Package: oligo

Version: 1.11.9

Command: /Library/Frameworks/R.framework/Versions/2.11/Resources/bin/R CMD check --no-vignettes oligo_1.11.9.tar.gz

StartedAt: 2009-12-07 18:08:49 -0800 (Mon, 07 Dec 2009)

EndedAt: 2009-12-07 18:12:13 -0800 (Mon, 07 Dec 2009)

EllapsedTime: 204.5 seconds

RetCode: 0

Status: WARNINGS

CheckDir: oligo.Rcheck

Warnings: 3

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.6-bioc/meat/oligo.Rcheck'
* using R version 2.11.0 Under development (unstable) (2009-11-30 r50622)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'oligo/DESCRIPTION' ... OK
* this is package 'oligo' version '1.11.9'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'oligo' 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 ... WARNING
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x314740c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x314740c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x314740c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x314740c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x314740c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x314740c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x314740c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x314740c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x314740c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x314740c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x314740c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x314740c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x314740c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x314740c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x314740c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x314740c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x314740c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x314740c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x314740c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x314740c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x314740c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x314740c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x314740c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x314740c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x314740c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x314740c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x314740c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x314740c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x314740c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x314740c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x314740c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x314740c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x314740c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x314740c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... WARNING
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x40fd0bc> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x40fd0bc> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x40fd0bc> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x40fd0bc> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
In R, the argument of a replacement function which corresponds to the right
hand side must be named 'value'.
* checking foreign function calls ... WARNING
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x412f41c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x412f41c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x412f41c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x412f41c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x412f41c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x412f41c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x412f41c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x412f41c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x412f41c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x412f41c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x412f41c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x412f41c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x412f41c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x412f41c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x412f41c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x412f41c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x412f41c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x412f41c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x412f41c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x412f41c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x412f41c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x412f41c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x412f41c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x412f41c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x412f41c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x412f41c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x412f41c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x412f41c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x412f41c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x412f41c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x412f41c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x412f41c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x412f41c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x412f41c> where hasMethods(g, env) errors: ‘end’, ‘start’, ‘width’
May need something like

  importFrom("stats", "end")
  importFrom("stats", "start")
  importFrom("IRanges", "width")

in NAMESPACE.
See the chapter 'System and foreign language interfaces' of the 'Writing R
Extensions' manual.
* checking R code for possible problems ... OK
* checking Rd files ... OK
* 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 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

WARNING: There were 3 warnings, see
  /Users/biocbuild/bbs-2.6-bioc/meat/oligo.Rcheck/00check.log
for details

* install options are ' --no-html'

* installing *source* package ‘oligo’ ...
** libs
** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -c ParserXYS.c -o ParserXYS.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -c baseProfile.c -o baseProfile.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -c basecontent.c -o basecontent.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -c rma2.c -o rma2.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -c rma_common.c -o rma_common.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -c trimmed.c -o trimmed.o
gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o oligo.so ParserXYS.o baseProfile.o basecontent.o rma2.o rma_common.o trimmed.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -c ParserXYS.c -o ParserXYS.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -c baseProfile.c -o baseProfile.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -c basecontent.c -o basecontent.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -c rma2.c -o rma2.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -c rma_common.c -o rma_common.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -c trimmed.c -o trimmed.o
gcc-4.2 -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o oligo.so ParserXYS.o baseProfile.o basecontent.o rma2.o rma_common.o trimmed.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - x86_64
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -c ParserXYS.c -o ParserXYS.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -c baseProfile.c -o baseProfile.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -c basecontent.c -o basecontent.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -c rma2.c -o rma2.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -c rma_common.c -o rma_common.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -c trimmed.c -o trimmed.o
gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o oligo.so ParserXYS.o baseProfile.o basecontent.o rma2.o rma_common.o trimmed.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** R
** inst
** preparing package for lazy loading
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)'.

Welcome to oligoClasses version 1.9.14
Creating a new generic function for "boxplot" in "oligo"
** help
*** installing help indices
** building package indices ...
* DONE (oligo)