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[Bioc-devel] Download and cache sesameData/ExperimentHub data during Bioconductor checks

8 messages · Gabriel Odom, Shepherd, Lori, Wanding Zhou

Original
Gabriel Odom
# 
Hi folks,
We are submitting the package coMethDMR to Bioconductor (https://github.com/Bioconductor/Contributions/issues/2064).
This package requires HM450 and EPIC data (probe IDs) available for package functionality. We currently have a check on package load that these two data components are in cache.
Our package passes checks on local and Travis (https://travis-ci.com/github/TransBioInfoLab/coMethDMR/builds/228394255), but instantly fails on Bioconductor (http://bioconductor.org/spb_reports/coMethDMR_buildreport_20210610114003.html).

What solutions have people used in the past to require access to such large data sets without including them in the package?
Warm regards and many thanks,
Gabriel
3 days later
Shepherd, Lori
# 
Let me check the location of the cache on the builders.

Did you create a specific cache for these files or were you using the default?




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263
Wanding Zhou
# 
Looks like sesameData build is experiencing the same problem.

http://bioconductor.org/checkResults/devel/data-experiment-LATEST/sesameData/nebbiolo2-buildsrc.html

error in evaluating the argument 'x' in selecting a method for
function 'query': Corrupt Cache: index file
  See AnnotationHub's TroubleshootingTheCache vignette section on corrupt cache
  cache: /home/biocbuild/.cache/R/ExperimentHub
  filename: experimenthub.index.rds

I will do some more test from my side as well. Thanks,


Wanding

On Mon, Jun 14, 2021 at 6:56 AM Kern, Lori <Lori.Shepherd at roswellpark.org>
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      Shepherd, Lori
    

    

      
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This is an issue on the Bioconductor builds. I will fix momentarily and should be reflected in tomorrow's build report.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Shepherd, Lori
    

    

      
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I'm looking at the caching code in sesameData.  I think there could be some code cleanup and some things things that should be changed.  I'll try to put together some comments and time pending a pull request.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Wanding Zhou
    

    

      
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Thank you for the fix and suggestions, Lori!

Wanding

On Mon, Jun 14, 2021 at 9:34 AM Kern, Lori <Lori.Shepherd at roswellpark.org>
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1 day later

    

      
      

        


  

        

      Gabriel Odom
    

    

      
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Thank you Lori and Wanding :)
We are using the default settings for the cache location. Our call to the sesameData:: package is simply sesameDataCache("HM450", showProgress = FALSE)
What should we do in the mean time?

        
On Jun 14, 2021, at 9:49 AM, Wanding Zhou <zhouwanding at gmail.com<mailto:zhouwanding at gmail.com>> wrote:

        
Note: This message originated from outside the FIU Faculty/Staff email system.

Thank you for the fix and suggestions, Lori!

Wanding

        
On Mon, Jun 14, 2021 at 9:34 AM Kern, Lori <Lori.Shepherd at roswellpark.org<mailto:Lori.Shepherd at roswellpark.org>> wrote:

        
I'm looking at the caching code in sesameData.  I think there could be some code cleanup and some things things that should be changed.  I'll try to put together some comments and time pending a pull request.

Cheers,

Lori Shepherd
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Wanding Zhou
    

    

      
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Hi Gabriel,
Yeah, that should be correct. The build seems fixed on Bioconductor I just
checked.

Wanding

        
On Tue, Jun 15, 2021 at 12:40 PM Gabriel Odom <godom at fiu.edu> wrote: