Package: snapCGH

Version: 1.0.0

Command: /loc/biocbuild/1.8d/R/bin/R CMD check snapCGH_1.0.0.tar.gz

RetCode: 0

Time: 89.8 seconds

Status: OK

CheckDir: snapCGH.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory '/loc/biocbuild/1.8d/Rpacks/snapCGH.Rcheck'
* using Version 2.3.1 (2006-06-01)
* checking for file 'snapCGH/DESCRIPTION' ... OK
* this is package 'snapCGH' version '1.0.0'
* 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 for sufficient/correct file permissions ... 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 library.dynam ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking Rd files ... 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
* 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 *source* package 'snapCGH' ...
** libs
gcc -I/loc/biocbuild/1.8d/R/include -I/loc/biocbuild/1.8d/R/include  -I/usr/local/include   -fpic  -g -O2 -std=gnu99 -Wall -c optimizer.c -o optimizer.o
gcc -shared -L/usr/local/lib64 -o snapCGH.so optimizer.o   
** R
** data
** inst
** preparing package for lazy loading
Loading required package: limma
Loading required package: DNAcopy
Loading required package: aCGH
Loading required package: cluster
Loading required package: survival
Loading required package: splines
Loading required package: multtest
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: sma

Attaching package: 'aCGH'


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

	 heatmap 

Loading required package: GLAD
[1] "Have fun with GLAD"

Attaching package: 'GLAD'


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

	 cluster 

Loading required package: cluster
** help
Warning messages:
1: incomplete final line found by readLines on './man/GEList.Rd' 
2: incomplete final line found by readLines on './man/filter.Rd' 
3: incomplete final line found by readLines on './man/find.param.four.Rd' 
4: incomplete final line found by readLines on './man/find.param.two.Rd' 
5: incomplete final line found by readLines on './man/fitBioHMM.Rd' 
6: incomplete final line found by readLines on './man/removeByWeights.Rd' 
7: incomplete final line found by readLines on './man/runDNAcopy.Rd' 
 >>> Building/Updating help pages for package 'snapCGH'
     Formats: text html latex example 
  GEList                            text    html    latex
  LargeDataObject                   text    html    latex   example
  SegList                           text    html    latex
  Viterbi.five                      text    html    latex
  Viterbi.four                      text    html    latex
  Viterbi.three                     text    html    latex
  Viterbi.two                       text    html    latex
  cbind                             text    html    latex
  chrominfo.Mb                      text    html    latex
  computeSD                         text    html    latex
  convert.output                    text    html    latex   example
  dim                               text    html    latex   example
  dimnames                          text    html    latex
  filter                            text    html    latex
  find.param.five                   text    html    latex
  find.param.four                   text    html    latex
  find.param.one                    text    html    latex
  find.param.three                  text    html    latex
  find.param.two                    text    html    latex
  findAberrations                   text    html    latex
  findAmplifications                text    html    latex
  findBreakPoints                   text    html    latex   example
  findGenomicEvents                 text    html    latex
  findOutliers                      text    html    latex
  findTranslocations                text    html    latex
  fit.model                         text    html    latex
  fitBioHMM                         text    html    latex
  fitHMM                            text    html    latex
  fractionAltered                   text    html    latex
  genomePlot                        text    html    latex   example
  heatmapGenome                     text    html    latex   example
  impute.lowess                     text    html    latex   example
  log2ratios                        text    html    latex
  mergeStates                       text    html    latex
  mod.chrominfo                     text    html    latex
  non.zero.length.distr.non.tiled   text    html    latex
  non.zero.length.distr.tiled       text    html    latex
  plotGainLoss                      text    html    latex   example
  plotSegmentationStates            text    html    latex   example
  plotSegmentedGenome               text    html    latex   example
  plotSummaryProfile                text    html    latex
  processCGH                        text    html    latex
  read.clonesinfo                   text    html    latex
  removeByWeights                   text    html    latex
  runDNAcopy                        text    html    latex
  runGLAD                           text    html    latex
  sim.structure                     text    html    latex   example
  subsetting                        text    html    latex   example
  summarize.clones                  text    html    latex
  threshold.func                    text    html    latex   example
  zero.length.distr.non.tiled       text    html    latex
  zero.length.distr.tiled           text    html    latex
** building package indices ...
* DONE (snapCGH)