"Recipe: Compile Rnw files" calls Anacondas version of R

[pehkawn]

Preliminary questions [Required]

I tried compiling a .Rnw with LaTeX Workshop, which rendered the error message "Error in readRDS(pfile): cannot read workspace version 3 written by R 3.1.2 (need R 3.5.0 or newer)"

Disable all the other extensions except for LaTeX Workshop, restart VS Code, and check that you still see this issue. [Required]

You still see this issue?: Yes

Make sure to visit the wiki FAQ before filling an issue.

You visited the wiki?: Yes

If your issue is with compiling a document (not having to do with finding the root file of a project), check first that you can compile manually.

You can compile a TeX document manually?: I can now.

Describe the bug [Required]

I googled around a bit. Seemingly this issue had to with having different versions of R. I have an older version of R installed in Anaconda, which I haven't used. My system $PATH points to the newest version, I installed via apt from the the official CRAN repos. LaTeX Workshop seem not to recognize this, and still tries to use the Anaconda version. Replacing the script opt/anaconda3/lib/R/bin/R with /lib/R/bin/R solved the issue.

To Reproduce

Steps to reproduce the behavior:

1. Install R in Anaconda, and install newest version of R from official repo.
2. Make sure $PATH points to the newest version
3. Open/create .Rnw file
4. Click on 'Build LaTeX project.
5. See error
6. Solution: Replace opt/anaconda3/lib/R/bin/R with /lib/R/bin/R

Expected behavior

Generation of PDF.

