lgatto / pRoloc

A unifying bioinformatics framework for organelle proteomics
http://lgatto.github.io/pRoloc/
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Biomart down? #77

Closed lmsimp closed 8 years ago

lmsimp commented 8 years ago

I believe Biomart is down. knitr output from pRoloc-goannotations (below). Also setAnnotationParams is hanging... can you verify the same happens with you @lgatto? Thanks.


processing file: pRoloc-goannotations.Rmd
  |...                                                              |   5%
   inline R code fragments

  |......                                                           |  10%
label: loadData (with options) 
List of 3
 $ echo   : logi TRUE
 $ message: logi FALSE
 $ warning: logi FALSE

Loading required package: MSnbase
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 objects are masked from 'package:stats':

    IQR, mad, 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,
    grep, grepl, intersect, is.unsorted, lapply, lengths, Map,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, Position, rank, rbind, Reduce, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unlist, unsplit

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: mzR
Loading required package: Rcpp
Loading required package: BiocParallel
Loading required package: ProtGenerics

This is MSnbase version 1.19.19 
  Read '?MSnbase' and references therein for information
  about the package and how to get started.

Attaching package: 'MSnbase'

The following object is masked from 'package:stats':

    smooth

The following object is masked from 'package:base':

    trimws

Loading required package: MLInterfaces
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: XML
Loading required package: cluster

This is pRoloc version 1.11.23 
  Read '?pRoloc' and references therein for information
  about the package and how to get started.

This is pRolocdata version 1.9.5.
Use 'pRolocdata()' to list available data sets.
  |..........                                                       |  15%
  ordinary text without R code

  |.............                                                    |  20%
label: queryparams
  |................                                                 |  25%
  ordinary text without R code

  |....................                                             |  30%
label: addGO (with options) 
List of 4
 $ echo   : logi TRUE
 $ message: logi FALSE
 $ warning: logi FALSE
 $ eval   : logi TRUE

Quitting from lines 50-53 (pRoloc-goannotations.Rmd) 
Error in value[[3L]](cond) : 
  Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.
Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
lgatto commented 8 years ago

It did work in the morning for me. Do you still have this?

lmsimp commented 8 years ago

Okay now, so I am closing