virtualArray 1.9.0
Andreas Heider
| Snapshot Date: 2014-10-09 17:20:02 -0700 (Thu, 09 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/virtualArray | | Last Changed Rev: 88840 / Revision: 95261 | | Last Changed Date: 2014-04-11 14:21:21 -0700 (Fri, 11 Apr 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | [ ERROR ] | skipped | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | ERROR | skipped | skipped |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | ERROR | skipped | skipped |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | ERROR | skipped | skipped |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.1-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
1 5874k 1 97016 0 0 71690 0 0:01:23 0:00:01 0:01:22 76330
77 5874k 77 4523k 0 0 1936k 0 0:00:03 0:00:02 0:00:01 2006k
100 5874k 100 5874k 0 0 2358k 0 0:00:02 0:00:02 --:--:-- 2439k
File stored at:
/tmp/RtmpAam4DV/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
4 689k 4 33304 0 0 26454 0 0:00:26 0:00:01 0:00:25 28033
100 689k 100 689k 0 0 363k 0 0:00:01 0:00:01 --:--:-- 377k
File stored at:
/tmp/RtmpAam4DV/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.
Packagehgug4112a.dbnot available. Atempting to install it.
Bioconductor version 3.0 (BiocInstaller 1.15.5), ?biocLite
for help
Installing package into ‘/tmp/RtmpNckKH4/Rinst220e280e5252’
(as ‘lib’ is unspecified)
also installing the dependency ‘org.Hs.eg.db’
trying URL 'http://bioconductor.org/packages/3.0/data/annotation/src/contrib/org.Hs.eg.db_3.0.0.tar.gz'
Content type 'application/x-gzip' length 61468422 bytes (58.6 Mb)
opened URL
=================================================
downloaded 58.6 Mb
trying URL 'http://bioconductor.org/packages/3.0/data/annotation/src/contrib/hgug4112a.db_3.0.0.tar.gz'
Content type 'application/x-gzip' length 1582331 bytes (1.5 Mb)
opened URL
==================================================
downloaded 1.5 Mb
* installing *source* package ‘org.Hs.eg.db’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (org.Hs.eg.db)
* installing *source* package ‘hgug4112a.db’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (hgug4112a.db)
Package hgug4112a.db has been successfully installed!
Loading required package: hgug4112a.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: GenomeInfoDb
Loading required package: S4Vectors
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 GSE26428: Annotating expression values with SYMBOL...
Error: processing vignette 'virtualArray.Rnw' failed with diagnostics:
chunk 12
Error : 2 errors; first error:
Error in eval(expr, envir, enclos): object 'hgu133plus2SYMBOL' not found
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:
49: tools::buildVignettes(dir = ".", tangle = TRUE)
48: tryCatch({
engine$weave(file, quiet = quiet)
setwd(startdir)
find_vignette_product(name, by = "weave", engine = engine)
}, error = function(e) {
stop(gettextf("processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)), domain = NA, call. = FALSE)
})
47: tryCatchList(expr, classes, parentenv, handlers)
46: tryCatchOne(expr, names, parentenv, handlers[[1L]])
45: doTryCatch(return(expr), name, parentenv, handler)
44: engine$weave(file, quiet = quiet)
43: ut
Execution halted