Im trying to save a plot to a file, when using the print command i get this error:
print "data"
Unknown device: pswrite
Unrecoverable error: undefined in .uninstallpagedevice
Operand stack:
defaultdevice
warning: broken pipe`
You should realy provide more infos when asking for help with software. What OS are you running? Which Octave version? Installed from repo or source? What graphics_toolkit?
But I've asked my crystal ball and I guess it's a problem with ghostscript. Ghostscript versions >= 9.09 removed the pswrite command, see also https://savannah.gnu.org/bugs/?41141
So install a older version of ghostscript or a newer version of GNU Octave or use the qt or fltk graphics_toolkit.
Related
I have a general question about how to effectively load any kind of external package into R. I have found that many sources detailing this information are simply insufficient, but I will leave out mentioning those respective URLs. I have successfully loaded external packages into R before, but I am having difficulties loading the fgui package.
In my specific case, I cannot load the library fgui into R Studio. First I download directly from CRAN with the command:
install.packages("fgui", lib="~/Documents/R_dir")
This works fine for me. My working directory is set to ~/Documents/R_dir
The next command I use is:
library("fgui", lib.loc="~/Documents/R_dir")
The error I get is:
Error : .onLoad failed in loadNamespace() for 'tcltk', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.1/Resources/library/tcltk/libs/tcltk.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.1/Resources/library/tcltk/libs/tcltk.so, 10): Library not loaded: /opt/X11/lib/libX11.6.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.1/Resources/library/tcltk/libs/tcltk.so
Reason: image not found
Error: package or namespace load failed for ‘fgui’
I have examined the thread "Error when trying to load library(ggplot2) in R" but it did not answer my question.
Please help me with any suggestions to get the package fgui to work properly in R Studio and feel free to address the more general issue of effectively loading external packages into R.
tcltk is not a typical package. It's probably already installed on your system and it cannot be installed using the usual install.packages procedure because it is not on CRAN (just like the base packages that come with R, like stats, etc.). Also, tcltk2 is not the same as tcltk; that is a package that expands upon (and depends on) the functionality of tcltk.
So, start with this:
> capabilities("tcltk")
tcltk
TRUE
If that comes back FALSE it means that your R was not built with tcltk support. You don't say what OS you're using, so it's a little bit difficult to help you.
That said, if you're on Linux, you need to rebuild R with tcltk support. This should be relatively straightforward. Basically, make sure Tcl and tk are available on your system in a standard location (something like sudo apt-get install tcl8.5-dev tk8.5-dev) and then rebuild R per usual procedures.
If you're on Mac OS, you're encountering the same error that John Fox describes here in relation to Rcmdr. In short, it's probably one of two things:
A file permission issue related to the directory where you have Tcl installed. To quote Fox: "You can verify the source of this problem by issuing the following command at the R command prompt:
system("ls -ld /usr/local /usr/local/lib /usr/local/lib/libtcl*")
# ls: /usr/local/lib: Permission denied
# ls: /usr/local/lib/libtcl*: Permission denied
# drwx------ 8 root wheel 272 Sep 24 10:21 /usr/local
If the output of the system command looks like the above, you should go to Terminal and do the following: sudo chmod -R a+rX /usr/local and enter your password to change directory permissions.
You have an out-dated version of X-Windows. Try running Mac OS Software Update.
It may also be solvable by creating a symbolic link as described in this answer.
This should never come up on Windows, unless you built R from source without tcl/tk support.
On Arch Linux, tk is a separate package from tcl and both need to be installed:
sudo pacman -S tcl tk
This is given that the output from capabilities("tcltk") with R is TRUE (which means your R is compiled with tcltk support as noted previously in the answers here, this should be the case if you installed it from the arch repos).
The official installation instructions for R say:
Note: the use of X11 (including tcltk) requires XQuartz to be
installed since it is no longer part of OS X. Always re-install
XQuartz when upgrading your OS X to a new major version.
So: Simply (re)install XQuartz if you want to use the tcltk package in R.
delete the X11 file on location : /opt
delete the X11 on application unitiltiy
reinstall X11 again
Problem solved...
