[R] save R object into a remote directory

[Henrik Bengtsson]

On Tue, Sep 6, 2016 at 2:00 AM, Rainer M Krug <Rainer at krugs.de> wrote:
> Please reply to the mailing list to keep the conversation available for
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>
> Simone Tenan <tenan.simone at gmail.com> writes:
>
>> Thanks Rainer,
>> it's very kind of you.
>> Unfortunately, I cannot save the (large) R object where the current R session is running. There is not enough memory and when I tried I got the error "error
>> writing to connection".
>
> OK - essential piece of information.

Assuming the remote machine you're logging into is running Linux:

Before anything else, did you try to save elsewhere than to your
/home/ folder/account? Try /tmp/.  That probably / hopefully doesn't
count to your account quota (and it gets wiped at every reboot).
There's also /var/tmp/ (a bit more persistent storage - survives
reboots).

/Henrik

PS. In R, the tempdir() function often points to a directory under
/tmp/, e.g.  tempdir() => "/tmp/RtmpWZPsip".  However, that will be
wiped by R itself when you quit the R session, so if you use tempdir()
you need to scp that file before you quit R.  It's probably better to
avoid tempdir() in your case.

>
> In this case, your best bet is trying to mount an a flder from your
> client on the server and than save there.
>
> Contact you administrator to find out if this is possible or (s)he has
> other suggestions.
>
>> For that reason I was trying to save the object of of the remote server.
>>
>> Best,
>
> Cheers,
>
> Rainer
>
>> Simone
>>
>> On 6 September 2016 at 10:30, Rainer M Krug <Rainer at krugs.de> wrote:
>>
>>  Simone Tenan <tenan.simone at gmail.com> writes:
>>
>>  > Hi all,
>>  > I'm using R remotely via ssh connection in linux. I need to save a large R
>>  > object from the remote server to my laptop. How can I specify the path in
>>  > the save() function?
>>
>>  You are working on the remote machine and there is no way that you can
>>  specify "out of the box" a save to client machine (I stand to be corrected).
>>
>>  You could mount a directory on the client on the server, but I would
>>  suggest to
>>
>>  1) save the object on the server (the where R is running on)
>>  2) use scp from the client to copy the file from the server to the
>>  client (the one you are typing on).
>>
>>  scp user at host1:file1 ./TheNameOfTheLocalFile
>>
>>  Cheers,
>>
>>  Rainer
>>
>>  >
>>  > Thanks much for your help,
>>  > Simone
>>  >
>>  > [[alternative HTML version deleted]]
>>  >
>>  > ______________________________________________
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>>
>>  --
>>  Rainer M. Krug
>>  email: Rainer<at>krugs<dot>de
>>  PGP: 0x0F52F982
>>
>>
>
> --
> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)
>
> Centre of Excellence for Invasion Biology
> Stellenbosch University
> South Africa
>
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> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.