Package: bgx

Version: 1.1.3

Command: /home/biocbuild/bbs-2.1-bioc/R/bin/R CMD build bgx

RetCode: 0

Time: 63.5 seconds

Status: OK

PackageFile: bgx_1.1.3.tar.gz

* checking for file 'bgx/DESCRIPTION' ... OK
* preparing 'bgx':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking whether 'INDEX' is up-to-date ... OK
* installing the package to re-build vignettes
* 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... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for gcc architecture flag... 
checking for x86 cpuid 0 output... a:756e6547:6c65746e:49656e69
checking for x86 cpuid 1 output... 6f6:1020800:4e3bd:bfebfbff
checking whether C compiler accepts -march=pentiumpro... no
checking whether C compiler accepts -mcpu=pentiumpro... no
checking whether C compiler accepts -mpentiumpro... yes
checking for gcc architecture flag... -mpentiumpro
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) x86_64-unknown-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... yes
checking for main in -lboost_program_options... yes
checking whether the Boost::Thread library is available... yes
checking for main in -lboost_thread... no
checking for main in -lboost_thread-gcc... no
checking for main in -l-std=gnu99... no
checking for main in -lboost_thread-gcc... (cached) no
checking for main in -l-std=gnu99-mt... no
checking for main in -lboost_thread-gcc... (cached) no
checking for main in -l-std=gnu99-mt-s... no
checking for main in -lboost_thread-gcc... (cached) no
checking for main in -l-std=gnu99-s... no
checking for main in -llibboost_thread... no
checking for main in -llibboost_thread-gcc... no
checking for main in -l-std=gnu99... (cached) no
checking for main in -llibboost_thread-gcc... (cached) no
checking for main in -l-std=gnu99-mt... (cached) no
checking for main in -llibboost_thread-gcc... (cached) no
checking for main in -l-std=gnu99-mt-s... (cached) no
checking for main in -llibboost_thread-gcc... (cached) no
checking for main in -l-std=gnu99-s... (cached) no
checking for main in -lboost_thread-mgw... no
checking for main in -lboost_thread-mgw... (cached) no
checking for main in -lboost_thread-mgw-mt... no
checking for main in -lboost_thread-mgw-mt-s... no
checking for main in -lboost_thread-mgw-s... no
configure: Could not link against boost_thread-mgw-s !
checking whether the Boost::IOStreams library is available... yes
checking for main in -lboost_iostreams... yes
checking whether the Boost::Serialization library is available... yes
checking for main in -lboost_serialization... yes
checking for main in -lboost_wserialization... yes
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... yes
checking the name of the Boost::UnitTestFramework library... 
checking for an ANSI C-conforming const... yes
checking for inline... inline
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/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 -mpentiumpro -DUSING_R -c bgx.cc -o bgx.o
g++ -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/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 -mpentiumpro -DUSING_R -c bgx_frontend.cc -o bgx_frontend.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/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 -mpentiumpro -c qnorm.c -o qnorm.o
g++ -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/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 -mpentiumpro -DUSING_R -c rundir.cc -o rundir.o
g++ -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/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 -mpentiumpro -DUSING_R -c sokal.cc -o sokal.o
g++ -shared -L/usr/local/lib64 -o bgx.so bgx.o bgx_frontend.o qnorm.o rundir.o sokal.o -lm   -L/home/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)
* creating vignettes ... OK
* cleaning src
* removing junk files
* checking for LF line-endings in source files
* checking for empty or unneeded directories
* building 'bgx_1.1.3.tar.gz'