I had to mess around with my R version to be able to get my secure gateway to connect to R mirrors. I did this by adding http_proxy=http://servername to both the properties tab in the R icon, and also by doing:
Sys.setenv(http_proxy=http://servername)
in Rstudio. Could get this to work in R, but not Rstudio. anyway no problem - I can install packages from within R, point RStudio at R and load the package. good.
So I try to create a (default) .Rmd file in Rstudio - when I run knitr, I get the following:
Error: 24:17: unexpected '/'
24: http_proxy=http:/
^
Execution halted
I can only imagine I am getting this because I messed around setting up the proxy. Would this make sense?
How do I clear/unset any proxy server in Rstudio?
Quote the string:
Sys.setenv(http_proxy = "http://servername")
If your on Windows, configure your proxy in IExplorer and use setInternet2(TRUE) function in your script to use IExplorer's proxy settings.
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 running Red Hat Enterprise Linux (RHEL) 8.5 with Linux kernel 4.18 and Gnome 3.32.2. In this system, I've got R 4.1.2 compiled with the tool asdf with shared libraries enabled. On top of that, I installed RStudio 2021.09.01-372 from an RPM from the official RStudio website.
When I start Rstudio, the first line of output after the usual R startup is an error:
Error in tools::startDynamicHelp() : internet routines cannot be loaded
I am unable to figure out what's causing this error, and with it I can't run things like refresh CRAN or update packages. But if I start a pure R session from the terminal (instead of Rstudio) this error does not occur.
Some things I tried:
Install the krb5 and libssh2 packages on my host system: Didn't help.
Starting a "pure" R session (both with and without the --vanilla argument) from the Terminal tab within Rstudio also gives this error. If I try to run update.packages() from this session, it pops up a window to select a CRAN mirror then fails with the following:
Warning: failed to download mirrors file (internet routines cannot be loaded); using local file '/home/[my username]/.asdf/installs/R/4.1.2/lib64/R/doc/CRAN_mirrors.csv'
Warning: unable to access index for repository https://cloud.r-project.org/src/contrib:
internet routines cannot be loaded
Warning message:
In download.file(url, destfile = f, quiet = TRUE) :
unable to load shared object '/home/penyuan/.asdf/installs/R/4.1.2/lib64/R/modules//internet.so':
/lib64/libssh.so.4: undefined symbol: EVP_KDF_ctrl, version OPENSSL_1_1_1b
But like I said, the strange thing is if I start an R session outside of Rstudio, these errors don't happen.
Within RStudio, the only workaround I can find is to run this command upon startup (suggested in this thread):
options(download.file.method="wget")
Once this is done, everything else seems to work, such as package updates.
However, I don't want to manually do this every time I start RStudio. So I tried to put it into ~/.Rprofile including a test print() as follows:
print("This is `~/.Rprofile`")
options(download.file.method="wget")
When I open RStudio, I can see the output from the print() call, but the options() command is not run because the original error shows up again. I still have to manually enter options(download.file.method="wget") every time.
I also tried to fold everything into a .First function in ~/.Rprofile as follows:
.First <- function() {
options(download.file.method="wget")
print("This is the `.First` function in `~/.Rprofile`")
}
Unfortunately, same result as before: print()'s output is seen, but options() is not run.
I also made sure that my ~/.Rprofile includes a trailing newline as discussed here. But this didn't help.
The above are the steps I've tried so far.
Why does this error only occur when running RStudio or a terminal within Rstudio? Why doesn't it happen if I start R from a terminal outside of Rstudio?
Is there a way to solve the problem so that the error doesn't happen in the first place? If it can't be solved, how do I set up my ~/.Rprofile so that options(download.file.method="wget") will be run?
Thank you.
I would like to build a simple webserver using Rook, however I am having strange errors when trying it in R-Studio:
The code
library(Rook)
s <- Rhttpd$new()
s$start()
print(s)
returns the rather useless error
"Error in listenPort > 0 :
comparison (6) is possible only for atomic and list types".
When trying the same code in a simple R-Console,everything works - so I would like to understand why that happens and how I can fix it.
RStudio is Version 0.99.484 and R is R 3.2.2
I've experienced same thing.
