snapCGH 1.8.0
John Marioni
| Snapshot Date: 2008-10-16 00:10:09 -0700 (Thu, 16 Oct 2008) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_2/madman/Rpacks/snapCGH | | Last Changed Rev: 31430 / Revision: 34573 | | Last Changed Date: 2008-04-29 16:50:18 -0700 (Tue, 29 Apr 2008) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | OK | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | OK | |
| wellington | Linux (openSUSE 10.3) / i686 | 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 |
* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.2-bioc/meat/snapCGH.Rcheck'
* using R version 2.7.2 (2008-08-25)
* using session charset: ISO8859-1
* checking for file 'snapCGH/DESCRIPTION' ... OK
* this is package 'snapCGH' version '1.8.0'
* 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 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'
processCGH: no visible binding for global variable 'RG'
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'
Found possibly global 'T' or 'F' in the following functions:
read.clonesinfo readPositionalInfo simulateData
* checking Rd files ... 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
* creating snapCGH-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating snapCGH-manual.tex ... OK
* checking snapCGH-manual.tex using pdflatex ... OK
installing R.css in E:/biocbld/bbs-2.2-bioc/meat/snapCGH.Rcheck
---------- Making package snapCGH ------------
adding build stamp to DESCRIPTION
making DLL ...
making optimizer.d from optimizer.c
gcc -std=gnu99 -Ie:/biocbld/bbs-2.2-bioc/R/include -O3 -Wall -c optimizer.c -o optimizer.o
windres --preprocessor="gcc -E -xc -DRC_INVOKED" -I e:/biocbld/bbs-2.2-bioc/R/include -i snapCGH_res.rc -o snapCGH_res.o
gcc -std=gnu99 -shared -s -o snapCGH.dll snapCGH.def optimizer.o snapCGH_res.o -Le:/biocbld/bbs-2.2-bioc/R/bin -lR
... DLL made
installing DLL
installing R files
installing inst files
installing data files
preparing package snapCGH for lazy loading
Loading required package: limma
Loading required package: tilingArray
Loading required package: Biobase
Loading required package: tools
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: affy
Loading required package: affyio
Loading required package: preprocessCore
Loading required package: RColorBrewer
Loading required package: grid
Loading required package: strucchange
Loading required package: zoo
Attaching package: 'zoo'
The following object(s) are masked from package:base :
as.Date.numeric
Loading required package: sandwich
Loading required package: vsn
Loading required package: lattice
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
Loading required package: geneplotter
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
Loading required package: xtable
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
Loading required package: pixmap
Loading required package: DNAcopy
Attaching package: 'DNAcopy'
The following object(s) are masked from package:tilingArray :
segment
Loading required package: GLAD
Loading required package: cluster
Loading required package: aCGH
Loading required package: multtest
Loading required package: sma
Attaching package: 'aCGH'
The following object(s) are masked from package:stats :
heatmap
installing man source files
installing indices
not zipping data
installing help
Note: unmatched right brace in file 'SegList.Rd' on or after line 30
Note: unmatched right brace in file 'SegList.Rd' on or after line 30
Note: unmatched right brace in file 'find.param.one.Rd' on or after line 18
Note: unmatched right brace in file 'find.param.one.Rd' on or after line 18
Note: removing empty section \examples
Note: removing empty section \examples
Note: removing empty section \examples
Note: removing empty section \examples
Note: unmatched right brace in file 'non.zero.length.distr.non.tiled.Rd' on or after line 9
Note: unmatched right brace in file 'non.zero.length.distr.non.tiled.Rd' on or after line 9
Note: removing empty section \examples
Note: removing empty section \examples
Note: unmatched right brace in file 'processCGH.Rd' on or after line 44
Note: unmatched right brace in file 'processCGH.Rd' on or after line 44
Note: removing empty section \examples
Note: removing empty section \examples
>>> 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
genomePlot text html latex chm
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
nudSegmentation text html latex chm
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
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-2.2-bioc\meat\snapCGH.Rcheck\00_pkg_src\snapCGH\chm\snapCGH.chm
Compile time: 0 minutes, 0 seconds
45 Topics
178 Local links
0 Internet links
1 Graphic
Created e:\biocbld\bbs-2.2-bioc\meat\snapCGH.Rcheck\00_pkg_src\snapCGH\chm\snapCGH.chm, 67,006 bytes
Compression decreased file by 86,308 bytes.
adding MD5 sums
* DONE (snapCGH)