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saezlab / MetaProViz

R-package to perform metabolomics pre-processing, differential metabolite analysis, metabolite clustering and custom visualisations.
https://saezlab.github.io/MetaProViz/
GNU General Public License v3.0
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Package load and dependencies installation #72

Closed dprymidis closed 3 months ago

dprymidis commented 10 months ago

image

When I load the package now I get this everytime.

Clusterprofiler is already installed. I think it cannot check if its installed because clusterprofiler is not cran but from bioconductor.

ChristinaSchmidt1 commented 10 months ago

I have checked this on both of my machines and I do not have this coming up. So maybe it is something machine specific after all?

dprymidis commented 9 months ago

Marc informed me that when he installed MetaProViz the packages from bioconductor ,EnhancedVolcano and Clusterprofiler were not installed automatically and he had to istall them manually. I also had this issue when Itested this.

ChristinaSchmidt1 commented 9 months ago

Thanks, in this case I will definetly add this information to the vignette. So the user is informed that this may happen and if this is the case that they shall manually install the package. I will also see if I can find what is the reason for this, so maybe its something we can prevent.

ChristinaSchmidt1 commented 9 months ago

I have done some reading and one reason might be that the package ‘EnhancedVolcano’ is not available for the version of R you have installed. Could you double check if this may be the issue for you and Marc?

ChristinaSchmidt1 commented 9 months ago

Does you thumbs up mean that this was indeed the issue why that was not installed for you?

dprymidis commented 9 months ago

No, We talked with Marc to check it out but didnt.

ChristinaSchmidt1 commented 3 months ago

I have now removed those dependencies as usethis::use_package can not import BiocManager packages. There are other functions like use_dev_package, but also here we can not import BiocManager packages. This afffects clusterProfiler and EnhancedVolcano. We can remove the dependency to clusterProfiler once we have added a helper function for the Fishers Exact test.