Error Installing OmnipathR when trying to install liana

[rstorch01]

Hello,

I am getting an error running remotes::install_github('saezlab/liana'):

• installing source package ‘OmnipathR’ ...
  ** using staged installation
  ** R
  ** inst
  ** byte-compile and prepare package for lazy loading
  Error: object ‘join_by’ is not exported by 'namespace:dplyr'
  Execution halted
  ERROR: lazy loading failed for package ‘OmnipathR’
• removing ‘/usr/local/R/4.0.2/lib64/R/library/OmnipathR’
  Downloading GitHub repo saezlab/OmnipathR@HEAD
  Skipping OmnipathR, it is already being installed
  checking for file ‘/tmp/RtmpbHkfqa/remotes6c692bf1f617/saezlab-liana-86adaca/DES✔ checking for file ‘/tmp/RtmpbHkfqa/remotes6c692bf1f617/saezlab-liana-86adaca/DESCRIPTION’
  ─ preparing ‘liana’:
  ✔ checking DESCRIPTION meta-information ...
  ─ checking for LF line-endings in source and make files and shell scripts
  ─ checking for empty or unneeded directories
  ─ building ‘liana_0.1.12.tar.gz’

ERROR: dependency ‘OmnipathR’ is not available for package ‘liana’

Please let me know if there is something else I need to do to get this to load successfully. Thank you.

[deeenes]

Hi,

Sorry for the late answer, somehow this one got lost during holidays. The error says when the installer checks if OmnipathR can be loaded, it has to load also the join_by function from dplyr, which exists only in dplyr since version 1.1.0. Most likely your dplyr is older than that, you can update it by install_packages('dplyr').

To resolve the issue I also set a minimum version for dplyr (7d148f9), so it's enough if you do remotes::install_github('OmnipathR')