Re: [Bioc-devel] biomaRt uswest mirror ERROR

[Shepherd, Lori]

Ok. Thanks Mike.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Mike Smith 
Sent: Tuesday, April 24, 2018 12:17:58 PM
To: Shepherd, Lori
Cc: bioc-devel@r-project.org
Subject: Re: biomaRt uswest mirror ERROR

Hi Lori,

There should be no issue with switching to an alternative mirror with regards 
to the content.

However, in the current release you will also need to set the argument 
ensemblRedirect = FALSE otherwise it'll end up at the uswest mirror regardless 
of the host you specify.  This is not the case in the devel version, as I've 
disabled the geo-redirect by default after talking to the people at Ensembl, 
and the host argument is always obeyed.

Cheers,

Mike

On 24 April 2018 at 17:30, Shepherd, Lori 
mailto:lori.sheph...@roswellpark.org>> wrote:

Hello,


OrganismDbi is failing.

http://bioconductor.org/checkResults/3.7/bioc-LATEST/OrganismDbi/malbec2-checksrc.html


It appears that this link is not available for the uswest mirror:

http://uswest.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt


when specifying the host = "uswest.ensembl.org"


Is there any consequence to changing this to the us east mirror instead of west 
as that one appears to be up?

It has been a week since this weblink has been unavailable and wasn't sure what 
the time frame of having it back up was.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

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Re: [Bioc-devel] biomaRt uswest mirror ERROR

[Mike Smith]

Hi Lori,

There should be no issue with switching to an alternative mirror with
regards to the content.

However, in the current release you will also need to set the argument
ensemblRedirect
= FALSE otherwise it'll end up at the uswest mirror regardless of the host
you specify.  This is not the case in the devel version, as I've disabled
the geo-redirect by default after talking to the people at Ensembl, and the
host argument is always obeyed.

Cheers,

Mike

On 24 April 2018 at 17:30, Shepherd, Lori 
wrote:

> Hello,
>
>
> OrganismDbi is failing.
>
> http://bioconductor.org/checkResults/3.7/bioc-LATEST/
> OrganismDbi/malbec2-checksrc.html
>
>
> It appears that this link is not available for the uswest mirror:
> http://uswest.ensembl.org:80/biomart/martservice?type=
> registry&requestid=biomaRt
>
>
> when specifying the host = "uswest.ensembl.org"
>
>
> Is there any consequence to changing this to the us east mirror instead of
> west as that one appears to be up?
>
> It has been a week since this weblink has been unavailable and wasn't sure
> what the time frame of having it back up was.
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> This email message may contain legally privileged and/or confidential
> information. If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited. If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.

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[Bioc-devel] biomaRt uswest mirror ERROR

[Shepherd, Lori]

Hello,


OrganismDbi is failing.

http://bioconductor.org/checkResults/3.7/bioc-LATEST/OrganismDbi/malbec2-checksrc.html


It appears that this link is not available for the uswest mirror:

http://uswest.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt


when specifying the host = "uswest.ensembl.org"


Is there any consequence to changing this to the us east mirror instead of west 
as that one appears to be up?

It has been a week since this weblink has been unavailable and wasn't sure what 
the time frame of having it back up was.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.
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