My university provided laptop was recently replaced and now when I try to knit my Rmd files if get the following error:
pandoc.exe: \\: openBinaryFile: invalid argument (Invalid argument)
Error: pandoc document conversion failed with error 1
Execution halted
These files used to knit perfectly on my old laptop and all of the code blocks within the file still run without errors.
The pandoc_available() function returns TRUE
The answers to similar questions that I have searched suggest it is something to do with the file paths but I am not familiar enough with this to make sense of what I should do. I tried mapping a network drive (Z:) to the folder where the Rmd file is stored and then changing the working directory in RStudio to that drive but it hasn't helped (and now I don't know how to change it back to ~ or what that referred to in the first place)
I have also tried downloading the latest version of Pandoc and a search on Windows Explorer shows that has installed in my user directory but I also have a version in C:\Program Files\RStudio\bin. That has also not helped.
I'm not sure if this is relevant but here is the information on the R version that I am running:
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
Can you tell me what other information is required to diagnose the problem and I will edit to include.
I am sorry this question is so poorly specified and would appreciate any help to improve it.
**** UPDATE ****
I have found that if I
(i) specify that I want a .md file in the YAML header,
(ii) create an .md file by knitting the markdown file,
(iii) copy that .md file manually to the Pandoc directory
(iv) run pandoc.exe -s -o test.knit.md test.html from the MSDOS command prompt within the Pandoc directory,
then I can create the html output file.
However, changing the working directory for RStudio to the Pandoc directory and running
x <- rmarkdown::render("test.Rmd", run_pandoc = FALSE, clean = FALSE)
knit_meta <- attr(x, "knit_meta")
rmarkdown::render( input = 'test.knit.md' , knit_meta = knit_meta )
as per https://stackoverflow.com/questions/38908766/how-to-generate-an-md-file-from-a-rmarkdown-file-containing-an-htmlwidget gives the same error as shown in my original post.
Does this prompt any thoughts that might lead to a solution to my problem?
The university IT people were able to solve my problem by uninstalling R and RStudio from the network drive and installing it on the C: drive and I am now able to knit successfully.
Related
With a colleague, we are working on this github repo. When I knit manuscript.Rmd, I get an error "Unable to load picture or PDF file 'nwr.by.freq.ITEM'." as in this commit. When she knits it, it works fine, as in this commit.
The error comes after all chunks have been done, so it's not a problem within R/RStudio. (Plus, we are using renv, and I already checked for discrepancies between versions of our R, Rstudio, and packages.) The problem must come from knitting, so in the pandoc stage or thereabouts.
Given that we have some phonetic symbols (which is why we need to generate the figure in a png, and then read it back in), we are using xelatex as our engine, as recommended here. I don't think these symbols are the problem -- but I do suspect the issue is a divergence between her latex engine and mine. I'm not totally sure how to check for that...
(I'll be trying to answer my own question, so you can just wait and see if I crack this alone!)
To begin with, I updated xelatex, which led to a missing apa6.cls error. Following papaja install instructions, I would ideally re-install mactex -- but while it downloads (since it takes 1h), I just installed tinytex with tinytex::install_tinytex(). At my first attempt to knit the document after that, tinytex downloaded many things. And then the knit went through! Problem solved.
I am trying to compile an rmarkdown document that includes a geographic plot into a PDF file. Here is a MWE:
---
title: "Problems with maps in tikz"
output: pdf_document
---
```{r setup, include=FALSE}
library(ggplot2)
library(sf)
```
## sf:png
Builds find when `nctikz` chunk is excluded.
```{r nc}
nc <- sf::st_read(system.file("shape/nc.shp", package = "sf"), quiet = TRUE)
ggplot(nc) +
geom_sf(aes(fill = AREA))
```
## sf:tikz
This graphic fails to build.
```{r nctikz, dev = 'tikz'}
ggplot(nc) +
geom_sf(aes(fill = AREA))
```
I am compiling this document using the "Knit" button in RStudio. I'm going to discuss each of the errors / warnings I get when I compile the document in case one leads to the others.
tinytex
Every time I try to run a chunk that includes dev = 'tikz', tinytex will try to reinstall the pgf TeX package, then discover it's already there, then give up trying to link it. I'm able to build document with non-geographic tikz outputs, however, so I've mostly just accepted this fact.
tlmgr search --file --global '/tikzlibrarytopaths.code.tex'
Trying to automatically install missing LaTeX packages...
tlmgr install pgf
tlmgr: package repository http://mirror.utexas.edu/ctan/systems/texlive/tlnet (not verified: gpg unavailable)
tlmgr install: package already present: pgf
tlmgr path add
add_link_dir_dir: /usr/local/share/info/dir exists; not making symlink.
