When I run apt install r-base it provides me with a slightly out-dated version of R. When I tried to look up how to get a newer version, much of what I found did something to the file /etc/apt/source.list. The content of this file is
#deb cdrom:[Linux Mint 18.3 _Sylvia_ - Release amd64 20171124]/ xenial contrib $
Most instructions suggest appending something like
deb http://cran.rstudio.com/bin/linux/debian wheezy-cran3/
But none of the various suggestions I've read have worked--presumably either because they were for non-Mint distros or they were for outdated versions of Mint. I tried taking something that I found, like
http://cran.ma.imperial.ac.uk/bin/linux/ubuntu trusty/
and editing it with the codename that I found elsewhere which seems to be the most recent, hence making it
http://cran.ma.imperial.ac.uk/bin/linux/ubuntu sylvia/
But when I ran the update it couldn't find the repo, presumably because places that have Trusty don't necessarily have Sylvia--although maybe it didn't work for some other reason. (And I notice the UK address which probably is bad for me to be using in America, but I don't really get how I'm supposed to find an address that will have the right files.)
Since I see a number of times when this question has been asked and solutions always seem to be short-lived, applying only so long as that particular version is hosted by that particular address and is the latest version--can I ask something where the answer might have a little more longevity: In general, how do you find the right thing to add to your /etc/apt/source.list file to make this work? How do you find the right repo source (same thing as a mirror?), the current codename, and so on? (It would also be nice to have a generalized procedure for how to solve this, because I basically ran into the same problem on my old computer with a 32-bit architecture, and would like to have R running on that too without having to ask the question a second time--but presumably the specific thing and place I'll have to download for that is different.)
Related
First of all, I am working on a Mac. I am trying to install Blotter from GitHub. I found several descriptions of how to do that but my RStudio tells me that I am missing Building tools and gives me a link (https://www.cnet.com/how-to/install-command-line-developer-tools-in-os-x/) where it is described to do that. So far so good. I downloaded Xcode and the command line tools for Mac and installed those. Nothing changed even after restarting R. Then I found this https://cran.r-project.org/bin/macosx/tools/. I installed it and during that, it told me that I had to do the following
"This package will install clang 6.0.0 for OS X 10.11 (El Capitan) or higher with OpenMP support in /usr/local/clang6
In order to use this compiler you have to add /usr/local/clang6/bin to the PATH environment variable such as
export PATH=/usr/local/clang6/bin:$PATH"
So I changed the environmental variable path as follows http://blog.tonytsai.name/blog/2018-05-07-setting-path-variable-for-gs-command-in-rstudio/.
How I changed the PATH variable.
Again I restarted R but still, nothing changed. I still get the notice that the building tool is missing.
Somehow it seems to me that I installed everything correctly but R doesn't recognize the Programmes. Does anyone have an idea? I tried to search for settings to tell R that I installed the command line tool but couldn't really find anything helpful.
Ok, a bit of an update.
Best I can see it that Blotter is built and stored on R-Forge packages under a package called RStrategist
In R console type/cut & paste this.
install.packages('RStrategist',repos='http://R-Forge.r-project.org')
See R forR-Forge for more details. Once this has been installed run instead.
library(RStrategist)
Unfortunately, I am not willing to install this package and see if it works mainly because 1) don't need it nor know how to use it, 2) not sure how good packages are from R-forge, though it seems legit, but, this brings me back to point one.
So before i read the updated answer of Conrad Thiele i was trying around bit. Basically i deleted R, R Studio, Xcode and Command Line tools. Then i installed Xcode, Command Line tools, R and RStudio. Then i followed the notice on https://cran.r-project.org about the tools and installed both stated tools. As mentioned in the original question the Clang package tells you to change the Environmental Variable. And there was the mistake i believe. I originally simply pasted "PATH=/usr/local/clang6/bin:$PATH" into the the ".Renviron" file. With reading up online i noticed that "export PATH=/usr/local/clang6/bin:$PATH" is actually a Command for the Mac Terminal. After executing it, it sill didn't work but then i remembered that i still had the Path "PATH=/usr/local/clang6/bin:$PATH" in the the ".Renviron" file. Once i deleted that it worked. So i guess the key was that with changing the Environmental Variable correctly R found the connection with the right tool. Patients paid off.
I just updated R from version 2.15.1 to version 3.0.0 on my MAC running 10.6.8 and now R crashes on startup.
