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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MicrobiomeProfiler.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings MicrobiomeProfiler_1.5.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MicrobiomeProfiler.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘MicrobiomeProfiler/DESCRIPTION’ ... OK
* this is package ‘MicrobiomeProfiler’ version ‘1.5.0’
* 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 ‘MicrobiomeProfiler’ 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 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
enrichCOG: no visible global function definition for ‘slot<-’
enrichHMDB: no visible global function definition for ‘slot<-’
enrichKO: no visible global function definition for ‘slot<-’
enrichMBKEGG: no visible global function definition for ‘slot<-’
enrichMDA: no visible global function definition for ‘slot<-’
enrichSMPDB: no visible global function definition for ‘slot<-’
Undefined global functions or variables:
  slot<-
Consider adding
  importFrom("methods", "slot<-")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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 ...
  ‘MicrobiomeProfiler.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘MicrobiomeProfiler.Rmd’ using rmarkdown
Error: processing vignette 'MicrobiomeProfiler.Rmd' failed with diagnostics:
there is no package called ‘BiocStyle’
--- failed re-building ‘MicrobiomeProfiler.Rmd’

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

Error: Vignette re-building failed.
Execution halted

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

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/MicrobiomeProfiler.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL MicrobiomeProfiler
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘MicrobiomeProfiler’ ...
** using staged installation
** R
** data
** 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 (MicrobiomeProfiler)

R version 4.3.0 alpha (2023-04-03 r84154)
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(MicrobiomeProfiler)

> test_check("MicrobiomeProfiler")
--> No gene can be mapped....
--> Expected input gene ID: K03737,K00668,K16881,K17360,K22186,K01783
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: COG0752,COG0624,COG0423,COG0722,COG0505,COG1155
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 44737,209880,174708,35783,196082,397864
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: PW_C001420,PW_C000117,PW_C002950,PW_C001875,PW_C002951,PW_C000746
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: C06192,C00258,C00279,C00492,C00040,C05761
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: HMDB0000158,HMDB0000043,HMDB0003791,HMDB0000223,HMDB0006454,HMDB0004067
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
> 
> 
> proc.time()
   user  system elapsed 
  9.967   0.528  10.484