recently I have created some Rmd script wchich create and send html file to specified recipients. Script works perfect, when i run from application level (R Studio). But it doesn't work, when i run it from Task Scheduler (bat file) - log file indicates an error:
ERROR: pandoc version 1.12.3 or higher is required and was not found
(see the help page ?rmarkdown::pandoc_available).
I have checked pandoc version n R Studio:
pandoc_available()
[1] TRUE
pandoc_version()
[1] ‘1.17.2’
Maybe application run from Task Scheduler do not use Pandoc library enclosed in R Studio, but try to find another Pandoc software instaled on my computer?
Any ideas? My operating system is Windows.
TK
Rstudio uses this environment variable to find where pandoc is installed on your machine:
Sys.getenv("RSTUDIO_PANDOC")
You need to add this location to system PATH
Related
I am using Rstudio in windows 10. I am triying to create a pdf from a .tex file. However, when I compile the PDF, the following error appears:
Running pdflatex.exe on file_name.tex...failed Error running C:/Users/user_name/AppData/Local/Programs/MiKTeX/miktex/bin/x64/pdflatex.exe (exit code -1073740791)
I am using a native installation of R, Rstudio and MikTeX. Not an envioronment with anaconda or similar.
If you are using RStudio, have you tried tinytex instead of MikTeX? In the Tools Menu>Global Options>Sweave, tick "use tinytex for compiling .tex files". Then install tinytex package. After installing tinytex package, write in console "tinytex::install_tinytex()". This will install the latex compiler tinytex. Try compiling your tex file using it.
I think that issue has to do with missing packages. In fact, MiKTeX doesnt preinstall most of them. I recommend to compile with TinyTeX, because it shows where the compilation stops (as I said, due to a missing package typically required in some sty file). This way you can track which are the missing packages and install them on the MiKTeX Console one by one.
I posted about this issue in an open discussion on Github. Drop the link here in case you need more details.
I just installed MacOS version of R from the CRAN web site. Within the R GUI application, everything works fine. However, I'm unable to run it from terminal. Trying to trigger R or Rscript in terminal yields a message indicating that neither command exists.
Also I do not see corresponded scripts in /Applications/R.app/Contents/.
How can I run R from terminal?
PS: I know brew installation will help. But I want this version of R from CRAN web site.
The R installer creates /Library/Frameworks/R.framework/ directory in addition to /Applications/R.app/.
So, you need add a correct directory to the Library dir. For my packages:
R_APP_DIR=/Library/Frameworks/R.framework/Versions/3.2/Resources/
export PATH=$R_APP_DIR:$PATH
I have been to their website. I have viewed a YouTube on a related subject. And, so far I don't really get it. My objective is to use Pandoc in conjunction with R Markdown to convert R Markdown HTML document into either Word or Pdf files.
You can install pandoc in several ways:
Using the x86 or x64 executable from here and installng like any other Windows app: pandoc downloads
Using the x86 or x64 flavor of the zip file (same link shown above), and unpack it on the folder of your preference. Then, set manually the path to that folder. Pandoc is only a couple of files pandoc.exe and pandoc-citeproc.exe. You may even copy then to your /bin folder of your preference if want to save adding another PATH.
Using the R package installr, and then run installr::install.pandoc().
It will automatically install the Windows msi and add the PATH for you.
You may review the user path in environment variables: C:\Users\user_name\AppData\Local\Pandoc\.
Reload the environment variables by restarting your PC.
If you have RStudio installed (and most R users do) then you already have a pandoc binary. Maybe just add that directory to your $PATH ?
If you have the Chocolatey package manager installed on your Windows machine, you can install the Pandoc package with:
choco install pandoc
I am checking my package and this is actually the last remaining problem. The pdf file cannot be compiled and the logfile tells me
2015-10-15 14:17:47,430+0200 INFO pdflatex - running 'initexmf --quiet --update-fndb' to refresh the file name database
2015-10-15 14:17:50,276+0200 FATAL pdflatex - GUI framework cannot be initialized.
