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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no GenomicFeatures_1.59.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc-longtests/meat/GenomicFeatures.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* 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 24.04.1 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘GenomicFeatures/DESCRIPTION’ ... OK
* this is package ‘GenomicFeatures’ version ‘1.59.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
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 for sufficient/correct file permissions ... OK
* checking whether package ‘GenomicFeatures’ can be installed ... OK
* checking installed package size ... OK
* checking package 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:::.getMetaValue’ ‘AnnotationDbi:::.valid.colnames’
  ‘AnnotationDbi:::.valid.metadata.table’
  ‘AnnotationDbi:::.valid.table.colnames’ ‘AnnotationDbi:::dbEasyQuery’
  ‘AnnotationDbi:::dbQuery’ ‘AnnotationDbi:::smartKeys’
  ‘BiocGenerics:::testPackage’
  ‘GenomeInfoDb:::getSeqlevelsReplacementMode’
  ‘GenomeInfoDb:::normarg_new2old’
  ‘GenomicRanges:::unsafe.transcriptLocs2refLocs’
  ‘GenomicRanges:::unsafe.transcriptWidths’
  ‘IRanges:::regroupBySupergroup’ ‘S4Vectors:::V_recycle’
  ‘S4Vectors:::decodeRle’ ‘S4Vectors:::extract_data_frame_rows’
  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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  FeatureDb-class.Rd: saveDb, loadDb
  extractUpstreamSeqs.Rd: mcols
  getPromoterSeq-methods.Rd: GRanges, GRangesList
  nearest-methods.Rd: GenomicRanges
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
 WARNING
directory ‘longtests’ not found
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc-longtests/meat/GenomicFeatures.Rcheck/00check.log’
for details.

* installing *source* package ‘GenomicFeatures’ ...
** this is package ‘GenomicFeatures’ version ‘1.59.1’
** using staged installation
** R
** 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 (GenomicFeatures)