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.
Related
When running R CMD check I get the following note:
checking for future file timestamps ... NOTE
unable to verify current time
I have seen this discussed here, but I am not sure which files it is checking for timestamps, so I'm not sure which files I should look at. This happens locally on my windows and remotely on different systems (using github actions).
Take a look at https://svn.r-project.org/R/trunk/src/library/tools/R/check.R
The check command relies on an external web resource:
now <- tryCatch({
foo <- suppressWarnings(readLines("http://worldclockapi.com/api/json/utc/now",
warn = FALSE))
This resource http://worldclockapi.com/ is currently not available.
Hence the following happens (see same package source):
if (is.na(now)) {
any <- TRUE
noteLog(Log, "unable to verify current time")
See also references:
https://community.rstudio.com/t/r-devel-r-cmd-check-failing-because-of-time-unable-to-verify-current-time/25589
So, unfortunately this requires a fix in the check function by the R development team ... or the web-resource coming online again.
To add to qasta's answer, you can silence this check by setting the _R_CHECK_SYSTEM_CLOCK_ environment variable to zero e.g Sys.setenv('_R_CHECK_SYSTEM_CLOCK_' = 0)
To silence this in a persistent manner, you can set this environment variable on R startup. One way to do so is through the .Renviron file, in the following manner:
install.packages("usethis") (If not installed already)
usethis::edit_r_environ()
Add _R_CHECK_SYSTEM_CLOCK_=0 to the file
Save, close file, restart R
I am new to Alfresco and I am trying to install alfresco in my debian server(via ssh access) following the installation guide. However, the installation stops and shows me this error :
Error: There has been an error.
initdb.bin: encoding mismatch
The encoding you selected (UTF8) and the encoding that the selected
locale uses (LATIN1) do not match. This would lead to misbehavior in
various character string processing functions. Rerun initdb.bin and either
do not specify an encoding explicitly, or choose a matching combination.
I tried updating the locales of the server but still the issue exists. How do I fix this?
I have successfully installed it by doing the following steps:
Commented out the Send_ENV in /etc/ssh/ssh_config variable in the local machine and Accept_ENV in /etc/ssh/sshd_config variable in the server.
Edited /etc/locale.gen to uncomment en_US.UTF-8.
Ran locale-gen
Edited /etc/locale.conf and added LANG=en_US.UTF-8.
Successfully installed alfresco.
I need authentication to use internet, say these are my variables:
Proxy : 1ncproxy1
Port : 80
Loggin : MyLoGiN
Pass : MyPaSs
How can I install a package in R and its addon packages ?
Such that the following would work:
install.packages("TSA", dependencies=TRUE)
Without our having internet connection failutes?
I tried this:
Sys.setenv("ftp_proxy" = "1ncproxy1","ftp_proxy_user"="MyLoGiN","ftp_proxy_password"="MyPaSs")#Port = 80
ButI get :
Warning: unable to access index for repository http://cran.ma.imperial.ac.uk/src/contrib
# or
cannot open: HTTP status was '407 Proxy Authentication Required'
Many thanks,
You are probably on Windows, so I would advice you to check the 'R on Windows FAQ' that came with your installation, particularly Question 2.19: The Internet download functions fail. You may need to restart R with the --internet2 option (IIRC) for the proxy settings to come into effect.
I always found this very cumbersome. An alternative is to install a proxy-aware webdownloader as eg wget (as a windows binary) where you set the proxy options in a file in your home directory. This is all from memory, I think the last time I was faced with such a proxy was in 2005 so YMMV.
As #juba states, I think you want to set the http_proxy. From ?download.file:
Usernames and passwords can be set for HTTP proxy transfers via
environment variable http_proxy_user in the form user:passwd.
Alternatively, http_proxy can be of the form
"http://user:pass#proxy.dom.com:8080/"
So, try: Sys.setenv(http_proxy="http://MyLoGiN:MyPaSs#1ncproxy1:80")
Be aware though:
These environment variables must be set before the download code is
first used: they cannot be altered later by calling Sys.setenv.
So you are best off calling it in your .Rprofile
+1 for Juba, above. This worked for me:
$ export http_proxy=http://username:password#the-proxy.mycompany.com:80
$ R
> install.packages("quantmod")
I tried to install swirl package, and had the same problem - proxy with authorisation.
After some experiments i found decision.
May be my answer will help for anybody.
On Windows 7 :
set 1 or more (if ou need) env variables http_proxy (https_proxy and ftp_proxy if you need) (If you dont know how - read there http://www.computerhope.com/issues/ch000549.htm )
Its look like that
env variables for proxy
format http_proxy="http://Proxyusername:ProxyUserPassw#proxyServName:ProxyPort"
Use '#' instead of %40
In RStudio Tools->Global Options->Packages release check box "Use Internet Explorer library /proxy for HTTP"
As Jeff Taylor wrote, R can indirectly make use of a proxy server. You need to specify the proxy server for both, http and https protocols, as follows:
$ export http_proxy=http://user:pass#proxy_server:port
$ export https_proxy=http://user:pass#proxy_server:port
$ R
> install.packages("<package_name>")
I just tested this solution and it works like a charm. The answer from Jeff was correct but unfortunatelly for most cases incomplete, as most of the servers are nowadays accesible over https.
I need authentication to use internet, say these are my variables:
Proxy : 1ncproxy1
Port : 80
Loggin : MyLoGiN
Pass : MyPaSs
How can I install a package in R and its addon packages ?
Such that the following would work:
install.packages("TSA", dependencies=TRUE)
Without our having internet connection failutes?
I tried this:
Sys.setenv("ftp_proxy" = "1ncproxy1","ftp_proxy_user"="MyLoGiN","ftp_proxy_password"="MyPaSs")#Port = 80
ButI get :
Warning: unable to access index for repository http://cran.ma.imperial.ac.uk/src/contrib
# or
cannot open: HTTP status was '407 Proxy Authentication Required'
Many thanks,
You are probably on Windows, so I would advice you to check the 'R on Windows FAQ' that came with your installation, particularly Question 2.19: The Internet download functions fail. You may need to restart R with the --internet2 option (IIRC) for the proxy settings to come into effect.
I always found this very cumbersome. An alternative is to install a proxy-aware webdownloader as eg wget (as a windows binary) where you set the proxy options in a file in your home directory. This is all from memory, I think the last time I was faced with such a proxy was in 2005 so YMMV.
As #juba states, I think you want to set the http_proxy. From ?download.file:
Usernames and passwords can be set for HTTP proxy transfers via
environment variable http_proxy_user in the form user:passwd.
Alternatively, http_proxy can be of the form
"http://user:pass#proxy.dom.com:8080/"
So, try: Sys.setenv(http_proxy="http://MyLoGiN:MyPaSs#1ncproxy1:80")
Be aware though:
These environment variables must be set before the download code is
first used: they cannot be altered later by calling Sys.setenv.
So you are best off calling it in your .Rprofile
+1 for Juba, above. This worked for me:
$ export http_proxy=http://username:password#the-proxy.mycompany.com:80
$ R
> install.packages("quantmod")
I tried to install swirl package, and had the same problem - proxy with authorisation.
After some experiments i found decision.
May be my answer will help for anybody.
On Windows 7 :
set 1 or more (if ou need) env variables http_proxy (https_proxy and ftp_proxy if you need) (If you dont know how - read there http://www.computerhope.com/issues/ch000549.htm )
Its look like that
env variables for proxy
format http_proxy="http://Proxyusername:ProxyUserPassw#proxyServName:ProxyPort"
Use '#' instead of %40
In RStudio Tools->Global Options->Packages release check box "Use Internet Explorer library /proxy for HTTP"
As Jeff Taylor wrote, R can indirectly make use of a proxy server. You need to specify the proxy server for both, http and https protocols, as follows:
$ export http_proxy=http://user:pass#proxy_server:port
$ export https_proxy=http://user:pass#proxy_server:port
$ R
> install.packages("<package_name>")
I just tested this solution and it works like a charm. The answer from Jeff was correct but unfortunatelly for most cases incomplete, as most of the servers are nowadays accesible over https.
I am facing problem while conecting R with internet in my office. May be this due to LAN settings. I tried the almost all possible ways I come across in the web (see below) but still in vain.
Method1: Invoking R using --internet2
Method2: Invoking R by setting ~/Rgui.exe http_proxy=http:/999.99.99.99:8080/ http_proxy_user=ask
Method3: Setting Setinternet2=TRUE
Method4:
curl <- getCurlHandle()
curlSetOpt(.opts = list(proxy = '999.99.99.99:8080'), curl = curl)
Res <- getURL('http://www.cricinfo.com', curl = curl)
In above all methods I can able to load packages directly from CRAN also able to download files using download.file command
But using getURL(RCurl), readHTMLTable(XML), htmlTreeParse(XML) commands I am unable to extract web data. I am getting ~<HEAD>\n<TITLE>Access Denied</TITLE>\n</HEAD>~ error.
How to set LAN proxy settings for XML package in R?
On Mac OS, I found the best solution here. Quoting the author, two simple steps are:
1) Open Terminal and do the following:
export http_proxy=http://staff-proxy.ul.ie:8080
export HTTP_PROXY=http://staff-proxy.ul.ie:8080
2) Run R and do the following:
Sys.setenv(http_proxy="http://staff-proxy.ul.ie:8080")
double-check this with:
Sys.getenv("http_proxy")
I am behind university proxy, and this solution worked perfectly. The major issue is to export the items in Terminal before running R, both in upper- and lower-case.
For RStudio just you have to do this:
Firstly, open RStudio like always, select from the top menu:
Tools-Global Options-Packages
Uncheck the option: Use Internet Explorer library/proxy for HTTP
And then close the Rstudio, furthermore you have to:
Find the file (.Renviron) in your computer, most probably you would find it here: C:\Users\your user name\Documents. Note that if it does not exist you can creat it just by writing this command in RStudio:
file.edit('~/.Renviron')
Add these two lines to the initials of the file:
options(internet.info = 0)
http_proxy="http://user_id:password#your_proxy:your_port"
And that's it..??!!!
