snapCGH 1.20.0
John Marioni
| Snapshot Date: 2011-03-30 23:22:56 -0700 (Wed, 30 Mar 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/snapCGH | | Last Changed Rev: 50293 / Revision: 54281 | | 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 |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* installing *source* package 'snapCGH' ...
** libs
gcc -I"E:/biocbld/bbs-2.7-bioc/R/include" -O3 -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:686:38: warning: 'gammaC[0][0]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[0][1]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[0][2]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[0][3]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[0][4]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[1][0]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[1][1]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[1][2]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[1][3]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[1][4]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[2][0]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[2][1]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[2][2]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[2][3]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[2][4]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[3][0]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[3][1]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[3][2]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[3][3]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[3][4]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[4][0]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[4][1]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[4][2]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[4][3]' may be used uninitialized in this function
optimizer.c:686:38: warning: 'gammaC[4][4]' may be used uninitialized in this function
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:412:38: warning: 'gammaC[0][0]' may be used uninitialized in this function
optimizer.c:412:38: warning: 'gammaC[0][1]' may be used uninitialized in this function
optimizer.c:412:38: warning: 'gammaC[0][2]' may be used uninitialized in this function
optimizer.c:412:38: warning: 'gammaC[0][3]' may be used uninitialized in this function
optimizer.c:412:38: warning: 'gammaC[1][0]' may be used uninitialized in this function
optimizer.c:412:38: warning: 'gammaC[1][1]' may be used uninitialized in this function
optimizer.c:412:38: warning: 'gammaC[1][2]' may be used uninitialized in this function
optimizer.c:412:38: warning: 'gammaC[1][3]' may be used uninitialized in this function
optimizer.c:412:38: warning: 'gammaC[2][0]' may be used uninitialized in this function
optimizer.c:412:38: warning: 'gammaC[2][1]' may be used uninitialized in this function
optimizer.c:412:38: warning: 'gammaC[2][2]' may be used uninitialized in this function
optimizer.c:412:38: warning: 'gammaC[2][3]' may be used uninitialized in this function
optimizer.c:412:38: warning: 'gammaC[3][0]' may be used uninitialized in this function
optimizer.c:412:38: warning: 'gammaC[3][1]' may be used uninitialized in this function
optimizer.c:412:38: warning: 'gammaC[3][2]' may be used uninitialized in this function
optimizer.c:412:38: warning: 'gammaC[3][3]' may be used uninitialized in this function
optimizer.c:585:1: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false
optimizer.c: In function 'fr_three':
optimizer.c:194:38: warning: 'gammaC[0][0]' may be used uninitialized in this function
optimizer.c:194:38: warning: 'gammaC[0][1]' may be used uninitialized in this function
optimizer.c:194:38: warning: 'gammaC[0][2]' may be used uninitialized in this function
optimizer.c:194:38: warning: 'gammaC[1][0]' may be used uninitialized in this function
optimizer.c:194:38: warning: 'gammaC[1][1]' may be used uninitialized in this function
optimizer.c:194:38: warning: 'gammaC[1][2]' may be used uninitialized in this function
optimizer.c:194:38: warning: 'gammaC[2][0]' may be used uninitialized in this function
optimizer.c:194:38: warning: 'gammaC[2][1]' may be used uninitialized in this function
optimizer.c:194:38: warning: 'gammaC[2][2]' may be used uninitialized in this function
optimizer.c: In function 'fr_two':
optimizer.c:25:38: warning: 'gammaC[0][0]' may be used uninitialized in this function
optimizer.c:25:38: warning: 'gammaC[0][1]' may be used uninitialized in this function
optimizer.c:25:38: warning: 'gammaC[1][0]' may be used uninitialized in this function
optimizer.c:25:38: warning: 'gammaC[1][1]' may be used uninitialized in this function
gcc -shared -s -static-libgcc -o snapCGH.dll tmp.def optimizer.o -LE:/biocbld/bbs-2.7-bioc/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.7-bioc/meat/snapCGH.buildbin-libdir/snapCGH/libs/i386
** 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)