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Package 233/354HostnameOS / ArchBUILDCHECKBUILD BIN
oligo 1.11.9
Benilton Carvalho
Bioconductor Changelog
Snapshot Date: 2009-12-07 11:32:00 -0800 (Mon, 07 Dec 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo
Last Changed Rev: 43391 / Revision: 43434
Last Changed Date: 2009-12-04 08:39:35 -0800 (Fri, 04 Dec 2009)
wilson1 Linux (openSUSE 11.1) / x86_64  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ WARNINGS ] OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 
Package: oligo
Version: 1.11.9
Command: E:\biocbld\bbs-2.6-bioc\R\bin\R.exe CMD check --no-vignettes oligo_1.11.9.tar.gz
StartedAt: 2009-12-07 17:45:56 -0800 (Mon, 07 Dec 2009)
EndedAt: 2009-12-07 17:48:38 -0800 (Mon, 07 Dec 2009)
EllapsedTime: 161.5 seconds
RetCode: 0
Status: WARNINGS
CheckDir: oligo.Rcheck
Warnings: 3

Command output

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.6-bioc/meat/oligo.Rcheck'
* using R version 2.11.0 Under development (unstable) (2009-10-22 r50179)
* using session charset: ISO8859-1
* 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 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 ... WARNING
Warning in get_S4_generics_with_methods(penv) :
  Generics g in env = <environment: 0x043c0408> 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: 0x043c0408> 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: 0x043c0408> 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: 0x043c0408> 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: 0x043c0408> 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: 0x043c0408> 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: 0x043c0408> 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: 0x043c0408> 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: 0x043c0408> 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: 0x043c0408> 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: 0x043c0408> 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: 0x043c0408> 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: 0x043c0408> 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: 0x043c0408> 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: 0x043c0408> 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: 0x043c0408> 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: 0x043c0408> 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: 0x043c0408> 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: 0x043c0408> 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: 0x043c0408> 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: 0x043c0408> 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: 0x043c0408> 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: 0x043c0408> 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: 0x043c0408> 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: 0x043c0408> 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: 0x043c0408> 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: 0x043c0408> 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: 0x043c0408> 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: 0x043c0408> 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: 0x043c0408> 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: 0x043c0408> 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: 0x043c0408> 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: 0x043c0408> 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: 0x043c0408> 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: 0x03975498> 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: 0x03975498> 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: 0x03975498> 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: 0x03975498> 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: 0x039ad1f4> 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: 0x039ad1f4> 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: 0x039ad1f4> 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: 0x039ad1f4> 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: 0x039ad1f4> 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: 0x039ad1f4> 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: 0x039ad1f4> 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: 0x039ad1f4> 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: 0x039ad1f4> 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: 0x039ad1f4> 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: 0x039ad1f4> 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: 0x039ad1f4> 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: 0x039ad1f4> 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: 0x039ad1f4> 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: 0x039ad1f4> 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: 0x039ad1f4> 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: 0x039ad1f4> 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: 0x039ad1f4> 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: 0x039ad1f4> 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: 0x039ad1f4> 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: 0x039ad1f4> 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: 0x039ad1f4> 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: 0x039ad1f4> 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: 0x039ad1f4> 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: 0x039ad1f4> 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: 0x039ad1f4> 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: 0x039ad1f4> 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: 0x039ad1f4> 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: 0x039ad1f4> 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: 0x039ad1f4> 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: 0x039ad1f4> 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: 0x039ad1f4> 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: 0x039ad1f4> 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: 0x039ad1f4> 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
  E:/biocbld/bbs-2.6-bioc/meat/oligo.Rcheck/00check.log
for details

oligo.Rcheck/00install.out:

* install options are ' --no-html'

* installing *source* package 'oligo' ...
** libs
  making DLL ...
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -Ie:/biocbld/bbs-2.6-bioc/R/src/extra/zlib -DHAVE_ZLIB  -I"e:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"     -O3 -Wall  -std=gnu99 -c ParserXYS.c -o ParserXYS.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -Ie:/biocbld/bbs-2.6-bioc/R/src/extra/zlib -DHAVE_ZLIB  -I"e:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"     -O3 -Wall  -std=gnu99 -c baseProfile.c -o baseProfile.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -Ie:/biocbld/bbs-2.6-bioc/R/src/extra/zlib -DHAVE_ZLIB  -I"e:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"     -O3 -Wall  -std=gnu99 -c basecontent.c -o basecontent.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -Ie:/biocbld/bbs-2.6-bioc/R/src/extra/zlib -DHAVE_ZLIB  -I"e:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"     -O3 -Wall  -std=gnu99 -c rma2.c -o rma2.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -Ie:/biocbld/bbs-2.6-bioc/R/src/extra/zlib -DHAVE_ZLIB  -I"e:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"     -O3 -Wall  -std=gnu99 -c rma_common.c -o rma_common.o
gcc -I"e:/biocbld/bbs-2.6-bioc/R/include" -Ie:/biocbld/bbs-2.6-bioc/R/src/extra/zlib -DHAVE_ZLIB  -I"e:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"     -O3 -Wall  -std=gnu99 -c trimmed.c -o trimmed.o
gcc -shared -s -o oligo.dll tmp.def ParserXYS.o baseProfile.o basecontent.o rma2.o rma_common.o trimmed.o -Le:/biocbld/bbs-2.6-bioc/R/bin -lR
  ... done
** 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 ...
** MD5 sums
* DONE (oligo)