Package: adSplit

Version: 1.8.0

Command: /loc/biocbuild/bbs-2.1-bioc/R/bin/R CMD check adSplit_1.8.0.tar.gz

RetCode: 0

Time: 317.8 seconds

Status: OK

CheckDir: adSplit.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory '/extra/loc/biocbuild/bbs-2.1-bioc/meat/adSplit.Rcheck'
* using R version 2.6.0 (2007-10-03)
* checking for file 'adSplit/DESCRIPTION' ... OK
* this is package 'adSplit' version '1.8.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'adSplit' 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 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 whether the name space 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
figure_ccimage: no visible global function definition for 'cc_image'
figure_ccimage: no visible binding for global variable 'res'
figure_induced: no visible binding for global variable 'rossResult'
figure_induced: no visible global function definition for 'oneGOGraph'
figure_induced: no visible global function definition for 'GOGraph'
figure_induced: no visible global function definition for 'join'
figure_induced: no visible global function definition for 'nodes'
figure_induced: no visible global function definition for 'edges'
image.splitSet: no visible binding for '<<-' assignment to 'root.dist'
image.splitSet: no visible binding for global variable 'root.dist'
image.splitSet: no visible global function definition for
  'collect.lines'
* 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 ... NOTE
S3 methods shown with full name in documentation object 'hist.splitSet':
  hist.splitSet

S3 methods shown with full name in documentation object 'image.splitSet':
  image.splitSet

S3 methods shown with full name in documentation object 'print.split':
  print.split

S3 methods shown with full name in documentation object 'print.splitSet':
  print.splitSet

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* 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 adSplit-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating adSplit-manual.tex ... OK
* checking adSplit-manual.tex ... OK

* Installing *source* package 'adSplit' ...
** libs
g++ -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c adSplit.cpp -o adSplit.o
g++ -shared -L/usr/local/lib -o adSplit.so adSplit.o   -L/loc/biocbuild/bbs-2.1-bioc/R/lib -lR
** R
** data
** inst
** preparing package for lazy loading
Loading required package: cluster
Loading required package: multtest
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: survival
Loading required package: splines
Loading required package: affy
Loading required package: affyio
Loading required package: preprocessCore
Loading required package: GO
Loading required package: KEGG
** help
 >>> Building/Updating help pages for package 'adSplit'
     Formats: text html latex example 
  adSplit-internal                  text    html    latex
  adSplit                           text    html    latex   example
  diana2means                       text    html    latex   example
  drawRandomPS                      text    html    latex   example
  golubKEGGSplits                   text    html    latex   example
  hist.splitSet                     text    html    latex   example
  image.splitSet                    text    html    latex   example
  makeEID2PROBESenv                 text    html    latex   example
  print.split                       text    html    latex
  print.splitSet                    text    html    latex   example
  randomDiana2means                 text    html    latex   example
** building package indices ...
* DONE (adSplit)