The problem is with your curl options – the RCurl package doesn't seem to use internet2.dll.
You need to specify the port separately, and will probably need to give your user login details as network credentials, e.g.,
opts <- list(
proxy = "999.999.999.999",
proxyusername = "mydomain\\myusername",
proxypassword = "mypassword",
proxyport = 8080
)
getURL("http://stackoverflow.com", .opts = opts)
Remember to escape any backslashes in your password. You may also need to wrap the URL in a call to curlEscape.
I had the same problem at my office and I solved it adding the proxy in the destination of the R shortcut; clik on right button of the R icon, preferences, and in the destination field add
"C:\Program Files\R\your_R_version\bin\Rgui.exe" http_proxy=http://user_id:passwod#your_proxy:your_port/
Be sure to put the directory where you have the R program installed. That works for me. Hope this help.
This post pertains to R proxy issues on *nix. You should know that R has many libraries/methods to fetch data over internet.
For 'curl', 'libcurl', 'wget' etc, just do the following:
Open a terminal. Type the following command:
sudo gedit /etc/R/Renviron.site
Enter the following lines:
http_proxy='http://username:password#abc.com:port/'
https_proxy='https://username:password#xyz.com:port/'
Replace username, password, abc.com, xyz.com and port with these settings specific to your network.
Quit R and launch again.
This should solve your problem with 'libcurl' and 'curl' method. However, I have not tried it with 'httr'. One way to do that with 'httr' only for that session is as follows:
library(httr)
set_config(use_proxy(url="abc.com",port=8080, username="username", password="password"))
You need to substitute settings specific to your n/w in relevant fields.
Inspired by all the responses related on the internet, finally I've found the solution to correctly configure the Proxy for R and Rstudio.
There are several steps to follow, perhaps some of the steps are useless, but the combination works!
Add environment variables http_proxy and https_proxy with proxy details.
variable name: http_proxy
variable value: https://user_id:password#your_proxy:your_port/
variable name: https_proxy
variable value: https:// user_id:password#your_proxy:your_port
If you start R from a desktop icon, you can add the --internet flag to the target line (right click -> Properties)
e.g."C:\Program Files\R\R-2.8.1\bin\Rgui.exe" --internet2
For RStudio just you have to do this:
Firstly, open RStudio like always, select from the top menu:
Tools-Global Options-Packages
Uncheck the option: Use Internet Explorer library/proxy for HTTP
Find the file (.Renviron) in your computer, most probably you would find it here: C:\Users\your user name\Documents.
Note that: if it does not exist you can create it just by writing this command in R:
file.edit('~/.Renviron')
Then add these six lines to the initials of the file:
options(internet.info = 0)
http_proxy = https:// user_id:password#your_proxy:your_port
http_proxy_user = user_id:password
https_proxy = https:// user_id:password0#your_proxy:your_port
https_proxy_user = user_id:password
ftp_proxy = user_id:password#your_proxy:your_port
Restart R. Type the following commands in R to assure that the configuration above works well:
Sys.getenv("http_proxy")
Sys.getenv("http_proxy_user")
Sys.getenv("https_proxy")
Sys.getenv("https_proxy_user")
Sys.getenv("ftp_proxy")
Now you can install the packages as you want by using the command like:
install.packages("mlr",method="libcurl")
It's important to add method="libcurl", otherwise it won't work.
On Windows 7 I solved this by going into my environment settings (try this link for how) and adding user variables http_proxy and https_proxy with my proxy details.
If you start R from a desktop icon, you can add the --internet flag to the target line (right click -> Properties) e.g.
"C:\Program Files\R\R-2.8.1\bin\Rgui.exe" --internet2
Simplest way to get everything working in RStudio under Windows 10:
Open up Internet Explorer, select Internet Options:
Open editor for Environment variables:
Add a variable HTTP_PROXY in form:
HTTP_PROXY=http://username:password#localhost:port/
Example:
HTTP_PROXY=http://John:JohnPassword#localhost:8080/
RStudio should work:
Tried all of these and also the solutions using netsh, winhttp etc.
Geek On Acid's answer helped me download packages from the server but none of these solutions worked for using the package I wanted to run (twitteR package).
The best solution is to use a software that let's you configure system-wide proxy.
FreeCap (free) and Proxifier (trial) worked perfectly for me at my company.
Please note that you need to remove proxy settings from your browser and any other apps that you have configured to use proxy as these tools provide system-wide proxy for all network traffic from your computer.
Find your R home with R.home("home")
Add following lines to Renviron.site in your R home
http_proxy=http://proxy.dom.com/
http_proxy_user=user:passwd
https_proxy=https://proxy.dom.com/
https_proxy_user=user:passwd
Open R -> R reads Renviron.site in its home -> it should work :)
My solution on a Windows 7 (32bit). R version 3.0.2
Sys.setenv(http_proxy="http://proxy.*_add_your_proxy_here_*:8080")
setInternt2
updateR(2)