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Package 44/389HostnameOS / ArchBUILDCHECKBUILD BIN
bgx 1.12.0
Ernest Turro
Snapshot Date: 2010-10-04 11:22:20 -0700 (Mon, 04 Oct 2010)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/bgx
Last Changed Rev: 46401 / Revision: 49923
Last Changed Date: 2010-04-22 11:21:23 -0700 (Thu, 22 Apr 2010)
wilson1 Linux (openSUSE 11.1) / x86_64  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: bgx
Version: 1.12.0
Command: /home/biocbuild/bbs-2.6-bioc/R/bin/R CMD check --no-vignettes --timings bgx_1.12.0.tar.gz
StartedAt: 2010-10-04 16:12:09 -0700 (Mon, 04 Oct 2010)
EndedAt: 2010-10-04 16:14:21 -0700 (Mon, 04 Oct 2010)
EllapsedTime: 131.7 seconds
RetCode: 0
Status:  OK 
CheckDir: bgx.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.6-bioc/meat/bgx.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'bgx/DESCRIPTION' ... OK
* this is package 'bgx' version '1.12.0'
* 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 package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... 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 ... NOTE
prepare_Rd: analysis.bgx.Rd:48-49: Dropping empty section \examples
prepare_Rd: mcmc.bgx.Rd:48-49: Dropping empty section \examples
prepare_Rd: readOutput.bgx.Rd:23-24: Dropping empty section \examples
prepare_Rd: saveAffinityPlot.bgx.Rd:18-19: Dropping empty section \details
prepare_Rd: saveAffinityPlot.bgx.Rd:20-21: Dropping empty section \value
prepare_Rd: saveAffinityPlot.bgx.Rd:26-27: Dropping empty section \examples
prepare_Rd: setupVars.bgx.Rd:21-22: Dropping empty section \details
prepare_Rd: setupVars.bgx.Rd:43-44: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... 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
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

bgx.Rcheck/00install.out:

* install options are ' --no-html'

* 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... 6f6:7020800:4e3bd:bfebfbff
checking whether C compiler accepts -march=pentiumpro... no
checking whether C compiler accepts -mcpu=pentiumpro... no
checking whether C compiler accepts -mpentiumpro... no
checking for gcc architecture flag... unknown
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-2.6-bioc/R/include -I ../boostIncl -I/usr/local/include    -fpic  -g -O2 -ffast-math -O3 -DUSING_R -c bgx.cc -o bgx.o
g++ -I/home/biocbuild/bbs-2.6-bioc/R/include -I ../boostIncl -I/usr/local/include    -fpic  -g -O2 -ffast-math -O3 -DUSING_R -c bgx_frontend.cc -o bgx_frontend.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include -I ../boostIncl -I/usr/local/include    -fpic  -g -O2 -g -O2  -ffast-math -O3 -c qnorm.c -o qnorm.o
g++ -I/home/biocbuild/bbs-2.6-bioc/R/include -I ../boostIncl -I/usr/local/include    -fpic  -g -O2 -ffast-math -O3 -DUSING_R -c rundir.cc -o rundir.o
g++ -I/home/biocbuild/bbs-2.6-bioc/R/include -I ../boostIncl -I/usr/local/include    -fpic  -g -O2 -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-2.6-bioc/R/lib -lR
rm -r ../boostIncl
installing to /loc/home/biocbuild/bbs-2.6-bioc/meat/bgx.Rcheck/bgx/libs
** R
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (bgx)

bgx.Rcheck/bgx-Ex.timings:

nameusersystemelapsed
bgx43.234 0.19243.580