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Package 382/419HostnameOS / ArchBUILDCHECKBUILD BIN
snapCGH 1.20.0
John Marioni
Snapshot Date: 2011-04-06 23:24:01 -0700 (Wed, 06 Apr 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/snapCGH
Last Changed Rev: 50293 / Revision: 54588
Last Changed Date: 2010-10-17 22:34:23 -0700 (Sun, 17 Oct 2010)
lamb2 Linux (openSUSE 11.2) / 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 ]

Summary

Package: snapCGH
Version: 1.20.0
Command: D:\biocbld\bbs-2.7-bioc\R\bin\R.exe CMD INSTALL --build --library=snapCGH.buildbin-libdir snapCGH_1.20.0.tar.gz
StartedAt: 2011-04-07 14:21:06 -0700 (Thu, 07 Apr 2011)
EndedAt: 2011-04-07 14:21:26 -0700 (Thu, 07 Apr 2011)
EllapsedTime: 19.3 seconds
RetCode: 0
Status:  OK  
PackageFile: snapCGH_1.20.0.zip
PackageFileSize: 1.138 MiB

Command output

* installing *source* package 'snapCGH' ...
** libs
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.7-bioc/R/include"         -O2 -Wall  -std=gnu99 -c optimizer.c -o optimizer.o
optimizer.c: In function 'fr_two':
optimizer.c:26:30: warning: unused variable 'temp3'
optimizer.c:26:23: warning: unused variable 'temp2'
optimizer.c:26:10: warning: unused variable 'denom'
optimizer.c: In function 'fr_three':
optimizer.c:195:30: warning: unused variable 'temp3'
optimizer.c:195:23: warning: unused variable 'temp2'
optimizer.c:195:10: warning: unused variable 'denom'
optimizer.c:194:69: warning: unused variable 'alphahat'
optimizer.c: In function 'fr_four':
optimizer.c:413:30: warning: unused variable 'temp3'
optimizer.c:413:23: warning: unused variable 'temp2'
optimizer.c:413:10: warning: unused variable 'denom'
optimizer.c:412:69: warning: unused variable 'alphahat'
optimizer.c: In function 'fr_five':
optimizer.c:687:30: warning: unused variable 'temp3'
optimizer.c:687:23: warning: unused variable 'temp2'
optimizer.c:687:10: warning: unused variable 'denom'
optimizer.c:686:69: warning: unused variable 'alphahat'
optimizer.c:943:4: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false
optimizer.c: In function 'fr_four':
optimizer.c:585:1: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false
x86_64-w64-mingw32-gcc -shared -s -static-libgcc -o snapCGH.dll tmp.def optimizer.o -LD:/biocbld/bbs-2.7-bioc/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.7-bioc/meat/snapCGH.buildbin-libdir/snapCGH/libs/x64
** R
** data
** inst
** preparing package for lazy loading

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



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



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
* MD5 sums
packaged installation of 'snapCGH' as snapCGH_1.20.0.zip

* DONE (snapCGH)