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orzechoj / piq-single

PIQ DNA footprinting. Cloned from https://bitbucket.org/thashim/piq-single
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Issue running PIQ #1

Open rm1238 opened 3 years ago

rm1238 commented 3 years ago

Hello,

I am having trouble trying to run PIQ. I am trying to run the test with a single motif with this command:

Rscript PIQ/pwmmatch.exact.r PIQ/common.global.r PIQ/pwms/JASPAR2020_CORE_vertebrates_non-redundant_pfms_jaspar.txt 8 /Volumes/CHACAL_0/8.ANALYSIS/MERGE/PIQ/motif.matches/

I get the following, which seems to be the correct reading of the arguments:

args <- commandArgs(trailingOnly = TRUE) print(args) [1] "PIQ/common.global.r"
[2] "PIQ/pwms/JASPAR2020_CORE_vertebrates_non-redundant_pfms_jaspar.txt" [3] "8"
[4] "/Volumes/CHACAL_0/8.ANALYSIS/MERGE/PIQ/motif.matches/"

commonfile = args[1] jaspardir = args[2] pwmid = as.double(args[3]) outdir = args[4]

outdir=paste0(outdir,'/') source(commonfile)

Then, this error shows up:

Error: With R version 3.5 or greater, install Bioconductor packages using BiocManager; see https://bioconductor.org/install

I updated all the core Bioconductor packages except 'cluster', 'mgcv’, and ‘reactome.db’, which for some reason I am unable to update due to a compiling error that I have been unable to sort out yet.

These are the versions I am currently running: Bioconductor version 3.9 , R 3.6.3 If you could provide any advice as to how I can get PIQ to work, it would be great.

Thank you for your time,

Ricardo

lindsaynhayes commented 2 years ago

@rm1238 I updated line 7 of common.global.r to new.repos["CRAN"] <- "http://cran.us.r-project.org/" the ucla link was broken