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buenrostrolab / FigR

Functional Inference of Gene Regulation
https://buenrostrolab.github.io/FigR/
MIT License
31 stars 10 forks source link

Unable to install FigR #10

Closed sylestiel closed 1 year ago

sylestiel commented 1 year ago

I tried the following: library(dplyr) library(FNN) library(BuenColors) library(chromVAR) library(doParallel) library(ComplexHeatmap) library(BSgenome.Mmusculus.UCSC.mm10) library(chromVAR) library(GenomicRanges) library(SummarizedExperiment) library(motifmatchr) devtools::install_github("buenrostrolab/FigR")

It gives me the following output:

devtools::install_github("buenrostrolab/FigR") Downloading GitHub repo buenrostrolab/FigR@HEAD Skipping 6 packages not available: BSgenome.Hsapiens.UCSC.hg19, ComplexHeatmap, chromVAR, GenomicRanges, SummarizedExperiment, motifmatchr ✔ checking for file ‘/private/var/folders/2c/zzjsgs_53vqflzjl28hf1x7r0000gn/T/Rtmp78zrSr/remotes10c362287973/buenrostrolab-FigR-5141359/DESCRIPTION’ ... ─ preparing ‘FigR’: ✔ checking DESCRIPTION meta-information ... ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories ─ building ‘FigR_0.1.0.tar.gz’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘FigR/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkWVAexg.woff’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘FigR/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkaVQ.woff’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘FigR/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkWVAexg.woff’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘FigR/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkaVQ.woff’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘FigR/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjWVAexg.woff’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘FigR/docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjaVQ.woff’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘FigR/docs/deps/bootstrap-5.1.0/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1x4gaVQ.woff’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘FigR/docs/deps/bootstrap-5.1.0/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0B4gaVQ.woff’ Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable: ‘FigR/docs/deps/bootstrap-5.1.0/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0B4gaVQ.woff’

ERROR: dependency ‘BSgenome.Hsapiens.UCSC.hg19’ is not available for package ‘FigR’

vkartha commented 1 year ago

Hi there - this was because we had listed needing a default genome package to begin with, but I have moved this from the dependencies, so that we assume users to have whichever genome package is associated with the reference specified already installed (as it appears, you have mm10 good to go and don't require hg19). If you try re-installing now I believe this should work

sylestiel commented 1 year ago

That did it! Thanks!