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

Tue Oct 31 10:21:21 CET 2017

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, Hervé Pagès <hpages at fredhutch.org> wrote:

> 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
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>
>
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-- 
Sokratis Kariotis
Scientific Programmer
Hidelab
Sheffield Institute for Translational Neuroscience
385a Glossop Rd, Sheffield, S10 2HQ

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