Problem installing package TxDb.Mmusculus.UCSC.mm10.knownGene
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@wolfgang-raffelsberger-2876
Last seen 8 hours ago
France

I'm having difficulty installing TxDb.Mmusculus.UCSC.mm10.knownGene on R-4.4.3 .

Following instructions from the Bioconductor website given for this package (https://bioconductor.org/packages/release/data/annotation/html/TxDb.Mmusculus.UCSC.mm10.knownGene.html) my attempts to install were not successful, The package BiocManager is installed and works properly for installing other BioC packages.

Here the code I used :

BiocManager::install("TxDb.Mmusculus.UCSC.mm10.knownGene")

I get :

Bioconductor version 3.20 (BiocManager 1.30.25), R 4.4.3 (2025-02-28 ucrt) Installing package(s) 'TxDb.Mmusculus.UCSC.mm10.knownGene' Warning message: package 'TxDb.Mmusculus.UCSC.mm10.knownGene' is not available as a binary package for Bioconductor version '3.20'

A version of this package for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages

My session :

sessionInfo( )

I get :

R version 4.4.3 (2025-02-28 ucrt) Platform: x86_64-w64-mingw32/x64 Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale: [1] LC_COLLATE=French_France.utf8 LC_CTYPE=French_France.utf8 LC_MONETARY=French_France.utf8 LC_NUMERIC=C
[5] LC_TIME=French_France.utf8

time zone: Europe/Paris tzcode source: internal

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

other attached packages: [1] TinnRcom_1.1.5 formatR_1.14 svSocket_1.1.5

loaded via a namespace (and not attached): [1] BiocManager_1.30.25 compiler_4.4.3 cli_3.6.4 tools_4.4.3 svMisc_1.4.3 rlang_1.1.5
[7] tcltk_4.4.3

TxDb.Mmusculus.UCSC.mm10.knownGene • 180 views
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I cannot reproduce this on Windows 11. Is rtools installed to allow compilation from source on Windows?

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Yes, rtools4.4 is installed (and works for making my own packages)

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shepherl 4.1k
@lshep
Last seen 2 hours ago
United States

Can you try BiocManager::install("TxDb.Mmusculus.UCSC.mm10.knownGene", type="source")

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Thank you, this solved the problem !

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