Logs

LaTeX Workshop extension log

[17:05:31] Initializing LaTeX Workshop.
[17:05:31] Extension root: /home/user/.vscode/extensions/james-yu.latex-workshop-8.23.0
[17:05:31] $PATH: /opt/anaconda3/bin:/opt/anaconda3/condabin:/home/user/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/opt/mplusdemo
[17:05:31] $SHELL: /bin/bash
[17:05:31] vscode.env.appName: Visual Studio Code
[17:05:31] vscode.env.remoteName: undefined
[17:05:31] vscode.env.uiKind: 1
[17:05:31] editor.acceptSuggestionOnEnter: "on"
[17:05:31] latex-workshop.bind.enter.key: true
[17:05:31] latex-workshop.docker.enabled: false
[17:05:31] latex-workshop.docker.image.latex: ""
[17:05:31] latex-workshop.hover.preview.mathjax.extensions: []
[17:05:31] latex-workshop.intellisense.package.enabled: true
[17:05:31] latex-workshop.intellisense.update.aggressive.enabled: false
[17:05:31] latex-workshop.intellisense.update.delay: 1000
[17:05:31] latex-workshop.latex.autoBuild.run: "onFileChange"
[17:05:31] latex-workshop.latex.outDir: "%DIR%"
[17:05:31] latex-workshop.latex.recipes: [
 {
  "name": "latexmk 🔃",
  "tools": [
   "latexmk"
  ]
 },
 {
  "name": "latexmk (latexmkrc)",
  "tools": [
   "latexmk_rconly"
  ]
 },
 {
  "name": "latexmk (lualatex)",
  "tools": [
   "lualatexmk"
  ]
 },
 {
  "name": "pdflatex ➞ bibtex ➞ pdflatex × 2",
  "tools": [
   "pdflatex",
   "bibtex",
   "pdflatex",
   "pdflatex"
  ]
 },
 {
  "name": "Compile Rnw files",
  "tools": [
   "rnw2tex",
   "latexmk"
  ]
 },
 {
  "name": "Compile Jnw files",
  "tools": [
   "jnw2tex",
   "latexmk"
  ]
 },
 {
  "name": "tectonic",
  "tools": [
   "tectonic"
  ]
 }
]
[17:05:31] latex-workshop.latex.tools: [
 {
  "name": "latexmk",
  "command": "latexmk",
  "args": [
   "-synctex=1",
   "-interaction=nonstopmode",
   "-file-line-error",
   "-pdf",
   "-outdir=%OUTDIR%",
   "%DOC%"
  ],
  "env": {}
 },
 {
  "name": "lualatexmk",
  "command": "latexmk",
  "args": [
   "-synctex=1",
   "-interaction=nonstopmode",
   "-file-line-error",
   "-lualatex",
   "-outdir=%OUTDIR%",
   "%DOC%"
  ],
  "env": {}
 },
 {
  "name": "latexmk_rconly",
  "command": "latexmk",
  "args": [
   "%DOC%"
  ],
  "env": {}
 },
 {
  "name": "pdflatex",
  "command": "pdflatex",
  "args": [
   "-synctex=1",
   "-interaction=nonstopmode",
   "-file-line-error",
   "%DOC%"
  ],
  "env": {}
 },
 {
  "name": "bibtex",
  "command": "bibtex",
  "args": [
   "%DOCFILE%"
  ],
  "env": {}
 },
 {
  "name": "rnw2tex",
  "command": "Rscript",
  "args": [
   "-e",
   "knitr::opts_knit$set(concordance = TRUE); knitr::knit('%DOCFILE_EXT%')"
  ],
  "env": {}
 },
 {
  "name": "jnw2tex",
  "command": "julia",
  "args": [
   "-e",
   "using Weave; weave(\"%DOC_EXT%\", doctype=\"tex\")"
  ],
  "env": {}
 },
 {
  "name": "jnw2texmintex",
  "command": "julia",
  "args": [
   "-e",
   "using Weave; weave(\"%DOC_EXT%\", doctype=\"texminted\")"
  ],
  "env": {}
 },
 {
  "name": "tectonic",
  "command": "tectonic",
  "args": [
   "--synctex",
   "--keep-logs",
   "%DOC%.tex"
  ],
  "env": {}
 }
]
[17:05:31] latex-workshop.viewer.pdf.internal.keyboardEvent: "auto"
[17:05:31] Creating a new file watcher.
[17:05:31] watcherOptions: {"useFsEvents":false,"usePolling":false,"interval":300,"binaryInterval":1000,"awaitWriteFinish":{"stabilityThreshold":250}}
[17:05:31] Creating PDF file watcher.
[17:05:31] watcherOptions: {"useFsEvents":false,"usePolling":false,"interval":300,"binaryInterval":1000,"awaitWriteFinish":{}}
[17:05:31] Creating Bib file watcher.
[17:05:31] watcherOptions: {"useFsEvents":false,"usePolling":false,"interval":300,"binaryInterval":1000,"awaitWriteFinish":{"stabilityThreshold":250}}
[17:05:31] Set $LATEXWORKSHOP_DOCKER_LATEX: ""
[17:05:31] [Server] Creating LaTeX Workshop http and websocket server.
[17:05:32] Bibtex format config: {"tab":"  ","case":"lowercase","left":"{","right":"}","trailingComma":false,"sort":["key"],"alignOnEqual":true,"sortFields":false,"fieldsOrder":[],"firstEntries":["string","xdata"]}
[17:05:32] LaTeX Workshop initialized.
[17:05:32] Bibtex format config: {"tab":"  ","case":"lowercase","left":"{","right":"}","trailingComma":false,"sort":["key"],"alignOnEqual":true,"sortFields":false,"fieldsOrder":[],"firstEntries":["string","xdata"]}
[17:05:32] Trigger characters for intellisense of LaTeX documents: ["\\",",","{"]
[17:05:32] Bibtex format config: {"tab":"  ","case":"lowercase","left":"{","right":"}","trailingComma":false,"sort":["key"],"alignOnEqual":true,"sortFields":false,"fieldsOrder":[],"firstEntries":["string","xdata"]}
[17:05:32] Current workspace folders: undefined
[17:05:32] Current workspaceRootDir: 
[17:05:32] Found root file from active editor: /home/user/path/lwe.Rnw
[17:05:32] Root file changed: from undefined to /home/user/path/lwe.Rnw
[17:05:32] Start to find all dependencies.
[17:05:32] Root file languageId: rsweave
[17:05:32] [Server] Server successfully started: {"address":"127.0.0.1","family":"IPv4","port":45283}
[17:05:32] Reset file watcher.
[17:05:32] Parsing a file and its subfiles: /home/user/path/lwe.Rnw
