[Bioc-devel] arm64 on Mac build fails due to problem with MPO.db
Matteo Tiberti
t|bert| @end|ng |rom c@ncer@dk
Thu Oct 19 10:19:08 CEST 2023
Hi all,
Regarding this problem with macOS arm64 builds, I just wanted to report that @Jennifer Wokaty<mailto:Jennifer.Wokaty using sph.cuny.edu> ‘s fix worked and our packages are now all green (as well as others that were failing earlier for the same reason, from a cursory check).
Thank you for the help with this issue
Best,
Matteo Tiberti
Danish Cancer Institute
Strandboulevarden 49
DK-2100 Copenhagen
Telephone: +45 35 25 73 07
– a part of the Danish Cancer Society
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From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Matteo Tiberti via Bioc-devel <bioc-devel using r-project.org>
Date: Friday, 13 October 2023 at 09.03
To: Jennifer Wokaty <Jennifer.Wokaty using sph.cuny.edu>, Hervé Pagès <hpages.on.github using gmail.com>, Zuguang Gu <jokergoo using gmail.com>, bioc-devel using r-project.org <bioc-devel using r-project.org>, Robert Castelo <robert.castelo using upf.edu>
Subject: Re: [Bioc-devel] arm64 on Mac build fails due to problem with MPO.db
@Jennifer Wokaty<mailto:Jennifer.Wokaty using sph.cuny.edu> great, thank you, happy the issue is on its way to be resolved. Looking forward to see them implemented on Thursday
@Robert Castelo<mailto:robert.castelo using upf.edu> @Zuguang Gu<mailto:jokergoo using gmail.com> thank you for your insights! These will come useful when trying to reduce the number of dependencies for our packages
Best,
Matteo Tiberti
Danish Cancer Institute
Strandboulevarden 49
DK-2100 Copenhagen
Telephone: +45 35 25 73 07
– a part of the Danish Cancer Society
[cid:image001.png using 01D9FDB3.68B00640]<https://www.cancer.dk/?utm_source=email&utm_medium=medarbejderemail&utm_campaign=medarbejderemail&utm_content=cancerdk>
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From: Jennifer Wokaty <Jennifer.Wokaty using sph.cuny.edu>
Date: Friday, 13 October 2023 at 02.00
To: Hervé Pagès <hpages.on.github using gmail.com>, Zuguang Gu <jokergoo using gmail.com>, bioc-devel using r-project.org <bioc-devel using r-project.org>, Matteo Tiberti <tiberti using cancer.dk>, Robert Castelo <robert.castelo using upf.edu>
Subject: Re: [Bioc-devel] arm64 on Mac build fails due to problem with MPO.db
There did seem to be an issue with the Annotation resource AH111553 that was preventing MPO.db from being installed. I've refreshed it and reinstalled MPO.db. I was able to manually install MoonlightR, Moonlight2R, as well as some of the other packages you mentioned after these changes. We should see this reflected in the report for next Thursday since the Mac ARM64 devel builds have already started. Thanks everyone for your help and this discussion.
Jennifer Wokaty (they/them)
Waldron Lab at CUNY SPH
Bioconductor Core Team
________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Hervé Pagès <hpages.on.github using gmail.com>
Sent: Thursday, October 12, 2023 3:33 PM
To: Zuguang Gu <jokergoo using gmail.com>; bioc-devel using r-project.org <bioc-devel using r-project.org>; Matteo Tiberti <tiberti using cancer.dk>; Robert Castelo <robert.castelo using upf.edu>
Subject: Re: [Bioc-devel] arm64 on Mac build fails due to problem with MPO.db
* This email originates from a sender outside of CUNY. Verify the sender before replying or clicking on links and attachments. *
On 10/12/23 12:25, Zuguang Gu wrote:
> The devel version of DOSE depends on MPO.db.
>
> I also found MoonlightR depends on DOSE only on its two functions:
> gseDO() and simplot().
