[Bioc-devel] affy's cleancdfname

Kasper Daniel Hansen khansen at stat.Berkeley.EDU
Tue Sep 27 19:44:22 CEST 2005

Seth et. al

When you are looking into all of this, I would like to have an easy  
way to set the cdf slot so the download process do not start, eg.  
setting it to "unknown". This could be quite relevant for people  
(like me) who needs to be able to read the cel files but do not have  
(and possibly will not get) a cdf environment. And right now (ok as  
far as I recall), even the show method on an AffyBatch object starts  
the entire existence checking/download etc. routine.


On Sep 27, 2005, at 9:45 AM, Seth Falcon wrote:

> Hi Jim,
> On 27 Sep 2005, jmacdon at med.umich.edu wrote:
>> Say I don't have the wherewithal to create a cdf package, so I am
>> just going to make the env and have it sitting in my .GlobalEnv.
>> hgfocuscdf <- make.cdf.env(dir()[11])
>> Reading CDF file.
>> Creating CDF environment
>> Wait for about 88 dots..................[snip]
>> Now I read in some HG-Focus celfiles.
>>> dat <- read.affybatch(filenames=list.celfiles()[1:3])
>> Warning message:
>> Incompatible phenoData object. Created a new one.
>> in: read.affybatch(filenames = list.celfiles()[1:3])
>> And I want to do something with the resulting AffyBatch.
>>> dat
>> Error in library("hgfocuscdf", lib.loc = "C:/rw2020dev/library") :
>> there is no package called 'hgfocuscdf'
>> AffyBatch object
>> size of arrays=448x448 features (4709 kb)
>> cdf=HG-Focus (??? affyids)
>> number of samples=3
>> Error in library("hgfocuscdf", lib.loc = "C:/rw2020dev/library") :
>> there is no package called 'hgfocuscdf'
>> In addition: Warning message:
>> missing cdf environment ! in: show(list())
>> Since cdfFromEnvironment() is called without user intervention,
>> there is no way for the end user to feed it the correct cdfname,
>> since it doesn't call cleancdfname(), it looks for 'HG-Focus', which
>> doesn't follow the normal naming rules for a cdfenv. Therefore you
>> either have to know a priori what getFromEnvironment() is going to
>> look for, or you have to figure it out after the fact and rename
>> your env.
>> Since none of the getFromXXX functions are actually called by the
>> end user, I think they all have to use cleancdfname() to keep things
>> consistent. This is the only way an end user has a fighting chance
>> of getting the name of their env right.
> This is an easy change.  I would like to be able to call
> cdfFromLibPath from cdfFromBioC, this means repeated calls to
> cleancdfname need to do nothing.  Do you see any problem with not
> appending "cdf" if the string already ends in "cdf"?
> To summarize, the proposed change:
> 1. Add call to cleancdfname() to all cdfFrom* funcs
> 2. Make cleancdfname idempotent so that repeated calls return the same
>    thing.  If it is already clean, don't make it dirty ;-)
>> There is another problem here that may be irrelevant given that Seth
>> wants to deprecate reposTools. If I use remove.packages() to remove
>> a BioC package (say, the hgfocuscdf package I removed for the above
>> exercise), it doesn't remove anything from liblisting.Rda, so as far
>> as reposTools is concerned, the package is still
>> installed. getCdfInfo() went through all the getFromXXX functions
>> and when it hit getFromBioC(), is.installed() said the package was
>> installed, but since it isn't actually installed anymore it errored
>> out.
> This will be fixed because we will rely on R built-in tools to detect
> whether or not a package is installed.
> Best,
> + seth
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