virtualArray 1.9.0
Andreas Heider
| Snapshot Date: 2014-10-09 16:20:10 -0700 (Thu, 09 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/virtualArray | | Last Changed Rev: 88840 / Revision: 95260 | | Last Changed Date: 2014-04-11 14:21:21 -0700 (Fri, 11 Apr 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | [ ERROR ] | skipped | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | ERROR | skipped | skipped |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | ERROR | skipped | skipped |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | ERROR | skipped | skipped |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data virtualArray
###
##############################################################################
##############################################################################
* 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, do.call,
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,
unsplit
Loading required package: plyr
Loading required package: preprocessCore
Warning: replacing previous import by ‘utils::relist’ when loading ‘virtualArray’
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")'.
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE23nnn/GSE23402/matrix/
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 --:--:-- 0:00:01 --:--:-- 0
7 5874k 7 432k 0 0 219k 0 0:00:26 0:00:01 0:00:25 227k
62 5874k 62 3657k 0 0 1231k 0 0:00:04 0:00:02 0:00:02 1261k
100 5874k 100 5874k 0 0 1724k 0 0:00:03 0:00:03 --:--:-- 1761k
File stored at:
/tmp/RtmpTNZ5g4/GPL570.soft
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE26nnn/GSE26428/matrix/
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
13 689k 13 94120 0 0 66792 0 0:00:10 0:00:01 0:00:09 70343
100 689k 100 689k 0 0 361k 0 0:00:01 0:00:01 --:--:-- 375k
File stored at:
/tmp/RtmpTNZ5g4/GPL6480.soft
Loading required package: BiocParallel
Loading required package: futile.logger
Now preprocessing raw data of GSE23402: Loading annotations...
Usinghgu133plus2as Bioconductor annotation package for datasetGSE23402.
Now preprocessing raw data of GSE26428: Loading annotations...
Usinghgug4112aas Bioconductor annotation package for datasetGSE26428.
Loading required package: hgu133plus2.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: hgug4112a.db
Loading required package: GenomeInfoDb
Loading required package: S4Vectors
Loading required package: AnnotationDbi
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:plyr’:
rename
Loading required package: IRanges
Loading required package: GenomeInfoDb
Attaching package: ‘IRanges’
The following object is masked from ‘package:plyr’:
desc
Loading required package: S4Vectors
Attaching package: ‘AnnotationDbi’
The following object is masked from ‘package:GenomeInfoDb’:
species
Loading required package: org.Hs.eg.db
Loading required package: DBI
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:plyr’:
rename
Loading required package: IRanges
Attaching package: ‘IRanges’
The following object is masked from ‘package:plyr’:
desc
Attaching package: ‘AnnotationDbi’
The following object is masked from ‘package:GenomeInfoDb’:
species
Loading required package: org.Hs.eg.db
Loading required package: DBI
Now preprocessing raw data of GSE26428: Collapsing expression values to their median...
Using identifier as id variables
Now preprocessing raw data of GSE23402: Collapsing expression values to their median...
Using identifier as id variables
Now preprocessing raw data of GSE26428: Annotating expression values with SYMBOL...
Now preprocessing raw data of GSE23402: Annotating expression values with SYMBOL...
Error: processing vignette 'virtualArray.Rnw' failed with diagnostics:
chunk 12
Error : 2 errors; first error:
Error in array(x, c(length(x), 1L), if (!is.null(names(x))) list(names(x), : 'data' must be of a vector type, was 'NULL'
For more information, use bplasterror(). To resume
calculation, re-call the function and set the
argument 'BPRESUME' 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: doTryCatch(return(expr), name, parentenv, handler)
Execution halted