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Package 320/353HostnameOS / ArchBUILDCHECKBUILD BIN
snapCGH 1.16.0
John Marioni
Snapshot Date: 2009-12-13 23:30:35 -0800 (Sun, 13 Dec 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_5/madman/Rpacks/snapCGH
Last Changed Rev: 42684 / Revision: 43539
Last Changed Date: 2009-10-27 16:33:29 -0700 (Tue, 27 Oct 2009)
wilson2 Linux (openSUSE 11.1) / x86_64 [ OK ] OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
Package: snapCGH
Version: 1.16.0
Command: /home/biocbuild/bbs-2.5-bioc/R/bin/R CMD build snapCGH
StartedAt: 2009-12-14 01:28:37 -0800 (Mon, 14 Dec 2009)
EndedAt: 2009-12-14 01:29:00 -0800 (Mon, 14 Dec 2009)
EllapsedTime: 23.5 seconds
RetCode: 0
Status: OK
PackageFile: snapCGH_1.16.0.tar.gz
PackageFileSize: 1001 KiB

Command output

* checking for file 'snapCGH/DESCRIPTION' ... OK
* preparing 'snapCGH':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* installing *source* package ‘snapCGH’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c optimizer.c -o optimizer.o
optimizer.c: In function ‘fr_two’:
optimizer.c:26: warning: unused variable ‘temp3’
optimizer.c:26: warning: unused variable ‘temp2’
optimizer.c:26: warning: unused variable ‘denom’
optimizer.c: In function ‘fr_three’:
optimizer.c:195: warning: unused variable ‘temp3’
optimizer.c:195: warning: unused variable ‘temp2’
optimizer.c:195: warning: unused variable ‘denom’
optimizer.c:194: warning: unused variable ‘alphahat’
optimizer.c: In function ‘fr_four’:
optimizer.c:413: warning: unused variable ‘temp3’
optimizer.c:413: warning: unused variable ‘temp2’
optimizer.c:413: warning: unused variable ‘denom’
optimizer.c:412: warning: unused variable ‘alphahat’
optimizer.c: In function ‘fr_five’:
optimizer.c:687: warning: unused variable ‘temp3’
optimizer.c:687: warning: unused variable ‘temp2’
optimizer.c:687: warning: unused variable ‘denom’
optimizer.c:686: warning: unused variable ‘alphahat’
optimizer.c:943: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false
optimizer.c: In function ‘fr_four’:
optimizer.c:585: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false
gcc -std=gnu99 -shared -L/usr/local/lib64 -o snapCGH.so optimizer.o -L/home/biocbuild/bbs-2.5-bioc/R/lib -lR
** R
** data
** inst
** preparing package for lazy loading
Loading required package: Biobase

Welcome to Bioconductor

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

Loading required package: pixmap

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.
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 

** help
*** installing help indices
** building package indices ...
* DONE (snapCGH)
* creating vignettes ... OK
* cleaning src
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'snapCGH_1.16.0.tar.gz'