Re: [Bioc-devel] Issue with GenomeInfoDb
Patch looks good. Thanks Kenneth!
H.
On 07/18/2017 06:59 AM, Weiss, Kenneth wrote:
Thanks for the info Martin.
Attached is the file in text format.
Cheers,
Ken
-Original Message-
From: Martin Morgan [mailto:martin.mor...@roswellpark.org]
Sent: Monday, July 17, 2017 4:00 PM
To: Weiss, Kenneth; bioc-devel@r-project.org
Cc: Mark Montague (markm...@umich.edu)
Subject: Re: [Bioc-devel] Issue with GenomeInfoDb
Thanks Ken the list filters attachements that are not of the following type
text/x-diff
multipart/mixed
multipart/alternative
text/plain
text/html
application/pgp-signature
application/postscript
application/pdf
image/png
message/rfc822
application/x-xz
application/x-gzip
so please feel free to send again (or to me and I'll see that it gets posted.
Martin
On 07/17/2017 02:37 PM, Weiss, Kenneth wrote:
Greetings,
Attached is the patch file GenomeInfoDb.patch noted below.
Cheers,
Ken
From: Weiss, Kenneth
Sent: Monday, July 17, 2017 11:33 AM
To: 'bioc-devel@r-project.org'
Cc: Mark Montague (markm...@umich.edu)
Subject: Issue with GenomeInfoDb
Greetings,
I provide support for an HPC cluster at the University of Michigan. Recently we
had a user approach us with the following problem:
I have an issue about using the following package/function in R.
*library("GenomeInfoDb")*
*GenomeInfoDb::Seqinfo(genome = "mm10")*
The function is getting a remote resource that works on the head node,
but not the worker nodes. The error on worker nodes is as follows.
*Error in .make_assembly_report_URL(assembly_accession)*
We have our cluster setup to use proxy variables to be able to access the
internet from our compute nodes. After some digging, my colleague, Mark
Montague, was able to come up with the following work around:
This is not a security issue. The problem is that our cluster compute nodes are
not connected to the Internet.
Because of this, compute nodes need to use a proxy server in order to
access things that are off campus. Usually this is not a problem, but
in this particular case there are actually three problems related to
GenomeInfoDb not working correctly with the proxy when running on compute nodes:
1. GenomeInfoDb doesn't recognize the FTP directory listing format our proxy
server uses.
2. GenomeInfoDb is not handing the download of assembly reports in the
same way it handles other downloads, which is a problem when the proxy is being
used.
3. R is not always using the proxy for FTP connections; this appears to be a
quirk of R.
To fix problems 1 and 2, you can install a modified version of
GenomeInfoDb to replace the one you currently have installed in your home
directory by running the following commands:
cd ~
git clone
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor-2Dmirror_GenomeInfoDb.git=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=x5iUx04safB-ad_8-p8FGpL1zsRp-htM3JOMBhRQ_dY=siFMZPPP0dRxS6L5ULywqPMJTSqsywp_ts54EFvugps=
cd GenomeInfoDb
git checkout release-3.4
patch -p 1 < /home/someuser/GenomeInfoDb.patch R CMD INSTALL .
To fix problem 3, you need to tell R to use libcurl to download files
rather than its default method. This needs to be done in every R script that
uses GenomeInfoDb. For example:
options(download.file.method="libcurl")
library("GenomeInfoDb")
GenomeInfoDb::Seqinfo(genome = "mm10")
Alternatively, you can put the "options" command above into a file
named /home/someuser/.Rprofile and it will take effect for all R scripts you
run.
Just thought you would like to know.
Cheers,
Ken
**
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Re: [Bioc-devel] Issue with GenomeInfoDb
Thanks for the info Martin.
Attached is the file in text format.
Cheers,
Ken
-Original Message-
From: Martin Morgan [mailto:martin.mor...@roswellpark.org]
Sent: Monday, July 17, 2017 4:00 PM
To: Weiss, Kenneth; bioc-devel@r-project.org
Cc: Mark Montague (markm...@umich.edu)
Subject: Re: [Bioc-devel] Issue with GenomeInfoDb
Thanks Ken the list filters attachements that are not of the following type
text/x-diff
multipart/mixed
multipart/alternative
text/plain
text/html
application/pgp-signature
application/postscript
application/pdf
image/png
message/rfc822
application/x-xz
application/x-gzip
so please feel free to send again (or to me and I'll see that it gets posted.
Martin
On 07/17/2017 02:37 PM, Weiss, Kenneth wrote:
> Greetings,
>
> Attached is the patch file GenomeInfoDb.patch noted below.
>
> Cheers,
> Ken
>
> From: Weiss, Kenneth
> Sent: Monday, July 17, 2017 11:33 AM
> To: 'bioc-devel@r-project.org'
> Cc: Mark Montague (markm...@umich.edu)
> Subject: Issue with GenomeInfoDb
>
> Greetings,
>
> I provide support for an HPC cluster at the University of Michigan. Recently
> we had a user approach us with the following problem:
>
> I have an issue about using the following package/function in R.
