curatedBreastData 1.5.0
Katie Planey
| Snapshot Date: 2016-09-21 09:20:16 -0700 (Wed, 21 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/curatedBreastData | | Last Changed Rev: 3763 / Revision: 3889 | | Last Changed Date: 2016-05-03 14:48:02 -0700 (Tue, 03 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | ERROR | skipped | | |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | [ ERROR ] | skipped | skipped | |
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### Running command:
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### chmod a+r curatedBreastData -R && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data curatedBreastData
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* checking for file 'curatedBreastData/DESCRIPTION' ... OK
* preparing 'curatedBreastData':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...Warning: running command '"D:/biocbld/bbs-3.4-bioc/R/bin/x64/Rscript" --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 1
ERROR
Loading required package: ggplot2
Loading required package: impute
Loading required package: XML
Loading required package: Biobase
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':
Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame,
cbind, colnames, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste,
pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff,
sort, table, tapply, union, unique, unsplit, which, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with 'browseVignettes()'. To
cite Bioconductor, see 'citation("Biobase")', and for packages
'citation("pkgname")'.
Loading required package: BiocStyle
Analyzing dataset 1 or dataset named study_1379_GPL1223_all
Warning in filterAndImputeSamples(study, studyName = "study", outputFile = paste0(outputFileDirectory, :
Just a warning: this function assumes your missing values
are proper NAs, not "null",etc.
Warning in collapseDupProbes(expr = exprSet@assayData$exprs, sampleColNames = colnames(exprSet@assayData$exprs), :
It's best to impute NA values before running this function
otherwise it may set averages to NA if there is 1 NA present.
This function just removes any genes whose key is NA.
Warning in collapseDupProbes(expr = exprSet@assayData$exprs, sampleColNames = colnames(exprSet@assayData$exprs), :
You may get a warning here because key names are duplicated
so it can't use them as row names. That's OK.
Error: processing vignette 'curatedBreastData-manual.Rnw' failed with diagnostics:
chunk 4
Error in .validate_assayDataElementReplace(obj, value) :
object and replacement value have different dimensions
Execution halted