I am using IDL version 5.5 and trying to write some output to a FITS formatted file. However, I keep getting % Variable is undefined: TEN. and % Attempt to call undefined procedure/function: 'FITS_WRITE'.
Is it just the case that IDL 5.5 is not equipped with FITS writing capabilities?
FITS_WRITE is a part of astrolib. You need to install old version suitable for IDL 5.5 to use it.
Related
I just spent an infuriating day trying to make a gif out of a series of jpg files in R. I installed ImageMagick to run the following code:
system("convert -delay 40 *.png example_4.gif")
but I get the following error message:
Warning message:
running command 'convert -delay 40 *.png example_4.gif' had status 4
which looks like a path error. Now I've looked for convert in the Imagemagick download and can't see it anywhere. Does anyone know where it is?
Alternately, is there another easier method of making a gif from a series of jpegs in R that isn't ridiculously long?
Thanks
Three options:
Consider using the magick R package instead of using system().
Change your script from convert ... to magick convert ....
Re-install imagemagick, and enable the "Install legacy utilities (e.g. convert)" option.
This change has been around since 7.0.1 (now up to 7.0.7), and is discussed in their porting guide, specifically in the section entitled "Command Changes".
Philosophically, I prefer to not install the legacy utilities, mostly because it can cause some confusion with command names. For instance, the non-ImageMagick convert.exe in windows tries to convert a filesystem ... probably not what you want to accidentally trigger (there is a very low chance that you could get the arguments right to actually make a change, but it's still not 0). The order of directories in your PATH will dictate which you are calling.
EDITs:
From comments, it seems like the difference between "static" and "dll" installers might disable the option to install legacy utilities such as convert.exe. So you can either switch to the "dll" to get the legacy option, or you are restricted to options 1 (magick R package) and 2 ("magick convert ...").
From further comments (thanks to fmw42 and MarkSetchell), it is clear that the old convert.exe and the current legacy mode of magick.exe convert are not the same as the currently recommended magick.exe (without "convert"); the first two are legacy and compatibility modes, but they do not accept all arguments currently supported by magick-alone. So the use of "convert" anywhere in the command should indicate use of v6, not the current v7. This answer is then merely a patch for continued use of the v6 mechanisms; one could argue a better solution would be to use magick.exe's v7 interface, completely removing the "convert" legacy mode.
My question is if an object in R saved to binary format using the save function can be different if saved from different (but recent) versions of R.
That is because I have a script that makes some calculations and save its results to a file. When reproducing the same calculations later, I decided to compare the two files using
diff --binary -s mv3p.Rdata mv3p.Rdata.backup
To my surprise the two files are different. However when analysing the contents in R, they are identical.
The new version is 3.3.1. I believe the older version have been created by R 3.3.0 but it could also be by 3.2.x, I am not 100% sure. I used the save command with only the object I wanted to save and the filename arguments.
So my question is : is it normal that the same object is written differently in different versions of R? is it documented somewhere? How can I be sure to be able to reproduce exactly the same file? On what can it depend (R version, OS, processor architecture, etc...)
Please , I am NOT asking if versions can be read by another version of R and I am NOT asking about very old R versions.
R data files also include the R version used to write it. That's one reason the files may be different. See here on documentation: http://biostat.mc.vanderbilt.edu/wiki/Main/RBinaryFormat
Also, you can use save(..., ascii=T) to see the difference in plain text.
This is an issue I am encountering for different pieces of codes I am writing in R.
Basically, I would like to generate a window that displays a picture (a .png file). Following for instance guidances from this or this, I come up with this kind of code:
library(tcltk)
tmpFile <- tempfile(fileext = ".png")
download.file("https://www.r-project.org/logo/Rlogo.png", tmpFile)
tcl("image","create","photo", "imageLogo", file=tmpFile)
win1 <- tktoplevel()
tkpack(ttklabel(win1, image="imageLogo", compound="image"))
This works fine under Mac OS, but not on Linux nor on Windows, where I am displayed such an error message:
[tcl] couldn't recognize data in image file
I can find some workarounds when I want to display graphs, using for instance packages tkrplot or igraph. Nonetheless, I would be really eager to understand why I got such errors when running my scripts on Linux or Windows, whereas it works just fine on Mac OS.
Apologies in case this issue is obvious, but I haven't found anything about potential differences with the tcltk package depending on the OS.
Tk's native support for PNG was added in 8.6. Prior to that, you need to have the tkimg extension loaded into Tk to add the image format handler required. If your installation of Tcl/Tk that R is using is set up right, you can probably make it work with:
tclRequire("Img")
once you've initialised things sufficiently. Yes, the name used internally is “Img” for historical reasons, but that's just impossible to search for! (This is the key thing in this mailing list message from way back.)
However, upgrading the versions of Tcl and Tk to 8.6 is likely to be a better move.
