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.
Related
So I was trying to install Rcpp using the checkpoint package (with a March 1st 2020 date).
Most of my packages were fine, but Rcpp specifically makes a lot of temporary directories that it then deletes, for example:
00LOCK-Rcpp/00new/Rcpp/include/Rcpp/generated/InternalFunctionWithStdFunction_call.h
This is 84 characters long and I belive some are longer.
Checkpoint creates numerous directories as well, for example with a custom library here:
"custom_library/.checkpoint/2020-03-01/lib/x86_64-w64-mingw32/3.6.0/"
This is 67 characters, of which 52 are only necessary when managing multiple checkpoint dates or versions.
This means that for a file path such as:
"C:/Users/USER/OneDrive - COMPANY/Documents/LargeDirectory/SubDirectory1/SubDirectory2/custom_library/.checkpoint/2020-03-01/lib/x86_64-w64-mingw32/3.6.0/Rcpp"
Assuming even temporary files can't exceed 255 chars then I have definitely < 60 characters left available for all of the Rcpp temporary objects.
I tested with the following code:
setwd("C:/Users/USERNAME/OneDrive - COMPANY/Documents/LargeDirectory/SubDirectory1/SubDirectory2/")
dir.create("custom_library)
checkpoint(as.Date("2020-03-01"),
checkpointLocation = paste0(
"SubDirectory2","/custom_library")
)
y
install.packages("Rcpp")
It fails because of numerous "no file or directory found" which I believe actually fails because 00LOCK-Rcpp/00new/Rcpp/include/Rcpp/ can't be created to then unzip all the .h files to it. I was curious so I ran the following:
setwd("~") # up to Documents
dir.create("Rcpptest")
.libPaths("Rcpptest")
install.packages("Rcpp")
And it installed fine.
Any ideas on how to make checkpoint either not create so many nested directories OR ignore the file_path 255 limit until the whole package installs?
For now, I will likely move the directory up a few levels but any insight into whether my guess is actually correct or if I'm missing something would be appreciated!
I believe you are correct -- this is, to the best of my knowledge, a limitation of the internal unzip implementation used by R, which is ultimately a limitation of the Windows APIs used by R. See https://learn.microsoft.com/en-us/windows/win32/fileio/naming-a-file for some more discussion.
There are a couple options for mitigating the issue that may be worth trying.
Use utils::shortPathName() to construct a so-called Windows 'short path'. This will help trim longer path components and bring the full path down in size.
Create a junction to your project using Sys.junction() to a local path with a shorter length, and move to that directory. See ?Sys.junction for more information -- a junction is basically like a Windows shortcut, or a symlink to a directory.
In each case, you should hopefully be able to construct a path that is "identical" to your current project directory, but short enough that things can function as expected.
I am translating the GUI of QGIS desktop software.
The current developing version is on transifex platform from which it can be extracted the corresponding .ts file.
the older versions of QGIS are archived on github.
I'd like to insert the missing strings translated in the newer version in the older version. Also some strings have been corrected in the new version and I'd like to replace them in the older.
I used lconvert in this form:
lconvert -i 2.18.ts 2.99.ts -o total.ts
But QT Linguist warns that in total.ts there are duplicated strings.
Is it possible to insert in the older version (2.18) only the strings that are the same from the newer (2.99)?
I ran three years ago with the ts-tools from Qt4 into the same problem.
The manual says that the call of lconvert (just like you laid it out) will merge the content (means: the translations from two sources) into a new file. And I expected "merge" to work like "make a superset out of both". But it did not.
I wrote myself a bash-script to merge it in a way I want to. Will try to find the file this evening.
(I know, right now the answer is - beside confirming the error - not helpful.)
My Octave crashes when I execute plot command. I found a solution in Assad Ebrahim's answer. He mentioned to switch the default toolkit to gnuplot, and change it in octave.rc file if I want to make the change permanently but I'm not clear about the permanent change in octaverc. When I open my octaverc with notepad++, it looks like this:
## System-wide startup file for Octave.
##
## This file should contain any commands that should be executed each
## time Octave starts for every user at this site.
EXEC_PATH (cstrcat (fullfile (OCTAVE_HOME, 'notepad++'), pathsep,
EXEC_PATH));
EXEC_PATH (cstrcat (fullfile (OCTAVE_HOME, 'bin'), pathsep, EXEC_PATH));
EDITOR (fullfile (OCTAVE_HOME, 'notepad++', 'notepad++.exe'));
What should I change and how?
First, the direct answer to your question is to append any command you want executed on startup to the end of the .octaverc file. So, to set a particular graphics toolkit you would add the line:
graphics_toolkit("gnuplot")
Or
graphics_toolkit("qt")
Or
graphics_toolkit("fltk")
For whichever toolkit you want.
Now, as pointed out by #Andy, if you are using Windows, it may be that you are misinterpreting a long delay for a crash. A still not entirely resolved windows bug concerns the fact that on the first plot Windows might need to create a font cache file. This can take a long time. Once this is complete, most subsequent plots will be much faster. Some info can be found about it at the following bug report page:
https://savannah.gnu.org/bugs/?45458
EDIT: in the time since this answer was posted, the bug linked above has been largely resolved. Part of the installation process now updates the font-cache file. If using a zip package rather than an executable installer, there is a batch file that should be run after extracting octave to ensure that this is done. Details are available at:
http://wiki.octave.org/Octave_for_Microsoft_Windows
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.