[Bioc-devel] Accepted packages can't find each other and fail build
Sokratis Kariotis
s.kariotis at sheffield.ac.uk
Fri Nov 3 12:04:08 CET 2017
Hey all,
I can see the landing pages for both packages now (pcxn and pcxnData) but
as I try to install them using:
source("https://bioconductor.org/biocLite.R")
biocLite("pcxnData")
I get the following:
BioC_mirror: https://bioconductor.orgUsing Bioconductor 3.5
(BiocInstaller 1.26.1), R 3.4.0 (2017-04-21).Installing package(s)
‘pcxnData’Warning message:package ‘pcxnData’ is not available (for R
version 3.4.0)
The same happens with the pcxn package but other unrelated packages
seem to install fine.
Regards,
Sokratis
On 1 November 2017 at 22:25, Hervé Pagès <hpages at fredhutch.org> wrote:
> FYI today's data-experiment builds completed and pcxnData is
> green:
>
>
> https://bioconductor.org/checkResults/3.6/data-experiment-LATEST/pcxnData/
>
> and propagated:
>
> https://bioconductor.org/packages/3.6/data/experiment/html/pcxnData.html
>
> Now the next step is that the software builds will be able
> to install pcxnData on tokay1 (Windows) and veracruz1 (Mac)
> from the public data-experiment repo so the results for
> pcxn should get cleared tomorrow:
>
> https://bioconductor.org/checkResults/3.6/bioc-LATEST/pcxn/
>
> It's a long (and admittedly confusing) ping-pong game between the
> software and data-expriment builds ;-)
>
> Thanks for your patience,
> H.
>
>
> On 11/01/2017 08:21 AM, Hervé Pagès wrote:
>
>> Hi Sokratis,
>>
>> Not sure why but it seems that for some reason the build machines
>> didn't manage to install pcxn so far. Until only now. I went on
>> build machine malbec1 to check whether it managed to install pcxn,
>> and it seems that it did:
>>
>> > "pcxn" %in% rownames(installed.packages())
>> [1] TRUE
>>
>> According to the log, it looks like this is the 1st time that it
>> gets installed on malbec1 (the data experiment builds just started
>> today and did the installation).
>>
>> So, if everything goes as expected, pcxnData should build successfully
>> today and pcxnData should propagate (granted of course that it also
>> passes CHECK). The build/check report for data-experiment packages
>> should update today around 5pm EST. It will take about 1 hour after
>> the report is updated for pcxnData to propagate to the public repo
>> and for its landing page to show up.
>>
>> Sorry for the inconvenience,
>>
>> H.
>>
>> On 11/01/2017 01:36 AM, Sokratis Kariotis wrote:
>>
>>> 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 <mailto: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
>>> <mailto: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
>>> <mailto: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
>>> <mailto: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
>>> <mailto: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>><mailto: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>><mailto: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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>>> <mailto:Bioc-devel at r-project.org> mailing list
>>>
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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://urldefense.proofpoint.com/v2/url?u=https-3A__maps.
>>> google.com_-3Fq-3D1100-2BFairview-2BAve.-2BN-26entry-
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>>> uibVSfgh5w2Y&e=>,
>>>
>>> M1-B514
>>> P.O. Box 19024
>>> Seattle, WA 98109-1024
>>>
>>> E-mail: hpages at fredhutch.org <mailto:hpages at fredhutch.org>
>>> Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
>>> Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
>>>
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>>>
>>>
>>> --
>>> Sokratis Kariotis
>>> Scientific Programmer
>>> Hidelab
>>> Sheffield Institute for Translational Neuroscience
>>> 385a Glossop Rd, Sheffield, S10 2HQ
>>>
>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__maps.
>>> google.com_-3Fq-3D385a-2BGlossop-2BRd-2C-2BSheffield-
>>> 2C-2BS10-2B2HQ-26entry-3Dgmail-26source-3Dg&d=DwMFaQ&
>>> c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXA
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>>>
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>>>
>>>
>>>
>>> --
>>> Sokratis Kariotis
>>> Scientific Programmer
>>> Hidelab
>>> Sheffield Institute for Translational Neuroscience
>>> 385a Glossop Rd, Sheffield, S10 2HQ
>>>
>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__maps.
>>> google.com_-3Fq-3D385a-2BGlossop-2BRd-2C-2BSheffield-
>>> 2C-2BS10-2B2HQ-26entry-3Dgmail-26source-3Dg&d=DwMFaQ&
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>>>
>>>
>>>
>>> --
>>> Sokratis Kariotis
>>> Scientific Programmer
>>> Hidelab
>>> Sheffield Institute for Translational Neuroscience
>>> 385a Glossop Rd, Sheffield, S10 2HQ
>>>
>>
>>
> --
> 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
>
--
Sokratis Kariotis
Scientific Programmer
Hidelab
Sheffield Institute for Translational Neuroscience
385a Glossop Rd, Sheffield, S10 2HQ
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