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"
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> 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
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