Broken AnnotationHub resource (AH21414 | grasp2)
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Entering edit mode
Peter Hickey ▴ 740
@petehaitch
Last seen 5 weeks ago
WEHI, Melbourne, Australia

The 'grasp2' resource appears to be broken with a HTTP 403 error in both release and devel

> suppressPackageStartupMessages(library(AnnotationHub))
> ah <- AnnotationHub()
snapshotDate(): 2016-05-12
> ah["AH21414"]
AnnotationHub with 1 record
# snapshotDate(): 2016-05-12
# names(): AH21414
# $dataprovider: NHLBI
# $species: Homo sapiens
# $rdataclass: SQLiteConnection
# $title: Bioconductor distribution of grasp2 v. 2.0.0.0
# $description: Build 2.0.0.0 of the grasp2 data base, with 2,082 GWAS studi...
# $taxonomyid: 9606
# $genome: hg19
# $sourcetype: GRASP
# $sourceurl: https://s3.amazonaws.com/NHLBI_Public/GRASP/GraspFullDataset2.zip
# $sourcelastmodifieddate: NA
# $sourcesize: NA
# $tags: SNP, Annotation, GRASP2
# retrieve record with 'object[["AH21414"]]'
> ah[["AH21414"]]
downloading from ‘https://annotationhub.bioconductor.org/fetch/25509’
retrieving 1 resource
Downloading: 240 B
Error: failed to load resource
  name: AH21414
  title: Bioconductor distribution of grasp2 v. 2.0.0.0
  reason: 1 resources failed to download
In addition: Warning message:
download failed
  hub path: ‘https://annotationhub.bioconductor.org/fetch/25509’
  cache path: ‘/home/other/phickey/.AnnotationHub/25509’
  reason: Forbidden (HTTP 403).
> sessionInfo()
R version 3.3.0 Patched (2016-05-20 r70657)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.5 (Santiago)

locale:
 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8
 [5] LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8
 [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] AnnotationHub_2.4.0 BiocGenerics_0.18.0 repete_0.0.0.9004
[4] devtools_1.11.1

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.5                   AnnotationDbi_1.34.2
 [3] knitr_1.12.3                  magrittr_1.5
 [5] IRanges_2.6.0                 munsell_0.4.3
 [7] xtable_1.8-2                  colorspace_1.2-6
 [9] R6_2.1.2                      stringr_1.0.0
[11] httr_1.1.0                    plyr_1.8.3
[13] tools_3.3.0                   Biobase_2.32.0
[15] DBI_0.4-1                     withr_1.0.1
[17] htmltools_0.3.5               digest_0.6.9
[19] interactiveDisplayBase_1.10.0 shiny_0.13.2
[21] pryr_0.1.2                    S4Vectors_0.10.0
[23] codetools_0.2-14              curl_0.9.7
[25] mime_0.4                      memoise_1.0.0
[27] RSQLite_1.0.0                 stringi_1.0-1
[29] BiocInstaller_1.22.1          scales_0.4.0
[31] stats4_3.3.0                  httpuv_1.3.3
> BiocInstaller::biocVersion()
[1] ‘3.3’
annotationhub grasp2 grasp2db • 1.4k views
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Entering edit mode
@valerie-obenchain-4275
Last seen 2.9 years ago
United States

Hi Pete,

Thanks for report. Should be fixed in the version with snapshot date of May 26.

> hub = AnnotationHub()
snapshotDate(): 2016-05-26

Valerie

 

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Entering edit mode

Yep, working for me too. Thanks, Valerie!

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