Question

Problems Installing biomaRt

1

Entering edit mode

ksci ▴ 20

@72e6b5a3

Last seen 2.7 years ago

United States

Having issues installing biomaRt. How do I fix this?

if (!require("BiocManager", force = TRUE)) install.packages("BiocManager")

BiocManager::install("biomaRt")

'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories: CRAN: https://mirror.las.iastate.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'

```

biomaRt • 6.1k views

ADD COMMENT • link updated 13 months ago by James W. MacDonald 67k • written 2.7 years ago by ksci ▴ 20

0

Entering edit mode

library(biomaRt)

I pressed enter to run biomaRT then this show up. Does it mean it worked?

ADD REPLY • link 2.7 years ago ksci ▴ 20

0

Entering edit mode

If you ran the code and it looked like nothing happen then yes it worked. Some packages print welcome message and other stuff, but biomaRt is silent at that point. If there was a problem you'd see an error message, most likely "there is no package called ‘biomaRt’".

As a quick test, after using library(biomaRt) you can try running one of the functions in biomaRt. For example, if I run the code below I get the output shown after. If there's a problem with biomaRt this will show an error instead.

library(biomaRt)
listEnsembl()

        biomart                version
1         genes      Ensembl Genes 105
2 mouse_strains      Mouse strains 105
3          snps  Ensembl Variation 105
4    regulation Ensembl Regulation 105

ADD REPLY • link 2.7 years ago Mike Smith ★ 6.6k

score 0 · Answer 1 · 2022-04-07

0

Entering edit mode

Mike Smith ★ 6.6k

@mike-smith

Last seen 2 days ago

EMBL Heidelberg

I don't see any actual errors here. There's admittedly lot of text, which might look intimidating but is totally normal and isn't particularly worrying. The important part is:

Warning message: package(s) not installed when version(s) same as current;

That's letting you know that BiocManager isn't going to install the biomaRt package because you've already got the most up-to-date version installed.

You should be able to use library(biomaRt) at this point.

ADD COMMENT • link 2.7 years ago Mike Smith ★ 6.6k

0

Entering edit mode

library(biomaRt) Error in library(biomaRt) : there is no package called ‘biomaRt’

This is what I see

ADD REPLY • link 2.7 years ago ksci ▴ 20

0

Entering edit mode

I am getting this same error. Has any one found out how to resolve it? I have tried re-installing bioMart, re-istalling and updating bioconductor. Nothing is working.

Thank you!

ADD REPLY • link 13 months ago sara_jean08 • 0

0

Entering edit mode

You need to show code.

ADD REPLY • link 13 months ago James W. MacDonald 67k

0

Entering edit mode

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?

ADD REPLY • link 2.7 years ago ksci ▴ 20