Package: ggtut

Version: 0.0.21

Command: mkdir ggtut.buildbin-libdir && E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --no-multiarch --library=ggtut.buildbin-libdir ggtut_0.0.21.tar.gz

StartedAt: 2011-07-06 16:53:47 -0700 (Wed, 06 Jul 2011)

EndedAt: 2011-07-06 16:56:54 -0700 (Wed, 06 Jul 2011)

EllapsedTime: 186.8 seconds

RetCode: 0

Status:  OK

PackageFile: ggtut_0.0.21.zip

PackageFileSize: 147.7 MiB

* installing *source* package 'ggtut' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: Biobase

Welcome to Bioconductor

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

Loading required package: GGBase
Loading required package: snpStats
Loading required package: survival
Loading required package: splines
Loading required package: Matrix
Loading required package: lattice

Attaching package: 'Matrix'

The following object(s) are masked from 'package:base':

    det

Loading required package: RSQLite
Loading required package: DBI
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: IRanges

Attaching package: 'IRanges'

The following object(s) are masked from 'package:Biobase':

    updateObject

The following object(s) are masked from 'package:base':

    Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union

Loading required package: rtracklayer
Loading required package: RCurl
Loading required package: bitops
Loading required package: org.Hs.eg.db

Loading required package: GenomicRanges
Loading package bit1.1-7

package:bit (c) 2008/2009 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

Loading package ff2.2-2
- getOption("fftempdir")=="E:/biocbld/bbs-2.9-data-experiment/tmpdir/RtmpmsZJgh"

- 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")==16095641.6 -- consider a different value for tuning your system

- getOption("ffmaxbytes")==804782080 -- consider a different value for tuning your system


Attaching package: 'GGtools'

The following object(s) are masked from 'package:Biobase':

    geneNames

Loading required package: tools
Loading required package: bit

Attaching package: 'bit'

The following object(s) are masked from 'package:base':

    xor

Attaching package ff

Attaching package: 'ff'

The following object(s) are masked from 'package:utils':

    write.csv, write.csv2

The following object(s) are masked from 'package:base':

    is.factor, is.ordered

Loading required package: illuminaHumanv1.db

To get a tailored smlSet, use getSS("GGdata", [chrvec]) 
available chromosomes are named  1 10 ... X Y 
Loading required package: biomaRt

Attaching package: 'biomaRt'

The following object(s) are masked from 'package:annotate':

    getGO

Loading required package: multtest
Loading required package: Biostrings

Attaching package: 'Biostrings'

The following object(s) are masked from 'package:ff':

    mismatch, pattern

Loading required package: BSgenome

Attaching package: 'BSgenome'

The following object(s) are masked from 'package:annotate':

    organism

Loading required package: BSgenome.Ecoli.NCBI.20080805
Loading required package: GO.db

Loading required package: limma
Loading required package: gplots
Loading required package: gtools
Loading required package: gdata
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.

gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.

Attaching package: 'gdata'

The following object(s) are masked from 'package:IRanges':

    trim

The following object(s) are masked from 'package:Biobase':

    combine

The following object(s) are masked from 'package:stats':

    nobs

The following object(s) are masked from 'package:utils':

    object.size

Loading required package: caTools

Attaching package: 'caTools'

The following object(s) are masked from 'package:IRanges':

    runmean

Loading required package: grid

Attaching package: 'gplots'

The following object(s) are masked from 'package:multtest':

    wapply

The following object(s) are masked from 'package:rtracklayer':

    space

The following object(s) are masked from 'package:IRanges':

    space

The following object(s) are masked from 'package:stats':

    lowess

Warning: replacing previous import 'space' when loading 'IRanges'
Warning: replacing previous import 'getSeq' when loading 'BSgenome'
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
To get a tailored smlSet, use getSS("GGdata", [chrvec]) 
available chromosomes are named  1 10 ... X Y 
Warning messages:
1: replacing previous import 'space' when loading 'IRanges' 
2: replacing previous import 'getSeq' when loading 'BSgenome' 
* MD5 sums
packaged installation of 'ggtut' as ggtut_0.0.21.zip

* DONE (ggtut)