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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:AnnotationDbi.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings AnnotationDbi_1.73.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/AnnotationDbi.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘AnnotationDbi/DESCRIPTION’ ... OK
* this is package ‘AnnotationDbi’ version ‘1.73.0’
* 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 ‘AnnotationDbi’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   4.3Mb
* 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 ... NOTE
Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
createORGANISMSeeds: no visible global function definition for
  ‘makeAnnDbMapSeeds’
Undefined global functions or variables:
  makeAnnDbMapSeeds
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'AnnDbPkg-checker.Rd':
  ‘[AnnotationForge:AnnDbPkg-maker]{AnnDbPkg-maker}’

Non-topic package-anchored link(s) in Rd file 'print.probetable.Rd':
  ‘[base:print.dataframe]{print.data.frame}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'Bimap-envirAPI.Rd':
mget
  Code: function(x, envir = as.environment(pos), mode = "any",
                 ifnotfound, inherits = FALSE, pos = -1L)
  Docs: function(x, envir, mode, ifnotfound, inherits)
  Argument names in code not in docs:
    pos
  Mismatches in argument default values:
    Name: 'envir' Code: as.environment(pos) Docs: 
    Name: 'mode' Code: "any" Docs: 
    Name: 'inherits' Code: FALSE Docs: 

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ...* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
AnnDbPkg-checker  35.453  0.628  36.355
organismKEGGFrame  0.183  0.003   6.509
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘AnnotationDbi_unit_tests.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: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/AnnotationDbi.Rcheck/00check.log’
for details.