Installation error

[brianlangseth-NOAA]

Describe how far you got

• [X] installed tinytex - But did not install, current version was 12-13-2022 so did not reinstall
• [X] installed pandoc - But did not install, rmarkdown::pandoc_available() equaled TRUE
• [X] installed sa4ss - Maybe, library(sa4ss) works, but following readme directions for cloned repo produce the warning below. Im surprised given my version of R (4.2.2)
• [X] ran sa4ss::session_test()
• [ ] set up my own draft
• [ ] compiled my own document

sa4ss install warning

── R CMD build ────────────────────────────────────────────────────────── ✔ checking for file 'U:\Other github repos\sa4ss/DESCRIPTION' ... ─ preparing 'sa4ss': (3.5s) ✔ checking DESCRIPTION meta-information ... ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories ─ building 'sa4ss_23.0.tar.gz'

Warning in install.packages : package ‘U:/Other github repos/sa4ss_23.0.tar.gz’ is not available for this version of R

A version of this package for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages

Place output from sa4ss::session_info() here if possible

$session_info $ADMB_HOME [1] "c:/ADMB/admb120-gcc493-win64"

$ALLUSERSPROFILE [1] "C:\ProgramData"

$APPDATA [1] "C:\Users\Brian.Langseth\AppData\Roaming"

$CLICOLOR_FORCE [1] "1"

$CommonProgramFiles [1] "C:\Program Files\Common Files"

$CommonProgramFiles(x86) [1] "C:\Program Files (x86)\Common Files"

$CommonProgramW6432 [1] "C:\Program Files\Common Files"

$COMPUTERNAME [1] "NWCLW04432672"

$ComSpec [1] "C:\WINDOWS\system32\cmd.exe"

$CURL_CA_BUNDLE [1] "C:/PROGRA~1/R/R-42~1.2/etc/curl-ca-bundle.crt"

$DEFLOGDIR [1] "C:\ProgramData\McAfee\Endpoint Security\Logs"

$DISPLAY [1] ":0"

$DriverData [1] "C:\Windows\System32\Drivers\DriverData"

$FPS_BROWSER_APP_PROFILE_STRING [1] "Internet Explorer"

$FPS_BROWSER_USER_PROFILE_STRING [1] "Default"

$GFORTRAN_STDERR_UNIT [1] "-1"

$GFORTRAN_STDOUT_UNIT [1] "-1"

$HOME [1] "c:/~"

$HOMEDRIVE [1] "G:"

$HOMEPATH [1] "\"

$HOMESHARE [1] "\\PICKINGFISH\USERS\Brian.Langseth"

$LDMS_PREFERRED_SERVER [1] "nwclandesk.nmfs.local"

$LOCALAPPDATA [1] "C:\Users\Brian.Langseth\AppData\Local"

$LOGONSERVER [1] "\\NWCDC1S2"

$MPLENGINE [1] "tkAgg"

$MSYS2_ENV_CONV_EXCL [1] "R_ARCH"

$NUMBER_OF_PROCESSORS [1] "12"

$OneDrive [1] "C:\Users\Brian.Langseth\OneDrive"

$OS [1] "Windows_NT"

$PATH [1] "c:\rtools42\x86_64-w64-mingw32.static.posix\bin;c:\rtools42\usr\bin;C:\Program Files\R\R-4.2.2\bin\x64;C:\Program Files (x86)\Common Files\Oracle\Java\javapath_target_193549250;C:\Rtools\bin;C:\Windows\System32;C:\Windows;C:\Windows\System32\wbem;C:\Windows\System32\WindowsPowerShell\v1.0;C:\Windows\System32\OpenSSH;C:\Program Files\Tumbleweed\Desktop Validator;C:\Program Files\Tumbleweed\Desktop Validator\x86;C:\Program Files (x86)\HID Global\ActivClient;C:\Program Files\HID Global\ActivClient;C:\admb\admb120-gcc493-win64\bin;C:\gnu\emacs\bin;C:\~\emacs\lisp\admb;C:\Program Files\Git\cmd;C:\Users\Brian.Langseth\AppData\Local\Programs\Quarto\bin;C:\admb\admb120-gcc493-win64\bin;C:\Rtools\mingw_64\bin;C:\gnu\emacs\bin;C:\Users\Brian.Langseth\AppData\Local\GitHubDesktop\bin;C:\Users\Brian.Langseth\AppData\Local\Programs\Quarto\bin"

$PATHEXT [1] ".COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH;.MSC"

$PROCESSOR_ARCHITECTURE [1] "AMD64"

$PROCESSOR_IDENTIFIER [1] "Intel64 Family 6 Model 158 Stepping 13, GenuineIntel"

$PROCESSOR_LEVEL [1] "6"

$PROCESSOR_REVISION [1] "9e0d"

$ProgramData [1] "C:\ProgramData"

$ProgramFiles [1] "C:\Program Files"

$ProgramFiles(x86) [1] "C:\Program Files (x86)"

$ProgramW6432 [1] "C:\Program Files"

$PSModulePath [1] "C:\Program Files\WindowsPowerShell\Modules;C:\WINDOWS\system32\WindowsPowerShell\v1.0\Modules"

$PUBLIC [1] "C:\Users\Public"

$PYTHONIOENCODING [1] "utf-8"

$QT_D3DCREATE_MULTITHREADED [1] "1"

$R_ARCH [1] "/x64"

$R_CLI_HAS_HYPERLINK_IDE_HELP [1] "true"

$R_CLI_HAS_HYPERLINK_IDE_RUN [1] "true"

