R SIG Debian - Jan 2012 - [R] fix and edit don't work: unable to open X Input

(moved from R-help)

I tried this on Ubuntu with R-2.14.1 built from source, and I do not get 
the segfault problem. (I don't at the moment have a debian binary R, or 
I would confirm whether I get the segfault problem.) My sessioninfo() is 
reporting additional information about namespace imports:

 > library(ggplot2)
Loading required package: reshape
Loading required package: plyr

Attaching package: ?reshape?

The following object(s) are masked from ?package:plyr?:

rename, round_any

Loading required package: grid
Loading required package: proto
 > sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: i686-pc-linux-gnu (32-bit)

locale:
[1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8
[5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] grid stats graphics grDevices utils datasets methods
[8] base

other attached packages:
[1] ggplot2_0.8.9 proto_0.3-9.2 reshape_0.8.4 plyr_1.7.1

loaded via a namespace (and not attached):
[1] tcltk_2.14.1 tools_2.14.1
 > fix(mpg)
 >

Paul Gilbert
> Date: Sun, 8 Jan 2012 15:32:49 -0600 From: Paul Johnson 
> <pauljohn32 at gmail.com> To: R-help <r-help at r-project.org>
Subject: [R]
> fix and edit don't work: unable to open X Input Method->segfault 
> Message-ID: 
> <CAErODj9+Fbg9bbC_1X3Use8eQQoq+Mg4Nb0hH1Yr7YnGp6G21A at
mail.gmail.com>
> Content-Type: text/plain; charset=windows-1252 I can't run fix() or 
> edit() anymore. Did I break my system? I'm running Debian Linux with 
> R-2.14.1. As far as I can tell, the R packages came from Debian's 
> testing "wheezy" repository. I would like to know if users on
other
> types of systems see the same problem. If no, then, obviously, it is a 
> Debian-only issue and I can approach it from that point of view. And 
> if no other Debian users see same, it means it is a me-only problem, 
> and that's discouraging :) I get this same R crash whether I try fix 
> when R is running in a terminal or in Emacs with ESS. I've not seen 
> this before, but Google leads to some bug reports on Ubuntu in 2007, 
> where it was claimed that the problem was fixed. The really bad part 
> is that the second try causes a segmentation fault in R itself.
>> >  library(ggplot2)
> Loading required package: reshape
> Loading required package: plyr
>
> Attaching package: ?reshape?
>
> The following object(s) are masked from ?package:plyr?:
>
>      rename, round_any
>
> Loading required package: grid
> Loading required package: proto
>
>> >  sessionInfo()
> R version 2.14.1 (2011-12-22)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=C                 LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] ggplot2_0.8.9 proto_0.3-9.2 reshape_0.8.4 plyr_1.6
>> >  fix(mpg)
> Error in dataentry(datalist, modes) : invalid device
> In addition: Warning message:
> In edit.data.frame(get(subx, envir = parent), title = subx, ...) :
>    unable to open X Input Method
>> >  fix(mpg)
>   *** caught segfault ***
> address (nil), cause 'unknown'
>
> Traceback:
>   1: edit.data.frame(get(subx, envir = parent), title = subx, ...)
>   2: edit(get(subx, envir = parent), title = subx, ...)
>   3: fix(mpg)
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> Selection:
>
>
> Same happens no matter what packages are loaded, so far as I can tell.
>   Here it is without ggplot2, in case you were suspicious of those
> particular datasets.
>
>
>> >  library(datasets)
>> >  datasets()
> Error: could not find function "datasets"
>> >  help(package=datasets)
>> >  fix(CO2)
> Error in dataentry(datalist, modes) : invalid device
> In addition: Warning message:
> In edit.data.frame(get(subx, envir = parent), title = subx, ...) :
>    unable to open X Input Method
>
>
>
> -- Paul E. Johnson Professor, Political Science 1541 Lilac Lane, Room 
> 504 University of Kansas

