microbiome / OMA

Orchestrating Microbiome Analysis

https://microbiome.github.io/OMA

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Installation scripts & instructions #361

Closed antagomir closed 5 months ago

antagomir commented 11 months ago

The current installation script (ch 2.1) installs Bioc versions of mia, miaViz, bluster.

However, OMA uses some stuff from the latest Github devel versions.

Update the current installation instructions to use those Github versions.

During 2024, stabilize OMA so that it is in sync with the latest Bioconductor devel version (and does not need some experimental and unstable Github development versions of the key packages).

antagomir commented 5 months ago

To NdG

RiboRings commented 5 months ago

Hi! I hope this is the right place to bring up installation issues, but I can also open a separate issue if needed.

When rendering the book locally, I get this warning. Consider adding these dependencies under Suggests: in DESCRIPTION or check if some of them can be replaced with base R functionality.

> BiocBook::preview(BiocBook::BiocBook('.'))
✖ Some dependencies found in book pages are not listed in DESCRIPTION: 
  • BiocManager
  • stats
  • reshape2
  • devtools
  • NetCoMi
  • SpiecEasi
  • SPRING
  • RColorBrewer
  • factoextra
  • grid
  • cluster
  • dada2
ℹ Consider adding these dependencies to DESCRIPTION

RiboRings commented 5 months ago

Also, the kableExtra package is used in some chapters but is not installed by the install_packages.R script:

Quitting from lines  at lines 86-90 [unnamed-chunk-6] (10_manipulation.qmd)
Error in `loadNamespace()`:
! there is no package called 'kableExtra'

Consider replacing kableExtra with a base R solution, or adding it to install_packages.R.

antagomir commented 5 months ago

I would add it to installation script unless there are particular problems with that. It has useful functionality.

Insaynoah commented 5 months ago

I added the package to the csv file that specifies the packages to install. However by default, the packages are installed using an url which I can't modify :


packages <- url("https://raw.githubusercontent.com/microbiome/OMA/devel/oma_packages.csv")
#packages <- "oma_packages.csv"

antagomir commented 5 months ago

You can modify the oma_packages.csv file at the root folder: https://github.com/microbiome/OMA

The URL also refers to the Github branch where this is released after your PR

Insaynoah commented 5 months ago

415 I added it to the PR so it should be good !