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Package 30/233HostnameOS / ArchBUILDCHECKBUILD BIN
bgx 1.2.2
Ernest Turro
Snapshot Date: 2008-04-09 12:13:20 -0700 (Wed, 09 Apr 2008)
Last Changed Rev: 29287 / Revision: 30966
Last Changed Date: 2007-12-20 14:53:35 -0800 (Thu, 20 Dec 2007)
lamb1 Linux (SUSE 10.1) / x86_64  OK  OK 
wilson2 Linux (openSUSE 10.3) / x86_64  OK  OK 
wellington Linux (openSUSE 10.3) / i686  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
lemming Windows Server 2003 (32-bit) / x64  OK  OK  OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK [ OK ] OK 
Package: bgx
Version: 1.2.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check bgx_1.2.2.tar.gz
StartedAt: 2008-04-09 15:10:43 -0700 (Wed, 09 Apr 2008)
EndedAt: 2008-04-09 15:15:28 -0700 (Wed, 09 Apr 2008)
EllapsedTime: 284.6 seconds
RetCode: 0
Status: OK
CheckDir: bgx.Rcheck
Warnings: 0

Command output

* checking for working latex ... OK
* using log directory '/Users/biocbuild/bbs-2.1-bioc/meat/bgx.Rcheck'
* using R version 2.6.2 (2008-02-08)
* checking for file 'bgx/DESCRIPTION' ... OK
* this is package 'bgx' version '1.2.2'
* checking package name space information ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating bgx-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating bgx-manual.tex ... OK
* checking bgx-manual.tex ... OK


* Installing *source* package 'bgx' ...
checking for gcc... gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -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 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 accepts -g... yes
checking for gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -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 -O3... yes
checking build system type... i386-apple-darwin8.11.1
checking host system type... i386-apple-darwin8.11.1
checking for gcc architecture flag... 
checking for x86 cpuid 0 output... unknown
checking for x86 cpuid 1 output... unknown
checking for gcc architecture flag... unknown
checking for gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 option to accept ISO C99... none needed
checking for main in -lm... yes
Untarring Boost header files...
checking for an ANSI C-conforming const... yes
checking for inline... inline
configure: creating ./config.status
config.status: creating src/Makevars
** libs
** arch - i386
g++ -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I ../boostIncl -msse3    -fPIC  -g -O2 -march=nocona -ffast-math -O3 -DUSING_R -c -o bgx.o
g++ -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I ../boostIncl -msse3    -fPIC  -g -O2 -march=nocona -ffast-math -O3 -DUSING_R -c -o bgx_frontend.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I ../boostIncl -msse3    -fPIC  -g -O2 -march=nocona -g -O2  -ffast-math -O3 -c qnorm.c -o qnorm.o
g++ -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I ../boostIncl -msse3    -fPIC  -g -O2 -march=nocona -ffast-math -O3 -DUSING_R -c -o rundir.o
g++ -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I ../boostIncl -msse3    -fPIC  -g -O2 -march=nocona -ffast-math -O3 -DUSING_R -c -o sokal.o
g++ -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -dynamiclib -Wl,-headerpad_max_install_names -Wl,-macosx_version_min -Wl,10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o bgx.o bgx_frontend.o qnorm.o rundir.o sokal.o -lm   -F/Library/Frameworks/R.framework/.. -framework R 
rm -r ../boostIncl
** 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: preprocessCore
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)