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wguo-research / scCancer

A package for automated processing of single cell RNA-seq data in cancer
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liger dependency error #45

Open nicholas-middelberg opened 5 months ago

nicholas-middelberg commented 5 months ago

Per the installation instructions on the wiki:

if(!checkPkg("liger")) install_github("MacoskoLab/liger")

image

This successfully installs the package, but as the liger README states, the package is installed under the name rliger, so when I try to install scCancer from github I get the following error:

ERROR: dependency ‘liger’ is not available for package ‘scCancer’

Does anyone have advice for fixing this issue?

sunyu1010 commented 4 months ago

I also encountered the same problem(ㄒoㄒ)

weiwei0029 commented 3 months ago

. Search and Replace liger References in the Code It's possible that some parts of the code still directly reference liger. You can search for liger in the scCancer package source code and replace it with rliger.

Unzip the scCancer-master.zip file. Search for liger in the unzipped folder: In RStudio, you can use the "Find in Files" feature (shortcut: Ctrl+Shift+F) to search for all occurrences of liger in the code and replace them with rliger. Save all modified files.

  1. Reinstall the Modified Package After making the replacements, try installing the modified package again
theAeon commented 3 weeks ago

Looks like the scCancer2 branch also has this fixed-you should be able to just do devtools::install_github("wguo-research/scCancer", ref = "scCancer2")

I would recommend this over the find-replace method as we made a LOT of breaking changes to liger in the years since the package name changed.