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

Hi all, Regarding this problem with macOS arm64 builds, I just wanted to report that @Jennifer Wokaty ‘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

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

@Jennifer Wokaty great, thank you, happy the issue is on its way to be resolved. Looking forward to see them implemented on Thursday @Robert Castelo @Zuguang Gu thank you for your insights! These

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

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

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 

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

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

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

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

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

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

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

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

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

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

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