ADaCGH2 1.3.0
Ramon Diaz-Uriarte
| Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ADaCGH2 | | Last Changed Rev: 54802 / Revision: 55359 | | Last Changed Date: 2011-04-13 15:36:43 -0700 (Wed, 13 Apr 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | OK | [ OK ] |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* installing *source* package 'ADaCGH2' ...
** libs
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.9-bioc/R/include" -O2 -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
x86_64-w64-mingw32-gcc -shared -s -static-libgcc -o ADaCGH2.dll tmp.def r_haarseg.o -LD:/biocbld/bbs-2.9-bioc/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/ADaCGH2.buildbin-libdir/ADaCGH2/libs/x64
** 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 bit1.1-7
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
Attaching package: 'bit'
The following object(s) are masked from 'package:base':
xor
Loading package ff2.2-2
- getOption("fftempdir")=="D:/biocbld/bbs-2.9-bioc/tmpdir/Rtmpld7bob"
- 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")==42928701.44 -- consider a different value for tuning your system
- getOption("ffmaxbytes")==2146435072 -- 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 ...
*** tangling vignette sources ...
'ADaCGH2.Rnw' using 'latin1'
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ADaCGH2' as ADaCGH2_1.3.0.zip
* DONE (ADaCGH2)