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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AnnotationHub.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings AnnotationHub_3.13.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/AnnotationHub.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'AnnotationHub/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AnnotationHub' version '3.13.0'
* 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 whether package 'AnnotationHub' 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'BiocFileCache:::.get_tbl_rid' 'S4Vectors:::selectSome'
  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 ... 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 ... ERROR
Running examples in 'AnnotationHub-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AnnotationHub-objects
> ### Title: AnnotationHub objects and their related methods and functions
> ### Aliases: class:AnnotationHub AnnotationHub-class class:Hub Hub-class
> ###   .Hub AnnotationHub refreshHub mcols,Hub-method cache cache,Hub-method
> ###   cache,AnnotationHub-method cache<- cache<-,Hub-method hubUrl
> ###   hubUrl,Hub-method hubCache hubCache,Hub-method hubDate
> ###   hubDate,Hub-method package package,Hub-method removeCache isLocalHub
> ###   isLocalHub,Hub-method isLocalHub<- isLocalHub<-,Hub-method
> ###   possibleDates snapshotDate snapshotDate,Hub-method snapshotDate<-
> ###   snapshotDate<-,Hub-method removeResources
> ###   removeResources,missing-method removeResources,character-method
> ###   dbconn,Hub-method dbfile,Hub-method .db_close recordStatus
> ###   recordStatus,Hub-method length,Hub-method names,Hub-method
> ###   fileName,Hub-method $,Hub-method [[,Hub,character,missing-method
> ###   [[,Hub,numeric,missing-method [,Hub,character,missing-method
> ###   [,Hub,logical,missing-method [,Hub,numeric,missing-method
> ###   [<-,Hub,character,missing,Hub-method
> ###   [<-,Hub,logical,missing,Hub-method [<-,Hub,numeric,missing,Hub-method
> ###   subset,Hub-method query query,Hub-method as.list.Hub
> ###   as.list,Hub-method c,Hub-method show,Hub-method
> ###   show,AnnotationHubResource-method
> ### Keywords: classes methods
> 
> ### ** Examples
> 
>   ## create an AnnotationHub object
>   library(AnnotationHub)
>   ah = AnnotationHub()
> 
>   ## Summary of available records
>   ah
AnnotationHub with 69666 records
# snapshotDate(): 2024-06-27
# $dataprovider: Ensembl, BroadInstitute, UCSC, Haemcode, FANTOM5,DLRP,IUPHA...
# $species: Homo sapiens, Mus musculus, Drosophila melanogaster, Rattus norv...
# $rdataclass: GRanges, TwoBitFile, BigWigFile, EnsDb, Rle, SQLiteFile, Chai...
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["AH5012"]]' 

             title                                             
  AH5012   | Chromosome Band                                   
  AH5013   | STS Markers                                       
  AH5014   | FISH Clones                                       
  AH5015   | Recomb Rate                                       
  AH5016   | ENCODE Pilot                                      
  ...        ...                                               
  AH117051 | Ensembl 112 EnsDb for Xiphophorus maculatus       
  AH117052 | Ensembl 112 EnsDb for Xenopus tropicalis          
  AH117053 | Ensembl 112 EnsDb for Zonotrichia albicollis      
  AH117054 | Ensembl 112 EnsDb for Zalophus californianus      
  AH117055 | Ensembl 112 EnsDb for Zosterops lateralis melanops
> 
>   ## Detail for a single record
>   ah[1]
AnnotationHub with 1 record
# snapshotDate(): 2024-06-27
# names(): AH5012
# $dataprovider: UCSC
# $species: Homo sapiens
# $rdataclass: GRanges
# $rdatadateadded: 2013-03-26
# $title: Chromosome Band
# $description: GRanges object from UCSC track 'Chromosome Band'
# $taxonomyid: 9606
# $genome: hg19
# $sourcetype: UCSC track
# $sourceurl: rtracklayer://hgdownload.cse.ucsc.edu/goldenpath/hg19/database...
# $sourcesize: NA
# $tags: c("cytoBand", "UCSC", "track", "Gene", "Transcript",
#   "Annotation") 
# retrieve record with 'object[["AH5012"]]' 
> 
>   ## and what is the date we are using?
>   snapshotDate(ah)
[1] "2024-06-27"
> 
>   ## how many resources?
>   length(ah)
[1] 69666
> 
>   ## from which resources, is data available?
>   head(sort(table(ah$dataprovider), decreasing=TRUE))

