I am trying to make a blog with blogdown using my windows machine, but get this error message when I use RStudio (File/New Project/New Directory/Website using blogdown/ ... and enter Directory name: "new"):
setwd("C:/Users/AndrésLagerlöf/OneDrive - Andrés Lagerlöf Konsulttjänst AB/R/blog")
'C:\Users\Andr‚sLagerl”f\AppData\Roaming\Hugo\hugo.exe" new site "new' is not recognized as an internal or external command,
operable program or batch file.
Error in shell(cmd, mustWork = TRUE, intern = intern) :
'"C:\Users\AndrésLagerlöf\AppData\Roaming\Hugo\hugo.exe" new site "new" --force -f toml' execution failed with error code 1
I do not know what to make out of this error message. Does anyone know how to fix this?
I use R version 4.0.0 and RStudio Version 1.2.5033.
Kind regards,
Andrés
You may consider installing Hugo to a path that does not contain multibyte characters. Per documentation ?blogdown::install_hugo:
If you want to install Hugo to a custom path, you can set the global option blogdown.hugo.dir to a directory to store the Hugo executable before you call install_hugo(), e.g., options(blogdown.hugo.dir = '~/Downloads/hugo_0.20.1/').
This is also mentioned in Appendix D.1 in the blogdown book. You'd better set this option in your .Rprofile (see Section 1.4 for how), so the setting won't be lost after you restart R.
Related
I'm updating the renv folder from a project in order to adjust the libraries, but it seems I'm having a permission problem. After running renv::init() and trying to installing manually the remaining libraries using install.packages() I always get the message
Error: failed to retrieve 'https://cran.rstudio.com/bin/windows/contrib/4.2/ipeadatar_0.1.6.zip' [error code 23]
1: curl: (23) Failure writing output to destination
2: curl: (23) Failure writing output to destination
Using .libPath() I can see that the renv was created in the "AppData" hidden folder
1] "C:/Users/André Ferreira/AppData/Local/R/cache/R/renv/library/MacroBRA_Wrld-09789847/R-4.2/x86_64-w64-mingw32"
So checking my permissions, I couldn't see anything wrong. Any thoughts about this problem? The thing it's that when I open my .Rmd file and try to knit, I receive the same message "1: curl: (23) Failure writing output to destination", now from rmarkdown retrieve installation, so it may be a configuration/permission problem.
Adding "C:\rtools42\usr\bin" and "C:\Program Files\R\R-4.2.1\bin" in the environment variable didn't help.
As I could see, opening an empty file from rstudio, I could use install.packages() without problem.
Although this doesn't solve the problem directly, you can also instruct renv to use a different library path with something like:
# use a project-local library path
RENV_PATHS_LIBRARY = renv/library
in your project's .Renviron file. Depending on your environment, you might also consider placing the library path in an alternate location.
See https://rstudio.github.io/renv/articles/packages.html#r-cmd-build-and-the-project-library for more details.
I am trying to run 'whitebox' packages in R.
To get started, I follow the steps in the link: https://github.com/giswqs/whiteboxR
install.packages("whitebox")
whitebox::install_whitebox()
Console:
------------------------------------------------------------------------
Could not find WhiteboxTools!
------------------------------------------------------------------------
Your next step is to download and install the WhiteboxTools binary:
> whitebox::install_whitebox()
If you have WhiteboxTools installed already run `wbt_init(exe_path=...)`':
> wbt_init(exe_path='/home/user/path/to/whitebox_tools')
For whitebox package documentation, ask for help:
> ??whitebox
For more information visit https://giswqs.github.io/whiteboxR/
------------------------------------------------------------------------
Performing one-time download of WhiteboxTools binary from
https://www.whiteboxgeo.com/WBT_Windows/WhiteboxTools_win_amd64.zip
(This could take a few minutes, please be patient...)
