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### Running command:
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###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:txdbmaker.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings txdbmaker_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/txdbmaker.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘txdbmaker/DESCRIPTION’ ... OK
* this is package ‘txdbmaker’ version ‘1.0.0’
* 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 ‘txdbmaker’ 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘AnnotationDbi:::dbEasyQuery’ ‘BiocGenerics:::testPackage’
  ‘GenomeInfoDb:::check_tax_id’
  ‘GenomeInfoDb:::lookup_organism_by_tax_id’
  ‘GenomeInfoDb:::lookup_tax_id_by_organism’
  ‘GenomeInfoDb:::make_circ_flags_from_circ_seqs’
  ‘S4Vectors:::anyMissingOrOutside’
  ‘S4Vectors:::extract_data_frame_rows’ ‘S4Vectors:::quick_togroup’
  ‘biomaRt:::martBM’ ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’
  ‘rtracklayer:::resourceDescription’
  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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in Rd file 'txdbmaker-package.Rd':
  ‘https://bioconductor.org/packages/release/bioc/vignettes/txdbmaker/inst/doc/txdbmaker.html’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
makeFeatureDbFromUCSC 119.732  3.640 318.934
makeTxDbFromBiomart    67.797  1.423 240.347
makeTxDbFromUCSC       18.482  0.084  35.224
makeTxDbFromGFF        11.805  0.140  11.968
makeTxDbFromEnsembl     1.073  0.011  13.133
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.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: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/txdbmaker.Rcheck/00check.log’
for details.