Hello,

Downloading the AnnotationHub object AH134 (the hg19 genome) does not currently work, even though the source URL for that object exists and can be manually downloaded. Here is a reproducible code example:

> library (AnnotationHub)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply,
    parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, xtabs

The following objects are masked from ‘package:base’:

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

> hub = AnnotationHub()
snapshotDate(): 2016-10-11

> hub[["AH134"]]
require(“Rsamtools”)
downloading from ‘https://annotationhub.bioconductor.org/fetch/134’
    ‘https://annotationhub.bioconductor.org/fetch/14095’
retrieving 2 resources
Downloading: 240 B    
Downloading: 240 B    
Error: failed to load resource
  name: AH134
  title: Homo_sapiens.GRCh37.69.dna.toplevel.fa
  reason: 2 resources failed to download
In addition: Warning messages:
1: download failed
  hub path: ‘https://annotationhub.bioconductor.org/fetch/134’
  cache path: ‘/Users/rbradley//.AnnotationHub/134’
  reason: Forbidden (HTTP 403).
2: download failed
  hub path: ‘https://annotationhub.bioconductor.org/fetch/14095’
  cache path: ‘/Users/rbradley//.AnnotationHub/14095’
  reason: Forbidden (HTTP 403).

> hub["AH134"]$sourceurl
[1] "ftp://ftp.ensembl.org/pub/release-69/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.69.dna.toplevel.fa.gz"

I confirmed that Bioconductor itself and all packages were updated. Here is my session info:

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.6 (El Capitan)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    parallel  grDevices utils     datasets  stats     graphics  methods   base     

other attached packages:
[1] Rsamtools_1.26.0     Biostrings_2.42.0    XVector_0.14.0       GenomicRanges_1.26.0 GenomeInfoDb_1.10.0  IRanges_2.8.0        S4Vectors_0.12.0     AnnotationHub_2.6.0
[9] BiocGenerics_0.20.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.7                   AnnotationDbi_1.36.0          zlibbioc_1.20.0               BiocParallel_1.8.0            xtable_1.8-2                 
 [6] R6_2.2.0                      httr_1.2.1                    Biobase_2.34.0                DBI_0.5-1                     htmltools_0.3.5              
[11] digest_0.6.10                 interactiveDisplayBase_1.12.0 shiny_0.14.1                  bitops_1.0-6                  curl_2.1                     
[16] RSQLite_1.0.0                 mime_0.5                      BiocInstaller_1.24.0          httpuv_1.3.3                 

Hi Robert,

Dan helped me sort this one out. It's due to an error I made a few months ago when I accidentally deleted a few ensembl 69 fastas from the hub. 

Looking at one of the problem urls:

https://annotationhub.bioconductor.org/fetch/134

curl -I https://annotationhub.bioconductor.org/fetch/134

shows that it redirects to:

http://s3.amazonaws.com/annotationhub/ensembl/release-69/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.69.dna.toplevel.fa.rz

However, looking in that folder in S3 there is no file with an .rz extension. The processing of these fastas involves downloading the .gz, unzipping, indexing and re-compressing as .rz. In our haste to replace the deleted files we accidentally uploaded the .gz files as replacements instead of the .rz files. 

I will rebuild the .rz files for Ensembl 69 but it probably won't happen until next week. Do you need version 69? None of the other versions >= 70 have this problem. GRCh37 dna toplevel is available in several other versions ...

Valerie