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Question: AnnotationHub Error HTTP status was '500 Internal Server Error'
0
gravatar for ness
22 months ago by
ness0
ness0 wrote:

I am trying to compare results obtained from an older version of R and Bioconductor to current. However, the script I used in Dec 2014 no longer works - it reports an error from AnnotationHub.

I suspect this is due to something that has changed, such as a link to a remote database or the lack of "https" support, but I can't figure out how to get around this. Can someone help?

Scott Ness, PhD - University of New Mexico Cancer Center

 

Here are the commands and the error:

R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.1.0 (64-bit)

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.

  Natural language support but running in an English locale

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.

> library(AnnotationHub)
Loading required package: IRanges
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 object is masked from ‘package:stats’:

    xtabs

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

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

> hub = AnnotationHub()
Error in file(con, "r") : cannot open the connection
In addition: Warning message:
In file(con, "r") :
  cannot open: HTTP status was '500 Internal Server Error'
> traceback()
8: file(con, "r")
7: readLines(file, warn = FALSE)
6: paste(readLines(file, warn = FALSE), collapse = "")
5: fromJSON(file = url, ...)
4: .parseJSON(url)
3: as.POSIXlt(.parseJSON(url))
2: .snapshotDate(hubUrl, snapshotVersion)
1: AnnotationHub()
> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)

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] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] AnnotationHub_1.4.0 IRanges_1.22.10     BiocGenerics_0.10.0

loaded via a namespace (and not attached):
 [1] annotate_1.42.1          AnnotationDbi_1.26.1     Biobase_2.24.0          
 [4] BiocInstaller_1.14.3     Category_2.30.0          colorspace_1.2-4        
 [7] DBI_0.3.1                digest_0.6.4             genefilter_1.46.1       
[10] GenomeInfoDb_1.0.2       GenomicRanges_1.16.4     ggplot2_1.0.0           
[13] graph_1.42.0             grid_3.1.1               gridSVG_1.4-0           
[16] GSEABase_1.26.0          gtable_0.1.2             htmltools_0.2.6         
[19] httpuv_1.3.2             httr_0.5                 interactiveDisplay_1.2.0
[22] lattice_0.20-29          MASS_7.3-35              Matrix_1.1-4            
[25] mime_0.2                 munsell_0.4.2            plyr_1.8.1              
[28] proto_0.3-10             R6_2.0.1                 RBGL_1.40.1             
[31] RColorBrewer_1.0-5       Rcpp_0.11.3              RCurl_1.95-4.3          
[34] reshape2_1.4             rjson_0.2.14             RJSONIO_1.3-0           
[37] RSQLite_1.0.0            scales_0.2.4             shiny_0.10.2.1          
[40] splines_3.1.1            stats4_3.1.1             stringr_0.6.2           
[43] survival_2.37-7          tools_3.1.1              XML_3.98-1.1            
[46] xtable_1.7-4             XVector_0.4.0           

ADD COMMENTlink modified 22 months ago • written 22 months ago by ness0
0
gravatar for James W. MacDonald
22 months ago by
United States
James W. MacDonald45k wrote:

You should upgrade to a current version of R and Bioconductor and try again.

ADD COMMENTlink written 22 months ago by James W. MacDonald45k
0
gravatar for ness
22 months ago by
ness0
ness0 wrote:

Thanks -  The new version works fine... but the problem is that the old version no longer works. 

This is a big problem for trying to publish results... if readers cannot reproduce results because 1-yr old software no longer works. Ideally, if one restores everything to the way it was a year ago, one should get the same results again. But that is not the case.

 

ADD COMMENTlink written 22 months ago by ness0
0
gravatar for Dan Tenenbaum
22 months ago by
Dan Tenenbaum ♦♦ 8.2k
United States
Dan Tenenbaum ♦♦ 8.2k wrote:

The old AnnotationHub server was offline. It is back online now.

Dan

 

ADD COMMENTlink written 22 months ago by Dan Tenenbaum ♦♦ 8.2k
0
gravatar for ness
22 months ago by
ness0
ness0 wrote:

Thanks very much!  Now I just need to figure out why my new and old analyses give different results...

:-)

Scott

ADD COMMENTlink written 22 months ago by ness0
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