##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:animalcules.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings animalcules_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/animalcules.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘animalcules/DESCRIPTION’ ... OK
* this is package ‘animalcules’ version ‘1.16.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘SummarizedExperiment::rownames’ by ‘biomformat::rownames’ when loading ‘animalcules’
  Warning: replacing previous import ‘SummarizedExperiment::colnames’ by ‘biomformat::colnames’ when loading ‘animalcules’
  Warning: replacing previous import ‘ape::where’ by ‘dplyr::where’ when loading ‘animalcules’
See ‘/home/biocbuild/bbs-3.17-bioc/meat/animalcules.Rcheck/00install.out’ for details.
* 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 loading without being on the library search path ... 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 ... ERROR
Running examples in ‘animalcules-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: find_taxonomy
> ### Title: Find the taxonomy for unlimited tids
> ### Aliases: find_taxonomy
> 
> ### ** Examples
> 
> taxonLevels <- find_taxonomy(tids=1200)
Error: HTTP failure: 400
<?xml version="1.0" encoding="UTF-8" ?>
<!DOCTYPE eEfetchResult PUBLIC "-//NLM//DTD efetch 20131226//EN" "https://eutils.ncbi.nlm.nih.gov/eutils/dtd/20131226/efetch.dtd">
<eFetchResult>
	<ERROR> Error: External viewer error: Empty Response. Bytes read: 0 Status: Timeout</ERROR>
</eFetchResult>
Execution halted
* 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 ...
  ‘animalcules.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘animalcules.Rmd’ using rmarkdown

Quitting from lines 29-32 [unnamed-chunk-1] (animalcules.Rmd)
Error: processing vignette 'animalcules.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building ‘animalcules.Rmd’

SUMMARY: processing the following file failed:
  ‘animalcules.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/animalcules.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL animalcules
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘animalcules’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘SummarizedExperiment::rownames’ by ‘biomformat::rownames’ when loading ‘animalcules’
Warning: replacing previous import ‘SummarizedExperiment::colnames’ by ‘biomformat::colnames’ when loading ‘animalcules’
Warning: replacing previous import ‘ape::where’ by ‘dplyr::where’ when loading ‘animalcules’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘SummarizedExperiment::rownames’ by ‘biomformat::rownames’ when loading ‘animalcules’
Warning: replacing previous import ‘SummarizedExperiment::colnames’ by ‘biomformat::colnames’ when loading ‘animalcules’
Warning: replacing previous import ‘ape::where’ by ‘dplyr::where’ when loading ‘animalcules’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘SummarizedExperiment::rownames’ by ‘biomformat::rownames’ when loading ‘animalcules’
Warning: replacing previous import ‘SummarizedExperiment::colnames’ by ‘biomformat::colnames’ when loading ‘animalcules’
Warning: replacing previous import ‘ape::where’ by ‘dplyr::where’ when loading ‘animalcules’
** testing if installed package keeps a record of temporary installation path
* DONE (animalcules)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 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)
Warning messages:
1: replacing previous import 'SummarizedExperiment::rownames' by 'biomformat::rownames' when loading 'animalcules' 
2: replacing previous import 'SummarizedExperiment::colnames' by 'biomformat::colnames' when loading 'animalcules' 
3: replacing previous import 'ape::where' by 'dplyr::where' when loading 'animalcules' 
> 
> test_check("animalcules")
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 38 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 38 ]
> 
> proc.time()
   user  system elapsed 
 24.921   1.204  26.662