Invalid characters
Tikz (in knitr) seems unable to handle the degree symbol as part of a tex file. As a note, the nctikz-1.tex object can be built by pdflatex without issue.
! Package inputenc Error: Invalid UTF-8 byte "B0.
Quitting from lines 24-27 (test.Rmd)
Error: Failed to compile test_files/figure-latex/nctikz-1.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See nctikz-1.log for more info.
Underscore in filepath
I can get around the invalid characters error by suppressing the axis titles theme(axis.text = element_blank()) on my plot, but this then introduces another error dealing with bringing in a file.
! Missing $ inserted.
<inserted text>
$
l.3975 ...72.27pt,interpolate=true]{nctikz-1_ras1}
};
Quitting from lines 24-27 (test.Rmd)
The full line that generates this error is
\node[inner sep=0pt,outer sep=0pt,anchor=south west,rotate= 0.00] at (423.16, 120.24) {
\pgfimage[width= 14.45pt,height= 72.27pt,interpolate=true]{nctikz-1_ras1}};
The image it's trying to reference is barely an image (I think it's for the legend).
Environment
I am building this document on MacOS with a whole pile of libraries. In an effort to isolate the issue, I also attempted to build the document on Rstudio.cloud (Ubuntu) in a brand new project. In this environment, only the issue with the math environment / underscore occurs.
! Missing $ inserted.
<inserted text>
$
l.4049 ...72.27pt,interpolate=true]{nctikz-1_ras1}
};
Quitting from lines 26-28 (test.Rmd)
Error: Failed to compile test_files/figure-latex/nctikz-1.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See nctikz-1.log for more info.
Not a full answer, but I would like to document my current state:
It makes sense to enable debugging by adding
```{r, include=FALSE}
options(tinytex.verbose = TRUE)
```
to the Rmd file as suggested.
The pgf issue is sort of a red herring. With debugging we see that it happens after some other error occurs (illegal character or underscore in file path). The corresponding regular expression was recently introduced and should probably be extended to check for actual error messages from Tikz/pgf.
I can reproduce the illegal character on Debian Linux. Somehow ° is written as 0xB0, i.e. Latin-1 encoded instead of UTF-8. I am not sure why/where this is happening. BTW, I can process the resulting tex file directly with pdflatex only from RStudio, since that re-encodes the 0xB0 as a question mark. If I use pdflatex via Emacs or directly on the command line, I get the same error message.
Removing the degree symbol from the output via
```{r nctikz, dev = 'tikz'}
ggplot(nc) +
theme(axis.text = element_blank()) +
geom_sf(aes(fill = AREA))
```
I can reproduce the "underscore in file path" issue. With debugging turned on, one sees that the issue is again somewhere else:
Package pgf Warning: File "nctikz-1_ras1" not found when defining image "pgflas
timage". Tried all extensions in ".pdf:.jpg:.jpeg:.png:" on input line 3975.
! Missing $ inserted.
<inserted text>
$
l.3975 ...72.27pt,interpolate=true]{nctikz-1_ras1}
};
! ==> Fatal error occurred, no output PDF file produced!
The file nctikz-1_ras1.png that is present in the same directory as nctikz-1.tex is not found. One can reproduce this issue directly using
tinytex::latexmk("<path>/nctikz-1.tex", install_packages = FALSE, clean = FALSE)
However, if one changes to the directory first, no such error occurs:
setwd("<path>")
tinytex::latexmk("./nctikz-1.tex", install_packages = FALSE, clean = FALSE)
I am trying to compile an RMarkdown document from an R script. This is the code I am running:
setwd("C:/Users/me/me_VN02_5676/myfolder")
rmarkdown::render("myrmd.Rmd",
output_file = "mypdf.pdf")
This results in the error:
Error: Failed to compile mypdf.tex.
In addition: Warning message:
running command '"pdflatex" -halt-on-error -interaction=batchmode "mypdf.tex"' had status 1
Does anyone know what is happening?
