Re: [O] minor bug in babel with silent output and remote R session
Hi all, Thomas Alexander Gerds t...@biostat.ku.dk writes: Hi Bastien I think that I can describe the problem a bit better now. It is not related to the silent option but occurs whenever :results value. Emacs freezes due to the following line in org-babel-comint-eval-invisibly-and-wait-for-file (while (not (file-exists-p file)) (sit-for (or period 0.25))) sorry for hijacking this thread. With a quite useless message... I experience freezes at that exact position also on local sessions sometimes. I have never reported, because I can't send the scripts where this happens and slight modifications to the causing source block usually 'fix' this. So I failed in creating a reproducible example that I can send so far. The main purpose of this message is the hope, that someone else has experienced and solved that problem before (maybe changing some ESS-setup?). I will try more to get a reproducible example and report if I get one. Best, Andreas
Re: [O] minor bug in babel with silent output and remote R session
hmm. I agree that this should be handled by ESS and I have not given up yet.
as indicated in my previous mail, I dont know how to test if an
R-session is remote because the command ess-remote deletes all local
variables. a hack would be to let the R-process evaluate
file.exists((file-name-directory org-babel-temp-file))
thanks
Eric Schulte schulte.e...@gmail.com writes:
It is a shame that this can't be handled gracefully either through ESS
or R code.
I agree it would be nice to raise a warning rather than hang waiting
for a file which won't ever exist. So, how can we tell from the Babel
source if the R session is remote?
Thanks,
Thomas Alexander Gerds t...@biostat.ku.dk writes:
yes, I am using ESS. ess-remote allows me to evaluate R-code from
the local emacs-session on a remote machine connected to via ssh.
there are two problems:
1) the remote machine cannot write to org-babel-temp-file because
the tmp-directory exists on the local machine. here we could add
if(!file.exists(dirname(transfer.file))){dir.create(dirname(transfer.file))}
in the middle of the variable org-babel-R-write-object-command this
would achieve that the file is at least generated on the remote
host.
2) however, still the transfer file does not exist on the local
machine. there are several possiblities:
a) tell org-babel-comint-eval-invisibly-and-wait-for-file that the
file is remote and then test if (concat / username @ host :
file) exists instead of file.
b) use tramp to transfer the file from the remote to the local
machine. the function ssh does define ssh-host and ssh-username,
however, calling ess-remote removes these variables again.
c) tell org-babel-comint-eval-invisibly-and-wait-for-file not to
wait for file if it is remote
my conclusion: it would be nice to have this functionality, but
perhaps it is not worth the efforts and it would be sufficient to
avoid the endless loop when waiting for a file which never will
generated.
cheers thomas
Eric Schulte schulte.e...@gmail.com writes:
Bastien b...@gnu.org writes:
Hi Thomas, thanks for the follow-up. Thomas Alexander Gerds
t...@biostat.ku.dk writes:
I think that I can describe the problem a bit better now. It is
not related to the silent option but occurs whenever :results
value. Emacs freezes due to the following line in
org-babel-comint-eval-invisibly-and-wait-for-file (while (not
(file-exists-p file)) (sit-for (or period 0.25))) it seems that R
cannot transfer the file and hence this is an endless loop.
I'm not knowledgeable enough in this area to provide a fix, maybe
someone else will.
Could this be a problem with whatever tool (I'm assuming ESS) you
are using to maintain the R session and generate the R file?
Perhaps babel needs to modify the R code used to create the file
(held in the `org-babel-R-write-object-command' variable). Could
you take a shot at providing another version of this variable? I
don't really use R myself.