>
> *library("GenomeInfoDb")*
> *GenomeInfoDb::Seqinfo(genome = "mm10")*
>
> The function is getting a remote resource that works on the head node,
> but not the worker nodes. The error on worker nodes is as follows.
> *Error in .make_assembly_report_URL(assembly_accession)*
>
> We have our cluster setup to use proxy variables to be able to access the
> internet from our compute nodes. After some digging, my colleague, Mark
> Montague, was able to come up with the following work around:
>
> This is not a security issue. The problem is that our cluster compute nodes
> are not connected to the Internet.
> Because of this, compute nodes need to use a proxy server in order to
> access things that are off campus. Usually this is not a problem, but
> in this particular case there are actually three problems related to
> GenomeInfoDb not working correctly with the proxy when running on compute
> nodes:
>
> 1. GenomeInfoDb doesn't recognize the FTP directory listing format our proxy
> server uses.
> 2. GenomeInfoDb is not handing the download of assembly reports in the
> same way it handles other downloads, which is a problem when the proxy is
> being used.
> 3. R is not always using the proxy for FTP connections; this appears to be a
> quirk of R.
>
> To fix problems 1 and 2, you can install a modified version of
> GenomeInfoDb to replace the one you currently have installed in your home
> directory by running the following commands:
>
> cd ~
> git clone https://github.com/Bioconductor-mirror/GenomeInfoDb.git
> cd GenomeInfoDb
> git checkout release-3.4
> patch -p 1 < /home/someuser/GenomeInfoDb.patch R CMD INSTALL .
>
> To fix problem 3, you need to tell R to use libcurl to download files
> rather than its default method. This needs to be done in every R script that
> uses GenomeInfoDb. For example:
>
> options(download.file.method="libcurl")
> library("GenomeInfoDb")
> GenomeInfoDb::Seqinfo(genome = "mm10")
>
> Alternatively, you can put the "options" command above into a file
> named /home/someuser/.Rprofile and it will take effect for all R scripts you
> run.
>
> Just thought you would like to know.
>
> Cheers,
> Ken
> **
> Electronic Mail is not secure, may not be read every day, and should
> not be used for urgent or sensitive issues
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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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diff --git a/R/assembly-utils.R b/R/assembly-utils.R
index 7d9c4f3..1073d2f 100644
--- a/R/assembly-utils.R
+++ b/R/assembly-utils.R
@@ -218,7 +218,9 @@
"AssignedMoleculeLocationOrType", "GenBankAccn",
"
Re: [Bioc-devel] Issue with GenomeInfoDb
Thanks Ken the list filters attachements that are not of the following type
text/x-diff
multipart/mixed
multipart/alternative
text/plain
text/html
application/pgp-signature
application/postscript
application/pdf
image/png
message/rfc822
application/x-xz
application/x-gzip
so please feel free to send again (or to me and I'll see that it gets
posted.
Martin
On 07/17/2017 02:37 PM, Weiss, Kenneth wrote:
Greetings,
Attached is the patch file GenomeInfoDb.patch noted below.
Cheers,
Ken
From: Weiss, Kenneth
Sent: Monday, July 17, 2017 11:33 AM
To: 'bioc-devel@r-project.org'
Cc: Mark Montague (markm...@umich.edu)
Subject: Issue with GenomeInfoDb
Greetings,
I provide support for an HPC cluster at the University of Michigan. Recently we
had a user approach us with the following problem:
I have an issue about using the following package/function in R.
*library("GenomeInfoDb")*
*GenomeInfoDb::Seqinfo(genome = "mm10")*
The function is getting a remote resource that works on the head node, but
not the worker nodes. The error on worker nodes is as follows.
*Error in .make_assembly_report_URL(assembly_accession)*
We have our cluster setup to use proxy variables to be able to access the
internet from our compute nodes. After some digging, my colleague, Mark
Montague, was able to come up with the following work around:
This is not a security issue. The problem is that our cluster compute nodes are
not connected to the Internet.
Because of this, compute nodes need to use a proxy server in order to access
things that are off campus. Usually this
is not a problem, but in this particular case there are actually three problems
related to GenomeInfoDb not working
correctly with the proxy when running on compute nodes:
1. GenomeInfoDb doesn't recognize the FTP directory listing format our proxy
server uses.
2. GenomeInfoDb is not handing the download of assembly reports in the same way
it handles other downloads, which is a
problem when the proxy is being used.
3. R is not always using the proxy for FTP connections; this appears to be a
quirk of R.
To fix problems 1 and 2, you can install a modified version of GenomeInfoDb to
replace the one you currently have
installed in your home directory by running the following commands:
cd ~
git clone https://github.com/Bioconductor-mirror/GenomeInfoDb.git
cd GenomeInfoDb
git checkout release-3.4
patch -p 1 < /home/someuser/GenomeInfoDb.patch
R CMD INSTALL .
