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Paul Gilbert | 9 Jan 2012 16:08
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Re: [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
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Johannes Ranke | 9 Jan 2012 22:17
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Re: [R] fix and edit don't work: unable to open X Input

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?
> >
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Paul Johnson | 10 Jan 2012 06:37
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Re: [R] fix and edit don't work: unable to open X Input

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.
(Continue reading)

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Dirk Eddelbuettel | 10 Jan 2012 06:53
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Re: [R] fix and edit don't work: unable to open X Input


Do you have x11 setup right?  Ie can you do (outside of R) 'xterm &' or
'xclock &' ?

In case you ssh to your machine, set the option in the config file, or use
'ssh -X some.where.com'.

Dirk

--

-- 
"Outside of a dog, a book is a man's best friend. Inside of a dog, it is too
dark to read." -- Groucho Marx
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Paul Johnson | 11 Jan 2012 00:02
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Re: [R] fix and edit don't work: unable to open X Input

Solution! In case you see this error:

On Mon, Jan 9, 2012 at 11:37 PM, Paul Johnson <pauljohn32 <at> gmail.com> wrote:
>
>> 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
>

The problem is a stray or mistaken configuration for multi-character
languages in your environment.  The problem is not the X11 display,
but rather in keyboard input, possibly a mismatch between what
keyboard input system you are actually using and that which is
specified in some environment variables.

This has cropped up from time-to-time concerning R:

https://bugs.launchpad.net/ubuntu/+source/r-base/+bug/48168

but it usually cures itself before anybody writes out a completely
clear explanation of what is wrong, how it went wrong, and what fix is
minimally sufficient to fix it.  I do not believe I intentionally
changed any input settings, but plenty of updates from Debian Wheezy
have flown by.

The posts in that ubuntu bug say check your locale and input settings,
in particular, Run this:
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Simon Blomberg | 12 Jan 2012 03:51
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Problems compiling packages from source: can't find -lquadmath.

Hi all,

I have recently installed Debian squeeze on a Dell T7500, but I have 
pinned R and friends to come from the unstable distribution. Currently I 
have these Debian packages installed (with dependencies):

r-base-core 2.14.1-1
r-base-dev 2.14.1-1

The problem comes when installing new source packages from CRAN using 
install.packages(). Below is a typical installation output:

* installing *source* package ‘gee’ ...
** libs
gfortran -fpic -O3 -pipe -g -c dgedi.f -o dgedi.o
gfortran -fpic -O3 -pipe -g -c dgefa.f -o dgefa.o
gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c ugee.c -o ugee.o
gcc -std=gnu99 -shared -o gee.so dgedi.o dgefa.o ugee.o -lblas 
-lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/lib64/R/lib -lR
/usr/bin/ld: cannot find -lquadmath
collect2: ld returned 1 exit status
make: *** [gee.so] Error 1
ERROR: compilation failed for package ‘gee’
* removing ‘/usr/local/lib/R/site-library/gee’

The downloaded packages are in
‘/tmp/Rtmp7Cgdu4/downloaded_packages’
Warning message:
In install.packages("gee") :
installation of package ‘gee’ had non-zero exit status
(Continue reading)

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Dirk Eddelbuettel | 12 Jan 2012 04:46
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Re: Problems compiling packages from source: can't find -lquadmath.


On 12 January 2012 at 12:51, Simon Blomberg wrote:
| Hi all,
| 
| I have recently installed Debian squeeze on a Dell T7500, but I have 
| pinned R and friends to come from the unstable distribution. Currently I 
| have these Debian packages installed (with dependencies):
| 
| r-base-core 2.14.1-1
| r-base-dev 2.14.1-1
| 
| The problem comes when installing new source packages from CRAN using 
| install.packages(). Below is a typical installation output:
| 
| * installing *source* package ‘gee’ ...
| ** libs
| gfortran -fpic -O3 -pipe -g -c dgedi.f -o dgedi.o
| gfortran -fpic -O3 -pipe -g -c dgefa.f -o dgefa.o
| gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c ugee.c -o ugee.o
| gcc -std=gnu99 -shared -o gee.so dgedi.o dgefa.o ugee.o -lblas 
| -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/lib64/R/lib -lR
| /usr/bin/ld: cannot find -lquadmath
| collect2: ld returned 1 exit status
| make: *** [gee.so] Error 1
| ERROR: compilation failed for package ‘gee’
| * removing ‘/usr/local/lib/R/site-library/gee’
| 
| The downloaded packages are in
| ‘/tmp/Rtmp7Cgdu4/downloaded_packages’
| Warning message:
(Continue reading)

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Simon Blomberg | 12 Jan 2012 05:14
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Re: Problems compiling packages from source: can't find -lquadmath.

