[Bioc-devel] Accepted packages can't find each other and fail build
Hervé Pagès
hpages at fredhutch.org
Wed Nov 1 23:25:50 CET 2017
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
>>
>> <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_wJYbW0WYiZvSXAJJKaaPhzWA&m=uyIFjpL7wep4FyufJhLYsoBHxnLP8tcCArZLZdua1MY&s=4qo8KXmEZAYrs1orxWWzZrYuQLlLsLtq57YxqhFOyb0&e=>
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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-3Dgmail-26source-3Dg&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=uyIFjpL7wep4FyufJhLYsoBHxnLP8tcCArZLZdua1MY&s=dchTsUqdQMAnLluyGzpxyuxQ1PEFqkvuibVSfgh5w2Y&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>
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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_wJYbW0WYiZvSXAJJKaaPhzWA&m=uyIFjpL7wep4FyufJhLYsoBHxnLP8tcCArZLZdua1MY&s=4qo8KXmEZAYrs1orxWWzZrYuQLlLsLtq57YxqhFOyb0&e=>
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>>
>> This email message may contain legally privileged and/or
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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_wJYbW0WYiZvSXAJJKaaPhzWA&m=uyIFjpL7wep4FyufJhLYsoBHxnLP8tcCArZLZdua1MY&s=4qo8KXmEZAYrs1orxWWzZrYuQLlLsLtq57YxqhFOyb0&e=>
>>
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>> This email message may contain legally privileged and/or
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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
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