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[Bioc-devel] bioconductor_docker:devel missing MAE and GenomeInfoDb

6 messages · Laurent Gatto, Nitesh Turaga, Robert Castelo +1 more

Original
Laurent Gatto
# 
I am setting up a repo/docker for the coming Bioc2021 workshops, and apparently packages ?GenomeInfoDb?, ?MultiAssayExperiment? are not available for this version of R [1] (they indeed fail on devel).  Surprisingly, they seemed to be available earlier in the day - my action failed for a different reason, much later in the process.

Laurent

[1] https://github.com/lgatto/QFeaturesScpWorkshop2021/runs/2070746544?check_suite_focus=true#step:8:157
Nitesh Turaga
# 
Hi Laurent,

Since you are using the devel version of `bioconductor_docker` it's possible that the packages failed to build on the build system. 

For example, http://bioconductor.org/checkResults/devel/bioc-LATEST/MultiAssayExperiment/ , MultiAsssayExperiment failed to build on devel. A better solution for this, is to use the release 3.12 version of 'bioconductor_docker:RELEASE_3_12'. 

This may be transient, and could be fixed by the maintainers.

Best,

Nitesh

?On 3/9/21, 4:51 PM, "Bioc-devel on behalf of Laurent Gatto" <bioc-devel-bounces at r-project.org on behalf of laurent.gatto at uclouvain.be> wrote:

    I am setting up a repo/docker for the coming Bioc2021 workshops, and apparently packages ?GenomeInfoDb?, ?MultiAssayExperiment? are not available for this version of R [1] (they indeed fail on devel).  Surprisingly, they seemed to be available earlier in the day - my action failed for a different reason, much later in the process.

    Laurent

    [1] https://github.com/lgatto/QFeaturesScpWorkshop2021/runs/2070746544?check_suite_focus=true#step:8:157


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Robert Castelo
# 
hi,

a possible workaround is to install directly from the repo using the 
syntax "Bioconductor/pkgname" in the call to 'BiocManager::install()'. 
this just worked in my current devel container:

BiocManager::install("Bioconductor/GenomeInfoDb")

while attempting to 'BiocManager::install("GenomeInfDb")' didn't. i 
think the following discussion we had on June last year in this list is 
relevant to his issue:

https://stat.ethz.ch/pipermail/bioc-devel/2020-June/016857.html

cheers,

robert.
On 3/10/21 3:11 PM, Nitesh Turaga wrote:

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Laurent Gatto
    

    

      
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Thank you Robert and Nitesh for your input.

The workshops at EuroBioc were using devel (as far as I can remember at least) which is why I am using bioconductor_docker:devel. For now, I will (try to) install these two packages from github.

Best wishes,

Laurent

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Marcel Ramos
    

    

      
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Hi Laurent,

This is a side-effect of the improvements to / migration of the build 
system (thanks Herv?!).
Any packages that were not building would be marked with that error because
the last-propagated version of the package would not be available.
I have updated MultiAssayExperiment to build and it should propagate today
(later this evening your time). Sorry for the inconvenience.

Best regards,

Marcel

        
On 3/10/21 10:10 AM, Laurent Gatto wrote:

            

      
      
      
    

        

      
      
    

        
---
Marcel Ramos
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics & Bioinformatics
Elm St. & Carlton St.
Buffalo, New York 14263



This email message may contain legally privileged and/or...{{dropped:4}}

  
  


  


      

    

    

      
      

        


  

        

      Laurent Gatto
    

    

      
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No worries at all, and thank you for following up.

Laurent