Hi Dirk,

I downgraded r-base-core, r-base-dev back to squeeze, and then upgraded 
them again to testing. It seems to have fixed the problem! Most packages 
are compiling happily now.

Thanks for your advice!

Simon.

On 12/01/12 13:46, Dirk Eddelbuettel wrote:
> On 12 January 2012 at 12:51, Simon Blomberg wrote:
> | Hi all,
> |
> | I have recently installed Debian squeeze on a Dell T7500, but I have
> | pinned R and friends to come from the unstable distribution. Currently I
> | have these Debian packages installed (with dependencies):
> |
> | r-base-core 2.14.1-1
> | r-base-dev 2.14.1-1
> |
> | The problem comes when installing new source packages from CRAN using
> | install.packages(). Below is a typical installation output:
> |
> | * installing *source* package ‘gee’ ...
> | ** libs
> | gfortran -fpic -O3 -pipe -g -c dgedi.f -o dgedi.o
> | gfortran -fpic -O3 -pipe -g -c dgefa.f -o dgefa.o
> | gcc -std=gnu99 -I/usr/share/R/include -fpic -O3 -pipe -g -c ugee.c -o ugee.o
> | gcc -std=gnu99 -shared -o gee.so dgedi.o dgefa.o ugee.o -lblas
(Continue reading)

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Jim Robison-Cox | 12 Jan 2012 19:05
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Can't install rjags on LinuxMint 12

Hi,

I'm trying to install rjags and R2jags with R version 2.14.1 (2011-12-22)
on
Linux Mint 12 machine using
software repository:
  deb http://cran.fhcrc.org/bin/linux/ubuntu oneiric/

jags seems to install OK, but rjags gives a weird error about not finding 
fprec symbol.

Here is a history of the problem including several attempts to work 
around it.
(Because of Ben Bolker's recent post, I first removed jags)

sudo apt-get remove jags
## The following packages will be REMOVED:
##  jags r-cran-rjags

  sudo apt-get install jags
## The following NEW packages will be installed:
##  jags
  ## Unpacking jags (from .../jags_3.2.0-1oneiric0_amd64.deb)

sudo apt-get install r-cran-rjags
##The following NEW packages will be installed:
   ##r-cran-rjags
   ## Unpacking r-cran-rjags (from .../r-cran-rjags_3.3-1_amd64.deb)

sudo apt-get install r-cran-r2jags
(Continue reading)

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Michael Rutter | 12 Jan 2012 20:16
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Re: Can't install rjags on LinuxMint 12


On 01/12/2012 01:05 PM, Jim Robison-Cox wrote:
> Hi,
>
> I'm trying to install rjags and R2jags with R version 2.14.1 (2011-12-22)
> on
> Linux Mint 12 machine using
> software repository:
> deb http://cran.fhcrc.org/bin/linux/ubuntu oneiric/
>
> jags seems to install OK, but rjags gives a weird error about not
> finding fprec symbol.
>
>
> Here is a history of the problem including several attempts to work
> around it.
> (Because of Ben Bolker's recent post, I first removed jags)
>
> sudo apt-get remove jags
> ## The following packages will be REMOVED:
> ## jags r-cran-rjags
>
> sudo apt-get install jags
> ## The following NEW packages will be installed:
> ## jags
> ## Unpacking jags (from .../jags_3.2.0-1oneiric0_amd64.deb)
>
> sudo apt-get install r-cran-rjags
> ##The following NEW packages will be installed:
> ##r-cran-rjags
(Continue reading)

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