Thanks,
-- Thomas A. Gerds -- Assoc. Prof. Department of Biostatistics
University of Copenhagen, Øster Farimagsgade 5, 1014 Copenhagen,
Denmark Office: CSS-15.2.07 (Gamle Kommunehospital) tel: 35327914
(sec: 35327901)
--
Thomas A. Gerds -- Assoc. Prof. Department of Biostatistics
University of Copenhagen, Øster Farimagsgade 5, 1014 Copenhagen, Denmark
Office: CSS-15.2.07 (Gamle Kommunehospital)
tel: 35327914 (sec: 35327901)
Re: [O] minor bug in babel with silent output and remote R session
yes, I am using ESS. ess-remote allows me to evaluate R-code from the local
emacs-session on a remote machine connected to via ssh.
there are two problems:
1) the remote machine cannot write to org-babel-temp-file because the
tmp-directory exists on the local machine. here we could add
if(!file.exists(dirname(transfer.file))){dir.create(dirname(transfer.file))}
in the middle of the variable org-babel-R-write-object-command
this would achieve that the file is at least generated on the remote host.
2) however, still the transfer file does not exist on the local
machine. there are several possiblities:
a) tell org-babel-comint-eval-invisibly-and-wait-for-file
that the file is remote and then test if
(concat / username @ host : file) exists instead of file.
b) use tramp to transfer the file from the remote to the local
machine. the function ssh does define ssh-host and ssh-username,
however, calling ess-remote removes these variables again.
c) tell org-babel-comint-eval-invisibly-and-wait-for-file not to wait
for file if it is remote
my conclusion: it would be nice to have this functionality, but perhaps
it is not worth the efforts and it would be sufficient to avoid the
endless loop when waiting for a file which never will generated.
cheers thomas
Eric Schulte schulte.e...@gmail.com writes:
Bastien b...@gnu.org writes:
Hi Thomas,
thanks for the follow-up.
Thomas Alexander Gerds t...@biostat.ku.dk writes:
I think that I can describe the problem a bit better now. It is not
related to the silent option but occurs whenever :results value.
Emacs freezes due to the following line in
org-babel-comint-eval-invisibly-and-wait-for-file
(while (not (file-exists-p file)) (sit-for (or period 0.25)))
it seems that R cannot transfer the file and hence this is an
endless loop.
I'm not knowledgeable enough in this area to provide a fix, maybe
someone else will.
Could this be a problem with whatever tool (I'm assuming ESS) you are
using to maintain the R session and generate the R file?
Perhaps babel needs to modify the R code used to create the file (held
in the `org-babel-R-write-object-command' variable). Could you take a
shot at providing another version of this variable? I don't really
use R myself.
Thanks,
--
Thomas A. Gerds -- Assoc. Prof. Department of Biostatistics
University of Copenhagen, Øster Farimagsgade 5, 1014 Copenhagen, Denmark
Office: CSS-15.2.07 (Gamle Kommunehospital)
tel: 35327914 (sec: 35327901)
Re: [O] minor bug in babel with silent output and remote R session
It is a shame that this can't be handled gracefully either through ESS
or R code.
I agree it would be nice to raise a warning rather than hang waiting for
a file which won't ever exist. So, how can we tell from the Babel
source if the R session is remote?
Thanks,
Thomas Alexander Gerds t...@biostat.ku.dk writes:
yes, I am using ESS. ess-remote allows me to evaluate R-code from the local
emacs-session on a remote machine connected to via ssh.
there are two problems:
1) the remote machine cannot write to org-babel-temp-file because the
tmp-directory exists on the local machine. here we could add
if(!file.exists(dirname(transfer.file))){dir.create(dirname(transfer.file))}
in the middle of the variable org-babel-R-write-object-command
this would achieve that the file is at least generated on the remote host.
