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NathanSkene / EWCE

Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.
https://nathanskene.github.io/EWCE/index.html
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Installation error: package 'ewceData' requires R >= 4.1 #31

Closed zhanglab2008 closed 3 years ago

zhanglab2008 commented 3 years ago

Hi, Thanks for writing this great tools. However, I came across an error across all operation systems (Windows, Mac and Ubuntu 20.4) when I installed the package.

ERROR: this R is version 4.0.4, package 'ewceData' requires R >= 4.1
Error: Failed to install 'ewceData' from GitHub:
  (converted from warning) installation of package ‘/tmp/Rtmp9xG1JD/file26f92ae904c2/ewceData_0.99.6.tar.gz’ had non-zero exit status

Could you suggest if this is a bug or if I miss something? Many thanks! Zhang

NathanSkene commented 3 years ago

Hi,

We're trying to get the package back onto bioconductor but their submission system has required that we break the master branch. I suggest installing an earlier commit from before 1 month ago. Would send a link but am on my phone at the moment! Will reply shortly with the specific command to use.

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Hi, Thanks for writing this great tools. However, I came across an error across all operation systems (Windows, Mac and Ubuntu 20.4) when I installed the package.

ERROR: this R is version 4.0.4, package 'ewceData' requires R >= 4.1

Error: Failed to install 'ewceData' from GitHub:

(converted from warning) installation of package ‘/tmp/Rtmp9xG1JD/file26f92ae904c2/ewceData_0.99.6.tar.gz’ had non-zero exit status

Could you suggest if this is a bug or if I miss something? Many thanks! Zhang

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zhanglab2008 commented 3 years ago

That works! Thanks!

madnessfish commented 3 years ago

Hi there! I have also encountered the same problem as @zhanglab2008. Would you mind posting the specific command? Thank you so much!!

numpde commented 3 years ago

edited: just skip to the next comment.

==

@madnessfish Maybe this earlier version (from ~Jan 26, 2021) works:

devtools::install_github("nathanskene/ewce@0aeef50")

although I couldn't make it work.

I made a hack 

devtools::install_github("numpde/EWCE", ref="hack")

by commenting a few lines that requires to

load("all_mgi.rda")
load("all_hgnc.rda")
load("mouse_to_human_homologs.rda")

the files from here.

Al-Murphy commented 3 years ago

Hi both, the data has been removed from the git history of EWCE as per a requirement of Bioconductor. EWCE will be reinstated on Bioconductor in the next release (likely April/May this year). To make EWCE usable for those with R < 4.1 in the meantime, we have made a separate repository based on a previous commit of EWCE and added back in the necessary data. See neurogenomics/EWCE for details and feel free to create issues on that repo if anything is wrong.

Al-Murphy commented 3 years ago

EWCE is available on bioconductor 3.13