Check installation of package dependences

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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Check installation of package dependences #41

Closed dprymidis closed 11 months ago

dprymidis commented 1 year ago

Each function requires installation of other packages. Check whether they are correctly installed. Maybe packages from CRAN need different installation from those from Bioconductor.

ChristinaSchmidt1 commented 1 year ago

Just a note here, I think we can do this as part of the DOCUMENTATION file since we can add packages there ours depends on. But will need to check this a bit more.

ChristinaSchmidt1 commented 11 months ago

[x] Check if required packages are installed as part of each function otherwise warning message
[x] Only load library of tidyverse (silent load)
[x] Check that all other packages are called for their function using ::
[x] Document all the packages we need to put into the DOUCMENTATION file (list can be added here)

List:

list <- c("tidyverse","ggplot2","factoextra","qcc","hash","reshape","gridExtra","inflection","patchwork","clusterProfiler","enrichplot","ggupset","alluvial","gtools","EnhancedVolcano","writexl","pheatmap","ggfortify" )

dprymidis commented 11 months ago

For 1. We check if the required packages are installed. If they are not we install them For 2. To use autoplot in PCA we have to also load ggfortify.

ChristinaSchmidt1 commented 11 months ago

[x] Check if ggfortify can be called using :::
[x] Move list into package documentation (Christina)

ChristinaSchmidt1 commented 11 months ago

Updated the package description. I only did not add alluvial, as this wont be in the first release. I will add another issue for alluvial specifically. feel free to close the issue once you checked ggfortify

dprymidis commented 11 months ago

ggfortify::: autoplot doesnt work. So, ggfortify will be loaded along with tidyverse in PCA.