I have been using R on commandline (BASH). I am unable to access the internet (download any packages). I have tried proxy system wide, and tested it with wget, which works. The "install.packages()" command however does not.
Per some user's advice, I also tried setting the proxy in .Rprofiles file. That didn't help either. Please advice.
I recently ran into the same issue on my work machine. Our Firm uses Cylance as its antivirus software. Cylance was quarantining the file "internet.dll" that R uses to access the Internet. Fortunately, however, it only does so in the 32-bit version of R. For me, there were two solutions:
First, I was able to download packages directly from the 32-bit version of R (outside of RStudio). This works fine. The downloaded packages will run in 64-bit RStudio.
The longer-term solution was to submit an IT service request to release this file from quarantine (that is, to "whitelist a blocked entity"). At my Firm this was promptly done, as there is (obviously) nothing unsafe about this R file.
Related
I have a new computer in the same network as the old one. In the new one, I first installed RStudio, then the latest version of R (I hope the order does not matter). Now, the new R installation gets "unable to access index for repository" error for every library. Simple task becomes hours of googling, during which I tried the following:
tick or untick use secure download method for http in global options (was ticked in the old computer)
try different, close my location repositories in global settings
copy the folder of an existing package (like ggplot2) from the old computer to the new one's library folder (does not become visible in packages pane)
uninstall and reinstall R
compare installations (the only difference is that in the old computer, folder RTools is under c:/program files while in the new one I accepted the standard location and folder (c:/Rtools40)
Please note that both computers are in the same corporate network, so the firewall and other network settings are the same.
Finally I found the reason: our company uses an internal repository that mirrors an external one. After inserting a custom repository, everything worked perfectly.
I hope this helps if someone runs to a similar problem.
Thanks everyone for your comments!
I have a problem with a custom local CRAN-mirror (jfrog) under windows on a machine without access to the internet:
in R 4.1.2, I have no problems accessing the mirror via https,
in R 4.2.0, I get errors that the index in PACKAGES can not be accessed via https.
After browsing the web and SO, I saw some more problems alike but none quite the same (see, e.g. here), I got around this issue by adding to my .Rprofile
options(repos = c(CRAN = "internalrepo"),
download.file.method = "curl",
download.file.extra = "-k -L")
to bypass checking SSL-certificates.
This works for me on a computer with access to the local network only, but it seems a bad idea on computers connected to the internet using a custom CRAN mirror.
Also, I would like to understand the cause of the problem. Did something change in the way that R handles SSL-certificates or did we break something in the installation of R 4.2?
sessionInfo() and Sys.getenv() do not show much difference between R 4.1.2 and R 4.2.0 but in R 4.2.0, I saw that there is an additional environment variable
CURL_CA_BUNDLE that points to the R installation directory /etc/curl-ca-bundle.crt
EDIT: 2022-12-14: I believe I tracked down the issue - it's SSL revocation checks that failed when a system only has access to a local network. A new flag was added to 4.2.1+ that can be set to TRUE, allowing SSL revocation checks to be given 'best-effort' attempts to contact, then bypassed. https://bugs.r-project.org/show_bug.cgi?id=18379 But if a machine has internet access, revocation checks will still be allowed to occur, which, I think, is probably the best we can hope for.
ORIGINAL: Just letting you know #clemenskuehn we have the same thing - local mirror working fine in 4.1.2 over HTTPS on some restricted data systems that aren't allowed internet access, then suddenly we update to 4.2.1 on our windows & linux boxes, and the windows machines only (linux works fine) aren't able to use the local mirror anymore,
"warning: unable to access index for repository https://mirror.oursite.com/cran/src/contrib:
cannot open URL 'https://mirror.oursite.com/cran/src/contrib/PACKAGES"
so it's not just you. Did you open a tracker with the R developers? Your workaround works for us so we might put it into production as a stopgap but it definitely be good if we didn't have to allow insecure connections, even though these systems can't get outbound access anyway.
I want to follow the advice I've read and heard to have both a main library in R_HOME/library and a user library. I'm using W10 on a desktop machine (not important, except that it gives me a name by which to refer to it), and I can't make R use the user library.
I have succeeded in doing that on a W10 laptop: C:/R/R-4.0.2/library contains some 30 recommended packages, and C:/Users/[username]/Documents/R/win-library/4.0 con contains a much larger number of packages in my user library.
As I recall, and as I wrote down when I did an upgrade on a server, all you have to do to create a site-library is to create a directory called C:/R/R-4.0.2/site-library, and R will use that the next time it starts.
To create a user library, create the directory C:/Users/[username]/Documents/R/win-library/4.0.
That seemed to work on my laptop, for I have seemingly a working R library and a user library there.
That seemed to work on the server, too: I have a library and a site-library.
In both cases, .libPaths() shows the same libraries that I see with Dired on the disk.
I tried to do the same thing on the desktop machine, and i can't make it work.
I created a directory C:/Users/[username]/Documents/R/win-library/4.0, restarted R, and ran .libPaths(); the only directory that was listed was C:/R/R-4.0.2/library.
Because I thought the Documents in that path seemed odd, I tried it again using C:/Users/[username]/R/win-library/4.0, still with no success.
https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Managing-libraries seems pertinent, but I'm not sure how to interpret the output of Sys.getenv("R_LIBL_USER). I get "\\[toplevel]\[nextlevel]\Home$\[username]/R/win-library/4.0", which I presume is a long-winded way to get to /Home$/[username]/R/win-library/4.0 (aka C:/Users/[username]/R/win-library/4.0.
Suggestions? I've tried a number of other suggestions from SO, all to no avail.
Question:
I am developing an R package. I have not yet submitted to CRAN (and it's not ready to at any rate). I want to send the package to friend for some preliminary testing (he's not a builder) and I just want to see if he can use a few features.
On my Mac version of RStudio, I can generate binaries easily. It creates a file called "iatgen_1.0.tgz"
Can my friend use that to install my early build on his windows machine? Or do I need to do something to that file to make it usable for a windows user. Let's assume I have NO access to a windows machine. What can I do from my mac to make this package usable by windows users?
I am posting my comment as an (extended) answer because I think it will help you. When I built my package, I did not have access to Windows either and was suffering from the same issue. I discovered the the Windows build service offered at http://win-builder.r-project.org/ and it worked great. You'll need to do a few things before you send it in, and this is all explained on the site.
First, build your source package with R CMD build. Next, check the package with R CMD check. If this succeeds, follow the rest of the instructions on the site and if all goes well they will send you a link to the temporary directory on their server where you can download the Windows build. If all does not go well, Mr. Ligges will send you an email with the detailed issues so you can fix them and try again.
Like I said, the service worked very well for me. The response was prompt and there were absolutely no problems.
i've been getting up to speed using R of late, and am wondering what the most efficient way is to clone an RStudio environment, especially the package installations, from one machine to another. i'd like to be able to switch from my desktop machine to my laptop, but i am adding packages very frequently to the desktop as i work and would like a simple way to make sure the same packages get installed on the laptop.
any help much appreciated
ps. not everything i'm installing is from CRAN...some are packages taken from github
If you have more than a couple of machine to maintain with the same R configuration, I think you should consider setting up your own local R repository.
And I will just redirect you to another SO question here:
Creating a local R package repository
You can also find the most useful information in the R manual.
Once this is done, you just have to update the local R repository and the packages will be updated on all machines, Windows or Unix
You can just copy and paste the folders in the R libraries between machines. As long as it is the same operating system on both machines there should not be any problem. If you want it to be automatically synchronised then place the R libraries into something like dropbox so that adding or updating a package will automatically appear on either machine with the next sync.