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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:bugphyzz.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings bugphyzz_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/bugphyzz.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘bugphyzz/DESCRIPTION’ ... OK
* this is package ‘bugphyzz’ version ‘1.1.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘bugphyzz’ 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 code 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 ... OK
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
physiologies       53.673  2.773 111.576
getTaxonSignatures 15.080  0.831  16.510
importBugphyzz     11.556  0.533  12.996
makeSignatures     11.535  0.496  12.811
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL bugphyzz
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘bugphyzz’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (bugphyzz)

R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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(bugphyzz)
> 
> test_check("bugphyzz")
Using data downloaded on 2024-11-26 17:02:17.

Attaching package: 'purrr'

The following object is masked from 'package:testthat':

    is_null

Importing binary data...
Replacing previous version downloaded on 2024-11-26 17:01:54.
Using data downloaded on 2024-11-28 17:01:29.
Importing multistate data...
Replacing previous version downloaded on 2024-11-26 17:01:58.
Using data downloaded on 2024-11-28 17:01:32.
Importing numeric data...
Replacing previous version downloaded on 2024-11-26 17:02:12.
Using data downloaded on 2024-11-28 17:01:43.
Importing binary data...
Replacing previous version downloaded on 2024-11-28 17:01:29.
Using data downloaded on 2024-11-28 17:01:48.
Importing multistate data...
Replacing previous version downloaded on 2024-11-28 17:01:32.
Using data downloaded on 2024-11-28 17:01:51.
Importing numeric data...
Replacing previous version downloaded on 2024-11-28 17:01:43.
Using data downloaded on 2024-11-28 17:02:02.
Replacing previous version downloaded on 2024-11-26 17:02:17.
Using data downloaded on 2024-11-28 17:02:07.
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Using data downloaded on 2024-11-28 17:02:07.
Using data downloaded on 2024-11-28 17:02:07.
All physiologies will be imported.
Finished COGEM pathogenicity rating.
Finished acetate producing.
Finished aerophilicity.
Finished animal pathogen.
Finished antimicrobial resistance.
Finished antimicrobial sensitivity.
Finished arrangement.
Finished biofilm formation.
Finished biosafety level.
Finished butyrate producing.
Finished coding genes.
Finished country.
Finished disease association.
Finished extreme environment.
Finished genome size.
Finished geographic location.
Finished gram stain.
Finished growth medium.
Finished growth temperature.
Finished habitat.
Finished halophily.
Finished health associated.
Finished hemolysis.
Finished host-associated.
Finished hydrogen gas producing.
Finished isolation site.
Finished lactate producing.
Finished length.
Finished metabolite production.
Finished metabolite utilization.
Finished motility.
Finished mutation rate per site per generation.
Finished mutation rate per site per year.
Finished optimal ph.
Finished pathogenicity human.
Finished plant pathogenicity.
Finished shape.
Finished sphingolipid producing.
Finished spore formation.
Finished spore shape.
Finished width.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 32 ]
> 
> proc.time()
   user  system elapsed 
124.599   6.677 206.341