Hi,

I just loaded ggplot2 and ran fix() both using R 2.14.1 from CRAN on Debian 
stable and Ubuntu 11.10 - no problems here . See one comment inline below.
> > Date: Sun, 8 Jan 2012 15:32:49 -0600 From: Paul Johnson
> > <pauljohn32 at gmail.com> To: R-help <r-help at
r-project.org> Subject: [R]
> > fix and edit don't work: unable to open X Input
Method->segfault
> > Message-ID:
> > <CAErODj9+Fbg9bbC_1X3Use8eQQoq+Mg4Nb0hH1Yr7YnGp6G21A at
mail.gmail.com>
> > Content-Type: text/plain; charset=windows-1252 I can't run fix()
or
> > edit() anymore. Did I break my system? I'm running Debian Linux
with
> > R-2.14.1. As far as I can tell, the R packages came from Debian's
> > testing "wheezy" repository. I would like to know if users
on other
> > types of systems see the same problem. If no, then, obviously, it is a
> > Debian-only issue and I can approach it from that point of view. And
> > if no other Debian users see same, it means it is a me-only problem,
> > and that's discouraging :) I get this same R crash whether I try
fix
> > when R is running in a terminal or in Emacs with ESS. I've not
seen
> > this before, but Google leads to some bug reports on Ubuntu in 2007,
> > where it was claimed that the problem was fixed. The really bad part
> > is that the second try causes a segmentation fault in R itself.
> > 
> >> >  library(ggplot2)
> > 
> > Loading required package: reshape
> > Loading required package: plyr
> > 
> > Attaching package: ?reshape?
> > 
> > The following object(s) are masked from ?package:plyr?:
> >      rename, round_any
> > 
> > Loading required package: grid
> > Loading required package: proto
> > 
> >> >  sessionInfo()
> > 
> > R version 2.14.1 (2011-12-22)
> > Platform: x86_64-pc-linux-gnu (64-bit)
> > 
> > locale:
> >   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> >   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> >   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
> >   [7] LC_PAPER=C                 LC_NAME=C
> >   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> > 
> > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> > 
> > attached base packages:
> > [1] grid      stats     graphics  grDevices utils     datasets 
methods
> > [8] base
> > 
> > other attached packages:
> > [1] ggplot2_0.8.9 proto_0.3-9.2 reshape_0.8.4 plyr_1.6
> > 
> >> >  fix(mpg)
> > 
> > Error in dataentry(datalist, modes) : invalid device
> > In addition: Warning message:
> > 
> > In edit.data.frame(get(subx, envir = parent), title = subx, ...) :
> >    unable to open X Input Method
Did you run R as root?

Kind regards,

Johannes

> >    
> >> >  fix(mpg)
> >   
> >   *** caught segfault ***
> > 
> > address (nil), cause 'unknown'
> > 
> > Traceback:
> >   1: edit.data.frame(get(subx, envir = parent), title = subx, ...)
> >   2: edit(get(subx, envir = parent), title = subx, ...)
> >   3: fix(mpg)
> > 
> > Possible actions:
> > 1: abort (with core dump, if enabled)
> > 2: normal R exit
> > 3: exit R without saving workspace
> > 4: exit R saving workspace
> > Selection:
> > 
> > 
> > Same happens no matter what packages are loaded, so far as I can tell.
> > 
> >   Here it is without ggplot2, in case you were suspicious of those
> > 
> > particular datasets.
> > 
> >> >  library(datasets)
> >> >  datasets()
> > 
> > Error: could not find function "datasets"
> > 
> >> >  help(package=datasets)
> >> >  fix(CO2)
> > 
> > Error in dataentry(datalist, modes) : invalid device
> > In addition: Warning message:
> > 
> > In edit.data.frame(get(subx, envir = parent), title = subx, ...) :
> >    unable to open X Input Method
> > 
> > -- Paul E. Johnson Professor, Political Science 1541 Lilac Lane, Room
> > 504 University of Kansas
> 
> _______________________________________________
> R-SIG-Debian mailing list
> R-SIG-Debian at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-debian

Thanks, Paul.

I'm not even sure r-sig-debian is the right place for me to whine
about this.  If other debian systems work, well, the problem can't be
the R package.

Checklist.

1. I'm not running R as root, nor am I remote (that was one suspicion)

2. Re-installed packages.  I configured a different CRAN repository,
at first I was encouraged because it seemed to be drawing in some
packages I was not aware of:


$ sudo apt-get install r-base r-base-dev
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following extra packages will be installed:
  cdbs dpatch gfortran libbz2-dev libjpeg8-dev libncurses5-dev libpcre3-dev
  libpcrecpp0 libreadline-dev libreadline6-dev libtinfo-dev patchutils
  r-base-html
Suggested packages:
  devscripts gfortran-multilib gfortran-doc ncurses-doc r-doc-info r-doc-pdf
The following NEW packages will be installed:
  cdbs dpatch gfortran libbz2-dev libjpeg8-dev libncurses5-dev libpcre3-dev
  libpcrecpp0 libreadline-dev libreadline6-dev libtinfo-dev patchutils r-base
  r-base-dev r-base-html
0 upgraded, 15 newly installed, 0 to remove and 8 not upgraded.
Need to get 1,877 kB of archives.
After this operation, 5,501 kB of additional disk space

===============
Oh, well. Start R, what do you get?
> fix(warpbreaks)
Error in dataentry(datalist, modes) : invalid device
In addition: Warning message:
In edit.data.frame(get(subx, envir = parent), title = subx, ...) :
  unable to open X Input Method

Bummer.
> sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base


3. Now, read the error message again. "X Input Method".

I've found the code where problem starts in R source.  I suspect my
locale and/or desktop environment and/or SCIM setup.  Here:

R-2.14.0/src/modules/X11/dataentry.c

  if(mbcslocale && DE->isEditor) {
        ioim = XOpenIM(iodisplay, NULL, NULL, NULL);
  if(!ioim) {
            XDestroyWindow(iodisplay, DE->iowindow);
            XCloseDisplay(iodisplay);
            warning("unable to open X Input Method");
            return TRUE;
        }

 XOpenIM has documentation, about complicated things like locale.
I'll report back if I find out what's wrong.

-- 
Paul E. Johnson
Professor, Political Science
1541 Lilac Lane, Room 504
University of Kansas