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.
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ordinary text without R code
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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
I believe Biomart is down.
knitr
output frompRoloc-goannotations
(below). AlsosetAnnotationParams
is hanging... can you verify the same happens with you @lgatto? Thanks.