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[Bioc-devel] GenomicFeatures

6 messages · Martin Morgan, Kasper Daniel Hansen, Obenchain, Valerie +1 more

Original
Kasper Daniel Hansen
# 
Seem broken in release.

And btw., because it is broken, when I run
  BiocManager::valid()
it doesn't report GenomicFeatures as out of date, despite the fact that I
have version 1.33.2 installed, and there are newer versions in the 1.33.x
hierarchy and the "right" (but broken) version in Bioc 3.8 is 1.34.0.

Best,
Kasper
Obenchain, Valerie
# 
Thanks Kasper. I'm looking into the error in GenomicFeatures.

Martin or Marcel may have more to add but I think BiocManager::install() 
can only report what versions are in the repo. GenomicFeatures 1.34.0 
has not built so doesn't yet exist in the repo.

We archive all versions in release but not in devel. The older 1.33.x 
versions don't exist in "released" Bioconductor 3.8.

Valerie
On 11/2/18 6:05 AM, Kasper Daniel Hansen wrote:
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Martin Morgan
# 
For which BiocManager::version() is this? BiocManager::valid() checks within versions, and if there's no GenomicFeatures to reference, then there is no way to flag it as out-of-date, sort of like a package you'd installed that was in neither CRAN nor Bioconductor.

Though of course we'd like GenomicFeatures to be available in 3.8

Martin

?On 11/2/18, 1:05 PM, "Bioc-devel on behalf of Kasper Daniel Hansen" <bioc-devel-bounces at r-project.org on behalf of kasperdanielhansen at gmail.com> wrote:

    Seem broken in release.
    
    And btw., because it is broken, when I run
      BiocManager::valid()
    it doesn't report GenomicFeatures as out of date, despite the fact that I
    have version 1.33.2 installed, and there are newer versions in the 1.33.x
    hierarchy and the "right" (but broken) version in Bioc 3.8 is 1.34.0.
    
    Best,
    Kasper
    
    
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    Bioc-devel at r-project.org mailing list
    https://stat.ethz.ch/mailman/listinfo/bioc-devel
Kasper Daniel Hansen
# 
Lates BiocManager

It is not flagging GenomicFeatures as out of date, presumably because it
doesn't exists in the repos. So in some sense it is all internally
consistent.  I was just surprised to not see it flagged as being out of
date.

I guess I am also confused about what happens at release.  Is the repos
wiped?  Because at some time pre-release GenomicFeatures existed in the
Bioc 3.8 repos, and (usually) that would mean it would fall back to this
previous version (seemingly 1.33.6 based on
  https://bioconductor.org/packages/release/bioc/html/GenomicFeatures.html
yet this package does not seem to exists (despite the URL)).

Ok, this is all a rather unfortunate and special case which I am not sure
how should be handled. I was just surprised at what I am seeing, but I am
also quite confident that when the package is fixed, it'll all work fine.

Best,
Kasper


On Fri, Nov 2, 2018 at 10:05 AM Martin Morgan <mtmorgan.bioc at gmail.com>
wrote:

  
  


  


      

    

    

      
      

        


  

        

      Obenchain, Valerie
    

    

      
      #
    

  


  

      
Historically we used to flush the repos before a release. At some point 
we stopped and I could not remember why. The situation you describe 
below is probably it.

When preparing for 3.8, we ran into the case where we had quite a few 
stale packages in the repos. Their 'staleness' was due to being renamed, 
deprecated, etc. These left around old landing pages and appeared in 
biocViews inappropriately. At the time it seemed like a good idea to 
flush the repo (release only) for a clean start. This would result in no 
products (landing page, tarball, ...) for packages that did not build in 
the new release. (We also had a hiccup with generating landing pages 
with stale links that we're working on. Should be fixed soon.)

While no landing page / nonavailability is motivation for maintainers to 
fix broken packages it's also an inconvenience for users and this is not 
good. For the next release we'll probably do some combination of the two 
- flush only packages not in the manifest.

Sorry for this inconvenience - my fault entirely.

Valerie

PS/BTW I've fixed GenomicFeatures and if it doesn't have an internet 
burp during the builds it should be available tomorrow.

        
On 11/2/18 8:36 AM, Kasper Daniel Hansen wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        
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      Hervé Pagès
    

    

      
      #
    

  


  

      
FYI I've temporarily disabled the makeTxDbFromBiomart() examples in 
GenomicFeatures that have been responsible for this 'R CMD check' 
TIMEOUT for 2-3 days in a row:

https://bioconductor.org/checkResults/3.8/bioc-LATEST/GenomicFeatures/malbec1-checksrc.html

Hopefully GenomicFeatures will pass CHECK on Linux tomorrow (it does on 
my laptop) and become available.

Thanks for your patience and sorry for the inconvenience.

H.

        
On 11/2/18 09:15, Obenchain, Valerie wrote: