Rstudio container becomes unresponsive after long runs about rocker

[dnadave]

image ID: 2504e529d3de

/home/dnadave> docker version
Client version: 1.3.1
Client API version: 1.15
Go version (client): go1.3.3
Git commit (client): 4e9bbfa
OS/Arch (client): linux/amd64
Server version: 1.3.1
Server API version: 1.15
Go version (server): go1.3.3
Git commit (server): 4e9bbfa

[cboettig]

believe it or not, the log looks fine. It looks like this problem is
connected to your particular command, I was able to replicate (I think)
this error by running that specific command on a my tiny droplet, though it
works fine on the image running locally.

Can you run docker pull rocker/rstudio and try this? For sake of
argument, can you confirm that this happens when you have only one
container instance running?

On Wed, Nov 5, 2014 at 3:52 PM, dnadave [email protected] wrote:

image ID: 2504e529d3de

/home/dnadave> docker version
Client version: 1.3.1
Client API version: 1.15
Go version (client): go1.3.3
Git commit (client): 4e9bbfa
OS/Arch (client): linux/amd64
Server version: 1.3.1
Server API version: 1.15
Go version (server): go1.3.3
Git commit (server): 4e9bbfa

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#76 (comment).

Carl Boettiger
UC Santa Cruz
http://carlboettiger.info/

[dnadave]

It's running right now. I'll let you know if/when it becomes
unresponsive. It might be tomorrow before I get back to you as I'm about
to leave for home, if that's not a problem.
On Nov 5, 2014 4:34 PM, "Carl Boettiger" [email protected] wrote:

believe it or not, the log looks fine. It looks like this problem is
connected to your particular command, I was able to replicate (I think)
this error by running that specific command on a my tiny droplet, though
it
works fine on the image running locally.

Can you run docker pull rocker/rstudio and try this? For sake of
argument, can you confirm that this happens when you have only one
container instance running?

On Wed, Nov 5, 2014 at 3:52 PM, dnadave [email protected] wrote:

image ID: 2504e529d3de

/home/dnadave> docker version
Client version: 1.3.1
Client API version: 1.15
Go version (client): go1.3.3
Git commit (client): 4e9bbfa
OS/Arch (client): linux/amd64
Server version: 1.3.1
Server API version: 1.15
Go version (server): go1.3.3
Git commit (server): 4e9bbfa

—
Reply to this email directly or view it on GitHub
#76 (comment).

Carl Boettiger
UC Santa Cruz
http://carlboettiger.info/

—
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#76 (comment).

[cboettig]

Yup, let me know. Also if you haven't already tested it, you might just
want to confirm that you can run this command successfully on a container
that isn't running RStudio, e.g.

docker run --rm -it rocker/r-base R
source('http://bioconductor.org/biocLite.R'); biocLite(all_group())

and make sure that runs successfully first. Looks like you're installing
all of bioconductor from source with that command, so I wouldna be too
surprised that something might go wrong that's not directly related to
RStudio....

On Wed, Nov 5, 2014 at 4:52 PM, David Henderson [email protected]
wrote:

It's running right now. I'll let you know if/when it becomes
unresponsive. It might be tomorrow before I get back to you as I'm about
to leave for home, if that's not a problem.
On Nov 5, 2014 4:34 PM, "Carl Boettiger" [email protected]
wrote:

believe it or not, the log looks fine. It looks like this problem is
connected to your particular command, I was able to replicate (I think)
this error by running that specific command on a my tiny droplet, though
it
works fine on the image running locally.

Can you run docker pull rocker/rstudio and try this? For sake of
argument, can you confirm that this happens when you have only one
container instance running?

On Wed, Nov 5, 2014 at 3:52 PM, dnadave [email protected]
wrote:

image ID: 2504e529d3de

/home/dnadave> docker version
Client version: 1.3.1
Client API version: 1.15
Go version (client): go1.3.3
Git commit (client): 4e9bbfa
OS/Arch (client): linux/amd64
Server version: 1.3.1
Server API version: 1.15
Go version (server): go1.3.3
Git commit (server): 4e9bbfa

—
Reply to this email directly or view it on GitHub
#76 (comment).

Carl Boettiger
UC Santa Cruz
http://carlboettiger.info/

—
Reply to this email directly or view it on GitHub
#76 (comment).

—
Reply to this email directly or view it on GitHub
#76 (comment).

Carl Boettiger
UC Santa Cruz
http://carlboettiger.info/

[dnadave]

It was basically unresponsive when I came in this morning. You do finally
get a click response, but it takes about 5-6 minutes to register.

I am installing all of Bioconductor. We're wanting to have a generic
container to load for all of the types of analyses we get contracted to
perform. Many of these require 32-48GB RAM to complete. We're hoping to
replace our hypervisor approach to managing resources with containers.

I'll try using the rbase container and see if I get the same results.

Thanks!!

Dave H
On Nov 5, 2014 8:12 PM, "Carl Boettiger" [email protected] wrote:

Yup, let me know. Also if you haven't already tested it, you might just
want to confirm that you can run this command successfully on a container
that isn't running RStudio, e.g.

docker run --rm -it rocker/r-base R
source('http://bioconductor.org/biocLite.R'); biocLite(all_group())

and make sure that runs successfully first. Looks like you're installing
all of bioconductor from source with that command, so I wouldna be too
surprised that something might go wrong that's not directly related to
RStudio....

On Wed, Nov 5, 2014 at 4:52 PM, David Henderson [email protected]

wrote:

It's running right now. I'll let you know if/when it becomes
unresponsive. It might be tomorrow before I get back to you as I'm about
to leave for home, if that's not a problem.
On Nov 5, 2014 4:34 PM, "Carl Boettiger" [email protected]
wrote:

believe it or not, the log looks fine. It looks like this problem is
connected to your particular command, I was able to replicate (I
think)
this error by running that specific command on a my tiny droplet,
though
it
works fine on the image running locally.

Can you run docker pull rocker/rstudio and try this? For sake of
argument, can you confirm that this happens when you have only one
container instance running?

On Wed, Nov 5, 2014 at 3:52 PM, dnadave [email protected]
wrote:

image ID: 2504e529d3de

/home/dnadave> docker version
Client version: 1.3.1
Client API version: 1.15
Go version (client): go1.3.3
Git commit (client): 4e9bbfa
OS/Arch (client): linux/amd64
Server version: 1.3.1
Server API version: 1.15
Go version (server): go1.3.3
Git commit (server): 4e9bbfa

—
Reply to this email directly or view it on GitHub
<
https://github.com/rocker-org/rocker/issues/76#issuecomment-61904227>.

Carl Boettiger
UC Santa Cruz
http://carlboettiger.info/

—
Reply to this email directly or view it on GitHub
#76 (comment).

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#76 (comment).

Carl Boettiger
UC Santa Cruz
http://carlboettiger.info/

—
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#76 (comment).

[dnadave]

The rbase container cannot connect to the internet. I can't even ping
anything.
On Nov 6, 2014 10:23 AM, "David Henderson" [email protected] wrote:

It was basically unresponsive when I came in this morning. You do finally
get a click response, but it takes about 5-6 minutes to register.

I am installing all of Bioconductor. We're wanting to have a generic
container to load for all of the types of analyses we get contracted to
perform. Many of these require 32-48GB RAM to complete. We're hoping to
replace our hypervisor approach to managing resources with containers.

I'll try using the rbase container and see if I get the same results.

Thanks!!

Dave H
On Nov 5, 2014 8:12 PM, "Carl Boettiger" [email protected] wrote:

Yup, let me know. Also if you haven't already tested it, you might just
want to confirm that you can run this command successfully on a container
that isn't running RStudio, e.g.

docker run --rm -it rocker/r-base R
source('http://bioconductor.org/biocLite.R'); biocLite(all_group())

and make sure that runs successfully first. Looks like you're installing
all of bioconductor from source with that command, so I wouldna be too
surprised that something might go wrong that's not directly related to
RStudio....

