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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:txdbmaker.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings txdbmaker_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/txdbmaker.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 12.7.1
* 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 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 92.706  3.113 203.471
makeTxDbFromBiomart   60.293  3.033 115.559
makeTxDbFromUCSC      13.804  0.203  23.147
makeTxDbFromGFF        9.435  0.066   9.531
makeTxDbFromEnsembl    0.735  0.024   9.259
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’
 ERROR
Running the tests in ‘tests/run_unitTests.R’ failed.
Last 13 lines of output:
  
  Error in BiocGenerics:::testPackage("txdbmaker") : 
    unit tests failed for package txdbmaker
  Calls: <Anonymous> -> <Anonymous>
  In addition: Warning messages:
  1: In .get_cds_IDX(mcols0$type, mcols0$phase) :
    The "phase" metadata column contains non-NA values for features of type
    exon. This information was ignored.
  2: In .get_cds_IDX(mcols0$type, mcols0$phase) :
    The "phase" metadata column contains non-NA values for features of type
    stop_codon. This information was ignored.
  3: In .extract_transcripts_from_GRanges(tx_IDX, gr, mcols0$type, mcols0$ID,  :
    the transcript names ("tx_name" column in the TxDb object) imported
    from the "Name" attribute are not unique
  Execution halted
* 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 ERROR, 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/txdbmaker.Rcheck/00check.log’
for details.