snapCGH 1.12.0
John Marioni
| Bioconductor Changelog | | Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/snapCGH | | Last Changed Rev: 39013 / Revision: 42512 | | Last Changed Date: 2009-04-20 16:24:12 -0700 (Mon, 20 Apr 2009) |
| wilson1 | 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 |
* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.4-bioc/meat/snapCGH.Rcheck'
* using R version 2.9.2 (2009-08-24)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'snapCGH/DESCRIPTION' ... OK
* this is package 'snapCGH' version '1.12.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'snapCGH' can be installed ... 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 name space can be loaded with stated dependencies ... 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'
runTilingArray: possible error in segment(log2ratios, maxk =
length(log2ratios), maxseg = min(length(log2ratios), maxSeg)): unused
argument(s) (maxk = length(log2ratios), maxseg =
min(length(log2ratios), maxSeg))
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 ... OK
* checking Rd files against version 2 parser ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK
* Installing *source* package 'snapCGH' ...
** libs
making DLL ...
gcc -I"e:/biocbld/bbs-2.4-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 -o snapCGH.dll tmp.def optimizer.o -Le:/biocbld/bbs-2.4-bioc/R/bin -lR
... done
** 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
[1] "Have fun with GLAD"
[1] "For smoothing it is possible to use either"
[1] "the AWS algorithm (Polzehl and Spokoiny, 2002)"
[1] "or the HaarSeg algorithm (Ben-Yaacov and Eldar, 2008)"
[1] ""
[1] "If you use the package with AWS, please cite:"
[1] "Hupe et al. (2004) and Polzehl and Spokoiny (2002)"
[1] ""
[1] "If you use the package with HaarSeg, please cite:"
[1] "Hupe et al. (2004) and (Ben-Yaacov and Eldar, 2008)"
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/Updating help pages for package 'snapCGH'
Formats: text html latex example chm
IDProbes text html latex chm
LargeDataObject text html latex example chm
SegList text html latex chm
Viterbi.five text html latex chm
Viterbi.four text html latex chm
Viterbi.three text html latex chm
Viterbi.two text html latex chm
cbind text html latex chm
chrominfo.Mb text html latex chm
compareSegmentations text html latex chm
convert.output text html latex example chm
dim text html latex example chm
dimnames text html latex chm
filter text html latex chm
find.param.five text html latex chm
find.param.four text html latex chm
find.param.one text html latex chm
find.param.three text html latex chm
find.param.two text html latex chm
findBreakPoints text html latex chm
fit.model text html latex chm
Note: removing empty section \examples in file 'genomePlot.Rd'
Note: removing empty section \examples in file 'genomePlot.Rd'
genomePlot text html latex chm
Note: removing empty section \examples in file 'heatmapGenome.Rd'
Note: removing empty section \examples in file 'heatmapGenome.Rd'
heatmapGenome text html latex chm
imputeMissingValues text html latex chm
log2ratios text html latex chm
mergeStates text html latex chm
non.zero.length.distr.non.tiled text html latex chm
non.zero.length.distr.tiled text html latex chm
Note: removing empty section \examples in file 'plotSegmentedGenome.Rd'
Note: removing empty section \examples in file 'plotSegmentedGenome.Rd'
plotSegmentedGenome text html latex chm
processCGH text html latex chm
read.clonesinfo text html latex chm
readPositionalInfo text html latex chm
removeByWeights text html latex chm
runBioHMM text html latex chm
runDNAcopy text html latex chm
runGLAD text html latex chm
runHMM text html latex chm
runTilingArray text html latex chm
Note: removing empty section \examples in file 'sim.structure.Rd'
Note: removing empty section \examples in file 'sim.structure.Rd'
sim.structure text html latex chm
zero.length.distr.non.tiled text html latex chm
zero.length.distr.tiled text html latex chm
zoomChromosome text html latex chm
zoomGenome text html latex chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\BBS-2~1.4-B\meat\SNAPCG~1.RCH\00_PKG~1\snapCGH\chm\snapCGH.chm
Compile time: 0 minutes, 0 seconds
44 Topics
178 Local links
0 Internet links
1 Graphic
Created e:\biocbld\BBS-2~1.4-B\meat\SNAPCG~1.RCH\00_PKG~1\snapCGH\chm\snapCGH.chm, 64,138 bytes
Compression decreased file by 87,210 bytes.
** building package indices ...
** MD5 sums
* DONE (snapCGH)