For Mac-OS users:
I struggled with this problem recently and found that R-3.1.2 has a bug, which assumes that otool is installed when it is not.
R-3.0.0 (and later) ships with Tck/Tk 8.6.0, so you shouldn't need to install that.
Simply upgrading to a more recent version of R (3.4.2) fixed the problem for me.
I had the same issue and went down a rabbit hole before discovering a simple fix. If you install R from bianry it will include tcltk by default. Just run the installer with the default installation. You can get the .dmg here: https://cran.r-project.org/bin/macosx/
Easiest answer for Mac users:
1- Install tcl-tk using brew:
brew install tcl-tk
2- Run the following code:
ln -s /usr/local/Cellar/tcl-tk/$version/lib/libtcl8.6.dylib /usr/local/lib/libtcl8.6.dylib
ln -s /usr/local/Cellar/tcl-tk/$version/lib/libtk8.6.dylib /usr/local/lib/libtk8.6.dylib
Problem solved!
I am trying to install octave through brew on mac (10.10.5 Yosemite). The command used is brew install octave . While installing, the process tries to install qt (version 4.8.7) which is essentially failing with the below error
Error : 'File already exists. /usr/local/Cellar/qt/4.8.7'.
When I check the file at this particular location, I don`t see any such directory, though the directory does appear and is created during the installation (probably getting removed later when the task fails).
Could someone please point out what I need to do exactly? Is Qt really required for Octave installation? If not then any way to skip it?
Does anyone have a link to clear instructions on how to install and configure the necessary latex packages to build R packages on a mac?
I have some scripts for building and checking R packages on a mac server. They seemed to work fine, but after upgrading to R 3.1.3, many of the packages started failing with
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
Running 'texi2dvi' on 'networkVignette.tex' failed.
Messages:
sh: /usr/local/bin/texi2dvi: No such file or directory
Calls: <Anonymous> -> texi2pdf -> texi2dvi
Execution halted
I found a thread which seemed to suggest I need a more recent version texinfo (5.2) than what is installed by default. And apparently I've I've got the wrong version installed in the wrong location?
which texi2pdf
/sw/bin/texi2pdf
texi2pdf --version
texi2pdf (GNU Texinfo 5.1) 5234
(same version is reported when running system('texi2pdf --version') in R )
This thread gives a link to a texinfo 5.2 source collection:
http://r.789695.n4.nabble.com/R-CMD-build-looking-for-texi2dvi-in-the-wrong-place-R-devel-td4701706.html
But I'm not familiar with installing executable from a tar.gz file on a mac. The R mac help pages I found suggest installing MacTex, which I tried but that didn't seem to help.
** Update: ** additional discussion of related problems on R-SIG-mac mailing list:
https://groups.google.com/forum/#!topic/r-sig-mac/xjyuFdl5Ezk
Update:
Here is where I'm currently at:
I removed my /sw directory to uninstall fink and all of its packages (couldn't figure out how to upgrade it)
installed homebrew
brew install texinfo installs version 5.2 the package,
but generates the message This formula is keg-only, which means it was not symlinked into /usr/local and actually installs in in /usr/local/Cellar/texinfo/5.2/bin which means it is not on the path and R won't find it.
manually symlink each of the texi2pdf, texi2dvi , etc as vincent suggests (this is because R has the /usr/local/bin location as default in the tools::texi2dvi function?
edited the /etc/paths file on the system to add /usr/local/bin so that finds the brew installed 5.2 version before it finds it before the osx system supplied version 4.6 version. This may not be necessary because R has it hardcoded?
All of this gets rid of the "can't find texi* errors", and gives me a bunch of latex errors (which I don't see on unix and windows builds) so I'm still kind of stuck.
