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
>