On Wed, Nov 5, 2014 at 4:52 PM, David Henderson [email protected]

wrote:

It's running right now. I'll let you know if/when it becomes
unresponsive. It might be tomorrow before I get back to you as I'm
about
to leave for home, if that's not a problem.
On Nov 5, 2014 4:34 PM, "Carl Boettiger" [email protected]
wrote:

believe it or not, the log looks fine. It looks like this problem is
connected to your particular command, I was able to replicate (I
think)
this error by running that specific command on a my tiny droplet,
though
it
works fine on the image running locally.

Can you run docker pull rocker/rstudio and try this? For sake of
argument, can you confirm that this happens when you have only one
container instance running?

On Wed, Nov 5, 2014 at 3:52 PM, dnadave [email protected]
wrote:

image ID: 2504e529d3de

/home/dnadave> docker version
Client version: 1.3.1
Client API version: 1.15
Go version (client): go1.3.3
Git commit (client): 4e9bbfa
OS/Arch (client): linux/amd64
Server version: 1.3.1
Server API version: 1.15
Go version (server): go1.3.3
Git commit (server): 4e9bbfa

—
Reply to this email directly or view it on GitHub
<
https://github.com/rocker-org/rocker/issues/76#issuecomment-61904227>.

Carl Boettiger
UC Santa Cruz
http://carlboettiger.info/

—
Reply to this email directly or view it on GitHub
#76 (comment).

—
Reply to this email directly or view it on GitHub
#76 (comment).

Carl Boettiger
UC Santa Cruz
http://carlboettiger.info/

—
Reply to this email directly or view it on GitHub
#76 (comment).

[cboettig]

That's very strange. I have no trouble pinging or installing things from
r-base.

I ran the same command overnight on my laptop in the rstudio container,
which finished without stalling or freezing, though I got error messages
about several packages being unavailable (possibly due to my inadequate
network connectivity).

It looks like I was running out of disk space when I was getting the errors
with my wimpy DO droplet. Still a bit puzzled why this should freeze for
you.

On Thu, Nov 6, 2014 at 10:23 AM, David Henderson [email protected]
wrote:

It was basically unresponsive when I came in this morning. You do finally
get a click response, but it takes about 5-6 minutes to register.

I am installing all of Bioconductor. We're wanting to have a generic
container to load for all of the types of analyses we get contracted to
perform. Many of these require 32-48GB RAM to complete. We're hoping to
replace our hypervisor approach to managing resources with containers.

I'll try using the rbase container and see if I get the same results.

Thanks!!

Dave H
On Nov 5, 2014 8:12 PM, "Carl Boettiger" [email protected]
wrote:

Yup, let me know. Also if you haven't already tested it, you might just
want to confirm that you can run this command successfully on a
container
that isn't running RStudio, e.g.

docker run --rm -it rocker/r-base R
source('http://bioconductor.org/biocLite.R'); biocLite(all_group())

and make sure that runs successfully first. Looks like you're installing
all of bioconductor from source with that command, so I wouldna be too
surprised that something might go wrong that's not directly related to
RStudio....

On Wed, Nov 5, 2014 at 4:52 PM, David Henderson <
[email protected]>

wrote:

It's running right now. I'll let you know if/when it becomes
unresponsive. It might be tomorrow before I get back to you as I'm
about
to leave for home, if that's not a problem.
On Nov 5, 2014 4:34 PM, "Carl Boettiger" [email protected]
wrote:

believe it or not, the log looks fine. It looks like this problem is
connected to your particular command, I was able to replicate (I
think)
this error by running that specific command on a my tiny droplet,
though
it
works fine on the image running locally.

Can you run docker pull rocker/rstudio and try this? For sake of
argument, can you confirm that this happens when you have only one
container instance running?

On Wed, Nov 5, 2014 at 3:52 PM, dnadave [email protected]
wrote:

image ID: 2504e529d3de

/home/dnadave> docker version
Client version: 1.3.1
Client API version: 1.15
Go version (client): go1.3.3
Git commit (client): 4e9bbfa
OS/Arch (client): linux/amd64
Server version: 1.3.1
Server API version: 1.15
Go version (server): go1.3.3
Git commit (server): 4e9bbfa

—
Reply to this email directly or view it on GitHub
<
https://github.com/rocker-org/rocker/issues/76#issuecomment-61904227>.

Carl Boettiger
UC Santa Cruz
http://carlboettiger.info/

—
Reply to this email directly or view it on GitHub
<
https://github.com/rocker-org/rocker/issues/76#issuecomment-61908423>.

—
Reply to this email directly or view it on GitHub
#76 (comment).

Carl Boettiger
UC Santa Cruz
http://carlboettiger.info/

—
Reply to this email directly or view it on GitHub
#76 (comment).

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#76 (comment).

Carl Boettiger
UC Santa Cruz
http://carlboettiger.info/

[eddelbuettel]

May we call this a local issue, or (as Carl suggested) related to a big BioC install, or ...

I "sort of forgot" I had a test instance of Rocker's rstudio running via boot2docker. If it stays up on friggin' Windows for a week, then I strongly suspect something else is going on at your end.

[dnadave]

I thought the no network thing strange, too. Especially since the network
works fine for the rstudio container.
On Nov 6, 2014 10:29 AM, "Carl Boettiger" [email protected] wrote:

That's very strange. I have no trouble pinging or installing things from
r-base.

I ran the same command overnight on my laptop in the rstudio container,
which finished without stalling or freezing, though I got error messages
about several packages being unavailable (possibly due to my inadequate
network connectivity).

It looks like I was running out of disk space when I was getting the errors
with my wimpy DO droplet. Still a bit puzzled why this should freeze for
you.

On Thu, Nov 6, 2014 at 10:23 AM, David Henderson [email protected]
wrote:

It was basically unresponsive when I came in this morning. You do finally
get a click response, but it takes about 5-6 minutes to register.

I am installing all of Bioconductor. We're wanting to have a generic
container to load for all of the types of analyses we get contracted to
perform. Many of these require 32-48GB RAM to complete. We're hoping to
replace our hypervisor approach to managing resources with containers.

I'll try using the rbase container and see if I get the same results.

Thanks!!

Dave H
On Nov 5, 2014 8:12 PM, "Carl Boettiger" [email protected]
wrote:

Yup, let me know. Also if you haven't already tested it, you might just
want to confirm that you can run this command successfully on a
container
that isn't running RStudio, e.g.

docker run --rm -it rocker/r-base R
source('http://bioconductor.org/biocLite.R'); biocLite(all_group())

and make sure that runs successfully first. Looks like you're
installing
all of bioconductor from source with that command, so I wouldna be too
surprised that something might go wrong that's not directly related to
RStudio....

On Wed, Nov 5, 2014 at 4:52 PM, David Henderson <
[email protected]>

wrote:

It's running right now. I'll let you know if/when it becomes
unresponsive. It might be tomorrow before I get back to you as I'm
about
to leave for home, if that's not a problem.
On Nov 5, 2014 4:34 PM, "Carl Boettiger" [email protected]
wrote:

believe it or not, the log looks fine. It looks like this problem
is
connected to your particular command, I was able to replicate (I
think)
this error by running that specific command on a my tiny droplet,
though
it
works fine on the image running locally.

Can you run docker pull rocker/rstudio and try this? For sake of
argument, can you confirm that this happens when you have only one
container instance running?

On Wed, Nov 5, 2014 at 3:52 PM, dnadave [email protected]
wrote:

image ID: 2504e529d3de

/home/dnadave> docker version
Client version: 1.3.1
Client API version: 1.15
Go version (client): go1.3.3
Git commit (client): 4e9bbfa
OS/Arch (client): linux/amd64
Server version: 1.3.1
Server API version: 1.15
Go version (server): go1.3.3
Git commit (server): 4e9bbfa

—
Reply to this email directly or view it on GitHub
<
https://github.com/rocker-org/rocker/issues/76#issuecomment-61904227>.

Carl Boettiger
UC Santa Cruz
http://carlboettiger.info/

—
Reply to this email directly or view it on GitHub
<
https://github.com/rocker-org/rocker/issues/76#issuecomment-61908423>.

—
Reply to this email directly or view it on GitHub
#76 (comment).

Carl Boettiger
UC Santa Cruz
http://carlboettiger.info/

—
Reply to this email directly or view it on GitHub
#76 (comment).

—
Reply to this email directly or view it on GitHub
#76 (comment).

Carl Boettiger
UC Santa Cruz
http://carlboettiger.info/

—
Reply to this email directly or view it on GitHub
#76 (comment).

[dnadave]

I also can't find netstat or ifconfig on the rbase container.
On Nov 6, 2014 10:29 AM, "Carl Boettiger" [email protected] wrote:

That's very strange. I have no trouble pinging or installing things from
r-base.

I ran the same command overnight on my laptop in the rstudio container,
which finished without stalling or freezing, though I got error messages
about several packages being unavailable (possibly due to my inadequate
network connectivity).

It looks like I was running out of disk space when I was getting the
errors
with my wimpy DO droplet. Still a bit puzzled why this should freeze for
you.

On Thu, Nov 6, 2014 at 10:23 AM, David Henderson [email protected]

wrote:

It was basically unresponsive when I came in this morning. You do
finally
get a click response, but it takes about 5-6 minutes to register.

I am installing all of Bioconductor. We're wanting to have a generic
container to load for all of the types of analyses we get contracted to
perform. Many of these require 32-48GB RAM to complete. We're hoping to
replace our hypervisor approach to managing resources with containers.

I'll try using the rbase container and see if I get the same results.

Thanks!!

Dave H
On Nov 5, 2014 8:12 PM, "Carl Boettiger" [email protected]
wrote:

Yup, let me know. Also if you haven't already tested it, you might
just
want to confirm that you can run this command successfully on a
container
that isn't running RStudio, e.g.

docker run --rm -it rocker/r-base R
source('http://bioconductor.org/biocLite.R'); biocLite(all_group())

and make sure that runs successfully first. Looks like you're
installing
all of bioconductor from source with that command, so I wouldna be too
surprised that something might go wrong that's not directly related to
RStudio....

On Wed, Nov 5, 2014 at 4:52 PM, David Henderson <
[email protected]>

wrote:

It's running right now. I'll let you know if/when it becomes
unresponsive. It might be tomorrow before I get back to you as I'm
about
to leave for home, if that's not a problem.
On Nov 5, 2014 4:34 PM, "Carl Boettiger" [email protected]
wrote:

believe it or not, the log looks fine. It looks like this problem
is
connected to your particular command, I was able to replicate (I
think)
this error by running that specific command on a my tiny droplet,
though
it
works fine on the image running locally.

Can you run docker pull rocker/rstudio and try this? For sake of
argument, can you confirm that this happens when you have only one
container instance running?

On Wed, Nov 5, 2014 at 3:52 PM, dnadave [email protected]

wrote:

image ID: 2504e529d3de

/home/dnadave> docker version
Client version: 1.3.1
Client API version: 1.15
Go version (client): go1.3.3
Git commit (client): 4e9bbfa
OS/Arch (client): linux/amd64
Server version: 1.3.1
Server API version: 1.15
Go version (server): go1.3.3
Git commit (server): 4e9bbfa

—
Reply to this email directly or view it on GitHub
<
https://github.com/rocker-org/rocker/issues/76#issuecomment-61904227>.

Carl Boettiger
UC Santa Cruz
http://carlboettiger.info/

—
Reply to this email directly or view it on GitHub
<
https://github.com/rocker-org/rocker/issues/76#issuecomment-61908423>.

—
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<
https://github.com/rocker-org/rocker/issues/76#issuecomment-61910249>.

