Install package without updating dependent package
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@23c4e923
Last seen 5 months ago
Japan

Hi,

I'm trying to install AnnotationForge, and it is said that the package "Matrix" is old.

> BiocManager::install("AnnotationForge")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01)
Old packages: 'Matrix'
Update all/some/none? [a/s/n]:

Matrix 1.4.0 is released in 2021/12/8. but in my environment, its compile is failing.

I'm trying to fix it, but anyway, can I install bioconductor packages without updating dependent package(in this case, Matrix)?

Regards.

Install AnnotationForge • 787 views
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Mike Smith ★ 5.5k
@mike-smith
Last seen 16 hours ago
EMBL Heidelberg / de.NBI

The simplest choice is to just select "n" at this point and it will keep the version of Matrix you already have, and AnnotationForge will probably still work fine. Since the new version of Matrix is so recent, it's very unlikely AnnotationForge will require that absolute latest version. In fact, it may be that AnnotationForge doesn't even need Matrix. The default behaviour is to check all installed packages to see if they are up-to-date, regardless of whether they are needed for this specific installation.

However if it gets annoying to keep saying "none" at this point, BiocManager::install() has the argument update for choosing whether other packages should be checked for updates. The manual page entry for this argument says "When FALSE, BiocManager::install() does not attempt to update old packages..." so you can, for example, do BiocManager::install("AnnotationForge", update = FALSE)

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Thank you for your kind reply!

I selected "n", then I got the following output.

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

So I have run the BiocManager::install() with "force" option,

BiocManager::install("AnnotationForge", force = TRUE)

Then it installed successfully and appears to be working fine!

Thank you.

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