[biomart-users] Problems with getBM function

[Claudia García Sánchez]

Hi,

I'm running this code lines since two years ago:

mart <- biomaRt::useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "mmusculus_gene_ensembl", host = 'www.ensembl.org')

biotype <- biomaRt::getBM(attributes = c("gene_biotype", "external_gene_name", "description"), mart = mart)

But I've obtained this error today:

Error: failed to load external entity "http://www.ensembl.org/info/website/archives/index.html?redirect=no"

What can I do to fix it? Is there any problem with this URL?

Thanks.

Claudia

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[Steffen Durinck-2]

Hi Claudia,

It seems that Ensembl changed their website's ability to be accessed by http and "broke" the biomaRt package.

This may lead to errors which look like this:

Error: failed to load external entity "http://www.ensembl.org/info/website/archives/index.html?redirect=no"

Details about this can be found at: https://support.bioconductor.org/p/134524/

I think a solution is to use the useEnsembl function instead of useMart or you could also install the dev version of biomaRt where this has been fixed.

Cheers,

Steffen

On Thu, Oct 15, 2020 at 6:08 AM Claudia García Sánchez <[hidden email]> wrote:

Hi,

I'm running this code lines since two years ago:

mart <- biomaRt::useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "mmusculus_gene_ensembl", host = 'www.ensembl.org')

biotype <- biomaRt::getBM(attributes = c("gene_biotype", "external_gene_name", "description"), mart = mart)

But I've obtained this error today:

Error: failed to load external entity "http://www.ensembl.org/info/website/archives/index.html?redirect=no"

What can I do to fix it? Is there any problem with this URL?

Thanks.

Claudia

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[Claudia García Sánchez]

Thank you very much Steffen.

I will try using useEnsembl function.

Claudia

El jue., 15 oct. 2020 a las 17:53, Steffen Durinck (<[hidden email]>) escribió:

Hi Claudia,

It seems that Ensembl changed their website's ability to be accessed by http and "broke" the biomaRt package.

This may lead to errors which look like this:

Error: failed to load external entity "http://www.ensembl.org/info/website/archives/index.html?redirect=no"

Details about this can be found at: https://support.bioconductor.org/p/134524/

I think a solution is to use the useEnsembl function instead of useMart or you could also install the dev version of biomaRt where this has been fixed.

Cheers,

Steffen

On Thu, Oct 15, 2020 at 6:08 AM Claudia García Sánchez <[hidden email]> wrote:

Hi,

I'm running this code lines since two years ago:

mart <- biomaRt::useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "mmusculus_gene_ensembl", host = 'www.ensembl.org')

biotype <- biomaRt::getBM(attributes = c("gene_biotype", "external_gene_name", "description"), mart = mart)

But I've obtained this error today:

Error: failed to load external entity "http://www.ensembl.org/info/website/archives/index.html?redirect=no"

What can I do to fix it? Is there any problem with this URL?

Thanks.

Claudia

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