Broken AnnotationHub resource (AH21414 | grasp2)
1
0
Entering edit mode
Peter Hickey ▴ 470
@petehaitch
Last seen 1 hour ago
Walter and Eliza Hall Institute of Medi…

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 • 779 views
ADD COMMENT
0
Entering edit mode
@valerie-obenchain-4275
Last seen 2.1 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

 

ADD COMMENT
0
Entering edit mode

Yep, working for me too. Thanks, Valerie!

ADD REPLY

Login before adding your answer.

Traffic: 345 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6