##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:AnnotationHubData.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings AnnotationHubData_1.39.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/AnnotationHubData.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘AnnotationHubData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AnnotationHubData’ version ‘1.39.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ... 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 73.074  1.555  74.631
* 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, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/AnnotationHubData.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL AnnotationHubData
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘AnnotationHubData’ ...
** this is package ‘AnnotationHubData’ version ‘1.39.2’
** 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)

R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("AnnotationHubData")

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

No methods found in package 'rtracklayer' for request: 'trackName<-' when loading 'AnnotationHubData'
INFO [2025-10-22 21:10:39] Preparer Class: ChEAImportPreparer
complete!
INFO [2025-10-22 21:10:40] Preparer Class: EncodeImportPreparer
getting file info: wgEncodeAffyRnaChipFiltTransfragsGm12878CellTotal.broadPeak.gz
getting file info: wgEncodeAffyRnaChipFiltTransfragsGm12878CytosolLongnonpolya.broadPeak.gz
getting file info: wgEncodeAffyRnaChipFiltTransfragsGm12878CytosolLongpolya.broadPeak.gz
getting file info: wgEncodeAffyRnaChipFiltTransfragsGm12878NucleolusTotal.broadPeak.gz
getting file info: wgEncodeAffyRnaChipFiltTransfragsGm12878NucleusLongnonpolya.broadPeak.gz
complete!
INFO [2025-10-22 21:10:41] Preparer Class: Grasp2ImportPreparer
complete!
INFO [2025-10-22 21:10:41] Preparer Class: NCBIImportPreparer
looking up value for: 495146
looking up value for: 4565
looking up value for: 8296
looking up value for: 214697
looking up value for: 111132
looking up value for: 3708
sh: 1: azcopy: not found
Processing 10 files.
complete!
INFO [2025-10-22 21:10:49] Preparer Class: RefNetImportPreparer
complete!
INFO [2025-10-22 21:10:49] Preparer Class: dbSNPVCFPreparer
ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/archive_1.0/2016/
complete!
Found invalid DispatchClass.

[1] "somethingNotThere"

For currently available DispatchClass run
    'AnnotationHub::DispatchClassList()'

Found invalid DispatchClass.

[1] "somethingNotThere"

For currently available DispatchClass run
    'AnnotationHub::DispatchClassList()'

Loading valid species information.
ftp://ftp.ensembl.org/pub/release-98/gtf/homo_sapiens/
ftp://ftp.ensembl.org/pub/release-98/gtf/homo_sapiens/
ftp://ftp.ensembl.org/pub/release-98/gtf/homo_sapiens/


RUNIT TEST PROTOCOL -- Wed Oct 22 21:12:58 2025 
*********************************************** 
Number of test functions: 20 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
AnnotationHubData RUnit Tests - 20 test functions, 0 errors, 0 failures
Number of test functions: 20 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In value[[3L]](cond) :
  gerstein-2012.tsv_0.0.1.RData: Could not resolve host: bioconductorhubs.blob.core.windows.net
2: In value[[3L]](cond) :
  hypoxiaSignaling-2006.tsv_0.0.1.RData: Could not resolve host: bioconductorhubs.blob.core.windows.net
3: In value[[3L]](cond) :
  stamlabTFs-2012.tsv_0.0.1.RData: Could not resolve host: bioconductorhubs.blob.core.windows.net
4: In value[[3L]](cond) :
  recon202.tsv_0.0.1.RData: Could not resolve host: bioconductorhubs.blob.core.windows.net
> 
> proc.time()
   user  system elapsed 
124.765   2.808 183.672