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

[Hervé Pagès]

Hi guys,

On 10/27/2017 05:50 AM, Obenchain, Valerie wrote:
> 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.
>

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.

> 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
>
> ________________________________
> From: Bioc-devel <bioc-devel-bounces at r-project.org><mailto:bioc-devel-bounces at r-project.org> on behalf of Sokratis Kariotis <s.kariotis at sheffield.ac.uk><mailto:s.kariotis at sheffield.ac.uk>
> Sent: Thursday, October 26, 2017 4:02:53 AM
> To: bioc-devel
> Subject: [Bioc-devel] Accepted packages can't find each other and fail build
>
> 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
> --
> Sokratis Kariotis
> Scientific Programmer
> Hidelab
> Sheffield Institute for Translational Neuroscience
> 385a Glossop Rd, Sheffield, S10 2HQ
>
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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