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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:keggorthology.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings keggorthology_2.63.0.tar.gz
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/keggorthology.Rcheck’
* using R Under development (unstable) (2025-10-28 r88973)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘keggorthology/DESCRIPTION’ ... OK
* this is package ‘keggorthology’ version ‘2.63.0’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘VJ Carey <stvjc@channing.harvard.edu>’

Unknown, possibly misspelled, fields in DESCRIPTION:
  ‘git_url’ ‘git_branch’ ‘git_last_commit’ ‘git_last_commit_date’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "VJ",
                    family = "Carey",
                    role = c("aut", "cre"),
                    email = "stvjc@channing.harvard.edu")
as necessary.

The Title field should be in title case. Current version is:
  ‘graph support for KO, KEGG Orthology’
In title case that is:
  ‘Graph Support for KO, KEGG Orthology’

The Description field should start with a capital letter.
* 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 ‘keggorthology’ 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 use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘DBI’
  All declared Imports should be used.
Package in Depends field not imported from: ‘hgu95av2.db’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getKOprobes: no visible binding for global variable ‘KOgraph’
getKOtags: no visible binding for global variable ‘KOgraph’
Undefined global functions or variables:
  KOgraph
* 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 sizes of PDF files under ‘inst/doc’ ...* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 3 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/keggorthology.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD INSTALL keggorthology
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library’
* installing *source* package ‘keggorthology’ ...
** this is package ‘keggorthology’ version ‘2.63.0’
** 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 (keggorthology)