Additional Notes
The PDF file is created when I use the Knit button in RStudio
This code does produce the .Tex file and when I run that it produces the pdf but render() does not produce the pdf
When I run the .R file via the command line it works! The PDF is created but why doesn't it work in R studio?
It would help to provide a Minimal Working Example so that we can attempt to replicate the problem. However, there may be two potential causes:
File Paths Look Incorrect
In R, they should be specified with a single forward slash: https://stat.ethz.ch/R-manual/R-devel/library/base/html/file.path.html
setwd("C:/Users/me/me_VN02_5676/myfolder")
rmarkdown::render("myrmd.Rmd",
output_file = paste0("mypdf.pdf")
)
PDF Output File May be Open
Another potential cause of this is that the PDF file is open, and therefore pandoc cannot save the output PDF. Try closing the PDF and render the document again.
Link to previous issue in Knitr which relates to this: https://github.com/yihui/knitr/issues/1209
I'm following this guide on building V8 but I am hitting some issues on the compilation step. I am running Windows 10 x64. I am trying to compile with options to embed the engine also.
Running the following command:
ninja -C out.gn/x64.release
Gives me this error:
ninja: Entering directory `out.gn/x64.release'
[1/471] LINK mksnapshot.exe mksnapshot.exe.pdb
FAILED: mksnapshot.exe mksnapshot.exe.pdb
C:/Workspace/depot_tools/win_tools-2_7_6_bin/python/bin/python.exe ../../build/toolchain/win/tool_wrapper.py link-wrapper environment.x64 False link.exe /nologo /OUT:./mksnapshot.exe /PDB:./mksnapshot.exe.pdb #./mksnapshot.exe.rsp
LINK : fatal error LNK1181: cannot open input file 'comdlg32.lib'
ninja: build stopped: subcommand failed.
Now I believe I have narrowed down the error to looking for the .lib files in the wrong directory. I have (had) multiple versions installed, so there were multiple folders in my Windows Kit install.
Windows Kits/10/Lib/10.0.16299.0
Windows Kits/10/Lib/10.0.15xxx.0
If I dragged and dropped the comdlg32.lib file from 10.0.16299.0 into the 10.0.15xxx.0 directory then the error changed to a LNK1181 error with a different input file. I did this a few times but I was unsure if this was going to cause issues with different versions and there was probably going to be a lot.
I uninstalled the 10.0.15xxx.0 version which left behind the folder I mentioned, so I removed that and after doing so I have started getting the LNK1181 error with a different input file (advapi32.lib I assume the very first file it can't find). This is how I came to the conclusion about the path being incorrect.
So I have tried a few things to change the path (I hoped just uninstalling the old version would fix it) such as:
Uninstalling the old version.
Going through registry entries to see if I can find an install path or something using that path, which I didn't. I did notice that there was still installation and data in the registry for the 10.0.15xxx.0 install, I might try deleting that from the registry directly as a last resort?
I have tried to explicitly set the path by setting <TargetUniversalCRTVersion>10.0.16299.0</TargetUniversalCRTVersion> in this file: C:\Program Files (x86)\Windows Kits\10\DesignTime\CommonConfiguration\Neutral\uCRT.props
I have never used Ninja before so I tried looking for a way to set some kind of lib-path in the command but couldn't really find anything.
I looked through the python scripts being executed to try and locate something to do with the libs path but couldn't see anything.
I would be grateful for any help and suggestions. Thanks.
You can try to compile v8 using Visual Studio as explained here: https://chromium.googlesource.com/chromium/src/+/master/docs/windows_build_instructions.md#using-the-visual-studio-ide
By running the following commands:
$ gn gen --ide=vs out.gn/x64.release
$ cd out.gn/x64.release
$ msbuild all.sln
You can see a full example here: https://github.com/phpv8/v8js/issues/272#issuecomment-262848754
Apparently this method is not officially supported anymore, but I had the same problem as you have and this solved the issue for me.
Note that after this I had another issue, the unit tests failed to be compiled due to a linking error, but I had the necessary libraries to use v8. So there may be deeper problem that is causing all of this that I'm missing.
Edit:
Also, you could try to set the following parameters with gn args:
visual_studio_path = "..."
visual_studio_version = "2017"
wdk_path = "..."
windows_sdk_path = "C:\Program Files (x86)\Windows Kits\10"
To set those parameters, do:
gn args out.gn/x64.release
This will open a text editor where you can write the extra parameters you are interested in.
