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Package 31/251HostnameOS / ArchBUILDCHECKBUILD BIN
bgx 1.3.0
Ernest Turro
Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bgx
Last Changed Rev: 27981 / Revision: 29143
Last Changed Date: 2007-10-13 04:46:15 -0700 (Sat, 13 Oct 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 
Package: bgx
Version: 1.3.0
Command: /home/biocbuild/bbs-2.2-bioc/R/bin/R CMD check bgx_1.3.0.tar.gz
StartedAt: 2007-12-11 03:08:42 -0800 (Tue, 11 Dec 2007)
EndedAt: 2007-12-11 03:11:08 -0800 (Tue, 11 Dec 2007)
EllapsedTime: 145.3 seconds
RetCode: 0
Status: OK
CheckDir: bgx.Rcheck
Warnings: 0

Command output

* checking for working latex ... OK
* using log directory '/home/biocbuild/bbs-2.2-bioc/meat/bgx.Rcheck'
* using R version 2.7.0 Under development (unstable) (2007-11-18 r43497)
* checking for file 'bgx/DESCRIPTION' ... OK
* this is package 'bgx' version '1.3.0'
* 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

bgx.Rcheck/00install.out:

* 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 -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... 6f6:6020800:4e3bd: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
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
g++ -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I ../boostIncl -I/usr/local/include    -fpic  -g -O2 -Wall -ffast-math -O3 -DUSING_R -c bgx.cc -o bgx.o
g++ -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I ../boostIncl -I/usr/local/include    -fpic  -g -O2 -Wall -ffast-math -O3 -DUSING_R -c bgx_frontend.cc -o bgx_frontend.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I ../boostIncl -I/usr/local/include    -fpic  -g -O2 -Wall -g -O2 -mpentiumpro  -ffast-math -O3 -c qnorm.c -o qnorm.o
g++ -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I ../boostIncl -I/usr/local/include    -fpic  -g -O2 -Wall -ffast-math -O3 -DUSING_R -c rundir.cc -o rundir.o
g++ -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include -I ../boostIncl -I/usr/local/include    -fpic  -g -O2 -Wall -ffast-math -O3 -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-2.2-bioc/R/lib -lR
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
Note: removing empty section \examples
Note: removing empty section \examples
Note: removing empty section \examples
Note: removing empty section \value
Note: removing empty section \details
Note: removing empty section \examples
Note: removing empty section \details
Note: removing empty section \examples
 >>> Building/Updating help pages for package 'bgx'
     Formats: text html latex example 
  analysis.bgx                      text    html    latex
  bgx                               text    html    latex   example
  mcmc.bgx                          text    html    latex
  readOutput.bgx                    text    html    latex
  saveAffinityPlot.bgx              text    html    latex
  setupVars.bgx                     text    html    latex
** building package indices ...
* DONE (bgx)