Finally and a bit lately, I would like to close this issue and sum up the different suggestions that were kindly made in response of my question:
R comes along with Tcl 8.5, even with the latest version 3.3.2, which means that there is no way for embedding a PNG file with the usual command into a window created thanks to Tcl/Tk. For some reasons it is working on Mac OS, but do not expect this to work easily on other OSs.
In order to display pictures, graphs, etc. in a window generated by Tcl/Tk in R, better look for either using the GIF support (when possible) or trying alternative solutions (see the question for possible alternative options).
In case one really wants to display PNG files, the solution consists of installing Tcl 8.5 (for instance ActiveTcl) along with the extension Img. In order to use the Tcl/Tk package that you've just installed on your computer, you can refer to the R FAQ for Windows for instance (as stated in the FAQ, you need to install Tcl 8.5 - I tried with Tcl 8.6, thereby hoping to solve my issue, but it didn't work). Basically, you need to set up an environment variable (MY_TCLTK) and put the path where the package Tcl/Tk is installed. Needless to be said, Tcl/Tk is commonly used in R in order to implement GUIs; if you have to go through very complex procedures to set up the system, the package definitely loses its advantages.
Finally, since Tcl 8.6 should be available soon or later with R (already implemented in the devel version), this issue will be de facto outdated.
I am attempting to automate the insertion of JPEG images into Powerpoint. I have a macro done for that already, except using R would be infinitely better for my purposes.
The package R2PPT should do this, I understand. However, I cannot use it. For example, when I try to use PPT.Open, I understand I can do it two different ways by calling method = "rcom" or method = "RDCOMClient". Using the latter, R will always crash, sending an error report to windows. Using the former, it tells me I need to install statconnDCOM , before giving the error:
Error in PPT.Open(x) : attempt to apply non-function.
I cannot install statconnDCOM freely, as I wouldn't call this work non-commercial. So if there isn't a way to get around this issue, are there at least some free alternatives to R2PPT so that I can save several hours of manual work with a simple R code? If there is a way for me to use R2PPT, that would be ideal.
Thanks!
Edit:
I'm using R version 2.15 and downloaded the most recent version of R2PPT. Powerpoint is 2007.
Do you have administrative privileges on this machine?
There is an issue with package RDCOMClient. It needs permissions to write file rdcom.err in the root of drive C:. If you don't have privileges to write to c:, there is a rather cumbersome workaround:
Close R
Create "c:\temp" folder if it doesn't exist.
Locate on your hard drive file rdcomclient.dll. It usually placed in \R\library\RDCOMClient\libs\i386\ and in \R\library\RDCOMClient\libs\x64\ (you need to patch file which corresponds your Windows version - 32 bit or 64 bit). It's recommended to make backup copy of this files before patching.
Open rdcomclient.dll in text editor (Notepad++, for example -http://notepad-plus-plus.org/)
Find in file string c:\rdcom.err - it occurs only once.
Go into overwrite mode (usually by pressing "Ins" key). It is very important that new path will have the same number of characters as original one. Type C:\temp\e.rr instead of c:\rdcom.err
Save the file.
Now all should work fine.
Arguably not an answer, but have you looked at using Sweave/knitr to render your presentations in LaTeX using something like Beamer? (As discussed on slide 17 here.)
Wouldn't help any with getting JPGs into a PowerPoint, but would certainly make putting R-output (numerical or graphical) into a presentation much easier!
Edit: if you want to use knitr (which I recommend), here's another reference.
I was wondering if it is possible to work between matlab and R to plot some data. I have a script in matlab which generates a text file. From this I was wondering if it was possible to open R from within matlab and plot the data from this text file and then return to matlab.
For example, if I save a text file called test.txt, in the path 'E:\', and then define the path of R which in my case will be:
pathR = 'C:\Program Files\R\R-2.14.1\bin\R';
Is it possible to run a script already written in R saved under test1.R (saved in the same directory as test.txt) in R from matlab?
If you're working with Windows (from the path it looks like you are), you can use the MATLAB R-link from the File Exchange to pass data from Matlab to R, execute commands there, and retrieve output.
I don't use R so this is not something I have done but I see no reason why you shouldn't be able to use the system function to call R from a Matlab session. Look in the product documentation under the section Run External Commands, Scripts, and Programs for this and related approaches.
There are some platform-specific peculiarities to be aware of and you may have to wrestle a little with what is returned (though since you are planning to have R create a plot which is likely to be a side-effect rather than what is returned you may not). As ever this is covered quite well in the product's documentation
After using R(D)COM and Matlab R-link for a while, I do not recommend it. The COM interface has trouble parsing many commands and it is difficult to debug the code. I recommend using a system command from Matlab as described in the R Wiki. This also avoids having to install RAndFriends.