To see the full list of parameters you can specify:
gn args --list out.gn/x64.release
I was following this guide https://medium.com/dailyjs/how-to-build-v8-on-windows-and-not-go-mad-6347c69aacd4 and also ran into the error
LINK1181: cannot open input file 'advapi32.lib'
I'm pretty sure it was because I had the wrong versions of the Windows 10 SDK. Similar to you I had versions:
Windows Kits/10/Lib/10.0.10240.0
Windows Kits/10/Lib/10.0.16299.0
But according to https://chromium.googlesource.com/chromium/src/+/master/docs/windows_build_instructions.md#Setting-up-Windows (Which I think is relevant) you need version 10.0.15063.0
After installing version 10.0.15063.0 (with the visual studio installer) to
Windows Kits/10/Lib/10.0.15063.0
I was able to continue with the build.
I'm trying to learn C++ programming with wxWidgets and CodeBlocks (with MinGW) and earlier today I succeeded in installing the software (after some trouble) to my Windows 7 computer with the guidance given to me in this post:
wxWidget 2.8.12 not working in Codeblocks
Later on the same day, I did the exact same steps on another Windows 7 machine and after creating a wxWidgets project and trying to compile and run it I got the following errors:
\wxWidgets-2.9.4\include: No such file or directory
\wxWidgets-2.9.4\lib\gcc_lib\mswu: No such file or directory
I have checked and these folders really do exist on those locations...so what seems to be the problem here again?...on the earlier post user asanth kumar guided me that if the steps given in the guide don't get the job done, then I'm missing an important compiler search path in my build options.
Ok, so what do I do? Where do I enter the search path? What is the search path, etc. I'm very new with wxWidgets and CodeBlocks so I don't know very much terminology. If anyone should know what to do, could you please give me like step by step instruction what to do e.g. like Click Project --> Build options --> ... and so on
I have used the latest CodeBlocks (12.11) and wxWidgets (2.9.4) installers
Thank you for any help :)
UPDATE:
here is the build log: (I'm using CodeBlocks 12.11 and wxWidgets 2.9.4)
-------------- Build: Debug in TEST (compiler: GNU GCC Compiler)---------------
windres.exe -I"C:\Users\Jonne\Omat ohjelmat\wxWidgets-2.9.4\include" -I"C:\Users\Jonne\Omat ohjelmat\wxWidgets-2.9.4\lib\gcc_lib\mswu" -J rc -O coff -i C:\Users\Jonne\DOCUME~1\CODEBL~1\TEST\resource.rc -o obj\Debug\resource.res
gcc: error: ohjelmat\wxWidgets-2.9.4\include: No such file or directory
gcc: error: ohjelmat\wxWidgets-2.9.4\lib\gcc_lib\mswu: No such file or directory
windres.exe: preprocessing failed.
Process terminated with status 1 (0 minutes, 0 seconds)
3 errors, 0 warnings (0 minutes, 0 seconds)
Here is also a picture where you can see Build options, global variables and build log on my CodeBlocks:
NOTICE FUTURE READERS: Install wxWidgets to a directory without whitespace in the path name. The problems in this post was because the directory path had spaces in it
When you create a wxWidgets project.Have you did this?
File->New->Project->wxWidgets Project->Click Go->Click on Next->click on the suitable wxWidgets 2...version->click Next->Give project Name->Click on Next->Click on Next
After that the Following below Screen comes in the Wizard. Give the wxWidgets Location(Path where You installed the wxWidgets 2.9.4)
After that click on Finish.
For Environment Variable Path Setting
Follow the Below Steps:
Right click on MyComputer->Click on Advanced Systems settings->click on Environment Variables->click on New->Give variable name=Path and variable value="C:\Program Files (x86)\CodeBlocks\MinGW\bin" -> click ok
`
Try The Following Steps.It will work.
Updates about Build settings:
I am having the same problem as this and I somehow solved my problem.
I transfer my wxWidget folder to another location path that don't have white space name on it's path. For example above, "C:\Users\Jonne*Omat ohjelmat*\wxWidgets-2.9.4\include"
the path has white space between Omat ohjelmat. Try transfering it where the path contains no white spaces. For me, I put it on C:\wxWidgets-3.1.2