snapCGH 1.22.0
John Marioni
| Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/snapCGH | | Last Changed Rev: 54808 / Revision: 59457 | | Last Changed Date: 2011-04-13 18:03:42 -0700 (Wed, 13 Apr 2011) |
| lamb1 | Linux (openSUSE 11.3) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | [ OK ] | OK |
| gewurz | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | WARNINGS | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory 'E:/biocbld/bbs-2.8-bioc/meat/snapCGH.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'snapCGH/DESCRIPTION' ... OK
* this is package 'snapCGH' version '1.22.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'snapCGH' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
generate.data: no visible binding for global variable
'zero.length.distr.non.tiled'
generate.data: no visible binding for global variable
'non.zero.length.distr.non.tiled'
generate.data: no visible binding for global variable
'zero.length.distr.tiled'
generate.data: no visible binding for global variable
'non.zero.length.distr.tiled'
heatmapGenome: no visible binding for global variable 'floor.func'
readPositionalInfo: no visible binding for global variable 'RGList'
simulateData: no visible binding for global variable
'zero.length.distr.non.tiled'
simulateData: no visible binding for global variable
'zero.length.distr.tiled'
simulateData: no visible binding for global variable
'non.zero.length.distr.non.tiled'
simulateData: no visible binding for global variable
'non.zero.length.distr.tiled'
* checking Rd files ... NOTE
prepare_Rd: genomePlot.Rd:51-57: Dropping empty section \examples
prepare_Rd: heatmapGenome.Rd:76-77: Dropping empty section \examples
prepare_Rd: plotSegmentedGenome.Rd:52-58: Dropping empty section \examples
prepare_Rd: sim.structure.Rd:57-58: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK
* installing *source* package 'snapCGH' ...
** libs
gcc -I"E:/biocbld/BBS-2˜1.8-B/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˜1.8-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.8-bioc/meat/snapCGH.Rcheck/snapCGH/libs/i386
** R
** data
** inst
** preparing package for lazy loading
######################################################################################
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
'browseVignettes()'. 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)