[BioC] affyPLM QC vignette is missing...

[Jenny Drnevich]

Hi Ben,

The QC Assessment .pdf vignette of affyPLM seems to be missing from 
the latest windows binary. I just updated all my packages to make 
sure I wasn't missing anything. The vignette is still available on 
the bioC webpage 
(http://bioconductor.org/packages/release/bioc/vignettes/affyPLM/inst/doc/QualityAssess.pdf) 
so I thought this must be a bug.

Thanks,
Jenny

 > source("http://bioconductor.org/biocLite.R")
 > update.packages(repos=biocinstallRepos(),ask=FALSE)
trying URL 
'http://bioconductor.org/packages/2.3/data/experiment/bin/windows/contrib/2.8/affydata_1.11.4.zip'
Content type 'application/zip' length 12730305 bytes (12.1 Mb)
opened URL
downloaded 12.1 Mb
### ... a bunch of packages being downloaded

package 'affydata' successfully unpacked and MD5 sums checked
package 'boot' successfully unpacked and MD5 sums checked
package 'Category' successfully unpacked and MD5 sums checked
package 'cluster' successfully unpacked and MD5 sums checked
package 'foreign' successfully unpacked and MD5 sums checked
package 'IRanges' successfully unpacked and MD5 sums checked
package 'lattice' successfully unpacked and MD5 sums checked
package 'mgcv' successfully unpacked and MD5 sums checked
package 'nlme' successfully unpacked and MD5 sums checked
package 'spam' successfully unpacked and MD5 sums checked

The downloaded packages are in
         C:\Documents and Settings\drnevich\Local 
Settings\Temp\RtmpTGrSYa\downloaded_packages
updating HTML package descriptions
 >
 > library(affyPLM)
Loading required package: affy
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: gcrma
Loading required package: matchprobes
Loading required package: splines
Loading required package: preprocessCore
 > openVignette()
Please select a vignette: (entries marked by '[-]' have no PDF file)

  1: affy - 1. Primer
  2: affy - 2. Built-in Processing Methods
  3: affy - 3. Custom Processing Methods
  4: affy - 4. Import Methods
  5: affyPLM - affyPLM: Advanced use of the MAplot function
  6: affyPLM - affyPLM: Fitting Probe Level Models
  7: affyPLM - affyPLM: the threestep function
  8: Biobase - An introduction to Biobase and ExpressionSets
  9: Biobase - Bioconductor Overview
10: Biobase - esApply Introduction
11: Biobase - Notes for eSet developers
12: Biobase - Notes for writing introductory 'how to' documents
13: Biobase - quick views of eSet instances
14: gcrma - gcrma1.2
15: matchprobes - Handling probe sequence information
16: affyPLM - affyPLM: Model Based QC Assessment of Affymetrix GeneChips [-]

Selection: 16
Error in openVignette() :
   Sorry, no PDF file could be found for this vignette.
Please reinstall the package with built vignettes.
 > sessionInfo()
R version 2.8.1 (2008-12-22)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
States.1252;LC_MONETARY=English_United 
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] splines   tools     stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
[1] affyPLM_1.18.1       preprocessCore_1.4.0 gcrma_2.14.1
[4] matchprobes_1.14.1   affy_1.20.2          Biobase_2.2.2

loaded via a namespace (and not attached):
[1] affyio_1.10.1
 >

Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at illinois.edu