[17:05:32] Parse fls file.
[17:05:32] Fls file found: /home/user/path/lwe.fls
[17:05:32] Parsing a file and its subfiles: /home/user/path/lwe.tex
[17:05:32] Parse aux file: /home/user/path/lwe.aux
[17:05:32] Added to file watcher: /home/user/path/lwe.Rnw
[17:05:32] Added to file watcher: /home/user/path/lwe.tex
[17:05:32] Snippet data loaded.
[17:05:32] Checking for duplicate labels: /home/user/path/lwe.Rnw.
[17:05:32] Checking for duplicate labels: /home/user/path/lwe.tex.
[17:05:34] Manager.fileWatcher.getWatched: {"/home/user/path":["lwe.Rnw","lwe.tex"]}
[17:05:34] Manager.filesWatched: ["/home/user/path/lwe.Rnw","/home/user/path/lwe.tex"]
[17:05:34] BibWatcher.bibWatcher.getWatched: {}
[17:05:34] BibWatcher.bibsWatched: []
[17:05:34] PdfWatcher.pdfWatcher.getWatched: {}
[17:05:34] PdfWatcher.pdfsWatched: []
[17:05:50] BUILD command invoked.
[17:05:50] The document of the active editor: file:///home/user/path/lwe.Rnw
[17:05:50] The languageId of the document: rsweave
[17:05:50] Current workspace folders: undefined
[17:05:50] Current workspaceRootDir: 
[17:05:50] Found root file from active editor: /home/user/path/lwe.Rnw
[17:05:50] Keep using the same root file: /home/user/path/lwe.Rnw
[17:05:50] Building root file: /home/user/path/lwe.Rnw
[17:05:50] Build root file /home/user/path/lwe.Rnw
[17:05:50] outDir: /home/user/path
[17:05:50] Recipe step 1: Rscript, -e,knitr::opts_knit$set(concordance = TRUE); knitr::knit('lwe.Rnw')
[17:05:50] Recipe step env: {}
[17:05:50] cwd: /home/user/path
[17:05:50] LaTeX build process spawned. PID: 1315817.
[17:05:50] Recipe returns with error: 1/null. PID: 1315817. message: Error in readRDS(pfile) : 
  klarte ikkje lesa arbeidsområde versjon 3, skriven av R 4.1.2 (treng R 3.5.0 eller nyare)
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Stoppa køyring
.
[17:05:50] The environment variable $PATH: /opt/anaconda3/bin:/opt/anaconda3/condabin:/home/user/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/opt/mplusdemo
[17:05:50] The environment variable $Path: undefined
[17:05:50] The environment variable $SHELL: /bin/bash
[17:05:50] Cleaning auxiliary files and retrying build after toolchain error.
[17:05:50] Clean glob matched files: {"globs":["*.aux","*.bbl","*.blg","*.idx","*.ind","*.lof","*.lot","*.out","*.toc","*.acn","*.acr","*.alg","*.glg","*.glo","*.gls","*.fls","*.log","*.fdb_latexmk","*.snm","*.synctex(busy)","*.synctex.gz(busy)","*.nav","*.vrb"],"outdir":"/home/user/path"}
[17:05:50] Cleaning file: /home/user/path/lwe.aux
[17:05:50] Cleaning file: /home/user/path/lwe.fls
[17:05:50] Cleaning file: /home/user/path/lwe.log
[17:05:50] Cleaning file: /home/user/path/lwe.fdb_latexmk
[17:05:50] Recipe step 1: Rscript, -e,knitr::opts_knit$set(concordance = TRUE); knitr::knit('lwe.Rnw')
[17:05:50] Recipe step env: {}
[17:05:50] cwd: /home/user/path
[17:05:50] LaTeX build process spawned. PID: 1315827.
[17:05:50] Recipe returns with error: 1/null. PID: 1315827. message: Error in readRDS(pfile) : 
  klarte ikkje lesa arbeidsområde versjon 3, skriven av R 4.1.2 (treng R 3.5.0 eller nyare)
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Stoppa køyring
.
[17:05:50] The environment variable $PATH: /opt/anaconda3/bin:/opt/anaconda3/condabin:/home/user/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/opt/mplusdemo
[17:05:50] The environment variable $Path: undefined
[17:05:50] The environment variable $SHELL: /bin/bash
[17:05:52] Manager.fileWatcher.getWatched: {"/home/user/path":["lwe.Rnw","lwe.tex"]}
[17:05:52] Manager.filesWatched: ["/home/user/pathmodelling/lwe.Rnw","/home/user/path/lwe.tex"]
[17:05:52] BibWatcher.bibWatcher.getWatched: {}
[17:05:52] BibWatcher.bibsWatched: []
[17:05:52] PdfWatcher.pdfWatcher.getWatched: {}
[17:05:52] PdfWatcher.pdfsWatched: []
[17:05:59] Current workspace folders: undefined
[17:05:59] Current workspaceRootDir: 
[17:05:59] Found root file from active editor: /home/user/path/lwe.Rnw
[17:05:59] Keep using the same root file: /home/user/path/lwe.Rnw
[17:06:01] Manager.fileWatcher.getWatched: {"/home/user/path":["lwe.Rnw","lwe.tex"]}
[17:06:01] Manager.filesWatched: ["/home/user/pathmodelling/lwe.Rnw","/home/user/path/lwe.tex"]
[17:06:01] BibWatcher.bibWatcher.getWatched: {}
[17:06:01] BibWatcher.bibsWatched: []
[17:06:01] PdfWatcher.pdfWatcher.getWatched: {}
[17:06:01] PdfWatcher.pdfsWatched: []
[17:06:11] LOG command invoked: default
[17:06:11] Current workspace folders: undefined
[17:06:11] Current workspaceRootDir: 
[17:06:11] Found root file from active editor: /home/user/path/lwe.Rnw
[17:06:11] Keep using the same root file: /home/user/path/lwe.Rnw
[17:06:13] Manager.fileWatcher.getWatched: {"/home/user/path":["lwe.Rnw","lwe.tex"]}
[17:06:13] Manager.filesWatched: ["/home/user/path/lwe.Rnw","/home/user/path/lwe.tex"]
[17:06:13] BibWatcher.bibWatcher.getWatched: {}
[17:06:13] BibWatcher.bibsWatched: []
[17:06:13] PdfWatcher.pdfWatcher.getWatched: {}
[17:06:13] PdfWatcher.pdfsWatched: []

