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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:fobitools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings fobitools_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/fobitools.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘fobitools/DESCRIPTION’ ... OK
* this is package ‘fobitools’ version ‘1.14.0’
* 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 ‘fobitools’ 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 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
annotate_foods: no visible binding for global variable ‘FOOD_NAME’
annotate_foods: no visible binding for global variable ‘FOOD_ID’
annotate_foods: no visible binding for global variable ‘words’
annotate_foods: no visible binding for global variable ‘words_joint’
annotate_foods: no visible binding for global variable ‘id_code’
annotate_foods: no visible binding for global variable ‘name’
annotate_foods: no visible binding for global variable ‘ref’
annotate_foods: no visible binding for global variable ‘detect’
annotate_foods: no visible binding for global variable ‘.’
annotate_foods: no visible binding for global variable ‘match_score’
fobi_graph: no visible binding for global variable ‘is_a_code’
fobi_graph: no visible binding for global variable ‘id_code’
fobi_graph: no visible binding for global variable ‘Contains’
fobi_graph: no visible binding for global variable ‘Property’
fobi_graph: no visible binding for global variable ‘name’
fobi_graph: no visible binding for global variable ‘BiomarkerOf’
fobi_graph: no visible binding for global variable ‘is_a_name’
fobi_graph: no visible binding for global variable ‘subOntology’
id_convert: no visible binding for global variable ‘BiomarkerOf’
id_convert: no visible binding for global variable ‘name’
id_convert: no visible binding for global variable ‘FOBI’
id_convert: no visible binding for global variable ‘HMDB’
id_convert: no visible binding for global variable ‘KEGG’
id_convert: no visible binding for global variable ‘PubChemCID’
id_convert: no visible binding for global variable ‘InChIKey’
id_convert: no visible binding for global variable ‘InChICode’
id_convert: no visible binding for global variable ‘ChemSpider’
id_convert: no visible binding for global variable ‘metaboliteNames’
id_convert: no visible binding for global variable ‘presence’
id_convert: no visible binding for global variable ‘.’
msea: no visible binding for global variable ‘BiomarkerOf’
msea: no visible binding for global variable ‘id_BiomarkerOf’
msea: no visible binding for global variable ‘name’
msea: no visible binding for global variable ‘FOBI’
msea: no visible binding for global variable ‘is_a_code’
msea: no visible binding for global variable ‘is_a_name’
msea: no visible binding for global variable ‘.’
msea: no visible global function definition for ‘unstack’
msea: no visible binding for global variable ‘pathway’
msea: no visible binding for global variable ‘size’
msea: no visible binding for global variable ‘className’
msea: no visible binding for global variable ‘classSize’
msea: no visible binding for global variable ‘log2err’
msea: no visible binding for global variable ‘ES’
msea: no visible binding for global variable ‘NES’
msea: no visible binding for global variable ‘pval’
msea: no visible binding for global variable ‘padj’
msea: no visible binding for global variable ‘leadingEdge’
ora: no visible binding for global variable ‘BiomarkerOf’
ora: no visible binding for global variable ‘id_BiomarkerOf’
ora: no visible binding for global variable ‘name’
ora: no visible binding for global variable ‘FOBI’
ora: no visible binding for global variable ‘is_a_code’
ora: no visible binding for global variable ‘is_a_name’
ora: no visible binding for global variable ‘.’
ora: no visible global function definition for ‘unstack’
ora: no visible binding for global variable ‘pathway’
ora: no visible binding for global variable ‘size’
ora: no visible binding for global variable ‘overlapGenes’
ora: no visible binding for global variable ‘className’
ora: no visible binding for global variable ‘classSize’
ora: no visible binding for global variable ‘overlap’
ora: no visible binding for global variable ‘pval’
ora: no visible binding for global variable ‘padj’
ora: no visible binding for global variable ‘overlapMetabolites’
parse_fobi: no visible binding for global variable ‘V2’
parse_fobi: no visible binding for global variable ‘V1’
parse_fobi: no visible binding for global variable ‘gf’
parse_fobi: no visible binding for global variable ‘name’
parse_fobi: no visible binding for global variable ‘id_code’
parse_fobi: no visible binding for global variable ‘Contains’
parse_fobi: no visible binding for global variable ‘disjoint_from’
parse_fobi: no visible binding for global variable ‘FOBI:050339’
parse_fobi: no visible binding for global variable ‘ChemSpider’
parse_fobi: no visible binding for global variable ‘KEGG’
parse_fobi: no visible binding for global variable ‘is_a_code’
parse_fobi: no visible binding for global variable ‘id_BiomarkerOf’
parse_fobi: no visible binding for global variable ‘id_Contains’
Undefined global functions or variables:
  . BiomarkerOf ChemSpider Contains ES FOBI FOBI:050339 FOOD_ID
  FOOD_NAME HMDB InChICode InChIKey KEGG NES Property PubChemCID V1 V2
  className classSize detect disjoint_from gf id_BiomarkerOf
  id_Contains id_code is_a_code is_a_name leadingEdge log2err
  match_score metaboliteNames name overlap overlapGenes
  overlapMetabolites padj pathway presence pval ref size subOntology
  unstack words words_joint
Consider adding
  importFrom("methods", "className")
  importFrom("utils", "unstack")
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 ... NOTE
  Note: found 199 marked UTF-8 strings
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... NOTE
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
parse_fobi 15.201  2.471  24.601
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/fobitools.Rcheck/00check.log’
for details.