##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data GlobalAncova
###
##############################################################################
##############################################################################


* checking for file ‘GlobalAncova/DESCRIPTION’ ... OK
* preparing ‘GlobalAncova’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘GlobalAncova.rnw’ using Sweave
Loading required package: corpcor
Loading required package: globaltest
Loading required package: survival
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following object is masked from ‘package:globaltest’:

    sort

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

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

Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Loading required package: org.Hs.eg.db



Error: processing vignette 'GlobalAncova.rnw' failed with diagnostics:
 chunk 2 (label = initialize) 
Error in library(vsn) : there is no package called ‘vsn’

--- failed re-building ‘GlobalAncova.rnw’

--- re-building ‘GlobalAncovaDecomp.rnw’ using Sweave
Warning in anova.lm(lm(dummy.formula, model.dat)) :
  ANOVA F-tests on an essentially perfect fit are unreliable
Warning in anova.lm(lm(dummy.formula, model.dat)) :
  ANOVA F-tests on an essentially perfect fit are unreliable
Warning in anova.lm(lm(dummy.formula, model.dat)) :
  ANOVA F-tests on an essentially perfect fit are unreliable
Warning in anova.lm(lm(dummy.formula, model.dat)) :
  ANOVA F-tests on an essentially perfect fit are unreliable
Warning in anova.lm(lm(dummy.formula, model.dat)) :
  ANOVA F-tests on an essentially perfect fit are unreliable
Warning in anova.lm(lm(dummy.formula, model.dat)) :
  ANOVA F-tests on an essentially perfect fit are unreliable
Warning in anova.lm(lm(dummy.formula, model.dat)) :
  ANOVA F-tests on an essentially perfect fit are unreliable
Warning in anova.lm(lm(dummy.formula, model.dat)) :
  ANOVA F-tests on an essentially perfect fit are unreliable
Warning in anova.lm(lm(dummy.formula, model.dat)) :
  ANOVA F-tests on an essentially perfect fit are unreliable
Warning in anova.lm(lm(dummy.formula, model.dat)) :
  ANOVA F-tests on an essentially perfect fit are unreliable
Warning in anova.lm(lm(dummy.formula, model.dat)) :
  ANOVA F-tests on an essentially perfect fit are unreliable
Warning in anova.lm(lm(dummy.formula, model.dat)) :
  ANOVA F-tests on an essentially perfect fit are unreliable
Warning in anova.lm(lm(dummy.formula, model.dat)) :
  ANOVA F-tests on an essentially perfect fit are unreliable
Warning in anova.lm(lm(dummy.formula, model.dat)) :
  ANOVA F-tests on an essentially perfect fit are unreliable
--- finished re-building ‘GlobalAncovaDecomp.rnw’

SUMMARY: processing the following file failed:
  ‘GlobalAncova.rnw’

Error: Vignette re-building failed.
Execution halted