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.
[Bioc-devel] biomaRt uswest mirror ERROR
3 messages · Mike Smith, Shepherd, Lori
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 <Lori.Shepherd at 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 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.
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 <grimbough at gmail.com>
Sent: Tuesday, April 24, 2018 12:17:58 PM
To: Shepherd, Lori
Cc: bioc-devel at r-project.org
Subject: Re: biomaRt uswest mirror ERROR
Sent: Tuesday, April 24, 2018 12:17:58 PM
To: Shepherd, Lori
Cc: bioc-devel at 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 <Lori.Shepherd at roswellpark.org<mailto:Lori.Shepherd at 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<http://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. 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.