[Bioc-devel] Accepted packages can't find each other and fail build
Hervé Pagès
hpages at fredhutch.org
Wed Nov 1 16:21:06 CET 2017
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
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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&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=uyIFjpL7wep4FyufJhLYsoBHxnLP8tcCArZLZdua1MY&s=4qo8KXmEZAYrs1orxWWzZrYuQLlLsLtq57YxqhFOyb0&e=>
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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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>
> --
> 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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