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.sheph...@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.kario...@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 <hpa...@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.sheph...@roswellpark.org <mailto:lori.sheph...@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.kario...@sheffield.ac.uk
> <mailto:s.kario...@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.sheph...@roswellpark.org
> <mailto:lori.sheph...@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.kario...@sheffield.ac.uk
> <mailto:s.kario...@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 <hpa...@fredhutch.org
> <mailto:hpa...@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-boun...@r-project.org
>
> <mailto:bioc-devel-boun...@r-project.org>><mailto:bioc-devel
> -boun...@r-project.org
>
> <mailto:bioc-devel-boun...@r-project.org>> on behalf of
> Sokratis Kariotis <s.kario...@sheffield.ac.uk
>
> <mailto:s.kario...@sheffield.ac.uk>><mailto:s.kario...@sheffield.ac.uk
> <mailto:s.kario...@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>
>
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__maps.g
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>
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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>
>
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__maps.g
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> >,
>
> M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpa...@fredhutch.org <mailto:hpa...@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://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
> <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
> <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: hpa...@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
> <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
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>
--
Sokratis Kariotis
Scientific Programmer
Hidelab
Sheffield Institute for Translational Neuroscience
385a Glossop Rd, Sheffield, S10 2HQ
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