BioC 3.3: BUILD report for DrugVsDisease on linux2.bioconductor.org

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data DrugVsDisease
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* checking for file ‘DrugVsDisease/DESCRIPTION’ ... OK
* preparing ‘DrugVsDisease’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: affy
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, as.vector,
    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, 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: limma

Attaching package: ‘limma’

The following object is masked from ‘package:BiocGenerics’:

    plotMA

Loading required package: biomaRt
Loading required package: ArrayExpress
Loading required package: GEOquery
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: DrugVsDiseasedata
Loading required package: cMap2data

Attaching package: ‘cMap2data’

The following object is masked from ‘package:DrugVsDiseasedata’:

    genelist

Loading required package: qvalue
trying URL 'http://www.ebi.ac.uk/arrayexpress/files/A-AFFY-33/A-AFFY-33.adf.txt'
Content type 'text/plain' length 2419735 bytes (2.3 MB)
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downloaded 2.3 MB

trying URL 'http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-22528/E-GEOD-22528.sdrf.txt'
Content type 'text/plain' length 8099 bytes
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downloaded 8099 bytes

trying URL 'http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-22528/E-GEOD-22528.idf.txt'
Content type 'text/plain' length 5376 bytes
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downloaded 5376 bytes

Copying raw data files

trying URL 'http://www.ebi.ac.uk/arrayexpress/files/E-GEOD-22528/E-GEOD-22528.raw.1.zip'
Content type 'application/zip' length 33986194 bytes (32.4 MB)
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downloaded 32.4 MB

Unpacking data files
ArrayExpress: Reading pheno data from SDRF
ArrayExpress: Reading data files
Loading required package: pd.hg.u133a
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘pd.hg.u133a’
Attempting to obtain 'pd.hg.u133a' from BioConductor website.
Checking to see if your internet connection works...
trying URL 'https://bioconductor.org/packages/3.3/data/annotation/src/contrib/pd.hg.u133a_3.12.0.tar.gz'
Content type 'unknown' length 9851796 bytes (9.4 MB)
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downloaded 9.4 MB

* installing *source* package ‘pd.hg.u133a’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (pd.hg.u133a)

The downloaded source packages are in
	‘/tmp/Rtmp3khWXS/downloaded_packages’
Loading required package: pd.hg.u133a
Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: XVector
Loading required package: RSQLite
Loading required package: DBI
Loading required package: oligoClasses
Welcome to oligoClasses version 1.33.0

Attaching package: ‘oligoClasses’

The following object is masked from ‘package:affy’:

    list.celfiles

Loading required package: oligo
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Welcome to oligo version 1.35.0
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Attaching package: ‘oligo’

The following object is masked from ‘package:limma’:

    backgroundCorrect

The following objects are masked from ‘package:affy’:

    MAplot, intensity, mm, mm<-, mmindex, pm, pm<-,
    pmindex, probeNames, rma

Platform design info loaded.
Read 53 items

 E-GEOD-22528  was successfully loaded into  ExpressionFeatureSet 


Error: processing vignette 'DrugVsDisease.Rnw' failed with diagnostics:
 chunk 2 
Error in .convertEnsembl(platform, values = rownames(exprdata)) : 
  Annotation file not available for this platform. Must be one of Affymetrix, HGU133A, HGU133A2 or HGU133Plus2. Alternatively upload an annotation file to process the data
Execution halted
BioC 3.3: BUILD report for DrugVsDisease on linux2.bioconductor.org

Summary

Command output
