I think I have managed to mess my zsh shell. I am getting the following message when I use the up or down arrow keys:
"_history-substring-search-end:13: _zsh_highlight: function definition file not found"
Just to give you some background:
I installed antigen using
curl https://cdn.rawgit.com/zsh-users/antigen/v1.4.0/bin/antigen.zsh > antigen.zsh
source antigen.zs
This worked fine.
Someone mentioned to install it via brew, so I installed it via brew. This is when antigen stopped working and the highlighter.
I tried installing antigen again via
curl https://cdn.rawgit.com/zsh-users/antigen/v1.4.0/bin/antigen.zsh > antigen.zsh
source antigen.zs
Antigen works while I am in the shell, but the highlighter is not working.
But when I re-launch a new shell and type the antigen command, I receive the following message:
"zsh: command not found: anitgen"
And also the following message when I use the up and down arrow keys:
"_history-substring-search-end:13: _zsh_highlight: function definition file not found"
How can I fix this?
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 have a '.js' script that I usually activate from the terminal using the command node script.js. As this is part of a process where I first do some data analysis in R, I want to avoid the manual step of opening the terminal and typing the command by simply having R do it for me. My goal would be something like this:
...R analysis
write.csv(df, "data.csv")
system('node script.js')
However, when I use that specific code, I get the error:
sh: 1: node: not found
Warning message:
In system("node script.js") : error in running command
Of course, the same command runs without problem if I type it directly on the terminal.
About my Software
I am using:
Linux computer with the PopOS!
RStudio 2021.09.1+372 "Ghost Orchid"
R version 4.0.4.
The error message node: not found indicates that it couldn't find the program node. It's likely in PATH in your terminal's shell, but not in system()'s shell (sh).
In your terminal, locate node by executing which node. This will show the full path to the executable. Use that full path in system() instead.
Alternatively, run echo $PATH in your terminal, and run system('echo $PATH') or Sys.getenv('PATH') in R. Add any missing directories to R's path with Sys.setenv(PATH = <your new path string>)
Note that system2() is recommended over system() nowadays - but for reasons unimportant for your case. See ?system and ?system2 for a comparison.
Examples
Terminal
$ which node
/usr/bin/node
R
system('/usr/bin/node script.js')
# alternatively:
system2('/usr/bin/node', c('script.js'))
or adapt your PATH permanently:
Terminal
% echo $PATH
/usr/local/bin:/home/caspar/programs:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin
R
> Sys.getenv('PATH')
[1] "/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/Applications/RStudio.app/Contents/MacOS/postback"
> Sys.setenv(PATH = "/home/caspar/programs:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/Applications/RStudio.app/Contents/MacOS/postback")
I am building a Shiny app using golem, and I need to use exiftool to rename photos. After using usethis::use_package('exifr') in my 02_dev.R script, exifr::read_exif() works fine, but when the app hits my system call to use exiftool (system('exiftool ...')), it gives the error "Warning: Error in system: 'exiftool' not found." I have exiftool and strawberry PERL installed on my computer (strawberry is in the C: drive), and I tried copying exiftool into my inst/app/www/ folder, but I am still getting the same message.
Edit: here is the full command that triggers the error: system("exiftool -r -d %Y%m%d_%H%M%S \"-filename<SWWLF2021/${userlabel;s/ //g}/",vals$pcode,"_${userlabel;s/ //g}_${DateTimeOriginal}_${triggermode;s/(.)(.*\\s)(.)(.*)/$1$3/}${sequence;s/(\\d)(.*)/_$1/}.%e\" "
where userlabel, DateTimeOriginal, triggermode, and sequence are all part of the photo metadata.
Is there a call I should be using in my 02_dev.R, or in golem_add_external_resources() in my app_ui script?
Sorry for a basic question. I'm trying run a R script called cuffdiff_gtf_attributes (please find it at enter link description here in R 3.3.1 installed on the Windows 7. The script is started with the below line:
#!/usr/bin/env Rscript
When I type cuffdiff_gtf_attributes in R, it says Error: object 'cuffdiff_gtf_attributes' not found. Also, I tried Rscript cuffdiff_gtf_attributes that returned me: Error: unexpected symbol in "Rscript cuffdiff_gtf_attributes".
Moreover, I tried source('cuffdiff_gtf_attributes.R')that seems to work and returned the usage of the script as bellow
Error:
usage: cuffdiff_gtf_attributes --input=<inputGTF> [--output=outputGTF] | --help
But, when I add the arguments as source('cuffdiff_gtf_attributes.R') --input=file.gtf, it says that: Error: object 'file.gtf' not found. I also tried this command as source('cuffdiff_gtf_attributes.R') --input file.gtf, it says that Error: unexpected symbol in "source('cuffdiff_gtf_attributes.R') --input file.gtf"
Sorry, I couldn't post a sample GTF file, you can find a short sample of it at enter link description here
Everything is the current path. Could you please help me out to execute the script?
Thanks in advance
This is a script file. You should run using Rscript instead for Rgui.exe. From a command prompt, navigate to the directory where file.gtf is and run:
"%Programfiles%\R\R-3.3.3\bin\Rscript" cuffdiff_gtf_attributes.R --input=file.gtf
On "./configure" of an open source project I get:
user agent OS = Linux
./configure: line 13957: syntax error near unexpected token 0.9.3'
./configure: line 13957: GOBJECT_INTROSPECTION_CHECK(0.9.3)'
make: *** [config.status] Error 2
Ubuntu 12.04 package "gobject-introspection" and "libgirepository1.0-dev" are present. Removing the GOBJECT_INTROSPECTION_CHECK line allows configure to complete, but the project fails a dependency later.
How can I get past this configure step cleanly? Googling for this issue shows bugs filed against numerous OS projects for this same blocking issue, but the usual answer is "install gobject-introspection".
As the OP discovered on his own he had to install the gobject-introspection package to get the m4 macros that were being used.
The error message has the raw macro in it, as configure scripts are generated from configure.in/configure.ac files via m4/etc the fact that the raw macro is in the output file indicates that the macro did not get translated at generation time.
The gobject-introspection m4 files were apparently installed after autogen.sh (or equivalent) was run to generate the configure script. Re-running the autogen.sh script should regenerate the configure script and run the macro correctly.