Package: GLAD

Version: 1.11.0

Command: /home/biocbuild/bbs-2.1-bioc/R/bin/R CMD check GLAD_1.11.0.tar.gz

RetCode: 0

Time: 49.5 seconds

Status: OK

CheckDir: GLAD.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory '/home/biocbuild/bbs-2.1-bioc/meat/GLAD.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-08-06 r42439)
* checking for file 'GLAD/DESCRIPTION' ... OK
* this is package 'GLAD' version '1.11.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'GLAD' 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 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
plotProfile.profileCGH: no visible binding for global variable
  'cytoband'
* 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 'arrayPersp':
  arrayPersp.default arrayPersp.arrayCGH

S3 methods shown with full name in documentation object 'arrayPlot':
  arrayPlot.default arrayPlot.arrayCGH

S3 methods shown with full name in documentation object 'as.data.frame.profileCGH':
  as.data.frame.profileCGH

S3 methods shown with full name in documentation object 'as.profileCGH':
  as.profileCGH.data.frame

S3 methods shown with full name in documentation object 'daglad':
  daglad.profileCGH

S3 methods shown with full name in documentation object 'glad':
  glad.profileCGH

S3 methods shown with full name in documentation object 'plotProfile':
  plotProfile.profileCGH

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 GLAD-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating GLAD-manual.tex ... OK
* checking GLAD-manual.tex ... OK

* Installing *source* package 'GLAD' ...
Configuring variable environment
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c distance.c -o distance.o
g++ -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c glad.cpp -o glad.o
glad.cpp: In function 'void detectOutliers(double*, int*, int*, int*, int*, int*, double*, int*)':
glad.cpp:112: warning: comparison between signed and unsigned integer expressions
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c glad-function.c -o glad-function.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c hclust.c -o hclust.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c laws.c -o laws.o
g++ -shared -L/usr/local/lib64 -o GLAD.so distance.o glad.o glad-function.o hclust.o laws.o   -L/home/biocbuild/bbs-2.1-bioc/R/lib -lR
** R
** data
** demo
** inst
** preparing package for lazy loading
Loading required package: aws
Loading required package: tcltk
Loading Tcl/Tk interface ... done
** help
 >>> Building/Updating help pages for package 'GLAD'
     Formats: text html latex example 
  ChrNumeric                        text    html    latex   example
  ColorBar                          text    html    latex   example
  GLAD-internal                     text    html    latex
  arrayCGH                          text    html    latex   example
  arrayPersp                        text    html    latex   example
  arrayPlot                         text    html    latex   example
  as.data.frame.profileCGH          text    html    latex   example
  as.profileCGH                     text    html    latex   example
  bladder                           text    html    latex   example
  cytoband                          text    html    latex   example
  daglad                            text    html    latex   example
  glad                              text    html    latex   example
  hclust                            text    html    latex   example
  kernel                            text    html    latex
  myPalette                         text    html    latex   example
  plotProfile                       text    html    latex   example
  profileCGH                        text    html    latex   example
  snijders                          text    html    latex   example
  tkdaglad                          text    html    latex   example
  veltman                           text    html    latex   example
** building package indices ...
* DONE (GLAD)