[Bioc-devel] arm64 on Mac build fails due to problem with MPO.db

Zuguang Gu jokergoo @end|ng |rom gm@||@com
Thu Oct 12 21:25:45 CEST 2023 

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")

}


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://bioconductor.org/packages/BiocPkgTools
>
> 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/
> >>
> >> <
> https://www.cancer.dk/?utm_source=email&utm_medium=medarbejderemail&utm_campaign=medarbejderemail&utm_content=cancerdk>
>
> >>
> >>
> >> www.cancer.dk <https://www.cancer.dk/international/> | Our privacy
> >> policy <https://www.cancer.dk/om-os/privatlivspolitik/>
> >>
> >> *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.
> >> miRspongeR<
> https://bioconductor.org/checkResults/3.18/bioc-mac-arm64-LATEST/miRspongeR/
> >
> >> <
> https://bioconductor.org/checkResults/3.18/bioc-mac-arm64-LATEST/miRspongeR/
> >
> >> miRSM<
> https://bioconductor.org/checkResults/3.18/bioc-mac-arm64-LATEST/miRSM/>
> >> <
> https://bioconductor.org/checkResults/3.18/bioc-mac-arm64-LATEST/miRSM/>
> >> MicrobiomeProfiler<
> https://bioconductor.org/checkResults/3.18/bioc-mac-arm64-LATEST/MicrobiomeProfiler/
> >
> >> <
> https://bioconductor.org/checkResults/3.18/bioc-mac-arm64-LATEST/MicrobiomeProfiler/
> >
> >> EasyCellType<
> https://bioconductor.org/checkResults/3.18/bioc-mac-arm64-LATEST/EasyCellType/
> >
> >> <
> https://bioconductor.org/checkResults/3.18/bioc-mac-arm64-LATEST/EasyCellType/
> >
> >> MetaPhOR<
> https://bioconductor.org/checkResults/3.18/bioc-mac-arm64-LATEST/MetaPhOR/
> >
> >> <
> https://bioconductor.org/checkResults/3.18/bioc-mac-arm64-LATEST/MetaPhOR/
> >
> >> meshes<
> https://bioconductor.org/checkResults/3.18/bioc-mac-arm64-LATEST/meshes/>
> >> <
> https://bioconductor.org/checkResults/3.18/bioc-mac-arm64-LATEST/meshes/>
> >> CBNplot<
> https://bioconductor.org/checkResults/3.18/bioc-mac-arm64-LATEST/CBNplot/>
> >> <
> https://bioconductor.org/checkResults/3.18/bioc-mac-arm64-LATEST/CBNplot/>
> >>     …) 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
> >> <cid:image001.png using 01D9FB90.6FE2D7A0>]<
> https://www.cancer.dk/?utm_source=email&utm_medium=medarbejderemail&utm_campaign=medarbejderemail&utm_content=cancerdk
> >
> >> <
> https://www.cancer.dk/?utm_source=email&utm_medium=medarbejderemail&utm_campaign=medarbejderemail&utm_content=cancerdk
> >
> >>
> >>
> >>     www.cancer.dk
> >> <http://www.cancer.dk><https://www.cancer.dk/international/>
> >>     <https://www.cancer.dk/international/> | Our privacy
> >>     policy<https://www.cancer.dk/om-os/privatlivspolitik/>
> >>     <https://www.cancer.dk/om-os/privatlivspolitik/>
> >>
> >>     _______________________________________________
> >>     Bioc-devel using r-project.org mailing list
> >>     https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >> --
> >> 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)
> Barcelona Biomedical Research Park (PRBB)
> Dr Aiguader 88
> E-08003 Barcelona, Spain
> telf: +34.933.160.514
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

	[[alternative HTML version deleted]]

More information about the Bioc-devel mailing list