Package: vsn

Version: 1.12.0

Command: /home/biocbuild/bbs-1.9/R/bin/R CMD check vsn_1.12.0.tar.gz

RetCode: 0

Time: 165.4 seconds

Status: WARNINGS

CheckDir: vsn.Rcheck

Warnings: 1

* checking for working latex ... OK
* using log directory '/home/biocbuild/bbs-1.9/meat/vsn.Rcheck'
* using R version 2.4.1 (2006-12-18)
* checking for file 'vsn/DESCRIPTION' ... OK
* this is package 'vsn' version '1.12.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'vsn' 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 non-ASCII characters ... 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 S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 for CRLF line endings in C/C++/Fortran sources/headers ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating vsn-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... WARNING
*** Weave Errors ***
File /home/biocbuild/bbs-1.9/meat/vsn.Rcheck/vsn/doc/vsn.Rnw :
Error:  chunk 16 (label=affy1) 
Error in vsn(intensity(abatch)[ind, ], niter = niter, strata = strind,  : 
The likelihood optimization did not converge. A likely reason is that the normalization parameters are not uniquely identifiable from the provided data.
Possibly, the columns of the data matrix are exactly co-linear or affine dependent - please verify the data to make sure there were no mix-ups.
* creating vsn-manual.tex ... OK
* checking vsn-manual.tex ... OK

WARNING: There was 1 warning, see
  /home/biocbuild/bbs-1.9/meat/vsn.Rcheck/00check.log
for details

* Installing *source* package 'vsn' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-1.9/R/include -I/home/biocbuild/bbs-1.9/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c vsn.c -o vsn.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o vsn.so vsn.o   
** R
** data
** inst
** help
 >>> Building/Updating help pages for package 'vsn'
     Formats: text html latex example 
  getIntensityMatrix                text    html    latex   example
  kidney                            text    html    latex   example
  lymphoma                          text    html    latex   example
  meanSdPlot                        text    html    latex   example
  normalize.AffyBatch.vsn           text    html    latex   example
  sagmbSimulateData                 text    html    latex   example
  vsn                               text    html    latex   example
  vsnPlotPar                        text    html    latex   example
  vsnh                              text    html    latex   example
** building package indices ...
* DONE (vsn)