goseq package loading issues
1
0
Entering edit mode
avinashi • 0
@23fda02d
Last seen 6 weeks ago

I am using goseq to run analysis on my RNA seq data. Previously it had worked for me, but recently, I am encountering an error when trying to load the package. The error reads as


> library(goseq)
Loading required package: BiasedUrn
Loading required package: geneLenDataBase
Error: package or namespace load failed for ‘geneLenDataBase’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 namespace ‘vctrs’ 0.3.4 is already loaded, but >= 0.3.5 is required
Error: package ‘geneLenDataBase’ could not be loaded

I have tried correcting this by updating the package using the below code:

update.packages('vctrs')

However, I still get the same error as before. I am also unable to reinstall this package since there are several other packages depending on this. Please advise on what step I should take to fix this problem. Thanks

DESeq2 goseq • 108 views
ADD COMMENT
1
Entering edit mode
@james-w-macdonald-5106
Last seen 20 hours ago
United States

Usually the fix for that sort of thing is to restart R (maybe using --vanilla, or certainly in a dir that doesn't have a .Rdata file floating around) and then do

library(BiocManager)
valid()

And then doing whatever you are told to do.

0
Entering edit mode

Hi, I tried doing this. When using valid (), I saw that there were packages that needed updating so I ran:

BiocManager::install(c(
    "broom", "cachem", "colorspace", "data.table", "ggraph", "matrixStats", "pkgload", "Rcpp", "RSQLite", "tibble",
    "vctrs"
  ), update = TRUE, ask = FALSE)

However, when running this, the warning I receive is as follows:

package ‘vctrs’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘vctrs’
Warning: restored ‘vctrs’

I read somewhere that I needed to use the following code to remove the lock directory, but I still recieve the same erros

library(pacman)
p_unlock()
ADD REPLY
0
Entering edit mode

Usually if there is a 00LOCK dir, it tells you that. What you are seeing may instead be due to more than one R session running concurrently, one of which has the vctrs package loaded.

ADD REPLY
0
Entering edit mode

Hi I ended up figuring this issue out. I checked multiple times and there was no other instances running, but whenever I tried to remove or update the package it woudl fail. I had to go directly into the library in my files where the packages are loaded and manually delete it and reinstall it.

ADD REPLY

Login before adding your answer.

Traffic: 434 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6