Question

Problems installing BiocManager

0

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ksci ▴ 20

@72e6b5a3

Last seen 2.0 years ago

United States

if (!require("BiocManager", quietly = TRUE))

install.packages("BiocManager") BiocManager::install() 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details replacement repositories: CRAN: https://rweb.crmda.ku.edu/cran

Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.3 (2022-03-10)

Did it even install?

If it didnt install how do I fix this? ```

BiocManager • 1.7k views

ADD COMMENT • link 2.1 years ago • updated 2.0 years ago ksci ▴ 20

Gordon Smyth · Answer 1 · 2022-04-07

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Gordon Smyth 50k

@gordon-smyth

Last seen 7 minutes ago

WEHI, Melbourne, Australia

You seem to be combining commands intended for different purposes out of context. All you actually need is:

install.packages("BiocManager")
library(BiocManager)
install("biomaRt")

And you should execute these commands one at a time, not all together.

ADD COMMENT • link 2.1 years ago Gordon Smyth 50k

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

replacement repositories:
    CRAN: https://rweb.crmda.ku.edu/cran

Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.3 (2022-03-10)
Warning message:
package(s) not installed when version(s) same as current; use `force = TRUE` to re-install: 'biomaRt'

I am getting this error still what am I doing wrong?

ADD REPLY • link updated 2.1 years ago by Gordon Smyth 50k • written 2.1 years ago by ksci ▴ 20

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There is no error. The output clearly shows that you have the BiocManager and biomaRt packages both installed already. So there seems to be no problem.

ADD REPLY • link 2.1 years ago Gordon Smyth 50k

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

What about this?

ADD REPLY • link 2.1 years ago ksci ▴ 20

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The message tells you that the version of the package that you already have installed is the same as the latest version on Bioconductor ("version same as current"), hence it won't re-download and re-install the package for no purpose.

Honestly, have you not tried simply typing library(biomaRt)?

ADD REPLY • link 2.1 years ago Gordon Smyth 50k

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yeah I finally got it to work thank you. It is my first time using bioconducotor so I am having a lot of issues.

ADD REPLY • link 2.0 years ago ksci ▴ 20