BioC 2.1: CHECK report for CALIB on wellington

* checking for working latex ... OK
* using log directory '/extra/loc/biocbuild/bbs-2.1-bioc/meat/CALIB.Rcheck'
* using R version 2.6.0 (2007-10-03)
* checking for file 'CALIB/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CALIB' version '1.4.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'CALIB' 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
getColClasses: no visible global function definition for 'namesInFun'
plotSpikeCI: no visible binding for global variable 'otherindex'
read.rg: no visible global function definition for 'readBlueFuseHeader'
read.spike: no visible binding for global variable 'files'
* 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 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 CALIB-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating CALIB-manual.tex ... OK
* checking CALIB-manual.tex ... OK

* Installing *source* package 'CALIB' ...
** 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 Design.cpp -o Design.o
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 Estimation.cpp -o Estimation.o
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 NormalizedData.cpp -o NormalizedData.o
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 ParameterofOneArray.cpp -o ParameterofOneArray.o
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 RawDataofOneArray.cpp -o RawDataofOneArray.o
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 SpikeofOneArray.cpp -o SpikeofOneArray.o
g++ -shared -L/usr/local/lib -o CALIB.so Design.o Estimation.o NormalizedData.o ParameterofOneArray.o RawDataofOneArray.o SpikeofOneArray.o   -L/loc/biocbuild/bbs-2.1-bioc/R/lib -lR
** R
** data
** inst
** preparing package for lazy loading
Loading required package: limma
** help
 >>> Building/Updating help pages for package 'CALIB'
     Formats: text html latex example 
  ParameterList-class               text    html    latex
  RG                                text    html    latex   example
  RGList_CALIB-class                text    html    latex
  SpikeList-class                   text    html    latex
  adjustP2                          text    html    latex   example
  calibReadMe                       text    html    latex   example
  cbind                             text    html    latex   example
  dim                               text    html    latex   example
  dimnames                          text    html    latex   example
  estimateParameter                 text    html    latex   example
  getColClasses                     text    html    latex   example
  merge                             text    html    latex   example
  normalizeData                     text    html    latex   example
  normdata                          text    html    latex   example
  parameter                         text    html    latex   example
  plotNormalizedData                text    html    latex   example
  plotSpikeCI                       text    html    latex   example
  plotSpikeHI                       text    html    latex   example
  plotSpikeRG                       text    html    latex   example
  plotSpikeSpotError                text    html    latex   example
  read.rg                           text    html    latex   example
  read.spike                        text    html    latex
  spike                             text    html    latex   example
  subsetting                        text    html    latex   example
** building package indices ...
* DONE (CALIB)

Package 42/234	Hostname	OS	Arch	BUILD	CHECK	BUILD BIN
CALIB 1.4.0 Hui Zhao Last Changed Date: 2007-10-02 17:41:09 -0700 Last Changed Rev: 27709	lamb1	Linux (SUSE 10.1)	x86_64	OK	OK
	wellington	Linux (SUSE 9.2)	i686	OK	[ OK ]
	liverpool	Windows Server 2003 R2 (32-bit)	x64	OK	OK	OK
	pitt	Mac OS X (10.4.10)	i386	OK	OK	OK

Command output