2015-10-15 14:17:50,276+0200 FATAL pdflatex - Info:
2015-10-15 14:17:50,276+0200 FATAL pdflatex - Source: Libraries\MiKTeX\UI\Qt\mikuiqt.cpp
2015-10-15 14:17:50,276+0200 FATAL pdflatex - Line: 50
Any idea where the problem could be?
This is known problem wit MikTex 2.9 when pdflatex encounters error
GUI framework cannot be initialized.
(found on my Windows 7 system in the file ~\AppData\Local\MiKTeX\2.9\miktex\log)
So far, I can offer following sequence of actions to remedy this:
In Windows Command prompt go to MiKTeX bin folder (e.g. C:\Program Files (x86)\MiKTeX 2.9\miktex\bin) and run utility mo.exe;
In General tab change 'Install missing packages on-the-fly:' option to No (this will disable GUI and error above won't be happening again);
Run R CMD that calls latex converter again (in my case
R CMD Rd2pdf man/
again to see new errors;
This time miktex won't complaint about GUI - instead it will be missing packages with error like this
! LaTeX Error: File `inconsolata.sty' not found.
Start MiKTeX package manager (again from mo.exe Packages tab) and install missing package one at the time by repeating steps 3.-5.
This might be not most effective way of fixing this so I appreciate corrections or alternative solutions.
I had this same issue, but for the newest versions of Miktex, mo.exe does not exist, and is replaced by the Miktex console. If you open it, go into settings and change the package on-the-fly setting from "Ask Me" to "Always", then the packages will install. If you do "Never" instead, then you'll have to do the individual package installation described by #topchef.
I ran into this problem just... A very easy solution for me that allowed me not to renege on the install on the fly option is to install TexStudio, open your .tex file in there, and compile it: you will be able to install all your MikTex packages on the fly as desired and retain control over what gets installed.
I had the same problem compiling Knit to PDF of a R markdown file in R studio. Once I changed from "Ask me" to "Always" in the MikTex console setting (see the screenshot posted above [Cara Wogsland]) it compiled without errors.
I am trying to do R CMD check before uploading my package to CRAN.
R CMD check --as-cran "my package folder".
However, it spits out this warning:
"checking for unstated dependencies in examples ... OK
WARNING
pdf is needed for checks on size reduction of PDFs"
I searched online but found no clue to solve this problem. This warning does not turn up when I run "R CMD check" only. And my package works with no problem. Could someone please tell me what might be wrong with my package?
qpdf is an external program necessary to reduce the size of pdf, it can be downloaded from the sourceforge site. You can install either the 32 bis or 64 bits version, both are working.
To install it, you download the file, and then copy the folder to your program folder.
Next you need to edit you system path to point to the bin folder by adding 'C:\Program Files\qpdf-version_numer\bin'. In a command batch (cmd) type qpdf to see if that has been set correctly, you should get the message
qpdf: an input file name is required
Usage: qpdf [options] infile outfile
For detailed help, run qpdf --help
Once this is done, the warning should be removed from your R CMD check
To add to Cedric's answer:
If you are running the 32-bit version of R, it is important that you download the 32-bit version of qpdf, which is the version linked from the SourceForge homepage. If you are running a 64-bit installation of R, you will need to do a bit of digging to locate the 64-bit version of qpdf, which is buried a little more deeply (version 7.0 is listed here).
Once you have extracted the zipped qpdf directory to your hard disk, perhaps under C:\Program Files, added C:\Program Files\qpdf-version_no\bin to your system PATH under the environment variables, and re-launched R so it picks up the new PATH, you need to convince Windows that pqdf is safe to run.
Navigate to C:\Program Files\qpdf-version_numer\bin and execute qpdf.exe (by double-clicking). Windows 10 throws up a security warning as it's an unrecognized executable file. You'll need to use the more options link to find the button to run the program. Once you've done this, Windows will recognize the file as safe to run and allow other programs, including R, to use it.