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

Tue Oct 31 16:20:39 CET 2017

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:

> 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
> ------------------------------
> *From:* Sokratis Kariotis <s.kariotis at sheffield.ac.uk>
> *Sent:* Tuesday, October 31, 2017 5:21:21 AM
> *To:* Hervé Pagès
> *Cc:* Obenchain, Valerie; Shepherd, Lori; bioc-devel
> *Subject:* Re: [Bioc-devel] Accepted packages can't find each other and
> fail build
>
> 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
>>> <https://maps.google.com/?q=385a+Glossop+Rd,+Sheffield,+S10+2HQ&entry=gmail&source=g>
>>>
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>> --
>> Hervé Pagès
>>
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N
>> <https://maps.google.com/?q=1100+Fairview+Ave.+N&entry=gmail&source=g>,
>> M1-B514
>> P.O. Box 19024
>> Seattle, WA 98109-1024
>>
>> E-mail: hpages at fredhutch.org
>> Phone:  (206) 667-5791
>> Fax:    (206) 667-1319
>>
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
>
> --
> Sokratis Kariotis
> Scientific Programmer
> Hidelab
> Sheffield Institute for Translational Neuroscience
> 385a Glossop Rd, Sheffield, S10 2HQ
> <https://maps.google.com/?q=385a+Glossop+Rd,+Sheffield,+S10+2HQ&entry=gmail&source=g>
>
> This email message may contain legally privileged and/or confidential
> information. If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited. If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.
>

-- 
Sokratis Kariotis
Scientific Programmer
Hidelab
Sheffield Institute for Translational Neuroscience
385a Glossop Rd, Sheffield, S10 2HQ

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