trying URL 'https://www.whiteboxgeo.com/WBT_Windows/WhiteboxTools_win_amd64.zip'
Content type 'application/zip' length 15383844 bytes (14.7 MB)
downloaded 14.7 MB
WhiteboxTools binary is located here: C:/Users/frsu0056/OneDrive - Umeå universitet/Documents/R/win-library/4.1/whitebox/WBT/whitebox_tools.exe
You can now start using whitebox
library(whitebox)
wbt_version()
After downloading i run:
library(whitebox)
if(wbt_init()==TRUE){print("all good")}#confirms if the whitebox_tools.exe exists in,'C:/Users/frsu0056/OneDrive - Umeå universitet/Documents/R/win-library/4.1/whitebox/WBT/whitebox_tools.exe'.
console:
[1] "all good"
Now, if I try to run any function in the whitebox package, it returns an odd error message
for example
wbt_version()
returns:
Error :
Error running WhiteboxTools
whitebox.exe_path: "C:/Users/frsu0056/OneDrive - Umeå universitet/Documents/R/win-library/4.1/whitebox/WBT/whitebox_tools.exe"; File exists? TRUE
Arguments: --version
Error in system(exeargs, intern = TRUE, ignore.stderr = ignore.stderr, : '"C:/Users/frsu0056/OneDrive - Umeå universitet/Documents/R/win-library/4.1/whitebox/WBT/whitebox_tools.exe"' not found
Yet, the wbt_init() returns TRUE so the file exists in the given directory. Nevertheless, the wbt_version() function can not find it.
And so the story goes for any function in the whitebox package. It just can't find the .exe file yet the file exists in the folder where it is supposed to be.
Anyone else get the same problem running this? And what could possibly be wrong here?
Below is the .exe file resting in the directory.
The problem with whitebox in my experience is that it cannot decode spaces. I don't think the problem is the one drive folder per se, just that there are spaces in the file path. I would suggest not having your packages installed in a one drive folder or any other folder where the path has spaces. To change the folder where your libraries are installed, refer to the solution: Change R default library path using .libPaths in Rprofile.site fails to work
I've seen the post about blogdown::serve_site() no longer serving the site and read the release notes for blogdown 0.21, but it didn't help with my problem.
My workflow is/was to write a post, then click "Serve Site" in RStudio and check out the newly generated files in the public/ folder of my project. I have a symbolic link of that folder in my ShinyApps directory so I can view my site via the Shiny server. This is great, because then my colleagues who also use the server can see my site as well.
Now this doesn't work anymore. While I get the updated site in RStudio directly, the files displayed by the Shiny server are not being updated. The only explanation I can find is this one:
The global option blogdown.generator.server has been deprecated. Now blogdown::serve_site() always use the Hugo server (which corresponds to options(blogdown.generator.server = TRUE) in previous version of blogdown), instead of the server created via the servr package (which corresponds to the default options(blogdown.generator.server = FALSE) before).
I don't know much about Hugo but I found that hugo server doesn't update the public/ directory, is that correct? What can I do now to update that?
The question was already answered on GitHub:
I need to build the site with blogdown::build_site(local=TRUE).
Edit: Turns out that the below was not the solution either for me. Therefore I posted an own question with a possible workaround:
Problem (and solution?) with rendering Hugo/blogdown site
Earlier (old) post:
With me this did not help. When updating blogdown and starting-up my R project, blogdown:::preview_site(startup = TRUE) automatically runs. Something I don't recall from earlier start-ups. I now always receive the same Error message:
Launching the server via the command:
hugo server --bind 127.0.0.1 -p 4321 --themesDir themes -t hugo-academic -D -F --navigateToChanged
sh: line 0: kill: (3262) - No such process
Error: It took more than 30 seconds to launch the server. There may be something wrong. The process has been killed. If the site needs more time to be built and launched, set options(blogdown.server.timeout) to a larger value.