>
> An analysis by the pkgndep package shows if you can reduce the
> dependency on both clusterProfiler and DOSE, a total of 46 upstream
> dependencies will be reduced (30 by clusterProfiler uniquely and 16 by
> both). You can use `pkgndep::dependency_database()` to query the
> dependencies, but the database was only updated to some version last year.
>
> MPO.db initializes an instance of AnnotationHub in its .onLoad(). I
> don't know whether that is the source of the error.
>
> .onLoad <- function(libname, pkgname) {
> ns <- asNamespace(pkgname)
> makeCachedActiveBinding("MPO.db", make_MPO.db, env=ns)
> namespaceExport(ns, "MPO.db")
> ah <- suppressMessages(AnnotationHub())
> dbfile <- ah[["AH111553", verbose=FALSE]]
> dbconn <- AnnotationDbi::dbFileConnect(dbfile)
> assign("dbconn", dbconn, envir=datacache)
> ann_objs <- createAnnObjs.MPO_DB("MPO", "MPO", dbconn, datacache)
> mergeToNamespaceAndExport(ann_objs, "MPO.db")
>
> }
I don't know either but we strongly recommend against .onLoad hooks
trying to access the internet. Once a package is installed, one should
be able to load it offline.
H.
>
>
> On Thu, 12 Oct 2023 at 20:37, Robert Castelo <robert.castelo using upf.edu>
> wrote:
>
> Hi,
>
> one of the kind of tools that Hervé is referring to is the package
> BiocPkgTools:
>
> https://urldefense.com/v3/__https://bioconductor.org/packages/BiocPkgTools__;!!PxiZbSOawA!I-l3hH8fBjv8Ra_NJu0m8IOjrAwWhFztC1P9ujN5jgHmAGRNmoDlVzYH3d7wQH2uhleJZVIjMu8dpbNpRcHCwF8G3MmVH8SmzHYbNw$<https://urldefense.com/v3/__https://bioconductor.org/packages/BiocPkgTools__;!!PxiZbSOawA!I-l3hH8fBjv8Ra_NJu0m8IOjrAwWhFztC1P9ujN5jgHmAGRNmoDlVzYH3d7wQH2uhleJZVIjMu8dpbNpRcHCwF8G3MmVH8SmzHYbNw$><https://urldefense.com/v3/__https://bioconductor.org/packages/BiocPkgTools__;!!PxiZbSOawA!I-l3hH8fBjv8Ra_NJu0m8IOjrAwWhFztC1P9ujN5jgHmAGRNmoDlVzYH3d7wQH2uhleJZVIjMu8dpbNpRcHCwF8G3MmVH8SmzHYbNw$>
>
> section "7 Dependency burden" in the vignette illustrates how to
> identify dependencies that you might want to get rid of.
>
> cheers,
>
> robert.
>
> On 12/10/23 18:24, Hervé Pagès wrote:
> > On 10/12/23 00:45, Matteo Tiberti wrote:
> >
> >> Hi Hervé,
> >>
> >> Thank you for your comment and for looking into our package – it
> >> would definitely make sense to try and not depend on
> clusterProfiler
> >> if it is that heavy of a dependency (and we don’t use it so
> much as
> >> you mention), more in general working in the direction of removing
> >> little-used or heavy dependencies would speed things up all around
> >> and reduce the chance of having failures because of
> changes/failures
> >> of dep. packages. We will try and reassess the package imports in
> >> this direction.
> >>
> >> It would be great if we could obtain e.g. a dependency graph –
> or at
> >> least know how many (unique) dependencies each of our deps has,
> e.g.
> >> I saw that miniCRAN can do something similar
> >>
> > I think there are a number of tools already that you can use to do
> > this kind of analysis e.g. basic low-level tools like
> > tools::package_dependencies() but also more high-level ones with
> > advanced functionalities like pkgndep (CRAN package) etc...
> >
> > H.