Carl Boettiger
UC Santa Cruz
http://carlboettiger.info/

—
Reply to this email directly or view it on GitHub
#76 (comment).

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Reply to this email directly or view it on GitHub
#76 (comment).

Carl Boettiger
UC Santa Cruz
http://carlboettiger.info/

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#76 (comment).

[cboettig]

You can apt-get install any tool you need. (or not I guess, if you don't
have network connectivity). I'd suggest you find or create a separate
Docker image that has the tools you need to debug this though; we can't
replicate your issue and debugging docker internet connections is beyond
our scope here.

On Thu, Nov 6, 2014 at 10:36 AM, David Henderson [email protected]
wrote:

I also can't find netstat or ifconfig on the rbase container.
On Nov 6, 2014 10:29 AM, "Carl Boettiger" [email protected]
wrote:

That's very strange. I have no trouble pinging or installing things from
r-base.

I ran the same command overnight on my laptop in the rstudio container,
which finished without stalling or freezing, though I got error messages
about several packages being unavailable (possibly due to my inadequate
network connectivity).

It looks like I was running out of disk space when I was getting the
errors
with my wimpy DO droplet. Still a bit puzzled why this should freeze for
you.

On Thu, Nov 6, 2014 at 10:23 AM, David Henderson <
[email protected]>

wrote:

It was basically unresponsive when I came in this morning. You do
finally
get a click response, but it takes about 5-6 minutes to register.

I am installing all of Bioconductor. We're wanting to have a generic
container to load for all of the types of analyses we get contracted
to
perform. Many of these require 32-48GB RAM to complete. We're hoping
to
replace our hypervisor approach to managing resources with containers.

I'll try using the rbase container and see if I get the same results.

Thanks!!

Dave H
On Nov 5, 2014 8:12 PM, "Carl Boettiger" [email protected]
wrote:

Yup, let me know. Also if you haven't already tested it, you might
just
want to confirm that you can run this command successfully on a
container
that isn't running RStudio, e.g.

docker run --rm -it rocker/r-base R
source('http://bioconductor.org/biocLite.R'); biocLite(all_group())

and make sure that runs successfully first. Looks like you're
installing
all of bioconductor from source with that command, so I wouldna be
too
surprised that something might go wrong that's not directly related
to
RStudio....

On Wed, Nov 5, 2014 at 4:52 PM, David Henderson <
[email protected]>

wrote:

It's running right now. I'll let you know if/when it becomes
unresponsive. It might be tomorrow before I get back to you as I'm
about
to leave for home, if that's not a problem.
On Nov 5, 2014 4:34 PM, "Carl Boettiger" [email protected]

wrote:

believe it or not, the log looks fine. It looks like this
problem
is
connected to your particular command, I was able to replicate (I
think)
this error by running that specific command on a my tiny
droplet,
though
it
works fine on the image running locally.

Can you run docker pull rocker/rstudio and try this? For sake
of
argument, can you confirm that this happens when you have only
one
container instance running?

On Wed, Nov 5, 2014 at 3:52 PM, dnadave <
[email protected]>

wrote:

image ID: 2504e529d3de

/home/dnadave> docker version
Client version: 1.3.1
Client API version: 1.15
Go version (client): go1.3.3
Git commit (client): 4e9bbfa
OS/Arch (client): linux/amd64
Server version: 1.3.1
Server API version: 1.15
Go version (server): go1.3.3
Git commit (server): 4e9bbfa

—
Reply to this email directly or view it on GitHub
<
https://github.com/rocker-org/rocker/issues/76#issuecomment-61904227>.

Carl Boettiger
UC Santa Cruz
http://carlboettiger.info/

—
Reply to this email directly or view it on GitHub
<
https://github.com/rocker-org/rocker/issues/76#issuecomment-61908423>.

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https://github.com/rocker-org/rocker/issues/76#issuecomment-61910249>.

Carl Boettiger
UC Santa Cruz
http://carlboettiger.info/

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<
https://github.com/rocker-org/rocker/issues/76#issuecomment-61925280>.