To fix problem 3, you need to tell R to use libcurl to download files rather
than its default method. This needs to be
done in every R script that uses GenomeInfoDb. For example:
options(download.file.method="libcurl")
library("GenomeInfoDb")
GenomeInfoDb::Seqinfo(genome = "mm10")
Alternatively, you can put the "options" command above into a file named
/home/someuser/.Rprofile and it will take effect
for all R scripts you run.
Just thought you would like to know.
Cheers,
Ken
**
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used for urgent or sensitive issues
___
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Re: [Bioc-devel] Issue with GenomeInfoDb
Greetings,
Attached is the patch file GenomeInfoDb.patch noted below.
Cheers,
Ken
From: Weiss, Kenneth
Sent: Monday, July 17, 2017 11:33 AM
To: 'bioc-devel@r-project.org'
Cc: Mark Montague (markm...@umich.edu)
Subject: Issue with GenomeInfoDb
Greetings,
I provide support for an HPC cluster at the University of Michigan. Recently we
had a user approach us with the following problem:
I have an issue about using the following package/function in R.
*library("GenomeInfoDb")*
*GenomeInfoDb::Seqinfo(genome = "mm10")*
The function is getting a remote resource that works on the head node, but
not the worker nodes. The error on worker nodes is as follows.
*Error in .make_assembly_report_URL(assembly_accession)*
We have our cluster setup to use proxy variables to be able to access the
internet from our compute nodes. After some digging, my colleague, Mark
Montague, was able to come up with the following work around:
This is not a security issue. The problem is that our cluster compute nodes are
not connected to the Internet.
Because of this, compute nodes need to use a proxy server in order to access
things that are off campus. Usually this
is not a problem, but in this particular case there are actually three problems
related to GenomeInfoDb not working
correctly with the proxy when running on compute nodes:
1. GenomeInfoDb doesn't recognize the FTP directory listing format our proxy
server uses.
2. GenomeInfoDb is not handing the download of assembly reports in the same way
it handles other downloads, which is a
problem when the proxy is being used.
3. R is not always using the proxy for FTP connections; this appears to be a
quirk of R.
To fix problems 1 and 2, you can install a modified version of GenomeInfoDb to
replace the one you currently have
installed in your home directory by running the following commands:
cd ~
git clone https://github.com/Bioconductor-mirror/GenomeInfoDb.git
cd GenomeInfoDb
git checkout release-3.4
patch -p 1 < /home/someuser/GenomeInfoDb.patch
R CMD INSTALL .
To fix problem 3, you need to tell R to use libcurl to download files rather
than its default method. This needs to be
done in every R script that uses GenomeInfoDb. For example:
options(download.file.method="libcurl")
library("GenomeInfoDb")
GenomeInfoDb::Seqinfo(genome = "mm10")
Alternatively, you can put the "options" command above into a file named
/home/someuser/.Rprofile and it will take effect
for all R scripts you run.
Just thought you would like to know.
Cheers,
Ken
**
Electronic Mail is not secure, may not be read every day, and should not be
used for urgent or sensitive issues
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Issue with GenomeInfoDb
Greetings,
I provide support for an HPC cluster at the University of Michigan. Recently we
had a user approach us with the following problem:
I have an issue about using the following package/function in R.
*library("GenomeInfoDb")*
*GenomeInfoDb::Seqinfo(genome = "mm10")*
The function is getting a remote resource that works on the head node, but
not the worker nodes. The error on worker nodes is as follows.
*Error in .make_assembly_report_URL(assembly_accession)*
We have our cluster setup to use proxy variables to be able to access the
internet from our compute nodes. After some digging, my colleague, Mark
Montague, was able to come up with the following work around:
This is not a security issue. The problem is that our cluster compute nodes are
not connected to the Internet.
Because of this, compute nodes need to use a proxy server in order to access
things that are off campus. Usually this
is not a problem, but in this particular case there are actually three problems
related to GenomeInfoDb not working
correctly with the proxy when running on compute nodes:
1. GenomeInfoDb doesn't recognize the FTP directory listing format our proxy
server uses.
2. GenomeInfoDb is not handing the download of assembly reports in the same way
it handles other downloads, which is a
problem when the proxy is being used.
3. R is not always using the proxy for FTP connections; this appears to be a
quirk of R.
To fix problems 1 and 2, you can install a modified version of GenomeInfoDb to
replace the one you currently have
installed in your home directory by running the following commands:
cd ~
git clone https://github.com/Bioconductor-mirror/GenomeInfoDb.git
cd GenomeInfoDb
git checkout release-3.4
patch -p 1 < /home/someuser/GenomeInfoDb.patch
R CMD INSTALL .
To fix problem 3, you need to tell R to use libcurl to download files rather
than its default method. This needs to be
done in every R script that uses GenomeInfoDb. For example:
options(download.file.method="libcurl")
library("GenomeInfoDb")
GenomeInfoDb::Seqinfo(genome = "mm10")
Alternatively, you can put the "options" command above into a file named
/home/someuser/.Rprofile and it will take effect
for all R scripts you run.
Just thought you would like to know.
Cheers,
Ken
**
Electronic Mail is not secure, may not be read every day, and should not be
used for urgent or sensitive issues
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