> >>
> >> Best,
> >>
> >>
> >> Matteo Tiberti
> >>
> >> *Danish Cancer Institute*
> >> Strandboulevarden 49
> >> DK-2100 Copenhagen
> >> *Telephone*: +45 35 25 73 07
> >> /– a part of the Danish Cancer Society/
> >>
> >>
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> >>
> >>
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> >>
> >> *From: *Hervé Pagès <hpages.on.github using gmail.com>
> >> *Date: *Wednesday, 11 October 2023 at 19.30
> >> *To: *Matteo Tiberti <tiberti using cancer.dk>, bioc-devel using r-project.org
> >> <bioc-devel using r-project.org>
> >> *Subject: *Re: [Bioc-devel] arm64 on Mac build fails due to
> problem
> >> with MPO.db
> >>
> >> Hi Matteo,
> >>
> >> Thanks for letting us know.
> >>
> >> FWIW the dependency on MPO.db is via clusterProfiler and DOSE.
> >>
> >> Not directly addressing the issue but note that clusterProfiler
> is a
> >> heavy-weight dependency that triggers the loading of 120+
> packages.
> >> All together, loading Moonlight2R with library(Moonlight2R)
> triggers
> >> the loading of 170+ packages which takes about 20 seconds.
> >>
> >> Have you considered trying to make Moonlight2R dependencies
> lighter?
> >> For example it seems that the only thing that the package uses
> from
> >> clusterProfiler is clusterProfiler::bitr(), which is a simple
> >> convenience wrapper around AnnotationDbi::select() used inside
> your
> >> GSEA() function. I wonder if some of these deps could perhaps be
> >> moved from Imports to Suggests, with the hope to make
> >> library(Moonlight2R) lighter and faster.
> >>
> >> Best,
> >>
> >> H.
> >>
> >> On 10/11/23 02:18, Matteo Tiberti via Bioc-devel wrote:
> >>
> >> Dear all,
> >>
> >> We are seeing a couple of build fails of our MoonlightR and
> >> Moonlight2R packages in the devel (3.18) MacOS arm64
> builder that
> >> seem to be related to the MPO.db package. This is the error
> >> message we get:
> >>
> >> * installing to library
> >>
> ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
> >>
> >> * installing *source* package ‘Moonlight2R’ ...
> >> ** using staged installation
> >> ** R
> >> ** data
> >> ** inst
> >> ** byte-compile and prepare package for lazy loading
> >> Warning: Couldn't set cache size: file is not a database
> >> Use `cache_size` = NULL to turn off this warning.
> >> Warning: Couldn't set synchronous mode: file is not a database
> >> Use `synchronous` = NULL to turn off this warning.
> >> Error: .onLoad failed in loadNamespace() for 'MPO.db', details:
> >> call: NULL
> >> error: file is not a database
> >> Execution halted
> >> ERROR: lazy loading failed for package ‘Moonlight2R’
> >> * removing
> >>
> ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Moonlight2R’
> >>
> >> We don’t have MPO.db as an explicit requirement for our
> packages,
> >> and it checks all green on its own build report. We poked
> around
> >> 3.18 MacOS arm64 build reports and saw several other
> packages with
> >> similar failures (e.g.
> >>
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> >> …) so we were wondering if there’s a more general problem
> with the
> >> builder/set up or if there is a general solution to this.
> >> Suggestions are welcome
> >>
> >> Thank you,
> >>
> >> Matteo Tiberti
> >>
> >> Danish Cancer Institute
> >> Strandboulevarden 49
> >> DK-2100 Copenhagen
> >> Telephone: +45 35 25 73 07
> >> – a part of the Danish Cancer Society
> >>
> >> [cid:image001.png using 01D9FB90.6FE2D7A0
> >>
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> >>
> >> --
> >> Hervé Pagès
> >> Bioconductor Core Team
> >> hpages.on.github using gmail.com
> >
>
> --
> Robert Castelo, PhD
> Associate Professor
> Dept. of Medicine and Life Sciences
> Universitat Pompeu Fabra (UPF)
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