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? Thanks much for your help, Simone [[alternative HTML version deleted]]
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]] > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.-- Rainer M. Krug email: Rainer<at>krugs<dot>de PGP: 0x0F52F982 -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 454 bytes Desc: not available URL: <https://stat.ethz.ch/pipermail/r-help/attachments/20160906/0283a3db/attachment.bin>
Please reply to the mailing list to keep the conversation available for everybody. I Send this mail to the mailing list as well. 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. 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]] > > > > ______________________________________________ > > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. > > -- > 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 Tel : +33 - (0)9 53 10 27 44 Cell: +33 - (0)6 85 62 59 98 Fax : +33 - (0)9 58 10 27 44 Fax (D): +49 - (0)3 21 21 25 22 44 email: Rainer at krugs.de Skype: RMkrug PGP: 0x0F52F982 -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 454 bytes Desc: not available URL: <https://stat.ethz.ch/pipermail/r-help/attachments/20160906/530a0360/attachment.bin>
On 06 Sep 2016, at 11:00 , Rainer M Krug <Rainer at krugs.de> wrote:> Please reply to the mailing list to keep the conversation available for > everybody. I Send this mail to the mailing list as well. > > 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. > > In this case, your best bet is trying to mount an a flder from your > client on the server and than save there.I think you can in principle do something with a socketConnection and SSH port forwarding, but it is not trivial.> Contact you administrator to find out if this is possible or (s)he has > other suggestions. >yep.>> 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]] >>> >>> ______________________________________________ >>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >>> https://stat.ethz.ch/mailman/listinfo/r-help >>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >>> and provide commented, minimal, self-contained, reproducible code. >> >> -- >> 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 > > Tel : +33 - (0)9 53 10 27 44 > Cell: +33 - (0)6 85 62 59 98 > Fax : +33 - (0)9 58 10 27 44 > > Fax (D): +49 - (0)3 21 21 25 22 44 > > email: Rainer at krugs.de > > Skype: RMkrug > > PGP: 0x0F52F982 > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.-- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
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 > everybody. I Send this mail to the mailing list as well. > > 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]] >> > >> > ______________________________________________ >> > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >> > https://stat.ethz.ch/mailman/listinfo/r-help >> > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >> > and provide commented, minimal, self-contained, reproducible code. >> >> -- >> 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 > > Tel : +33 - (0)9 53 10 27 44 > Cell: +33 - (0)6 85 62 59 98 > Fax : +33 - (0)9 58 10 27 44 > > Fax (D): +49 - (0)3 21 21 25 22 44 > > email: Rainer at krugs.de > > Skype: RMkrug > > PGP: 0x0F52F982 > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.