Package: stam

Version: 1.7.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check stam_1.7.0.tar.gz

RetCode: 0

Time: 951.6 seconds

Status: OK

CheckDir: stam.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory '/Users/biocbuild/2.0d/Rpacks/stam.Rcheck'
* using R version 2.5.0 Under development (unstable) (2006-10-21 r39702)
* checking for file 'stam/DESCRIPTION' ... OK
* this is package 'stam' version '1.7.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'stam' 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 syntax errors ... OK
* checking R files for non-ASCII characters ... 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 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 for CRLF line endings in C/C++/Fortran sources/headers ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating stam-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating stam-manual.tex ... OK
* checking stam-manual.tex ... OK

* Installing *source* package 'stam' ...
** libs
** arch - i386
gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -msse3  -D__NO_MATH_INLINES  -fPIC  -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c util.c -o util.o
/var/tmp//ccLSEuRG.s:837:indirect jmp without `*'
/var/tmp//ccLSEuRG.s:852:indirect jmp without `*'
/var/tmp//ccLSEuRG.s:867:indirect jmp without `*'
/var/tmp//ccLSEuRG.s:882:indirect jmp without `*'
/var/tmp//ccLSEuRG.s:897:indirect jmp without `*'
/var/tmp//ccLSEuRG.s:912:indirect jmp without `*'
/var/tmp//ccLSEuRG.s:931:indirect jmp without `*'
/var/tmp//ccLSEuRG.s:946:indirect jmp without `*'
/var/tmp//ccLSEuRG.s:961:indirect jmp without `*'
/var/tmp//ccLSEuRG.s:976:indirect jmp without `*'
/var/tmp//ccLSEuRG.s:991:indirect jmp without `*'
/var/tmp//ccLSEuRG.s:1006:indirect jmp without `*'
/var/tmp//ccLSEuRG.s:1021:indirect jmp without `*'
/var/tmp//ccLSEuRG.s:1036:indirect jmp without `*'
/var/tmp//ccLSEuRG.s:1051:indirect jmp without `*'
/var/tmp//ccLSEuRG.s:1066:indirect jmp without `*'
/var/tmp//ccLSEuRG.s:1081:indirect jmp without `*'
/var/tmp//ccLSEuRG.s:1096:indirect jmp without `*'
/var/tmp//ccLSEuRG.s:1111:indirect jmp without `*'
/var/tmp//ccLSEuRG.s:1130:indirect jmp without `*'
gcc-4.0 -arch i386 -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o stam.so util.o   -F/Library/Frameworks/R.framework/.. -framework R
** arch - ppc
gcc-4.0 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c util.c -o util.o
gcc-4.0 -arch ppc -std=gnu99 -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o stam.so util.o   -F/Library/Frameworks/R.framework/.. -framework R
** R
** data
** inst
** save image
Loading required package: GO
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

    Vignettes contain introductory material. To view, type
    'openVignette()' or start with 'help(Biobase)'. For details
    on reading vignettes, see the openVignette help page.

Loading required package: pamr
Loading required package: cluster
Loading required package: annaffy
Loading required package: KEGG
** help
 >>> Building/Updating help pages for package 'stam'
     Formats: text html latex example 
  golubTrain.cv                     text    html    latex
  golubTrain.fit                    text    html    latex
  image.stamPrediction              text    html    latex
  plot.stamCV                       text    html    latex
  plot.stamFit                      text    html    latex
  plot.stamPrediction               text    html    latex
  stam-internal                     text    html    latex
  stam.cv                           text    html    latex   example
  stam.evaluate                     text    html    latex   example
  stam.fit                          text    html    latex   example
  stam.graph.plot                   text    html    latex
  stam.net                          text    html    latex   example
  stam.predict                      text    html    latex   example
  stam.rgb.colors                   text    html    latex   example
  stam.serve                        text    html    latex   example
  stam.writeHTML                    text    html    latex   example
  stamCV-class                      text    html    latex
  stamEval-class                    text    html    latex
  stamFit-class                     text    html    latex
  stamINode-class                   text    html    latex
  stamLeaf-class                    text    html    latex
  stamNet-class                     text    html    latex
  stamNode-class                    text    html    latex
  stamPrediction-class              text    html    latex
** building package indices ...
* DONE (stam)