2) however, still the transfer file does not exist on the local
machine. there are several possiblities:
a) tell org-babel-comint-eval-invisibly-and-wait-for-file
that the file is remote and then test if
(concat / username @ host : file) exists instead of file.
b) use tramp to transfer the file from the remote to the local
machine. the function ssh does define ssh-host and ssh-username,
however, calling ess-remote removes these variables again.
c) tell org-babel-comint-eval-invisibly-and-wait-for-file not to wait
for file if it is remote
my conclusion: it would be nice to have this functionality, but perhaps
it is not worth the efforts and it would be sufficient to avoid the
endless loop when waiting for a file which never will generated.
cheers thomas
Eric Schulte schulte.e...@gmail.com writes:
Bastien b...@gnu.org writes:
Hi Thomas,
thanks for the follow-up.
Thomas Alexander Gerds t...@biostat.ku.dk writes:
I think that I can describe the problem a bit better now. It is not
related to the silent option but occurs whenever :results value.
Emacs freezes due to the following line in
org-babel-comint-eval-invisibly-and-wait-for-file
(while (not (file-exists-p file)) (sit-for (or period 0.25)))
it seems that R cannot transfer the file and hence this is an
endless loop.
I'm not knowledgeable enough in this area to provide a fix, maybe
someone else will.
Could this be a problem with whatever tool (I'm assuming ESS) you are
using to maintain the R session and generate the R file?
Perhaps babel needs to modify the R code used to create the file (held
in the `org-babel-R-write-object-command' variable). Could you take a
shot at providing another version of this variable? I don't really
use R myself.
Thanks,
--
Thomas A. Gerds -- Assoc. Prof. Department of Biostatistics
University of Copenhagen, Øster Farimagsgade 5, 1014 Copenhagen, Denmark
Office: CSS-15.2.07 (Gamle Kommunehospital)
tel: 35327914 (sec: 35327901)
--
Eric Schulte
http://cs.unm.edu/~eschulte
Re: [O] minor bug in babel with silent output and remote R session
Bastien b...@gnu.org writes: Hi Thomas, thanks for the follow-up. Thomas Alexander Gerds t...@biostat.ku.dk writes: I think that I can describe the problem a bit better now. It is not related to the silent option but occurs whenever :results value. Emacs freezes due to the following line in org-babel-comint-eval-invisibly-and-wait-for-file (while (not (file-exists-p file)) (sit-for (or period 0.25))) it seems that R cannot transfer the file and hence this is an endless loop. I'm not knowledgeable enough in this area to provide a fix, maybe someone else will. Could this be a problem with whatever tool (I'm assuming ESS) you are using to maintain the R session and generate the R file? Perhaps babel needs to modify the R code used to create the file (held in the `org-babel-R-write-object-command' variable). Could you take a shot at providing another version of this variable? I don't really use R myself. Thanks, -- Eric Schulte http://cs.unm.edu/~eschulte
Re: [O] minor bug in babel with silent output and remote R session
Hi Thomas, thanks for the follow-up. Thomas Alexander Gerds t...@biostat.ku.dk writes: I think that I can describe the problem a bit better now. It is not related to the silent option but occurs whenever :results value. Emacs freezes due to the following line in org-babel-comint-eval-invisibly-and-wait-for-file (while (not (file-exists-p file)) (sit-for (or period 0.25))) it seems that R cannot transfer the file and hence this is an endless loop. I'm not knowledgeable enough in this area to provide a fix, maybe someone else will. Best, -- Bastien
Re: [O] minor bug in babel with silent output and remote R session