TLDR: This pull request solves the problem: https://github.com/jeffreyhorner/Rook/pull/31
RStudio is treated in different way and Rook port is same as tools:::httpdPort value. The problem is that in current Rook master tools:::httpdPort is assigned directly. It's a function that's why we need to evaluate it first.
If you want to have it solved right now, without waiting for merge into master: install devtools and load package from my fork #github.
install.packages("devtools")
library(devtools)
install_github("filipstachura/Rook")
I'm having trouble roxygenizing a package. It was last working several months ago and I haven't checked since, so not sure if a snippet of code I added broke it, if my system's configuration changed, or if roxygen2 changed.
I've tried calling it through devtools::document, in a --vanilla R sesssion with roxygen2::roxygenize('taRifx') from the directory above it, roxygenize('.') from the project base directory, tried running as root in case it was a permissions thing, etc.
Here's the RStudio version:
==> roxygenize('.', roclets=c('rd'))
* checking for changes ... ERROR
Error in file(con, "r") : cannot open the connection
Package code is here:
https://github.com/gsk3/taRifx
How do I fix this?
You'll need to change line 1242 of the Rfunctions.R file to #examples instead of #example. For proper formatting you'll also need to change the # in email addresses to ##.
I'm trying to get R (running on Windows) to download some packages from the Internet, but the download fails because I can't get it to correctly use the necessary proxy server. The output text when I try the Windows menu option Packages > Install package(s)... and select a CRAN mirror is:
> utils:::menuInstallPkgs()
--- Please select a CRAN mirror for use in this session ---
Warning: unable to access index for repository http://cran.opensourceresources.org/bin/windows/contrib/2.12
Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.12
Error in install.packages(NULL, .libPaths()[1L], dependencies = NA, type = type) :
no packages were specified
In addition: Warning message:
In open.connection(con, "r") :
cannot open: HTTP status was '407 Proxy Authentication Required'
I know the address and port of the proxy, and I also know the address of the automatic configuration script. I don't know what the authentication is called, but when using the proxy (in a browser and some other applications), I enter a username and password in a dialog window that pops up.
To set the proxy, I tried each of the following:
Sys.setenv(http_proxy="http://proxy.example.com:8080")
Sys.setenv("http_proxy"="http://proxy.example.com:8080")
Sys.setenv(HTTP_PROXY="http://proxy.example.com:8080")
Sys.setenv("HTTP_PROXY"="http://proxy.example.com:8080")
For authentication, I similarly tried setting the http_proxy_user environment variable to:
ask
user:passwd
Leaving it untouched
Am I using the right commands in the right way?
You have two options:
Use --internet2 or setInternet2(TRUE) and set the proxy details in the control panel, in Internet Options
Do not use either --internet2 or setInternet2(FALSE), but specify the environment variables
EDIT: One trick is, you cannot change your mind between 1 and 2, after you have tried it in a session, i.e. if you run the command setInternet2(TRUE) and try to use it e.g. install.packages('reshape2'), should this fail, you cannot then call setInternet2(FALSE). You have to restart the R session.
As of R version 3.2.0, the setInternet2 function can set internet connection settings and change them within the same R session. No need to restart.
When using option 2, one way (which is nice and compact) to specify the username and password is http_proxy="http://user:password#proxy.example.com:8080/"
In the past, I have had most luck with option 2
If you want internet2 to be used everytime you use R you could add the following line to the Rprofile.site file which is located in R.x.x\etc\Rprofile.site
utils::setInternet2(TRUE)
I've solved my trouble editing the file .Renviron as documented in Proxy setting for R.
EDITED
The solutions based on the setInternet2 statement do not work with the recent R versions because setInternet2 is declared defunct.
I'm using the 4.2.1 (on Win 11Pro) while I never had any problems in previous versions .
So to solve the problem need to modify some config files in order to fix the proxy issue not only for packages installation but, in general, also to acced to a remote resource (ie. boundary maps in my case).
The question "Proxy setting for R" collect a lot of solutions. I've found that this one has solved both my problems (packages installation and remote resources) explaining step-by-step how to edit the file .Renviron
Other solutions based on the customization of the file Renviron.site for me doesn't work
install.packages("RCurl")
that will solve your problem.