon000
simpson_index0.0010.0000.000
upsample_counts0.0170.0010.018