Hi Bastien I think that I can describe the problem a bit better now. It is not related to the silent option but occurs whenever :results value. Emacs freezes due to the following line in org-babel-comint-eval-invisibly-and-wait-for-file (while (not (file-exists-p file)) (sit-for (or period 0.25))) it seems that R cannot transfer the file and hence this is an endless loop. it may be possible to fix this using tramp, e.g. by setting the default-directory in the buffer which runs the remote-session, or by adding a more thorough check of whether the R-session is remote. to this end let me note that there are at least two ways to start a remote R session in emacs: 1) M-x shell 2) M-x ssh via ssh.el (not part of emacs) Cheers Thomas Bastien b...@gnu.org writes: Hi Thomas, Thomas Alexander Gerds t...@biostat.ku.dk writes: Using the silent option together with a remote R session block (started via ssh.el and ess-remote), like this: #+BEGIN_SRC R :results silent :exports results :session *ssh gauss* :cache yes a=1 1 #+END_SRC produces: , |[1] 1 Warning message: | In file.rename(tfile, transfer.file) : cannot rename file | /tmp/RtmpQwlyCf/file7c9b78867f6c' to | /tmp/babel-4977UIT/R-4977ucf', reason 'No such file or directory' | ` and emacs freezes. No big deal because C-g gets me out of it, but slightly annoying. with `:results output' instead of `:results: silent' everything works fine. Please let us know if the documentation* needs some clarification here, or if this is a bug -- maybe someone will have time to look at it. Thanks, * Better to check against the latest documentation from our master branch, of course. -- Thomas A. Gerds -- Assoc. Prof. Department of Biostatistics University of Copenhagen, Øster Farimagsgade 5, 1014 Copenhagen, Denmark Office: CSS-15.2.07 (Gamle Kommunehospital) tel: 35327914 (sec: 35327901)
Re: [O] minor bug in babel with silent output and remote R session
Hi Thomas, Thomas Alexander Gerds t...@biostat.ku.dk writes: Using the silent option together with a remote R session block (started via ssh.el and ess-remote), like this: #+BEGIN_SRC R :results silent :exports results :session *ssh gauss* :cache yes a=1 1 #+END_SRC produces: , |[1] 1 | Warning message: | In file.rename(tfile, transfer.file) : | cannot rename file '/tmp/RtmpQwlyCf/file7c9b78867f6c' to '/tmp/babel-4977UIT/R-4977ucf', reason 'No such file or directory' | ` and emacs freezes. No big deal because C-g gets me out of it, but slightly annoying. with `:results output' instead of `:results: silent' everything works fine. Please let us know if the documentation* needs some clarification here, or if this is a bug -- maybe someone will have time to look at it. Thanks, * Better to check against the latest documentation from our master branch, of course. -- Bastien
Re: [O] minor bug in babel with silent output and remote R session
Bastien writes: #+BEGIN_SRC R :results silent :exports results :session *ssh gauss* :cache yes […] with `:results output' instead of `:results: silent' everything works fine. Please let us know if the documentation* needs some clarification here, or if this is a bug -- maybe someone will have time to look at it. Looking at the session argument it looks like this is supposed to be a remote R session. I'd think the session results would end up at the remote side and need to be copied from there. Regards, Achim. -- +[Q+ Matrix-12 WAVE#46+305 Neuron microQkb Andromeda XTk Blofeld]+ Samples for the Waldorf Blofeld: http://Synth.Stromeko.net/Downloads.html#BlofeldSamplesExtra
[O] minor bug in babel with silent output and remote R session
Using the silent option together with a remote R session block (started via ssh.el and ess-remote), like this: #+BEGIN_SRC R :results silent :exports results :session *ssh gauss* :cache yes a=1 1 #+END_SRC produces: , |[1] 1 | Warning message: | In file.rename(tfile, transfer.file) : | cannot rename file '/tmp/RtmpQwlyCf/file7c9b78867f6c' to '/tmp/babel-4977UIT/R-4977ucf', reason 'No such file or directory' | ` and emacs freezes. No big deal because C-g gets me out of it, but slightly annoying. with `:results output' instead of `:results: silent' everything works fine. best, Thomas
Re: [O] minor bug in babel with silent output and remote R session
