[Bioc-devel] arm64 on Mac build fails due to problem with MPO.db
Robert Castelo
robert@c@@te|o @end|ng |rom up|@edu
Thu Oct 12 20:37:26 CEST 2023
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
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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)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
E-08003 Barcelona, Spain
telf: +34.933.160.514
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