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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_1.37.2.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) (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
* checking for file ‘AnnotationHubData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AnnotationHubData’ version ‘1.37.2’
* 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 ... NOTE
No methods found in package ‘rtracklayer’ for request: ‘trackName<-’ when loading ‘AnnotationHubData’

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘stringr’
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’
.ucscTableQuery: no visible global function definition for
  ‘trackName<-’
needToRerunNonStandardOrgDb: no visible binding for global variable
  ‘results’
needToRerunNonStandardOrgDb: no visible binding for global variable
  ‘specData’
needToRerunNonStandardOrgDb: no visible binding for global variable
  ‘currentMetadata’
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:
  currentMetadata results seqname specData trackName<-
* checking Rd files ... WARNING
Fatal error: cannot create 'R_TempDir'
* checking Rd metadata ... NOTE
Fatal error: cannot create 'R_TempDir'
* checking Rd cross-references ... INFO
Fatal error: cannot create 'R_TempDir'
* checking for missing documentation entries ... WARNING
Fatal error: cannot create 'R_TempDir'
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Fatal error: cannot create 'R_TempDir'
Fatal error: cannot create 'R_TempDir'
* checking Rd \usage sections ... WARNING
Fatal error: cannot create 'R_TempDir'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Fatal error: cannot create 'R_TempDir'
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... NOTE
Fatal error: cannot create 'R_TempDir'
* checking for unstated dependencies in examples ... WARNING
Fatal error: cannot create 'R_TempDir'
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ...Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Error: inferior call failed
Execution halted

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###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL AnnotationHubData
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’
* installing *source* package ‘AnnotationHubData’ ...
** this is package ‘AnnotationHubData’ version ‘1.37.2’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘rtracklayer’ for request: ‘trackName<-’ when loading ‘AnnotationHubData’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘rtracklayer’ for request: ‘trackName<-’ when loading ‘AnnotationHubData’
** testing if installed package can be loaded from final location
No methods found in package ‘rtracklayer’ for request: ‘trackName<-’ when loading ‘AnnotationHubData’
** testing if installed package keeps a record of temporary installation path
* DONE (AnnotationHubData)