Back to Multiple platform build/check report for BioC 3.12
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for animalcules on malbec1

This page was generated on 2020-08-13 11:21:26 -0400 (Thu, 13 Aug 2020).

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 54/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
animalcules 1.5.1
Yue Zhao
Snapshot Date: 2020-08-12 14:52:00 -0400 (Wed, 12 Aug 2020)
URL: https://git.bioconductor.org/packages/animalcules
Branch: master
Last Commit: 36c4fb6
Last Changed Date: 2020-06-18 11:25:25 -0400 (Thu, 18 Jun 2020)
malbec1 Linux (Ubuntu 18.04.4 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: 1.5.1
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:animalcules.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings animalcules_1.5.1.tar.gz
StartedAt: 2020-08-13 06:11:26 -0400 (Thu, 13 Aug 2020)
EndedAt: 2020-08-13 06:17:38 -0400 (Thu, 13 Aug 2020)
EllapsedTime: 371.4 seconds
RetCode: 0
Status:  OK 
CheckDir: animalcules.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:animalcules.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings animalcules_1.5.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/animalcules.Rcheck’
* using R version 4.0.2 (2020-06-22)
* 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 ‘1.5.1’
* 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
find_biomarker         12.812  0.020  12.859
dimred_tsne            10.252  0.020  10.309
differential_abundance  8.776  0.176   8.961
* 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-3.12-bioc/meat/animalcules.Rcheck/00check.log’
for details.



Installation output

animalcules.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL animalcules
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-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 4.0.2 (2020-06-22) -- "Taking Off Again"
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: 2 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 49.912   1.012  53.238 

Example timings

animalcules.Rcheck/animalcules-Ex.timings

nameusersystemelapsed
alpha_div_boxplot0.9280.0481.401
alpha_div_test0.0080.0000.013
counts_to_logcpm0.0040.0000.003
counts_to_relabu0.0040.0000.005
df_char_to_factor0.0040.0000.001
differential_abundance8.7760.1768.961
dimred_pca0.3040.0080.482
dimred_pcoa0.2920.0080.442
dimred_tsne10.252 0.02010.309
dimred_umap0.3880.0040.393
diversities0.0000.0000.001
diversities_help000
diversity_beta_boxplot0.3240.0040.331
diversity_beta_heatmap0.3680.0080.374
diversity_beta_test0.1480.0000.150
do_alpha_div_test0.0720.0000.074
filter_categorize0.3560.0040.365
filter_summary_bar_density0.5480.0040.552
filter_summary_pie_box0.3160.0080.324
find_biomarker12.812 0.02012.859
find_taxon_mat0.2280.0080.800
find_taxonomy0.0920.0040.632
find_taxonomy_3000.0440.0000.664
gini_simpson000
grep_tid000
inverse_simpson0.0000.0000.001
is_categorical0.0000.0000.001
is_integer0000
is_integer10.0000.0040.000
mae_pick_organisms0.2800.0000.283
mae_pick_samples0.2320.0000.235
pct2str000
percent000
relabu_barplot2.1600.0122.178
relabu_boxplot0.1720.0080.178
relabu_heatmap0.2320.0040.237
run_animalcules000
shannon000
simpson_index000
upsample_counts0.0200.0000.032