Package: stam

Version: 1.7.0

Command: /loc/biocbuild/bbs-2.1-bioc/R/bin/R CMD build stam

RetCode: 1

Time: 1363.3 seconds

Status: ERROR

PackageFile: None

* checking for file 'stam/DESCRIPTION' ... OK
* preparing 'stam':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* Installing *source* package 'stam' ...
** libs
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c util.c -o util.o
gcc -std=gnu99 -G -L/usr/local/lib -o stam.so util.o   -L/loc/biocbuild/bbs-2.1-bioc/R/lib -lR
** R
** data
** inst
** preparing package for lazy loading
Loading required package: GO
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: pamr
Loading required package: cluster
Loading required package: survival
Loading required package: splines
Loading required package: annaffy
Loading required package: KEGG
** help
Note: unmatched right brace in 'golubTrain.cv' on or after line 10
Note: unmatched right brace in 'golubTrain.fit' on or after line 10
Note: unmatched right brace in 'stamPrediction-class' on or after line 52
 >>> 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 ...
Warning: 'golubTrain.cv' looks like a pre-2.4.0 S4 object: please recreate it
Warning: 'golubTrain.fit' looks like a pre-2.4.0 S4 object: please recreate it
* DONE (stam)
* creating vignettes ... ERROR
Loading required package: Biobase

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: GO
Loading required package: pamr
Loading required package: cluster
Loading required package: survival
Loading required package: splines
Loading required package: annaffy
Loading required package: KEGG
Loading required package: affy
Loading required package: affyio
Loading required package: preprocessCore
Loading required package: limma
Loading required package: hu6800

Error: processing vignette 'tr_2004_03.Rnw' failed with diagnostics:
 chunk 10 
Error in .Object@scores[a, ] <- alpha[a] * scaled.performance + (1 - alpha[a]) *  : 
  nothing to replace with
In addition: Warning messages:
1: In min(v) : no non-missing arguments to min; returning Inf
2: In max(v) : no non-missing arguments to max; returning -Inf
3: In min(v) : no non-missing arguments to min; returning Inf
4: In max(v) : no non-missing arguments to max; returning -Inf
Execution halted