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Package 353/389HostnameOS / ArchBUILDCHECKBUILD BIN
snapCGH 1.18.0
John Marioni
Snapshot Date: 2010-10-04 11:22:20 -0700 (Mon, 04 Oct 2010)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/snapCGH
Last Changed Rev: 47149 / Revision: 49923
Last Changed Date: 2010-05-26 11:24:55 -0700 (Wed, 26 May 2010)
wilson1 Linux (openSUSE 11.1) / 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 

Summary

Package: snapCGH
Version: 1.18.0
Command: chmod a+r snapCGH -R && E:\biocbld\bbs-2.6-bioc\R\bin\R.exe CMD build snapCGH
StartedAt: 2010-10-04 14:11:10 -0700 (Mon, 04 Oct 2010)
EndedAt: 2010-10-04 14:11:55 -0700 (Mon, 04 Oct 2010)
EllapsedTime: 45.4 seconds
RetCode: 0
Status:  OK  
PackageFile: snapCGH_1.18.0.tar.gz
PackageFileSize: 1.101 MiB

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
  making DLL ...
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include"         -O3 -Wall  -std=gnu99 -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'
gcc -shared -s -static-libgcc -o snapCGH.dll tmp.def optimizer.o -LE:/biocbld/bbs-2.6-bioc/R/bin -lR
installing to E:/biocbld/bbs-2.6-bioc/tmpdir/Rinst118005996/snapCGH/libs
  ... done
** R
** data
** inst
** preparing package for lazy loading

**************************************************************************
   The data format for the CNA object will be changed in version 1.23.0 
     Instead of a data frame it will be a list of 3 (or more) objects 
     chrom and maploc will be vectors and CN/LOH data will be a matrix 
**************************************************************************



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



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: Biobase

Welcome to Bioconductor

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

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* 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_1.18.0.tar.gz'