LaTeX compiler logs

Error in readRDS(pfile) : 
  klarte ikkje lesa arbeidsområde versjon 3, skriven av R 4.1.2 (treng R 3.5.0 eller nyare)
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Stoppa køyring

Desktop [Required]

Please write exact version numbers. Please don't write latest instead of exact numbers.

• OS: Ubuntu 21.04 LTS
• VS Code version: 1.63.2
• Extension version: 8.23.0
• TeX distribution version: TeX Live revision 56458

[jlelong]

It is very important to have access to the logs to identify the issue. So please add them to your initial post.

This is likely an issue with how you set your environment variable PATH. See https://github.com/James-Yu/LaTeX-Workshop/wiki/Install#setting-path-environment-variable

[pehkawn]

Compiling .tex works fine, so I doubt this is issue is with TeX Live path. I can call tlmgr from any directory, so it has to be added to $PATH.

I changed back to the original opt/anaconda3/lib/R/bin/R and have added the output from LaTeX Compiler.

[jlelong]

Compiling .tex works fine, so I doubt this is issue is with TeX Live path. I can call tlmgr from any directory, so it has to be added to $PATH.

You did not get my point. If LW is not using the correct version of R, this is because the value of PATH in VS Code is wrong and contains opt/anaconda3/lib/R/bin/R before /lib/R/bin/R. This has nothing to do with the TeX Live path.

Please post the complete logs of the extension starting from Initializing LaTeX Workshop.

You will find the value of PATH as seen by VS Code in the logs of the extension.

[pehkawn]

Sorry, I got a bit confused there why you wanted me to check TeXLive's path and what you wanted me to do.

I reset folder names, and tried compiling again in a new window. I have attached the full log from both LaTeX Workshop extension and LaTeX compiler.

[jlelong]

From the extension logs

[17:05:50] The environment variable $PATH: /opt/anaconda3/bin:/opt/anaconda3/condabin:/home/user/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/opt/mplusdemo

This is why the R version from anaconda3 is used and not the one provided by the system. Now, you have to figure out where the is value for the PATH is set (have a look at files /etc also).

When, you launch VS Code from a terminal using code -n ., it inherits the values of the environment variables from your shell. This is well explained here. Indeed, I recommend to read the whole article.

[pehkawn]

If you are referring to /opt/anaconda3/bin:/opt/anaconda3/condabin in path, I was already aware of this issue because it created problems in the past.

I tried to explain in my other post on issue #3029, I deleted the R file in /opt/anaconda3/bin a while back. I then also had issues with two shell wrappers for R in $PATH, opt/anaconda3/bin/R and /usr/local/bin/R, each pointing to different home directories, R_HOME_DIR=/opt/anaconda3/lib/R and R_HOME_DIR=/lib/R/bin/R, respectively. There was no shell wrapper for the R executable in $PATH when I tried to compile the .Rnw.

Typing "R" in terminal yields:

~$ R --version
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

Which means R 4.1.2 must be set in $PATH, right?

[jlelong]

Which means R 4.1.2 must be set in $PATH, right?

Not necessarily, The PATH used by VS Code when running a recipe is

/opt/anaconda3/bin:/opt/anaconda3/condabin:/home/user/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/opt/mplusdemo

This value of the PATH may be different from the one you have in a terminal (even in the terminal pane of VS Code). Check by running echo $PATH.

[17:05:50] Recipe step 1: Rscript, -e,knitr::opts_knit$set(concordance = TRUE); knitr::knit('lwe.Rnw')```

Note that the recipe for compiling .rnw files looks for a Rscript executable and not directly for R. You may have a Rscript pointing to the wrong R version.

[pehkawn]

Note that the recipe for compiling .rnw files looks for a Rscript executable and not directly for R. You may have a Rscript pointing to the wrong R version.

Hmm, that may actually be what's causing it. There is an Rscript in /opt/anaconda3/bin which would be in VS Code's $PATH
Typing in terminal gives

$ Rscript --version
R scripting front-end version 3.2.2 (2015-08-14)

As mentioned, replacing the R file in the same directory with the one in /lib/R/bin/R resolved the issue. I can only assume the reason it worked is that Rscript, even if it's an older version, now can retrieve information from the newest R version. Anyway, both R and Rscript are now removed from /opt/anaconda3/bin.
Typing in terminal now returns

~$ Rscript --version
R scripting front-end version 4.1.2 (2021-11-01)

Hopefully, this will prevent any further issues.
Anyway, thank you so much for your help today.