qiime2R IRanges installation issue

Other Bioinformatics Tools
1

Hello @jbisanz
Thank you for this package! I am trying to install it in R 3. 6.1 and I get this error:
Error: Failed to install 'qiime2R' from GitHub:
(converted from warning) cannot remove prior installation of package ‘IRanges'

Could you please help me figure it out how to fix it? I would appreciate it very much,

Maritsa Cruz

2

Hi @macruz258,

Welcome to the forum! I split this out into a separate topic since it deals with a different version of R and addresses what looks to be a different issue.

Best,
Justine

1 Like
4

Hmm, I just updated to 3.6.1 from 3.6.0 and did not run into this issue on my OSX machine. Are you using a shared server where you might not have appropriate permissions?

IRanges is a dependency of Biostrings which is used for importing fasta files in qiime2R. I would try to remove the old version and install the newest one as below:

remove.packages("IRanges")
BiocManager::install("IRanges")
library(IRanges)
devtools::install_github("jbisanz/qiime2R")
2 Likes
6

Thank you Jordan for your quick answer! It looks like it is installed now with this code you provided. I will contact you if I run into another issue. Btw, I use a windows computer. I thought that might have been the issue at the beginning. Thanks again!

1 Like
7

I had similar problem, then I noticed this message within error message:

Installation paths not writeable, unable to update packages
path: /usr/lib/R/library
packages:
boot, cluster, codetools, foreign, lattice, nlme, spatial

Now, I had these packages installed. So I just activated each of them

library(boot, lib.loc = "/usr/lib/R/library")
library(cluster, lib.loc = "/usr/lib/R/library")
library(codetools, lib.loc = "/usr/lib/R/library")
library(foreign, lib.loc = "/usr/lib/R/library")
library(lattice, lib.loc = "/usr/lib/R/library")

then I tried this again...

if (!requireNamespace("devtools", quietly = TRUE)){install.packages("devtools")}
devtools::install_github("jbisanz/qiime2R")

And it WORKED! Hooray!!!

1 Like