Package: ADaCGH2

Version: 1.1.0

Command: E:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD INSTALL --build --library=ADaCGH2.buildbin-libdir ADaCGH2_1.1.0.tar.gz

StartedAt: 2011-02-24 20:17:53 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 20:18:18 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 24.9 seconds

RetCode: 0

Status:  OK

PackageFile: ADaCGH2_1.1.0.zip

PackageFileSize: 440.9 KiB

* installing *source* package 'ADaCGH2' ...

  Using auto-selected zip option '--use-zip-data'

** libs
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include"          -O3 -Wall  -std=gnu99 -c r_haarseg.c -o r_haarseg.o
r_haarseg.c: In function 'ad_HaarConv':
r_haarseg.c:65:12: warning: unused variable 'totalNorm'
r_haarseg.c: In function 'ad_FindLocalPeaks':
r_haarseg.c:152:8: warning: "/*" within comment
r_haarseg.c:176:8: warning: "/*" within comment
r_haarseg.c:128:9: warning: unused variable 'j'
r_haarseg.c: In function 'ad_HaarConv':
r_haarseg.c:59:12: warning: 'lowWeightSum' may be used uninitialized in this function
r_haarseg.c:60:12: warning: 'highWeightSum' may be used uninitialized in this function
r_haarseg.c:63:12: warning: 'lowNonNormed' may be used uninitialized in this function
r_haarseg.c:64:12: warning: 'highNonNormed' may be used uninitialized in this function
gcc -shared -s -static-libgcc -o ADaCGH2.dll tmp.def r_haarseg.o -LE:/biocbld/bbs-2.8-bioc/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.8-bioc/meat/ADaCGH2.buildbin-libdir/ADaCGH2/libs/i386
** 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: pixmap
Loading required package: cluster
Loading required package: survival
Loading required package: splines
Loading required package: multtest

Attaching package: 'aCGH'

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

    heatmap

Loading required package: limma
Loading required package: DNAcopy

**************************************************************************
   The plan to change the data format for CNA object has been postponed   
 in order to ensure backward compatibility with older versions of DNAcopy 
**************************************************************************


Attaching package: 'DNAcopy'

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

    segment



######################################################################################



Have fun with GLAD



For smoothing it is possible to use either

the AWS algorithm (Polzehl and Spokoiny, 2002)

or the HaarSeg algorithm (Ben-Yaacov and Eldar, Bioinformatics,  2008)



If you use the package with AWS, please cite:

Hupe et al. (Bioinformatics, 2004) and Polzehl and Spokoiny (2002)



If you use the package with HaarSeg, please cite:

Hupe et al. (Bioinformatics, 2004) and (Ben-Yaacov and Eldar, Bioinformatics, 2008)



For fast computation it is recommanded to use

the daglad function with smoothfunc=haarseg



######################################################################################



New options are available in daglad: see help for details.



Attaching package: 'snapCGH'

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

    prop.na

Loading required package: snow

Attaching package: 'snow'

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

    enquote

Loading required package: tools
Loading required package: bit
Loading package bit1.1-6

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


Attaching package: 'bit'

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

    xor

Loading package ff2.2-1

- getOption("fftempdir")=="E:/biocbld/bbs-2.8-bioc/tmpdir/RtmpZ71IS9"

- 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 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

Setting adacgh_changepoints to DNAcopy:::changepoints
Setting adacgh_trimmed.variance to DNAcopy:::trimmed.variance
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ADaCGH2' as ADaCGH2_1.1.0.zip

* DONE (ADaCGH2)