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[Bioc-devel] Accepted packages can't find each other and fail build

8 messages · Sokratis Kariotis, Obenchain, Valerie, Hervé Pagès +1 more

Original
Sokratis Kariotis
# 
Hey all,

I created 2 packages that got accepted (pcxn and pcxnData) where pcxn
depends on the data coming from pcxnData. However, in the vignettes of
pcxnData I am using library(pcxn) to demonstrate what can you do with the
data. As a result both packages fail building in BioC 3.6 as they can't
find each other. In a previous pair of packages I am maintaining (pathprint
and pathprintGEOData) I could use the first library in the data package
vignette and building was fine. Is it necessary to remove library(pcxn)
from pcxnData to get them build? Thanks in advance!

Cheers
Shepherd, Lori
# 
We have already taken care of this on our end and you shouldn't need to do anything else.  As always changes reflected may take a few days to reflect in the build reports.


The solution is to add a .BBSoptions file with ForceInstall: TRUE to the software package.  Since there is a circular dependency this will force install the software package even though there will be ERRORs because of the missing data package.  On the next build of the data packages, the data package will then successfully build finding the software package. Then following, the software package will also build finding the data package.


Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263
1 day later
Obenchain, Valerie
# 
Hi Sokratis,

I added the .BBSoptions file to pcxn when it should have been added to pcxnData. The .BBSoptions file should be put in the package that 'Suggests' (not 'Depends') on the other. In this case it's pcxnData that needs the .BBSoptions. Sorry for the mix up, this has been fixed.

The data package should install with today's builds and be clean on the Saturday report. The software package should then install with the Saturday builds and be clean on the Sunday report.

Valerie
On 10/26/2017 04:26 AM, Shepherd, Lori wrote:
We have already taken care of this on our end and you shouldn't need to do anything else.  As always changes reflected may take a few days to reflect in the build reports.


The solution is to add a .BBSoptions file with ForceInstall: TRUE to the software package.  Since there is a circular dependency this will force install the software package even though there will be ERRORs because of the missing data package.  On the next build of the data packages, the data package will then successfully build finding the software package. Then following, the software package will also build finding the data package.


Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263
Hervé Pagès
# 
Hi guys,
On 10/27/2017 05:50 AM, Obenchain, Valerie wrote:
This is what should happen:

   - pcxnData should install with today's data-exp builds (they
     started this morning) but vignette will still fail (pcxn still
     missing)

   - pcxn won't install (will be back to NotNeeded) but should pass
     build/check and propagate on Saturday afternoon

   - on Sunday morning, the data exp builds will find pcxn **on line**
     (because now it propagated) so will be able to install it so
     vignette will finally build and the package will propagate

Thanks for taking care of this,

H.

  
    

      
      
    

  


  


      

    

    
3 days later

    

      
      

        


  

        

      Sokratis Kariotis
    

    

      
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Hi all,

There was an error in the pcxn package (and pcxnData as a resut of not
finding pcxn since it didnt build) which I fixed yesterday morning, but it
doesnt seem to accept my changes as the version in the build report is not
the last one I created but the erroneous one (2 days ago). I checked the
upstream of my package and it has my latest changes.

Regards,
Sokratis

        
On 27 October 2017 at 16:57, Herv? Pag?s <hpages at fredhutch.org> wrote:

        

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Shepherd, Lori
    

    

      
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The latest version bump change you made to 0.99.27 was yesterday Oct 30 right before we said to stop committing so we could make the release branch.  That change did make it into both the RELEASE_3_6 and the master branch and should appear in  the next build report for both versions.


Note:  It can take 12-24 hours to see version bumps and changes on the build report. The daily builders runs once per day to build all the packages; while a version bump is absolutely required, it is not built instantaneously on a version bump.


Please be sure to pull from upstream before making further changes as we have bumped the versions in both the release and devel versions of packages for the release.



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Sokratis Kariotis
    

    

      
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Does the same hold for the pcxnData package? I can't see the RELEASE_3_6 as
in pcxn.

-Sokratis

On 31 October 2017 at 11:38, Shepherd, Lori <Lori.Shepherd at roswellpark.org>
wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Shepherd, Lori
    

    

      
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It should be the same and you should be able to see the RELEASE_3_6 branch


git fetch --all

git branch -a


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263