BioC experimental data: BUILD report for ggtut on morelia

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ggtut
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* checking for file ‘ggtut/DESCRIPTION’ ... OK
* preparing ‘ggtut’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: GGBase
Loading required package: snpStats
Loading required package: survival
Loading required package: Matrix
Loading required package: data.table
Loading required package: parallel

Attaching package: ‘GGtools’

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

    getCall

Loading required package: Biobase
Loading required package: BiocGenerics

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:Matrix’:

    as.vector

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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: illuminaHumanv1.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

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

    expand.grid


Attaching package: ‘IRanges’

The following object is masked from ‘package:data.table’:

    shift

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

    expand

Loading required package: org.Hs.eg.db
Loading required package: DBI


To get a tailored smlSet, use getSS("GGdata", [chrvec])

available chromosomes are named 1, 10, ..., X, Y

Loading required package: ff
Loading required package: bit
Attaching package bit
package:bit (c) 2008-2012 Jens Oehlschlaegel (GPL-2)
creators: bit bitwhich
coercion: as.logical as.integer as.bit as.bitwhich which
operator: ! & | xor != ==
querying: print length any all min max range sum summary
bit access: length<- [ [<- [[ [[<-
for more help type ?bit

Attaching package: ‘bit’

The following object is masked from ‘package:data.table’:

    setattr

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

    xor

Attaching package ff
- getOption("fftempdir")=="/tmp/RtmpSXQWYD"

- getOption("ffextension")=="ff"

- getOption("ffdrop")==TRUE

- getOption("fffinonexit")==TRUE

- getOption("ffpagesize")==65536

- getOption("ffcaching")=="mmnoflush"  -- consider "ffeachflush" if your system stalls on large writes

- getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system

- getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system


Attaching package: ‘ff’

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

    clone, clone.default, clone.list

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

    write.csv, write.csv2

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

    is.factor, is.ordered

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicFeatures
Loading required package: ChIPpeakAnno
Loading required package: grid
Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

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

    mismatch, pattern

Loading required package: VennDiagram
Loading required package: futile.logger

Loading required package: Rsamtools
Loading required package: cheung2010
Loading required package: hgfocus.db

To get a tailored smlSet, use getSS("cheung2010", [chrvec])
available chromosomes are named chr1chr10...chr8chr9

Loading required package: SNPlocs.Hsapiens.dbSNP.20120608
Loading required package: BSgenome
Loading required package: rtracklayer
  Please note that the SNPlocs.Hsapiens.dbSNP.20120608 package contains
  outdated dbSNP data and will be deprecated in the near future. We
  highly recommend that you use a SNPlocs package based on a more recent
  dbSNP build for your analyses instead. See available.SNPs() for the
  list of SNPlocs packages currently available and make sure to pick up
  the most recent one.
Loading required package: hmyriB36
To get a tailored smlSet, use getSS("hmyriB36", [chrvec])
available chromosomes are named  1, 10, ..., X, Y

Attaching package: ‘SNPlocs.Hsapiens.dbSNP144.GRCh37’

The following objects are masked from ‘package:SNPlocs.Hsapiens.dbSNP.20120608’:

    .loadAlleles, .loadLoc, getSNPcount, getSNPlocs, rsid2alleles,
    rsid2loc, rsidsToGRanges

NOTE: expanding gene ranges by radius 50000 leads to negative start positions that are reset to 1.
opening ff /private/tmp/Rtmp5NqJ9M/Rinst16fec88fc2c3/ggtut/ffarchives/twfilt_perm17/17_tssco1_1.ff
opening ff /private/tmp/Rtmp5NqJ9M/Rinst16fec88fc2c3/ggtut/ffarchives/twfilt17/17_tssco1_1.ff
opening ff /private/tmp/Rtmp5NqJ9M/Rinst16fec88fc2c3/ggtut/ffarchives/twfilt17/17_tsinds1_1.ff
'select()' returned 1:1 mapping between keys and columns

Error: processing vignette 'tut15.Rnw' failed with diagnostics:
 chunk 58 (label = lkm) 
Error in lapply(killchr(select(Homo.sapiens, keys = m, keytype = "ENTREZID",  : 
  error in evaluating the argument 'X' in selecting a method for function 'lapply': Error in gsub("chr", "", x) : 
  error in evaluating the argument 'x' in selecting a method for function 'gsub': Error in select(Homo.sapiens, keys = m, keytype = "ENTREZID", columns = "TXCHROM") : 
  error in evaluating the argument 'x' in selecting a method for function 'select': Error: object 'Homo.sapiens' not found
Calls: killchr -> gsub

Execution halted
BioC experimental data: BUILD report for ggtut on morelia

Summary

Command output