Running blogdown::build_site(local = TRUE) results in an even longer Error message starting with:
ERROR 2020/11/13 15:55:56 render of "page" failed: execute of template failed: template: _default/single.html:6:5: executing "_default/single.html" at <partial "page_header.html" .>: error calling partial: execute of template failed: template: partials/page_header.html:92:7: executing "partials/page_header.html" at <partial "page_metadata" (dict "page" $page "is_list" 0 "share" true)>: error calling partial: "/Users/frederick/Dropbox/EUR/R_work/r_website/r_website_project/themes/hugo-academic/layouts/partials/page_metadata.html:63:31": execute of template failed: template: partials/page_metadata.html:63:31: executing "partials/page_metadata.html" at <.>: range can't iterate over R
Solution for me
For me, it helped to roll-back to blogdown version 0.20 like so:
packageVersion("blogdown")
#> [1] '0.21'
library("devtools")
#> Loading required package: usethis
install_version("blogdown", version = "0.20", repos = "http://cran.us.r-project.org")
#> Downloading package from url: http://cran.us.r-project.org/src/contrib/Archive/blogdown/blogdown_0.20.tar.gz
packageVersion("blogdown")
#> [1] '0.20'
Created on 2020-11-13 by the reprex package (v0.3.0)
Now everything is back to "normal".
im using R and quite new at rmarkdown. i want to knit my rmarkdown into pdf formatted file and i already read that i need to install tinytex package.
i enter the code as instructed on https://yihui.org/tinytex/
install.packages('tinytex')
tinytex::install_tinytex()
and i got this error code
Starting to install TinyTeX to C:\Users*****\AppData\Roaming\TinyTeX. It will take a few minutes.
Automated TeX Live installation using profile: ../tinytex.profile
Loading https://mirror.unpad.ac.id/ctan/systems/texlive/tlnet/tlpkg/texlive.tlpdb
C:\Users*****\AppData\Local\Temp\RtmpW6xVT8\install-tl-20191206\install-tl: TLPDB::from_file could not initialize from: https://mirror.unpad.ac.id/ctan/systems/texlive/tlnet/tlpkg/texlive.tlpdb
C:\Users*****\AppData\Local\Temp\RtmpW6xVT8\install-tl-20191206\install-tl: Maybe the repository setting should be changed.
C:\Users*****\AppData\Local\Temp\RtmpW6xVT8\install-tl-20191206\install-tl: More info: https://tug.org/texlive/acquire.html
TinyTeX installed to C:\Users*****\AppData\Roaming\TinyTeX
Please quit and reopen your R session and IDE (if you are using one, such as RStudio or Emacs) and check if tinytex:::is_tinytex() is TRUE.
Warning message:
In file.remove("TinyTeX/install-tl.log") :
cannot remove file 'TinyTeX/install-tl.log', reason 'No such file or directory'
i restart my r and rstudio, run tinytex::is_tinytex(), returned FALSE.
i guess the repository cannot be accessed anymore so i tried to change the repo but still it doesnt change.
can anyone help me with solution? thanks
UPDATE :
i tried to run this as Yihui Xie told me :
tinytex::install_tinytex(repository = 'http://dante.ctan.org/tex-archive/')
and
tinytex::install_tinytex(repository = 'http://mirrors.ibiblio.org/CTAN/')
and return this
trying URL
'http://dante.ctan.org/tex-archive/systems/texlive/tlnet/install-tl.zip'
length 22539829 bytes (21.5 MB) downloaded 21.5 MB trying URL
'https://yihui.name/gh/tinytex/tools/pkgs-custom.txt' Content length
81 bytes downloaded 351 bytes trying URL
'https://yihui.name/gh/tinytex/tools/tinytex.profile' Content length
81 bytes downloaded 295 bytes Starting to install TinyTeX to
C:\Users\Kandu\AppData\Roaming/TinyTeX. It will take a few minutes.
