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

Sokratis Kariotis s.kariotis at sheffield.ac.uk
Fri Nov 3 14:00:27 CET 2017


I didn't see that, you are right they now install properly. Thank you all
for your help with these packages.

Cheers,
Sokratis

On 3 November 2017 at 11:52, Shepherd, Lori <Lori.Shepherd at roswellpark.org>
wrote:

> 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:* Hervé Pagès
> *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.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
> <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
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>         --
>         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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>     --
>     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
> 385a Glossop Rd, Sheffield, S10 2HQ
> <https://maps.google.com/?q=385a+Glossop+Rd,+Sheffield,+S10+2HQ&entry=gmail&source=g>
>
>
>
> --
> 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
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>
>
>
>
> --
> 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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-- 
Sokratis Kariotis
Scientific Programmer
Hidelab
Sheffield Institute for Translational Neuroscience
385a Glossop Rd, Sheffield, S10 2HQ

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