Package: snapCGH

Version: 1.1.7

Command: D:\biocbld\1.9d\R\bin\R.exe CMD check snapCGH_1.1.7.tar.gz

RetCode: 0

Time: 321.0 seconds

Status: WARNINGS

CheckDir: snapCGH.Rcheck

Warnings: 1

* checking for working latex ... OK
* using log directory 'D:/biocbld/1.9d/Rpacks/snapCGH.Rcheck'
* using R version 2.4.0 alpha (2006-09-10 r39242)
* checking for file 'snapCGH/DESCRIPTION' ... OK
* this is package 'snapCGH' version '1.1.7'
* checking package dependencies ... WARNING
package 'methods' is used but not declared
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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 syntax errors ... OK
* checking R files for non-ASCII characters ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... 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 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

WARNING: There was 1 warning, see
  D:/biocbld/1.9d/Rpacks/snapCGH.Rcheck/00check.log
for details

installing R.css in D:/biocbld/1.9d/Rpacks/snapCGH.Rcheck


---------- Making package snapCGH ------------
  adding build stamp to DESCRIPTION
  making DLL ...
making optimizer.d from optimizer.c
gcc   -Id:/biocbld/1.9d/R/include  -Wall -O2 -std=gnu99   -c optimizer.c -o optimizer.o
windres --include-dir d:/biocbld/1.9d/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/1.9d/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\1.9d\Rpacks\snapCGH.Rcheck\00_pkg_src\snapCGH\chm\snapCGH.chm


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


Created d:\biocbld\1.9d\Rpacks\snapCGH.Rcheck\00_pkg_src\snapCGH\chm\snapCGH.chm, 66,684 bytes
Compression decreased file by 84,764 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()' or start with 'help(Biobase)'. For details
    on reading vignettes, see the openVignette help page.

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: colorspace

Creating a new generic function for 'plot' in 'colorspace'

Attaching package: 'colorspace'


	The following object(s) are masked from package:grDevices :

	 hcl 

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: pixmap

Loading required package: DNAcopy


Attaching package: 'DNAcopy'


	The following object(s) are masked from package:tilingArray :

	 segment 

Loading required package: aCGH

Loading required package: cluster

Loading required package: multtest

Loading required package: sma


Attaching package: 'aCGH'


	The following object(s) are masked from package:stats :

	 heatmap 

Loading required package: GLAD


Attaching package: 'GLAD'


	The following object(s) are masked from package:survival :

	 cluster 

  adding MD5 sums

* DONE (snapCGH)