This seems very hackish, so there must be a cleaner way? But it sounds like stuff with tex and mac is very sketchy at the moment? https://tex.stackexchange.com/questions/208181/why-did-my-tex-related-gui-program-stop-working-in-mac-os-x-yosemite
This worked for me on Mavericks and on Yosemite:
ln -s /usr/bin/texi2dvi /usr/local/bin/texi2dvi
ln -s /usr/bin/texi2pdf /usr/local/bin/texi2pdf
On my Lion system both the command which texi2pdf at a Terminal/bash prompt and from a R.app GUI prompt tell me that I have that program in:
system("which texi2pdf")
#/opt/local/bin/texi2pdf
That is a location typical for MacPorts installation. I think the /usr/local/bin/ is what the binary R version "expects". I'm not really that UNIX savvy, but I think the you can modify the PATH environment variable so that R will be able to find your installation. (Whether it will be compatible I cannot say since so much detail is missing from your question.) My Tex installation is MacTex, which I got from https://www.tug.org/mactex/. I admit to having a cobbled-together system:
system("echo $PATH")
# /opt/local/bin:/opt/local/sbin:/sw/bin:/sw/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/texbin:/usr/X11/bin:/usr/X11R6/bin
That gets set at the beginning of an R session because this is the first line in my .Rprofile-(invisible)file:
Sys.setenv(PATH="/opt/local/bin:/opt/local/sbin:/sw/bin:/sw/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/texbin:/usr/X11/bin:/usr/X11R6/bin")
I think /sw/bin/ installations signify a fink install, which I have had very little success with. Simon Urbanek suggests not using any package installers, but then leaves the rest of us UNIX weenies very little in the way of worked examples of how to install that various external packages that underpin the many interesting and oh-so-useful R packages. So I feel your pain, but I'm not running for President.
So I suppose you could try this at your R console before again attempting one of the earlier unsuccessful installs:
Sys.setenv(PATH=paste( Sys.getenv()$PATH, # should be the character string of the $PATH
"/sw/bin/", sep=":")
)
Wish I could offer guarantees, but if it breaks the only guarantee is that you get to keep all the pieces.
I ran into a similar error message using Mavericks 10.9.5 (factory configured) and R 3.1.
It turns out that I didn't have pdfLaTex. I went to this page: http://tug.org/mactex/ and downloaded the MacTex installation package. It's big (>2GB) but after I installed it, my R package build problems went away.
Hope this might be helpful to anyone else who runs into this error message.
I am trying to install rgl package (0.92.858) for R (2.14.2) under Mac OS X (Lion 10.7.3). When I try to load it (library(rgl)), I get the following error:
Error : .onLoad failed in loadNamespace() for 'rgl', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/2.14/Resources/library/rgl/libs/x86_64/aglrgl.so':
dlopen(/Library/Frameworks/R.framework/Versions/2.14/Resources/library/rgl/libs/x86_64/aglrgl.so, 6): Symbol not found: __ZN3gui13OSXGUIFactory12hasEventLoopEv
Referenced from: /Library/Frameworks/R.framework/Versions/2.14/Resources/library/rgl/libs/x86_64/aglrgl.so
Expected in: dynamic lookup
I have a Mac with Norwegian keyboard. Maybe this has something to do with the issue? However, I get the same error, even though I change the language to U.S. Has anyone experienced similar problem? Any way solving it?
I was having this problem with rgl 0.93.996 on OSX 10.9.2, but then after reinstalling several times I saw "Installing rgl - error: X11 not found but required, configure aborted"
A quick search took me here https://stat.ethz.ch/pipermail/r-sig-mac/2012-March/009077.html
Then I was finally able to get it to work by downloading XQuartz https://www.xquartz.org So it was X11 that was the problem in my case.
It requires building from the source as there is a problem with the path to libpng.dylib path if using the built in source install. The process is:
1) Download the source files from http://download.r-forge.r-project.org/src/contrib/rgl_0.92.879.tar.gz
- You need to download the source files from here since you have to manually install the program.
2) Unzip the files to a convenient location. You can do this by double clicking on the .tar file
3) Open Terminal and navigate to the directory that you placed the files in. I put them on my desktop so the command is:
cd ~/Desktop
4) In Terminal run
R CMD INSTALL --with-libpng-prefix=/usr/X11/lib/ rgl
You can then delete all the files you downloaded. Note that I am running Mac OS X 10.7.3 with R 2.15.0. The specific paths may be slightly different if you are on a different version. You do not need the rgl folder or files after you install them and they can be deleted.