                                                                                                   Ensembl 
                                                                                                     35862 
                                                                                            BroadInstitute 
                                                                                                     18248 
                                                                                                      UCSC 
                                                                                                     11202 
                                                                                                  Haemcode 
                                                                                                       945 
FANTOM5,DLRP,IUPHAR,HPRD,STRING,SWISSPROT,TREMBL,ENSEMBL,CELLPHONEDB,BADERLAB,SINGLECELLSIGNALR,HOMOLOGENE 
                                                                                                       872 
                                                                                                NCBI,DBCLS 
                                                                                                       514 
> 
>   ## from which species, is data available ?
>   head(sort(table(ah$species),decreasing=TRUE))

           Homo sapiens            Mus musculus Drosophila melanogaster 
                  26652                    1858                     468 
      Rattus norvegicus              Bos taurus         Pan troglodytes 
                    344                     341                     327 
> 
>   ## what web service and local cache does this AnnotationHub point to?
>   hubUrl(ah)
[1] "https://annotationhub.bioconductor.org"
>   hubCache(ah)
[1] "F:\\biocbuild\\AnnotationHub_cache"
> 
>   ### Examples ###
> 
>   ## One can  search the hub for multiple strings
>   ahs2 <- query(ah, c("GTF", "77","Ensembl", "Homo sapiens"))
> 
>   ## information about the file can be retrieved using
>   ahs2[1]
AnnotationHub with 1 record
# snapshotDate(): 2024-06-27
# names(): AH28812
# $dataprovider: Ensembl
# $species: Homo sapiens
# $rdataclass: GRanges
# $rdatadateadded: 2015-03-25
# $title: Homo_sapiens.GRCh38.77.gtf
# $description: Gene Annotation for Homo sapiens
# $taxonomyid: 9606
# $genome: GRCh38
# $sourcetype: GTF
# $sourceurl: ftp://ftp.ensembl.org/pub/release-77/gtf/homo_sapiens/Homo_sap...
# $sourcesize: 44454526
# $tags: c("GTF", "ensembl", "Gene", "Transcript", "Annotation") 
# retrieve record with 'object[["AH28812"]]' 
> 
>   ## one can further extract information from this show method
>   ## like the sourceurl using:
>   ahs2$sourceurl
[1] "ftp://ftp.ensembl.org/pub/release-77/gtf/homo_sapiens/Homo_sapiens.GRCh38.77.gtf.gz"
>   ahs2$description
[1] "Gene Annotation for Homo sapiens"
>   ahs2$title
[1] "Homo_sapiens.GRCh38.77.gtf"
> 
>   ## We can download a file by name like this (using a list semantic):
>   gr <- ahs2[[1]]
loading from cache
require("GenomicRanges")
Warning in readChar(con, 5L, useBytes = TRUE) :
  truncating string with embedded nuls
Warning: file '56602aa83f89_34252' has magic number 'X'
  Use of save versions prior to 2 is deprecated
Error: failed to load resource
  name: AH28812
  title: Homo_sapiens.GRCh38.77.gtf
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'runTests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  'F:/biocbuild/bbs-3.20-bioc/meat/AnnotationHub.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL AnnotationHub
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'AnnotationHub' ...
** 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 (AnnotationHub)

R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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("AnnotationHub")

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, unique, unsplit, which.max, which.min

Using 'localHub=TRUE'
  If offline, please also see BiocManager vignette section on offline use
require("xxx_foo")


RUNIT TEST PROTOCOL -- Tue Jul 23 22:02:09 2024 
*********************************************** 
Number of test functions: 20 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
AnnotationHub 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: call dbDisconnect() when finished working with a connection 
2: download failed
  hub path: 'bogus/url'
  cache resource: 'AHInvalid : 5012'
  reason: all(rtype == "web" | file.exists(fpath)) is not TRUE 
> 
> proc.time()
   user  system elapsed 
  49.67   10.57   64.59