[BioC] BioC2006, issues with makePlatformDesign package

[Robert Citek]

Hello Rafa, Benilton, and others,

I didn't get a chance to sit on the "Advancing in Feature-Level  
Analyses for Microarray Data" workshop[1] while at BioC2006, so I  
thought I'd try to work from the slides.  However, I'm running into  
some issues, which is not surprising given that I'm new to R and  
BioConductor.  As an example of one issue, I'd like to try out the  
makePlatformDesign package as explained on slide 56 of the tutorial- 
slides using our own data.  Here is the transcript of the results,  
where R's working directory is C:/tmp:

<quote>
R : Copyright 2006, The R Foundation for Statistical Computing
Version 2.3.1 (2006-06-01)
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

   Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

 > library(makePlatformDesign)
Loading required package: affyio
Loading required package: oligo
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

     Vignettes contain introductory material. To view, type
     'openVignette()' or start with 'help(Biobase)'. For details
     on reading vignettes, see the openVignette help page.

Warning messages:
1: package 'makePlatformDesign' was built under R version 2.4.0
2: package 'affyio' was built under R version 2.4.0
3: package 'oligo' was built under R version 2.4.0
 >
 > makePDpackage("d:/2006-01-30_Orion_ogha2.ndf",
+               "d:/77786_532.xys",
+               manufacturer="nimblegen", type="tiling")
nimblegen tiling
The package will be called pd20060130orionogha2
Reading d:/2006-01-30_Orion_ogha2.ndf
Assuming a simple design (NOT multiple-wells).
Creating package in C:/tmp/pd20060130orionogha2
[1] "pd20060130orionogha2"
 >
 > install.packages("C:/tmp/pd20060130orionogha2", repos=NULL)
Error in gzfile(file, "r") : unable to open connection
In addition: Warning messages:
1: error 1 in extracting from zip file
2: cannot open compressed file 'pd20060130orionogha2/DESCRIPTION'
 >
<quote>

We've googled for the error message "Error in gzfile ..." without any  
fruitful hits.  Any ideas why we are getting this error?  Wrong  
version of R?  Wrong version of BioConductor?  Wrong configuration?   
Wrong sequence of commands?  Wrong data format?  Something else?

Trying to install the package from the command line yielded these  
results:

<quote>
C:\tmp>R CMD INSTALL pd20060130orionogha2
'R' is not recognized as an internal or external command,
operable program or batch file.

C:\tmp>path
PATH=D:\oracle\ora92\bin;C:\Program Files\Oracle\jre\1.3.1\bin;C: 
\Program Files\Oracle\jre\1.1.8\bin;C:\WINDOWS\system32;C:\WINDOWS;C: 
\WINDOWS\System32\Wbem;D:\j2sdk1.4.2_05\bin;
</quote>

I suspect this is because the path to R needs to specified in the  
PATH variable.  When we explicitly used the path to R, we then got  
errors about requiring perl.  Before we go down the path of missing  
dependencies (e.g. perl, gcc, and who knows what else) I thought I'd  
post here to make sure that we were not overlooking the obvious.

This is for R running on Windows 2003 server.

[1] http://www.bioconductor.org/workshops/2006/BioC2006/labs/bcarvalho/

Regards,
- Robert Citek <rwcitek at oriongenomics.com>