Question

goseq package loading issues

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avinashi • 0

@23fda02d

Last seen 3.8 years 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 • 1.8k views

ADD COMMENT • link 3.8 years ago avinashi • 0

score 1 · Answer 1 · 2021-02-24

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 7 days 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.

ADD COMMENT • link 3.8 years ago James W. MacDonald 67k

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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 • link 3.8 years ago avinashi • 0

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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 • link 3.8 years ago James W. MacDonald 67k

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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 • link 3.8 years ago avinashi • 0