Question

DEseq2 loading library problem

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shilabr • 0

@shilabr-22171

Last seen 5.2 years ago

Hello I have already installed the DEseq2 package on my R (3.6.1) however i cant load the library and I get the same error to all the different approaches i have taken to solve the problem. This is the error:

 library(DESeq2)
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Error: package or namespace load failed for ‘GenomeInfoDb’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘GenomeInfoDbData’
Error: package ‘GenomeInfoDb’ could not be loaded

Can anyone help? Thank you in advance!

deseq2 • 1.2k views

ADD COMMENT • link updated 5.2 years ago by Martin Morgan 25k • written 5.2 years ago by shilabr • 0

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This seems like a weird one, and not quite sure where to begin. Something seems hosed with your installation. Does this happen when you start a fresh R sesion? If so, something weird might be getting loaded (from an .RData) on startup.

Perhaps a useful place to start would be to update your post by restarting R so that it is a clean workspace, and copy/paste the output of ls() and BiocManager::valid().

For instance, mine looks like this:

> ls()
character(0)
> BiocManager::valid()
Bioconductor version 3.9 (BiocManager 1.30.8), ?BiocManager::install for help

* sessionInfo()

R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] BiocManager_1.30.8 compiler_3.6.1     tools_3.6.1

Bioconductor version '3.9'

  * 2 packages out-of-date
  * 4 packages too new

create a valid installation with

  BiocManager::install(c(
    "data.table", "dtplyr", "gganimate", "gifski", "gsl", "UCSCXenaShiny"
  ), update = TRUE, ask = FALSE)

more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date

Warning message:
2 packages out-of-date; 4 packages too new

ADD REPLY • link 5.2 years ago Steve Lianoglou ★ 13k

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Entering edit mode

It looks like you're missing a package GenomeInfoDbData, so you might try

BiocManager::install("GenomeInfoDbData")`

This might work but a better approach is to ask how you managed to get into a situation where this dependency was not installed? Have you always used BiocManager::install() to install packages?

Please also add the output of sessionInfo() to your question or as a comment. Here's mine:

> sessionInfo()
R version 3.6.1 Patched (2019-10-04 r77256)
Platform: x86_64-apple-darwin17.7.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS:   /Users/ma38727/bin/R-3-6-branch/lib/libRblas.dylib
LAPACK: /Users/ma38727/bin/R-3-6-branch/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] compiler_3.6.1

ADD REPLY • link 5.2 years ago Martin Morgan 25k