Issue running PIQ

[rm1238]

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]

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