Thomas Alexander Gerds t...@biostat.ku.dk writes: Using the silent option together with a remote R session block (started via ssh.el and ess-remote), like this: #+BEGIN_SRC R :results silent :exports results :session *ssh gauss* :cache yes a=1 1 #+END_SRC produces: , |[1] 1 | Warning message: | In file.rename(tfile, transfer.file) : | cannot rename file '/tmp/RtmpQwlyCf/file7c9b78867f6c' to | /tmp/babel-4977UIT/R-4977ucf', reason 'No such file or directory' | ` and emacs freezes. No big deal because C-g gets me out of it, but slightly annoying. with `:results output' instead of `:results: silent' everything works fine. Are you sure this problem is related to the :results silent header argument? I would expect this problem to arise *any* time results are requested from a remove R session. This is because R and Emacs use the file system to hand results back and forth, and when the R session refers to a remote file system, this communication fails. One possible solution would be to use the :dir header argument to specify to the code block the machine on which the execution is taking place. Best, best, Thomas -- Eric Schulte http://cs.unm.edu/~eschulte
Re: [O] minor bug in babel with silent output and remote R session
yes, I am quite sure. here is the org code , | | #+BEGIN_SRC R :results silent :exports results :session *ssh gauss* :cache yes | a=1 | 1 | #+END_SRC | | #+BEGIN_SRC R :results output :exports results :session *ssh gauss* :cache yes | a=1 | 1 | #+END_SRC | | #+RESULTS[2013-03-13 17:26:16 4d5d8eeab67e30060345cd66f44466bd168af55a]: | : [1] 1 ` and here the contents of the *ssh gauss* buffer , | | Last login: Wed Mar 13 08:41:53 2013 from 10.128.132.66 | IFSV default server Policy. | NFS monteret home under /home/ifsv | $ R | WARNING: ignoring environment value of R_HOME | | R version 2.15.2 (2012-10-26) -- Trick or Treat | Copyright (C) 2012 The R Foundation for Statistical Computing | ISBN 3-900051-07-0 | Platform: x86_64-unknown-linux-gnu (64-bit) | | R is free software and comes with ABSOLUTELY NO WARRANTY. | You are welcome to redistribute it under certain conditions. | Type 'license()' or 'licence()' for distribution details. | | Natural language support but running in an English locale | | R is a collaborative project with many contributors. | Type 'contributors()' for more information and | 'citation()' on how to cite R or R packages in publications. | | Type 'demo()' for some demos, 'help()' for on-line help, or | 'help.start()' for an HTML browser interface to help. | Type 'q()' to quit R. | | options(STERM='iESS', str.dendrogram.last=', editor='emacsclient', show.error.locations=TRUE) | [Previously saved workspace restored] | |[1] 1 | Warning message: | In file.rename(tfile, transfer.file) : | cannot rename file '/tmp/RtmpLkxWKf/file8bd75fb3ce' to '/tmp/babel-8270IwX/R-8270vVe', reason 'No such file or directory' | a=1 | 1 | 'org_babel_R_eoe' | a=1 | 1 | [1] 1 | 'org_babel_R_eoe' | [1] org_babel_R_eoe | ` cheers Thomas Eric Schulte schulte.e...@gmail.com writes: Thomas Alexander Gerds t...@biostat.ku.dk writes: Using the silent option together with a remote R session block (started via ssh.el and ess-remote), like this: #+BEGIN_SRC R :results silent :exports results :session *ssh gauss* :cache yes a=1 1 #+END_SRC produces: , |[1] 1 Warning message: | In file.rename(tfile, transfer.file) : cannot rename file | /tmp/RtmpQwlyCf/file7c9b78867f6c' to | /tmp/babel-4977UIT/R-4977ucf', reason 'No such file or directory' | ` and emacs freezes. No big deal because C-g gets me out of it, but slightly annoying. with `:results output' instead of `:results: silent' everything works fine. Are you sure this problem is related to the :results silent header argument? I would expect this problem to arise *any* time results are requested from a remove R session. This is because R and Emacs use the file system to hand results back and forth, and when the R session refers to a remote file system, this communication fails. One possible solution would be to use the :dir header argument to specify to the code block the machine on which the execution is taking place. Best, best, Thomas
