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

Wed Nov 1 09:36:59 CET 2017

Hey all,

After the release I can see the release page of the pcxn package but not
pcxnData package. In the build page it says it cannot find the pcxn package
and fails.

Regards,
Sokratis

On 31 October 2017 at 16:33, Shepherd, Lori <Lori.Shepherd at roswellpark.org>
wrote:

> 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
> ------------------------------
> *From:* Sokratis Kariotis <s.kariotis at sheffield.ac.uk>
> *Sent:* Tuesday, October 31, 2017 11:20:39 AM
> *To:* Shepherd, Lori
> *Cc:* Hervé Pagès; Obenchain, Valerie; bioc-devel
>
> *Subject:* Re: [Bioc-devel] Accepted packages can't find each other and
> fail build
>
> 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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>>>>
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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
> <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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