##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomicFeatures.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings GenomicFeatures_1.51.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/GenomicFeatures.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GenomicFeatures/DESCRIPTION' ... OK
* this is package 'GenomicFeatures' version '1.51.4'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocGenerics', 'S4Vectors', 'IRanges', 'GenomeInfoDb',
  'GenomicRanges', 'AnnotationDbi'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 whether package 'GenomicFeatures' 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 R 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
':::' call which should be '::': 'rtracklayer:::tableNames'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'AnnotationDbi:::.getMetaValue' 'AnnotationDbi:::.valid.colnames'
  'AnnotationDbi:::.valid.metadata.table'
  'AnnotationDbi:::.valid.table.colnames' 'AnnotationDbi:::dbEasyQuery'
  'AnnotationDbi:::dbQuery' 'AnnotationDbi:::smartKeys'
  'BiocGenerics:::testPackage' 'GenomeInfoDb:::check_tax_id'
  'GenomeInfoDb:::getSeqlevelsReplacementMode'
  'GenomeInfoDb:::lookup_organism_by_tax_id'
  'GenomeInfoDb:::lookup_tax_id_by_organism'
  'GenomeInfoDb:::make_circ_flags_from_circ_seqs'
  'GenomeInfoDb:::normarg_new2old'
  'GenomicRanges:::unsafe.transcriptLocs2refLocs'
  'GenomicRanges:::unsafe.transcriptWidths'
  'IRanges:::regroupBySupergroup' 'S4Vectors:::V_recycle'
  'S4Vectors:::anyMissingOrOutside' 'S4Vectors:::decodeRle'
  '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 ... WARNING
checkRd: (5) FeatureDb-class.Rd:31-34: \item in \describe must have non-empty label
checkRd: (5) TxDb-class.Rd:30-33: \item in \describe must have non-empty label
checkRd: (5) TxDb-class.Rd:34-39: \item in \describe must have non-empty label
checkRd: (5) TxDb-class.Rd:40-43: \item in \describe must have non-empty label
checkRd: (5) TxDb-class.Rd:44-52: \item in \describe must have non-empty label
checkRd: (5) TxDb-class.Rd:53-59: \item in \describe must have non-empty label
checkRd: (5) TxDb-class.Rd:60-65: \item in \describe must have non-empty label
checkRd: (5) TxDb-class.Rd:66-71: \item in \describe must have non-empty label
checkRd: (5) TxDb-class.Rd:72-80: \item in \describe must have non-empty label
checkRd: (5) select-methods.Rd:21-25: \item in \describe must have non-empty label
checkRd: (5) select-methods.Rd:26-50: \item in \describe must have non-empty label
checkRd: (5) select-methods.Rd:51-55: \item in \describe must have non-empty label
checkRd: (5) select-methods.Rd:56-62: \item in \describe must have non-empty label
* 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
makeFeatureDbFromUCSC      75.32   3.25  105.38
coverageByTranscript       59.42   1.83   61.27
makeTxDbFromBiomart        52.11   2.24  181.34
coordinate-mapping-methods 44.05   2.37   53.50
exonicParts                33.37   1.41   35.66
extractTranscriptSeqs      12.00   0.59   12.68
transcriptLocs2refLocs      7.02   1.14    8.25
makeTxDbFromUCSC            7.75   0.19   27.34
makeTxDbFromGFF             6.84   0.03    6.89
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'run_unitTests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... 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, 2 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/GenomicFeatures.Rcheck/00check.log'
for details.