BioC 2.13: BUILD report for virtualArray on zin1

* checking for file ‘virtualArray/DESCRIPTION’ ... OK
* preparing ‘virtualArray’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
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’:

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

Loading required package: plyr
Loading required package: preprocessCore
Creating a generic function for ‘hist’ from package ‘graphics’ in package ‘affyPLM’
Setting options(‘download.file.method.GEOquery’=‘curl’)
Warning: replacing previous import by ‘methods::new’ when loading ‘virtualArray’
Warning: replacing previous import by ‘stats::density’ when loading ‘virtualArray’
Warning: replacing previous import by ‘utils::installed.packages’ when loading ‘virtualArray’
Warning: replacing previous import by ‘utils::read.csv’ when loading ‘virtualArray’
Warning: replacing previous import by ‘utils::read.table’ when loading ‘virtualArray’
Warning: replacing previous import by ‘utils::write.table’ when loading ‘virtualArray’
To support our work please cite:
Thanks.
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")’.

Found 1 file(s)
GSE23402_series_matrix.txt.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 11 5874k   11  685k    0     0   351k      0  0:00:16  0:00:01  0:00:15  367k
100 5874k  100 5874k    0     0  2144k      0  0:00:02  0:00:02 --:--:-- 2211k
File stored at: 
/tmp/Rtmpy78Qxd/GPL570.soft
Found 1 file(s)
GSE26428_series_matrix.txt.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:01 --:--:--     0
100  689k  100  689k    0     0   344k      0  0:00:02  0:00:02 --:--:--  358k
File stored at: 
/tmp/Rtmpy78Qxd/GPL6480.soft
Loading required package: BiocParallel

Error: processing vignette ‘virtualArray.Rnw’ failed with diagnostics:
 chunk 12 
Error in LastError$store(results = results, is.error = is.error, throw.error = TRUE) : 
  Errors occurred during execution. First error message:
Error in as.character.default(x): no method for coercing this S4 class to a vector

For more information, use bplasterror().
To resume calculation, re-call the function and set the argument ‘resume’ to TRUE or wrap
the previous call in bpresume().

First traceback:
50: tools::buildVignettes(dir = ".", tangle = TRUE)
49: tryCatch({
        engine$weave(file, quiet = quiet)
        setwd(startdir)
        find_vignette_product(name, by = "weave", engine = engine)
    }, error = function(e) {
        stop(gettextf("processing vignette ‘%s’ failed with diagnostics:\n%s", 
            file, conditionMessage(e)), domain = NA, call. = FALSE)
    })
48: tryCatchList(expr, classes, parentenv, handlers)
47: tryCatchOne(expr, names, parentenv, handlers[[1L]])
46: doTryCatc
Execution halted
BioC 2.13: BUILD report for virtualArray on zin1

Summary

Command output
