Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-24 15:05:39 -0400 (Fri, 24 Sep 2021).

CHECK results for animalcules on nebbiolo1

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 58/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
animalcules 1.8.1  (landing page)
Yue Zhao
Snapshot Date: 2021-09-23 04:50:12 -0400 (Thu, 23 Sep 2021)
git_url: https://git.bioconductor.org/packages/animalcules
git_branch: RELEASE_3_13
git_last_commit: 5a3dc66
git_last_commit_date: 2021-06-02 12:17:59 -0400 (Wed, 02 Jun 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: 1.8.1
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:animalcules.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings animalcules_1.8.1.tar.gz
StartedAt: 2021-09-23 08:49:16 -0400 (Thu, 23 Sep 2021)
EndedAt: 2021-09-23 08:53:41 -0400 (Thu, 23 Sep 2021)
EllapsedTime: 264.9 seconds
RetCode: 0
Status:   OK  
CheckDir: animalcules.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:animalcules.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings animalcules_1.8.1.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/animalcules.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.8.1’
* 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 ... 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
differential_abundance 7.624  0.472   8.095
find_biomarker         6.118  0.028   6.147
* 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-3.13-bioc/meat/animalcules.Rcheck/00check.log’
for details.



Installation output

animalcules.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL animalcules
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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)

Tests output

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-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")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 38 ]
> 
> proc.time()
   user  system elapsed 
 29.563   1.625  31.738 

Example timings

animalcules.Rcheck/animalcules-Ex.timings

nameusersystemelapsed
alpha_div_boxplot0.5100.0880.604
alpha_div_test0.0040.0000.004
counts_to_logcpm0.0020.0000.001
counts_to_relabu0.0030.0000.003
df_char_to_factor0.0010.0000.001
differential_abundance7.6240.4728.095
dimred_pca0.1420.0380.181
dimred_pcoa0.1120.0110.122
dimred_tsne4.8120.0684.880
dimred_umap0.3530.0240.376
diversities0.0010.0010.001
diversities_help000
diversity_beta_boxplot0.2140.0130.228
diversity_beta_heatmap0.1830.0120.194
diversity_beta_test0.1130.0040.117
do_alpha_div_test0.0470.0000.047
filter_categorize0.2760.0360.312
filter_summary_bar_density1.1580.3921.550
filter_summary_pie_box0.2010.0120.213
find_biomarker6.1180.0286.147
find_taxon_mat0.1450.0000.784
find_taxonomy0.0390.0000.703
find_taxonomy_3000.0440.0010.659
gini_simpson000
grep_tid0.0000.0000.001
inverse_simpson0.0010.0000.000
is_categorical000
is_integer00.0000.0000.001
is_integer10.0010.0000.001
mae_pick_organisms0.2060.0040.209
mae_pick_samples0.1460.0040.149
pct2str0.0010.0000.001
percent000
relabu_barplot0.9460.0350.981
relabu_boxplot0.1190.0000.118
relabu_heatmap0.1220.0080.130
run_animalcules000
shannon000
simpson_index000
upsample_counts0.0120.0000.012