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

Thu Oct 12 18:24:09 CEST 2023

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 
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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.
>     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/>
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> -- 
> Hervé Pagès
> Bioconductor Core Team
> hpages.on.github using gmail.com

-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.github using gmail.com