Hi all, Regarding this problem with macOS arm64 builds, I just wanted to report that @Jennifer Wokaty<mailto:jennifer.wok...@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 [cid:image001.png@01DA0275.664D1D90]<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: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Matteo Tiberti via Bioc-devel <bioc-devel@r-project.org> Date: Friday, 13 October 2023 at 09.03 To: Jennifer Wokaty <jennifer.wok...@sph.cuny.edu>, Hervé Pagès <hpages.on.git...@gmail.com>, Zuguang Gu <joker...@gmail.com>, bioc-devel@r-project.org <bioc-devel@r-project.org>, Robert Castelo <robert.cast...@upf.edu> Subject: Re: [Bioc-devel] arm64 on Mac build fails due to problem with MPO.db @Jennifer Wokaty<mailto:jennifer.wok...@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.cast...@upf.edu> @Zuguang Gu<mailto:joker...@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@01D9FDB3.68B00640]<https://www.cancer.dk/?utm_source=email&utm_medium=medarbejderemail&utm_campaign=medarbejderemail&utm_content=cancerdk> http://www.cancer.dk/<https://www.cancer.dk/international/><http://www.cancer.dk/%3chttps:/www.cancer.dk/international/%3e> | Our privacy policy<https://www.cancer.dk/om-os/privatlivspolitik/> From: Jennifer Wokaty <jennifer.wok...@sph.cuny.edu> Date: Friday, 13 October 2023 at 02.00 To: Hervé Pagès <hpages.on.git...@gmail.com>, Zuguang Gu <joker...@gmail.com>, bioc-devel@r-project.org <bioc-devel@r-project.org>, Matteo Tiberti <tibe...@cancer.dk>, Robert Castelo <robert.cast...@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-boun...@r-project.org> on behalf of Hervé Pagès <hpages.on.git...@gmail.com> Sent: Thursday, October 12, 2023 3:33 PM To: Zuguang Gu <joker...@gmail.com>; bioc-devel@r-project.org <bioc-devel@r-project.org>; Matteo Tiberti <tibe...@cancer.dk>; Robert Castelo <robert.cast...@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.cast...@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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>>
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>
>>
>> *From: *Hervé Pagès <hpages.on.git...@gmail.com>
>> *Date: *Wednesday, 11 October 2023 at 19.30
>> *To: *Matteo Tiberti <tibe...@cancer.dk>, bioc-devel@r-project.org
>> <bioc-devel@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@01D9FB90.6FE2D7A0
>>
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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
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Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
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