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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MicrobiomeProfiler.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MicrobiomeProfiler_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/MicrobiomeProfiler.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MicrobiomeProfiler/DESCRIPTION’ ... OK
* this is package ‘MicrobiomeProfiler’ version ‘1.4.0’
* 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 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/MicrobiomeProfiler.Rcheck/00check.log’
for details.

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MicrobiomeProfiler
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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: K00616,K00039,K01962,K16339,K22539,K00103
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: COG0137,COG2053,COG0077,COG4830,COG1911,COG0169
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 140625,104397,40544,209879,821,28037
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: PW_C001388,PW_C000197,PW_C000977,PW_C000105,PW_C000749,PW_C000544
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: C00532,C06019,C01099,C05745,C05345,C20878
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: HMDB0000026,HMDB0000294,HMDB0000935,HMDB0001429,HMDB0000300,HMDB0000517
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
> 
> 
> proc.time()
   user  system elapsed 
  9.215   0.586   9.823