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saezlab / OmnipathR

R client for the OmniPath web service
https://r.omnipathdb.org/
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Wrong version packages #72

Closed Icekirakira closed 1 year ago

Icekirakira commented 1 year ago

Hi,

Thanks for collating such a great database.

I am trying to install version 3.16 (for R 4.2), but the installation package seems to be of a lower version. Thus, I am unable to use this version for get_collectri. Could you kindly look into this issue?

Here is the code and the feedback I get.

BiocManager::install('OmnipathR', version = '3.16', force =T) 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cran.rstudio.com/ Bioconductor version 3.16 (BiocManager 1.30.20), R 4.2.0 (2022-04-22) Installing package(s) 'OmnipathR' trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/OmnipathR_3.5.25.tar.gz'

deeenes commented 1 year ago

Hi, 3.16 is an expired version of Bioconductor. We backported CollecTRI to the current stable version 3.17. Some features that we recently introduced for a better processing of CollecTRI are not yet in either BioC devel or 3.17, it takes time until we get successful builds there. I recommend to install it directly from github:

library(remotes)
remotes::install_github('saezlab/OmnipathR')