Package: bgx

Version: 1.1.3

Command: /loc/biocbuild/bbs-2.1-bioc/R/bin/R CMD check bgx_1.1.3.tar.gz

RetCode: 1

Time: 134.1 seconds

Status: ERROR

CheckDir: bgx.Rcheck

Warnings: NA

* checking for working latex ... OK
* using log directory '/extra/loc/biocbuild/bbs-2.1-bioc/meat/bgx.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-04-17 r41210)
* checking for file 'bgx/DESCRIPTION' ... OK
* this is package 'bgx' version '1.1.3'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'bgx' 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 ... 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 compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating bgx-Ex.R ... OK
* checking examples ... ERROR
Running examples in 'bgx-Ex.R' failed.
The error most likely occurred in:

> ### * bgx
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: bgx
> ### Title: Fully Bayesian integrated approach to the analysis of Affymetrix
> ###   GeneChip data
> ### Aliases: bgx standalone.bgx
> ### Keywords: manip
> 
> ### ** Examples
> 
>   if(require(affydata) && require(hgu95av2cdf)) {
+     data(Dilution)
+     eset <- bgx(Dilution, samplesets=c(2,2), probeAff=F, burnin=2048, iter=8192,
+       genes=c(12500:12599), output="all", basepath=".")
+   }
Loading required package: affydata
Loading required package: hgu95av2cdf
Analysing 4 array(s) in 2 condition(s):
	- condition 1: 2 array(s)
	- condition 2: 2 array(s)
Analysing genes  12500:12599 
Error in setupVars.bgx(data = aData, samplesets = samplesets, genes = genes,  : 
	F used instead of FALSE
Execution halted

* Installing *source* package 'bgx' ...
checking for gcc... gcc -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking for C compiler vendor... gnu
checking whether C compiler accepts -ffast-math... yes
checking whether C compiler accepts -fomit-frame-pointer... yes
checking whether C compiler accepts -O3... yes
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking for gcc architecture flag... 
checking for x86 cpuid 0 output... 5:756e6547:6c65746e:49656e69
checking for x86 cpuid 1 output... f41:6020800:641d:bfebfbff
checking whether C compiler accepts -march=prescott... yes
checking for gcc architecture flag... -march=prescott
checking for gcc -std=gnu99 option to accept ISO C99... none needed
checking for main in -lm... yes
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking build system type... (cached) i686-pc-linux-gnu
checking for boostlib >= 1.31.0... yes
checking whether the Boost::Filesystem library is available... yes
checking for main in -lboost_filesystem... yes
checking whether the Boost::Program_Options library is available... no
checking whether the Boost::Thread library is available... yes
checking for main in -lboost_thread... yes
checking whether the Boost::IOStreams library is available... no
checking whether the Boost::Serialization library is available... no
checking whether the Boost::Signals library is available... yes
checking for main in -lboost_signals... yes
checking whether the Boost::Date_Time library is available... yes
checking for main in -lboost_date_time... yes
checking whether the Boost::Regex library is available... yes
checking for main in -lboost_regex... yes
checking whether the Boost::UnitTestFramework library is available... no
checking for an ANSI C-conforming const... yes
checking for inline... inline
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/include -I/usr/local/include    -fpic  -g -O2 -Wall -g -O2 -ffast-math -fomit-frame-pointer -O3 -march=prescott -DUSING_R -c bgx.cc -o bgx.o
g++ -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/include -I/usr/local/include    -fpic  -g -O2 -Wall -g -O2 -ffast-math -fomit-frame-pointer -O3 -march=prescott -DUSING_R -c bgx_frontend.cc -o bgx_frontend.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/include -I/usr/local/include    -fpic  -g -O2 -Wall -g -O2 -ffast-math -fomit-frame-pointer -O3 -march=prescott -c qnorm.c -o qnorm.o
g++ -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/include -I/usr/local/include    -fpic  -g -O2 -Wall -g -O2 -ffast-math -fomit-frame-pointer -O3 -march=prescott -DUSING_R -c rundir.cc -o rundir.o
g++ -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/include -I/usr/local/include    -fpic  -g -O2 -Wall -g -O2 -ffast-math -fomit-frame-pointer -O3 -march=prescott -DUSING_R -c sokal.cc -o sokal.o
g++ -shared -L/usr/local/lib -o bgx.so bgx.o bgx_frontend.o qnorm.o rundir.o sokal.o -lm   -L/loc/biocbuild/bbs-2.1-bioc/R/lib -lR
** R
** inst
** preparing package for lazy loading
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: affy
Loading required package: affyio
Loading required package: gcrma
Loading required package: matchprobes
Loading required package: splines
** help
 >>> Building/Updating help pages for package 'bgx'
     Formats: text html latex example 
  analysis.bgx                      text    html    latex   example
  bgx                               text    html    latex   example
  mcmc.bgx                          text    html    latex   example
  readOutput.bgx                    text    html    latex   example
  saveAffinityPlot.bgx              text    html    latex   example
  setupVars.bgx                     text    html    latex   example
** building package indices ...
* DONE (bgx)