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

Fri, Nov 3, 2017 4:52 AM

The data package and software package are in Bioc 3.6 not Bioc 3.5.  You will need to update BiocInstaller in order to have access to the packages.


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: Friday, November 3, 2017 7:04:08 AM
To: Herv? Pag?s
Cc: Shepherd, Lori; bioc-devel
Subject: Re: [Bioc-devel] Accepted packages can't find each other and fail build

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.org
Using 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, Herv? Pag?s <hpages at fredhutch.org<mailto: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, Herv? Pag?s 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> <mailto: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>
    <mailto: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:* Herv? Pag?s; 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>
    <mailto: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>
        <mailto:s.kariotis at sheffield.ac.uk<mailto:s.kariotis at sheffield.ac.uk>>>
        *Sent:* Tuesday, October 31, 2017 5:21:21 AM
        *To:* Herv? Pag?s
        *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, Herv? Pag?s <hpages at fredhutch.org<mailto:hpages at fredhutch.org>
        <mailto: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>>><mailto: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>>><mailto: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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            --
            Herv? Pag?s

            Program in Computational Biology
            Division of Public Health Sciences
            Fred Hutchinson Cancer Research Center
            1100 Fairview Ave. N

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

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


--
Herv? Pag?s

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<mailto:hpages at fredhutch.org>
Phone:  (206) 667-5791<tel:%28206%29%20667-5791>
Fax:    (206) 667-1319<tel:%28206%29%20667-1319>



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


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

Thread (6 messages)