Package: aCGH

Version: 1.6.0

Command: /loc/biocbuild/1.8d/R/bin/R CMD check aCGH_1.6.0.tar.gz

RetCode: 0

Time: 370.2 seconds

Status: OK

CheckDir: aCGH.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory '/extra/loc/biocbuild/1.8d/Rpacks/aCGH.Rcheck'
* using Version 2.3.1 (2006-06-01)
* checking for file 'aCGH/DESCRIPTION' ... OK
* this is package 'aCGH' version '1.6.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'aCGH' 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
* checking for portable compilation flags in Makevars ... OK
* creating aCGH-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating aCGH-manual.tex ... OK
* checking aCGH-manual.tex ... OK

* Installing *source* package 'aCGH' ...
** libs
g++ -I/loc/biocbuild/1.8d/R/include -I/loc/biocbuild/1.8d/R/include -g3 -I/usr/local/include   -fpic  -g -O2 -Wall -c hmm.cpp -o hmm.o
g++ -shared -L/usr/local/lib -o aCGH.so hmm.o -lm  
** R
** data
** demo
** inst
** save image
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
** help
 >>> Building/Updating help pages for package 'aCGH'
     Formats: text html latex example 
  aCGH                              text    html    latex   example
  aCGH.process                      text    html    latex   example
  aCGH.read.Sprocs                  text    html    latex   example
  aCGH.test                         text    html    latex   example
  clusterGenome                     text    html    latex   example
  colorectal                        text    html    latex   example
  computeSD.func                    text    html    latex
  fga.func                          text    html    latex   example
  find.genomic.events               text    html    latex
  find.hmm.states                   text    html    latex   example
  findAber.func                     text    html    latex
  findAmplif.func                   text    html    latex
  findOutliers.func                 text    html    latex
  findTrans.func                    text    html    latex
  gainLoss                          text    html    latex   example
  heatmap                           text    html    latex   example
  human.chrom.info.Jul03            text    html    latex
  human.chrom.info.May04            text    html    latex
  impute.HMM                        text    html    latex   example
  impute.lowess                     text    html    latex   example
  mergeFunc                         text    html    latex
  mergeLevels                       text    html    latex   example
  plotFreqStat                      text    html    latex   example
  plotGenome                        text    html    latex   example
  plotHmmStates                     text    html    latex   example
  plotSummaryProfile                text    html    latex   example
  states.hmm.func                   text    html    latex
  summarize.clones                  text    html    latex   example
  threshold.func                    text    html    latex   example
** building package indices ...
* DONE (aCGH)