Automated TeX Live installation using profile: ../tinytex.profile
Loading
https://mirror.unpad.ac.id/ctan/systems/texlive/tlnet/tlpkg/texlive.tlpdb
C:\Users\Kandu\AppData\Local\Temp\Rtmp8OFCvK\install-tl-20191209\install-tl:
TLPDB::from_file could not initialize from:
https://mirror.unpad.ac.id/ctan/systems/texlive/tlnet/tlpkg/texlive.tlpdb
C:\Users\Kandu\AppData\Local\Temp\Rtmp8OFCvK\install-tl-20191209\install-tl:
Maybe the repository setting should be changed.
C:\Users\Kandu\AppData\Local\Temp\Rtmp8OFCvK\install-tl-20191209\install-tl:
More info: https://tug.org/texlive/acquire.html TinyTeX installed to
C:\Users\Kandu\AppData\Roaming/TinyTeX Please quit and reopen your R
session and IDE (if you are using one, such as RStudio or Emacs) and
check if tinytex:::is_tinytex() is TRUE. Warning messages:
1: In
file.remove("TinyTeX/install-tl.log") : cannot remove file
'TinyTeX/install-tl.log', reason 'No such file or directory'
2: In
in_dir(target, { : The repository
http://dante.ctan.org/tex-archive/systems/texlive/tlnet does not seem
to be accessible. Reverting to the default CTAN mirror.
idk why but it keep trying to download from https://mirror.unpad.ac.id.
any explanation?
At the moment, the mirror https://mirror.unpad.ac.id does not seem to have a valid SSL certificate, so the site is not accessible. You can find other accessible mirrors at https://ctan.org/mirrors/mirmon. To specify the mirror, use the repository argument. Below are two possible examples:
tinytex::install_tinytex(repository = 'http://mirrors.ibiblio.org/pub/mirrors/CTAN/')
tinytex::install_tinytex(repository = 'http://dante.ctan.org/tex-archive/')
I wanted to run this example script: http://mazamascience.com/WorkingWithData/?p=912 from Windows command line. So I opened the command line and typed Rscript tryCatch.R 1. However, I keep getting the error message Error: R not found. I did set the PATH environment variable as C:\Programme\R\R-3.0.1\bin. If I just type R.exe, it does start R, but it cannot find the packages that are to be loaded at start (e.g. package 'utils' in options<"defaultPackages"> was not found). I guess I have to set another path to the libraries somewhere, but I haven't got any idea where to do this.
UPDATE: After explicitly typing PATH C:\Programme\R\R-3.0.1\bin (rather than just adding this to the value of the environment variable PATH) it seems that R is found. However, a new problem occurs: In normalizePath<path.expand(path), winslash, mustWork>: path[2] = "C:/Programme/R/R-3.0.1/library": Access denied, the same than for the methods library. Then: Calls: .First ... library -> .getRequiredPackages2 -> library -> normalizePath Execution stopped. I'm using Windows 7 and I do have administrator rights.
Rscript is very handy (R CMD BATCH is the old way to ) specially under windows, But generally under I create a batch file to avoid all path's headache.
For example say launcher.bat:
#echo off
C:
PATH C:\Programme\R\R-3.0.1\bin;%path%
cd PATH_TO_YOUR_RSCRIPT
Rscript tryCatch.R 1
pause
And open a console(using cmd) , go where you have stored your launcher.bat and launch it. Or from the R cosnole using shell:
shell('path_to_launcher\launcher.bat')
I've found out that it was a language-specific problem on Windows 7, similar to what is described here: https://stat.ethz.ch/pipermail/r-help/2011-May/276932.html
After changing PATH to C:\Program Files\R\R-3.0.1\bin the script is properly executed from the command prompt.
Thanks to everyone who tried to help!
I ran into this problem under windows 7, apparently, when setting environment variables>user variables the path is not added into the PATH, so the user must add this path in system variables > PATH
at the end just add the path to your .EXE files and voila.