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#76 (comment).

Carl Boettiger
UC Santa Cruz
http://carlboettiger.info/

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#76 (comment).

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#76 (comment).

Carl Boettiger
UC Santa Cruz
http://carlboettiger.info/

[dnadave]

I have to say it is a bit weird. I first tried some of the standard docker
tools in the docker tutorials and had networking, etc.

One thing I've found is that I can ping internal IPs by address, but name
resolution is not working, even if I specify a DNS server in the docker
command. I cannot ping google even if I specify the IP address.
On Nov 6, 2014 10:41 AM, "Carl Boettiger" [email protected] wrote:

You can apt-get install any tool you need. (or not I guess, if you don't
have network connectivity). I'd suggest you find or create a separate
Docker image that has the tools you need to debug this though; we can't
replicate your issue and debugging docker internet connections is beyond
our scope here.

On Thu, Nov 6, 2014 at 10:36 AM, David Henderson [email protected]

wrote:

I also can't find netstat or ifconfig on the rbase container.
On Nov 6, 2014 10:29 AM, "Carl Boettiger" [email protected]
wrote:

That's very strange. I have no trouble pinging or installing things
from
r-base.

I ran the same command overnight on my laptop in the rstudio
container,
which finished without stalling or freezing, though I got error
messages
about several packages being unavailable (possibly due to my
inadequate
network connectivity).

It looks like I was running out of disk space when I was getting the
errors
with my wimpy DO droplet. Still a bit puzzled why this should freeze
for
you.

On Thu, Nov 6, 2014 at 10:23 AM, David Henderson <
[email protected]>

wrote:

It was basically unresponsive when I came in this morning. You do
finally
get a click response, but it takes about 5-6 minutes to register.

I am installing all of Bioconductor. We're wanting to have a generic
container to load for all of the types of analyses we get contracted
to
perform. Many of these require 32-48GB RAM to complete. We're hoping
to
replace our hypervisor approach to managing resources with
containers.

I'll try using the rbase container and see if I get the same
results.

Thanks!!

Dave H
On Nov 5, 2014 8:12 PM, "Carl Boettiger" [email protected]
wrote:

Yup, let me know. Also if you haven't already tested it, you might
just
want to confirm that you can run this command successfully on a
container
that isn't running RStudio, e.g.

docker run --rm -it rocker/r-base R
source('http://bioconductor.org/biocLite.R');
biocLite(all_group())

and make sure that runs successfully first. Looks like you're
installing
all of bioconductor from source with that command, so I wouldna be
too
surprised that something might go wrong that's not directly
related
to
RStudio....

On Wed, Nov 5, 2014 at 4:52 PM, David Henderson <
[email protected]>

wrote:

It's running right now. I'll let you know if/when it becomes
unresponsive. It might be tomorrow before I get back to you as
I'm
about
to leave for home, if that's not a problem.
On Nov 5, 2014 4:34 PM, "Carl Boettiger" <
[email protected]>

wrote:

believe it or not, the log looks fine. It looks like this
problem
is
connected to your particular command, I was able to replicate
(I
think)
this error by running that specific command on a my tiny
droplet,
though
it
works fine on the image running locally.

Can you run docker pull rocker/rstudio and try this? For
sake
of
argument, can you confirm that this happens when you have only
one
container instance running?

On Wed, Nov 5, 2014 at 3:52 PM, dnadave <
[email protected]>

wrote:

image ID: 2504e529d3de

/home/dnadave> docker version
Client version: 1.3.1
Client API version: 1.15
Go version (client): go1.3.3
Git commit (client): 4e9bbfa
OS/Arch (client): linux/amd64
Server version: 1.3.1
Server API version: 1.15
Go version (server): go1.3.3
Git commit (server): 4e9bbfa

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Carl Boettiger
UC Santa Cruz
http://carlboettiger.info/

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[eddelbuettel]

I'll close this as a mostly local issue, ok?