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### Running command:
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###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:AnnotationHubData.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings AnnotationHubData_1.37.0.tar.gz
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/AnnotationHubData.Rcheck’
* using R Under development (unstable) (2024-11-14 r87333)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘AnnotationHubData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AnnotationHubData’ version ‘1.37.0’
* 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 ‘AnnotationHubData’ 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' imports not declared from:
  ‘AzureStor’ ‘stringr’
'loadNamespace' or 'requireNamespace' call not declared from: ‘AzureStor’
Missing objects imported by ':::' calls:
  ‘AnnotationHub:::.db_connection’
  ‘GenomicFeatures:::.makeUCSCChrominfo’
  ‘GenomicFeatures:::lookup_organism_by_UCSC_genome’
Unexported objects imported by ':::' calls:
  ‘BiocCheck:::getParent’ ‘GenomeInfoDb:::check_tax_id’
  ‘GenomeInfoDb:::fetch_species_index_from_Ensembl_FTP’
  ‘GenomeInfoDb:::lookup_organism_by_tax_id’
  ‘GenomeInfoDb:::lookup_tax_id_by_organism’
  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
.NCBIMetadataFromUrl: no visible binding for global variable ‘results’
.NCBIMetadataFromUrl: no visible binding for global variable ‘specData’
.makeComplexGR: no visible binding for global variable ‘seqname’
needToRerunNonStandardOrgDb: no visible binding for global variable
  ‘results’
needToRerunNonStandardOrgDb: no visible binding for global variable
  ‘specData’
oldAWSS3_needToRerunNonStandardOrgDb: no visible binding for global
  variable ‘results’
oldAWSS3_needToRerunNonStandardOrgDb: no visible binding for global
  variable ‘specData’
trackWithAuxiliaryTablesToGRanges: no visible binding for global
  variable ‘seqname’
Undefined global functions or variables:
  results seqname specData
* checking Rd files ... NOTE
checkRd: (-1) makeAnnotationHubMetadata.Rd:31-36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) makeAnnotationHubMetadata.Rd:40-187: Lost braces in \itemize; meant \describe ?
* 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 include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
validationFunctions 55.037  0.917  55.957
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘AnnotationHubData_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, 2 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/AnnotationHubData.Rcheck/00check.log’
for details.