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Package 39/319HostnameOS / ArchBUILDCHECKBUILD BIN
bgx 1.8.0
Ernest Turro
Bioconductor Changelog
Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/bgx
Last Changed Rev: 39013 / Revision: 42512
Last Changed Date: 2009-04-20 16:24:12 -0700 (Mon, 20 Apr 2009)
wilson1 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ OK ] OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
Package: bgx
Version: 1.8.0
Command: E:\biocbld\bbs-2.4-bioc\R\bin\R.exe CMD check --no-vignettes bgx_1.8.0.tar.gz
StartedAt: 2009-10-20 16:20:50 -0700 (Tue, 20 Oct 2009)
EndedAt: 2009-10-20 16:24:14 -0700 (Tue, 20 Oct 2009)
EllapsedTime: 203.9 seconds
RetCode: 0
Status: OK
CheckDir: bgx.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.4-bioc/meat/bgx.Rcheck'
* using R version 2.9.2 (2009-08-24)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'bgx/DESCRIPTION' ... OK
* this is package 'bgx' version '1.8.0'
* 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 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 files against version 2 parser ... 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
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

bgx.Rcheck/00install.out:

* Installing *source* package 'bgx' ...
** libs
  making DLL ...
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -I ../boostIncl    -DUSING_R -march=i486 -ffast-math -O3   -O2 -Wall  -c bgx.cc -o bgx.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -I ../boostIncl    -DUSING_R -march=i486 -ffast-math -O3   -O2 -Wall  -c bgx_frontend.cc -o bgx_frontend.o
gcc -I"e:/biocbld/bbs-2.4-bioc/R/include" -I ../boostIncl    -DUSING_R -march=i486 -ffast-math -O3  -std=c99   -O3 -Wall  -std=gnu99 -c qnorm.c -o qnorm.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -I ../boostIncl    -DUSING_R -march=i486 -ffast-math -O3   -O2 -Wall  -c rundir.cc -o rundir.o
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -I ../boostIncl    -DUSING_R -march=i486 -ffast-math -O3   -O2 -Wall  -c sokal.cc -o sokal.o
g++ -shared -s -o bgx.dll tmp.def bgx.o bgx_frontend.o qnorm.o rundir.o sokal.o -Le:/biocbld/bbs-2.4-bioc/R/bin -lR
  ... done
** 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)'.

Loading required package: Biostrings
Loading required package: IRanges

Attaching package: 'IRanges'


	The following object(s) are masked from package:base :

	 cbind,
	 duplicated,
	 order,
	 pmax,
	 pmax.int,
	 pmin,
	 pmin.int,
	 rank,
	 rbind,
	 rep.int,
	 sapply,
	 sort,
	 table,
	 unique 

** help
*** installing help indices
 >>> Building/Updating help pages for package 'bgx'
     Formats: text html latex example chm 
Note: removing empty section \examples in file 'analysis.bgx.Rd'
Note: removing empty section \examples in file 'analysis.bgx.Rd'
  analysis.bgx                      text    html    latex           chm
  bgx                               text    html    latex   example chm
Note: removing empty section \examples in file 'mcmc.bgx.Rd'
Note: removing empty section \examples in file 'mcmc.bgx.Rd'
  mcmc.bgx                          text    html    latex           chm
Note: removing empty section \examples in file 'readOutput.bgx.Rd'
Note: removing empty section \examples in file 'readOutput.bgx.Rd'
  readOutput.bgx                    text    html    latex           chm
Note: removing empty section \value in file 'saveAffinityPlot.bgx.Rd'
Note: removing empty section \details in file 'saveAffinityPlot.bgx.Rd'
Note: removing empty section \examples in file 'saveAffinityPlot.bgx.Rd'
Note: removing empty section \value in file 'saveAffinityPlot.bgx.Rd'
Note: removing empty section \details in file 'saveAffinityPlot.bgx.Rd'
Note: removing empty section \examples in file 'saveAffinityPlot.bgx.Rd'
  saveAffinityPlot.bgx              text    html    latex           chm
Note: removing empty section \details in file 'setupVars.bgx.Rd'
Note: removing empty section \examples in file 'setupVars.bgx.Rd'
Note: removing empty section \details in file 'setupVars.bgx.Rd'
Note: removing empty section \examples in file 'setupVars.bgx.Rd'
  setupVars.bgx                     text    html    latex           chm
Microsoft HTML Help Compiler 4.74.8702

Compiling e:\biocbld\BBS-2~1.4-B\meat\BGX~1.RCH\00_PKG~1\bgx\chm\bgx.chm


Compile time: 0 minutes, 1 second
7	Topics
35	Local links
0	Internet links
1	Graphic


Created e:\biocbld\BBS-2~1.4-B\meat\BGX~1.RCH\00_PKG~1\bgx\chm\bgx.chm, 27,330 bytes
Compression decreased file by 4,031 bytes.
** building package indices ...
** MD5 sums
* DONE (bgx)