Question

Problem installing ChAMP on a MacBook

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Galia • 0

@cf6c003e

Last seen 5 months ago

Israel

Hello, I'm a bit new to R, I'm trying to install ChAMP with Bioconductor version 3.19 and R 4.4 I'm on a MacBook M3 Pro, Sonoma 14.1 I keep getting the following error: Warning message: package ChAMP is not available for Bioconductor version 3.19 A version of this package for your version of R might be available elsewhere,

Any help will be appreciated

ChAMP • 676 views

ADD COMMENT • link updated 6 months ago by shepherl 4.1k • written 6 months ago by Galia • 0

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Did you run these lines? https://www.bioconductor.org/packages/release/bioc/html/ChAMP.html

It is good practice to include code and error messages.

ADD REPLY • link 6 months ago ATpoint ★ 4.5k

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Yes, I ran those lines, I'm copying the full transcript (I just copied the error before). Note that I don't update the requested packages, because I already did updated them and it keeps showing this. Also I am successfully using minfi

> BiocManager::install("ChAMP")
'getOption("repos")' replaces Bioconductor standard repositories, see help("repositories",
package = "BiocManager") for details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/
Bioconductor version 3.19 (BiocManager 1.30.23), R 4.4.0 (2024-04-24)
Installing package(s) ChAMP
Old packages: cachem, DelayedArray, SparseArray
Update all/some/none? [a/s/n]: 
n
Warning message:
package ChAMP is not available for Bioconductor version 3.19

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

ADD REPLY • link 6 months ago Galia • 0

score 2 · Answer 1 · 2024-05-16

Its a little deceiving. ChAMP has not propagated yet for users because one of its dependencies has not yet built for 3.19. The goseq packages needed by ChAMP is unavailable; this is indicated by the red radio buttons on the build page where if you hoover you can see why the propagation was blocked. https://bioconductor.org/checkResults/release/bioc-LATEST/ChAMP/ The goseq package has been made aware and I believe there is some discussion of transitioning of maintainers.