Package: snapCGH

Version: 1.4.0

Command: D:\biocbld\bbs-2.0-bioc\R\bin\R.exe CMD check snapCGH_1.4.0.tar.gz

RetCode: 0

Time: 295.9 seconds

Status: OK

CheckDir: snapCGH.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory 'D:/biocbld/bbs-2.0-bioc/meat/snapCGH.Rcheck'
* using R version 2.5.0 (2007-04-23)
* checking for file 'snapCGH/DESCRIPTION' ... OK
* this is package 'snapCGH' version '1.4.0'
* 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 ... OK
* 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 for CRLF line endings in C/C++/Fortran sources/headers ... 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 ... OK

installing R.css in D:/biocbld/bbs-2.0-bioc/meat/snapCGH.Rcheck


---------- Making package snapCGH ------------
  adding build stamp to DESCRIPTION
  making DLL ...
making optimizer.d from optimizer.c
gcc   -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c optimizer.c -o optimizer.o
windres -I d:/biocbld/bbs-2.0-bioc/R/include  -i snapCGH_res.rc -o snapCGH_res.o
gcc  -shared -s  -o snapCGH.dll snapCGH.def optimizer.o snapCGH_res.o  -Ld:/biocbld/bbs-2.0-bioc/R/bin    -lR
  ... DLL made
  installing DLL
  installing R files
  installing inst files
  installing data files
  installing man source files
  installing indices
  not zipping data
  installing help
 >>> 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   example chm
  heatmapGenome                     text    html    latex   example 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   example 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
  runPicard                         text    html    latex           chm
  sim.structure                     text    html    latex   example chm
  subsetting                        text    html    latex   example 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 d:\biocbld\bbs-2.0-bioc\meat\snapCGH.Rcheck\00_pkg_src\snapCGH\chm\snapCGH.chm


Compile time: 0 minutes, 0 seconds
46	Topics
179	Local links
0	Internet links
1	Graphic


Created d:\biocbld\bbs-2.0-bioc\meat\snapCGH.Rcheck\00_pkg_src\snapCGH\chm\snapCGH.chm, 67,608 bytes
Compression decreased file by 87,596 bytes.
  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: 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 :

	 rapply 

Loading required package: sandwich
Loading required package: vsn
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
Loading required package: geneplotter
Loading required package: annotate
Loading required package: lattice
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: aws
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 

  adding MD5 sums

* DONE (snapCGH)