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[Bioc-devel] widgettools download problem w/ getBioC

8 messages · Cyrus Harmon, Seth Falcon

Original
Cyrus Harmon
# 
on both R 2.1.0 and the latest SVN sources, when using getBioC 
(develOK=TRUE) I get an error attempting to download widgetTools from  
BIOCRel1.6/src/contrib. I figure there are three possibilities:

1. The repository is in an unstable state as it gets prepped for the  
1.6 release
2. somehow widgetTools got messed up

or

3. another operator error on my part

Anyone else seeing this error?

Thanks,

Cyrus
Seth Falcon
# 
I just replied to Cyrus off-list by accident... here's what I said:

Cyrus Harmon <ch-bioc@bobobeach.com> writes:
That would be the issue: getBioC (the current version on the site)
doesn't know about the updated repository layouts.

Since you asked, please try:

source("http://www.bioconductor.org/getBioC-1.6.R")
And then
getBioC(...)  

The script now accepts a pkgs argument that should allow you to
specify a character vector of Bioconductor packages to install.

if you want the default package set, then getBioC() should do it.

The develOK arg is no longer supported.  The Bioconductor package
repository you will access depends on the version of R you use.  2.0
=> Bioc 1.5, 2.1 => Bioc 1.6, and 2.2 => Bioc 1.7 (not yet available).

Would love to hear how this works/doesn't work for you.  And if you
have time to report back, please indicate sessionInfo() output as
well.

Thanks!

+ seth
Cyrus Harmon
#
On May 18, 2005, at 4:23 PM, Seth Falcon wrote:

            

      
      
      
    

        
That's what I figured. The web pages that describe current releases  
and timelines could use an update. (I think there's one page that  
says that 1.5 is scheduled for release in Nov. 04 :-) ).

            

      
      
      
    

        
Will do. Before I go off and do this, a couple quick questions:

1. What R versions are supported? I'm happy to do this on both  
R-2.1.0 and R-SVN-current-as-of-today, but if either is known to not  
be supported, it will save me time tracking this down. I'm not too  
interested in pre-2.1.0 releases, although I imagine others might be.

2. What to do about previous bioconductor installations? Do we  
support getBioC for 1.6 on top of existing packages? Is there an  
expectation that users blow away there old versions? Either approach  
seems like it might be reasonable, but I'll skip testing the install- 
over-previous-bioconductor thing if that's unsupported/known-not-to- 
work.

            

      
      
      
    

        
Sounds good!

            

      
      
      
    

        
Again, sounds like an improvement.

            

      
      
      
    

        
My pleasure! Congrats on the impending (or completed? I'm still not  
sure...) release!

Cyrus

  
  


  


      

    

    

      
      

        


  

        

      Cyrus Harmon
    

    

      
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On May 18, 2005, at 4:39 PM, Cyrus Harmon wrote:

        

            

      
      
      
    

        
I'm getting 404 errors looking for the 2.2 binary release directory  
when I run getBioC. Perhaps getBioC should check the version and warn  
if we're using 2.2?

            

      
      
      
    

        
Is there an easy (or otherwise recommended) way to uninstall a BioC  
installation?

Thanks again,

Cyrus

  
  


  


      

    

    

      
      

        


  

        

      Cyrus Harmon
    

    

      
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Perhaps this a user-settable thing I'm missing, but now it seems that  
every time I call getBioC I download all of the packages. I'm using  
getBioC v0.1 from the getBioC-1.6.R URL. Isn't there some sort of  
package cache that can be used for this?

(Also, the fact that the build script is v0.1 and we're using  
getBioC-1.6 might confuse users a bit)

Thanks,

Cyrus

  
  


  


      

    

    

      
      

        


  

        

      Seth Falcon
    

    

      
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Cyrus Harmon <ch-bioc@bobobeach.com> writes:

            

      
      
      
    

        
2.1.x

and 2.0.x should continue to work as before.

We do not yet have things setup for 2.2.x, but will within a couple
days for sure.

            

      
      
      
    

        
Well, this would only come up if you have a separate package library.
It should work to install over existing packages, but I don't know for
sure.  I will try it!

I think the recommendation will be to install into a clean package
library.

            

      
      
      
    

        
Well, we're sneaking it in ;-)

Things are just about there.  We will be testing overnight and plan to
make an official announcement and website update tomorrow.

Thanks again for your help.

+ seth

  
  


  


      

    

    

      
      

        


  

        

      Seth Falcon
    

    

      
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Cyrus Harmon <ch-bioc@bobobeach.com> writes:

            

      
      
      
    

        
Well, it does detect 2.2 it is just that the 2.2 appropriate Bioc
package repositories don't yet exist.  But perhaps you are right that
until we do have those in place some other message would be friendlier
:-)

            

      
      
      
    

        
That depends on how you installed it initially.  I like to install
into a separate package library directory.  Then I can nuke that to
uninstall.

HTH,

+ seth

  
  


  


      

    

    

      
      

        


  

        

      Cyrus Harmon
    

    

      
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With getBioC-1.6 on R 2.1.0, I'm still getting makecdfenv 1.5.1 which  
breaks when compiling with GCC 4 on big-endian machines because of  
the bogus destination = ~destination line that needs to be commented  
out. Any chance the package maintainer can apply this change and bump  
makecdfenv before bioc 1.6 hits the streets?

Thanks,

Cyrus