Problem with DESeq2 installation using in R 1.4.1717
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Nahid • 0
@44c7543a
Last seen 11 hours ago
Sweden

I try to install DESeq2 using bellow code in R 1.4.1717

BiocManager::install("DESeq2")

Got this error

Warning message: package(s) not installed when version(s) same as current; use force = TRUE to re-install: 'DESeq2'

DESeq2 Problem installation with • 126 views
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R 1.4? Do you mean R 4.1?

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Probably 1.4.1717 is referring to the latest RStudio IDE version released which is 1.4.1717 not to the version of R.

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@james-w-macdonald-5106
Last seen 1 day ago
United States

Any time you get a message that starts with 'Warning', you can be sure that it isn't an error. An error starts with the word 'Error', as one might expect.

In addition, the warning you got seems to be pretty clear? It says you already have DESeq2 installed, and that the version you have installed is the same as what you are trying to install, and if you really want to re-install you can use force = TRUE.

Can you say what you found confusing about that warning? Perhaps it could be worded differently?

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Thanks but when I want to use library(DESeq2) get this message 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

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The error is fired when the GenomeInfoDb package is trying to load, which appears to be a dependency of GenomicRanges, which is DESeq2 may be using (through SummarizedExperiment, maybe?)

Anyway, try reinstalling the GenomeInfoDb package and reloading DESeq2 again to see if that does it.