I was still having issues installing from source with special flags or any of the other suggestions in comments and things above. I am using Mac OS X 10.7.3 on a 64-bit MacBook Pro and R 2.15.0
I continued to get the following when loading the rgl package:
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/2.14/Resources/library/rgl/libs/x86_64/aglrgl.so'
I tried the following sub-optimal solution works: Delete the aglrgl.so file. Then try loading the package again.
(This is a suggestion I took from a post by Duncan Murdoch
)
A quick way to delete this file is to type the following into the terminal:
open -a Finder /Library/Frameworks/R.framework/Versions/2.15/Resources/library/rgl/libs/x86_64/
In the new Finder window that pops up, delete the aglrgl.so file, and then close the window. Open the R-GUI, and try loading rgl: library("rgl"). It should work fine, and unfortunately use X11 for the 3D graphics instead of the native Quartz window. For me, this is better than nothing.
The problem is now documented on R-forge :
http://r-forge.r-project.org/tracker/index.php?func=detail&aid=1996&group_id=234&atid=946
You basically have to delete the incriminated file, aglrgl.so. R gives you the file's path in the displayed error message.
The new Mac binary version of rgl 0.92.861 installs on 2.14.2 without error and runs the example code.
Okay solution in my case (OS X Yosemite), first download the RGL source (not binaries) in http://cran.r-project.org/src/contrib/rgl_0.95.1247.tar.gz, extract it, and build the library using this command:
R CMD INSTALL --disable-cocoa --x-includes=/usr/X11/ rgl
and it works like a charm.
I have spent a lot of time trying to solve this, but still no luck. I am trying to get Rgraphviz to work with R 2.14.1 on a Max OS X Lion
These are the steps I took in order to install and use Rgraphviz on Mac OS X Lion:
Installed graphviz via: sudo port install graphviz
Checked that the installation was successful : pkg-config --modversion libgvc
Result: 2.28.0 <- That means its OK
Under R 2.14.1
source("http://www.bioconductor.org/biocLite.R")
biocLite("Rgraphviz")
Whenever I try to use the library I get the following error
Error : .onLoad failed in loadNamespace() for 'Rgraphviz', details:
call: value[[3L]](cond)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rgraphviz/libs/i386/Rgraphviz.so':
dlopen(/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rgraphviz/libs/i386/Rgraphviz.so, 6): Library not loaded: /usr/local/lib/libgvc.5.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rgraphviz/libs/i386/Rgraphviz.so
Check that (1) graphviz is installed on your system; (2) the installed version of
graphviz matches '2.26.3'; this is the version used to build this Rgraphviz
package; (3) graphviz is accessible to R, e.g., the path to the graphviz 'bin'
directory is in the system 'PATH' variable. See additional instructions in the
'README' file of the Rgraphviz 'source' distribution, available at
Some things I notice
The graphviz suggested in the "help" file is 2.26.3 and the graphviz installed by Mac Ports is 2.28.0, but as it is a newer version I don't think this makes a difference, and besides I can not find v 2.26.3
Suggestion number (3) seems to be the key, but I can't find/don't have a bin directory under graphbiz
Also when I run a locate Rgraphviz.so there are no results.
Any clue towards a solution will be much appreciated,
Thanks a lot!
Thanks for the final answer, the installation seems to work for me! (I still have to check that the package runs properly). Just a quick observation: Graphviz was installed in /usr/local on my machine so that the above command had to be entered as follows:
sudo R CMD INSTALL --configure-args='--with-graphviz=/usr/local' Rgraphviz_1.32.0.tar.gz
One more fail point. If you used Fink to install graphviz, you may still, like me, encounter separate build errors even after you use the configure arguments to point to graphviz, which now look like:
R CMD INSTALL --configure-args='--with-graphviz=/sw' Rgraphviz_1.34.0.tar.gz
The installation will fail during build errors for LL_funcs.c because it is looking for libraries that do not install unless you ALSO install graphviz-dev. You will see this:
In file included from LL_funcs.c:1:
common.h:31:17: error: gvc.h: No such file or directory
common.h:32:22: error: gvplugin.h: No such file or directory
common.h:35:20: error: gvcext.h: No such file or directory
common.h:39:20: error: gvcjob.h: No such file or directory
followed by many more build errors of course. Just be sure to
fink install graphviz-dev