$R_CLI_HAS_HYPERLINK_IDE_VIGNETTE [1] "true"

$R_COMPILED_BY [1] "gcc 10.4.0"

$R_DOC_DIR [1] "C:/PROGRA~1/R/R-42~1.2/doc"

$R_HOME [1] "C:/PROGRA~1/R/R-42~1.2"

$R_LIBS_SITE [1] "C:/PROGRA~1/R/R-42~1.2/site-library"

$R_LIBS_USER [1] "C:\Users\Brian.Langseth\AppData\Local/R/win-library/4.2"

$R_RTOOLS42_PATH [1] "c:/rtools42/x86_64-w64-mingw32.static.posix/bin;c:/rtools42/usr/bin"

$R_USER [1] "C:/~"

$RMARKDOWN_MATHJAX_PATH [1] "C:/Program Files/RStudio/resources/mathjax-27"

$RS_LOCAL_PEER [1] "\\.\pipe\52483-rsession"

$RS_RPOSTBACK_PATH [1] "C:/Program Files/RStudio/bin/rpostback"

$RS_SHARED_SECRET [1] "bcb9472c-38ce-441d-aee7-9108e0dd1044"

$RSTUDIO [1] "1"

$RSTUDIO_CLI_HYPERLINKS [1] "true"

$RSTUDIO_CONSOLE_COLOR [1] "256"

$RSTUDIO_CONSOLE_WIDTH [1] "80"

$RSTUDIO_MSYS_SSH [1] "C:/Program Files/RStudio/bin/msys-ssh-1000-18"

$RSTUDIO_PANDOC [1] "C:/Program Files/RStudio/bin/quarto/bin/tools"

$RSTUDIO_PROGRAM_MODE [1] "desktop"

$RSTUDIO_SESSION_PID [1] "17696"

$RSTUDIO_SESSION_PORT [1] "52483"

$RSTUDIO_USER_IDENTITY [1] "Brian.Langseth"

$RSTUDIO_WINUTILS [1] "C:/Program Files/RStudio/bin/winutils"

$RTOOLS40_HOME [1] "C:\rtools40"

$SESSIONNAME [1] "Console"

$SystemDrive [1] "C:"

$SystemRoot [1] "C:\WINDOWS"

$TEMP [1] "C:\Users\BRIAN~1.LAN\AppData\Local\Temp"

$TERM [1] "xterm-256color"

$TMP [1] "C:\Users\BRIAN~1.LAN\AppData\Local\Temp"

$USERDNSDOMAIN [1] "NMFS.LOCAL"

$USERDOMAIN [1] "NMFS"

$USERDOMAIN_ROAMINGPROFILE [1] "NMFS"

$USERNAME [1] "Brian.Langseth"

$USERPROFILE [1] "C:\Users\Brian.Langseth"

$windir [1] "C:\WINDOWS"

$pandoc_version [1] ‘2.18’

$pandoc_location pandoc ""

$sed_location [1] "C:\Rtools\bin\sed.exe"

$tried <simpleError: LaTeX failed to compile _main.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See _main.log for more info.>

Warning message: pandoc was not found on your system.

[kellijohnson-NOAA]

Sorry for this @brianlangseth-NOAA I think that my one off code for finding if pandoc is available is broken. I have switched to using {rmarkdown} to see if pandoc is available b/c if you look at your list it clearly is even though I was not able to find its location. Also, a better test would be if you can just move on to the next step in the readme that would really show me that the test is broken. lol Thanks for reporting. Let me know here if my fix (90ed577) works for you.

[brianlangseth-NOAA]

No dice. sa4ss::session_test() gave me the same warning "pandoc was not found on your system."

Ignoring that and trying library(sa4ss) sa4ss::draft(authors = "Kelli F. Johnson", create_dir = TRUE) setwd("doc") bookdown::render_book("00a.Rmd", clean = FALSE, output_dir = getwd()) setwd("..")

Gives me a whole lot of red text about

"! warning: kpathsea: configuration file texmf.cnf not found in these directories"

and ultimately outputting the classic error

"Error: LaTeX failed to compile _main.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See _main.log for more info."

[shcaba]

One additional note on getting pandoc to work with VS Code (and maybe will help here?): I recently updated my Rstudio, and I can get sa4ss stuff working on it with no issue. But when I went back to VS Code to render documents, it would not find pandoc. I had to remember that I needed to go into the PATH portion of my environmental variables and change the pandoc path linked to RStudio to the new updated RStudio path. It may be worth pointing out in the sa4ss readme page regarding confirming pandoc works is that it should include adding the quarto/bin/tools pathway of the Rstudio folder.

[iantaylor-NOAA]

I didn't remember how I installed Pandoc, so I just did it again by downloading pandoc-3.0-windows-x86_64.msi from https://pandoc.org/installing.html, running it without any admin priviledges (which produced the message screenshot below), and then confirming that "C:\Users\ian.taylor\AppData\Local\Pandoc\" was already in my path from the last time I installed it. This approach is independent of any RStudio location.

[brianlangseth-NOAA]

Thanks all for the help. My solution (really Kelli's, thanks @kellijohnson-NOAA) was to figure out that my issue was with tinytex. The red text I alluded to above indicated that files in my tinytex folder were missing. Reinstalling through Rstudio did not resolve the issue however uninstalling and reinstalling in R itself solved the issue.

Thus, based on the steps in the Readme, doing the tinytext steps in R itself and not Rstudio, and then doing the rest of the steps within Rstudio solved my issue.