I get the error:
Error in getLoadedDLLs() : there is no .Internal function 'getLoadedDLLs'
Error in checkConflicts(value) :
".isMethodsDispatchOn" is not a BUILTIN function
Any ideas on how to go about?
The most common cause of this is having a corrupted ".Rdata" file in your working directory. Using the Mac Finder.app you will not by default be able to see files that begin with a ".", so-called dotfiles. Those files can be "seen" if you execute a change to the plist controlling the behavior of Finder.app. Open a Terminal.app window and run this bit of code:
defaults write com.apple.Finder AppleShowAllFiles YES
Then /point/-/click/-/hold/ on Dock-Finder-icon, and choose "Relaunch"
If you to do so, you can then change it back with the obvious modfication to that procedure. I happen to like seeing the hidden files so that's the way I run my Mac all the time, but some people may feel it is too dangerous to expose the "hidden secrets" to their own bumbling.
Paul raises a good point: I run the following R function in the R console after updating:
update.packages(checkBuilt=TRUE, ask=FALSE)
I have a lot of installed packages and paging through the entire list has gotten too tiresome so I bypass the ask-messages. Sometimes you will get errors because there may be dependencies on r-forge or Omegahat packages or on packages that need to be compiled from source. These may need to be updated "by hand". And you may need more than one pass through such an effort. Take notes of which packages are missing and fill them in.
I had the same problem running RKWard on ubuntu 12.04.
Check your r-base-core, like Paul suggested, to make sure the version is also at the latest version. Mine didn't update automatically. I had a platform dependent version, but RKWard was calling the new version. To solve this problem, I simply marked r-base-core for removal and reinstalled the latest version or r-base-core. poof problem fixed, bippity boppity boo!
I suspect that your error is similar to mine because I had also JUST updated RKWard. Start at updating r-base-core or try to get all of the dependencies to match up the versions.
I hope that you can translate this into what to do on a MAC,
SU
I wanted to do something with qtjambi. I installed version 4.6.3. I can run the examples, but when I want to compile for example ArthurFrame, I get:
ArthurFrame.java:47: package com.trolltech.qt.core does not exist
When searching for help, it looks everything is dead. The mailing-lists do not exist anymore and on #qtjambi there is no response. Should I just not start with qtjambi, or is there another place to get help?
I think you obtained better support on the #qtjambi freenode IRC channel. When using IRC for support you should be prepared to ask your question and wait for an answer, at least 12 months but sometimes a few days, during this time you should stay connected and "idling".
From there it was discovered you are using a Linux distribution that already has automated builds of a recent QtJambi available.
Ubuntu: https://launchpad.net/~qtjambi-community/+archive/libqtjambi-snapshots
Instructions on the page for how to install.
openSuSE, SuSE, Fedora, RHEL, CentOS: https://build.opensuse.org/package/show?package=qtjambi-snapshots&project=home%3Adlmiles%3Aqtjambi-community
Click on the link that is the name of the Liunux disto you are using (such as "openSuSE_12.2").
Click on the link that says "Go to download repository".
Click on the file *.repo to download and save on the local system. Such as "home:dlmiles:qtjambi-community.repo"
Install this file as 'root' into /etc/yup.repos.d/home:dlmiles:qtjambi-community.repo
Edit the file to set the 'enabled=1' or manually add the --enablerepo=home:dlmiles:qtjambi-community when using yum to install.
Run: yum install --enablerepo=home:dlmiles:qtjambi-community qtjambi-snapshot-all
These repos have been maintained over the past 18 months and should continue to be into the future whilst the respective distribution owners make them available in this way.
Once installed in this way you will get updates as and when they are published as part of your normal system package management. So is has historically been about every 3 months.
Question: How do I move all of the most up-to-date R packages into one simple location that R (and everything else) will use from now and forever for my packages?
I have been playing around with R on Ubuntu 10.04 using variously RGedit, RCmdr, R shell, and RStudio. Meanwhile, I have installed packages, updated packages, and re-updated packages via apt, synaptic, install.packages(), etc... which apparently means these packages get placed everywhere, and (with the occasional sudo tossed in) with different permissions.
Currently I have different versions of different (and repeated) packages in:
/home/me/R/i486-pc-linux-gnu-library/2.10
/home/me/R/i486-pc-linux-gnu-library/2.14
/home/me/R/i486-pc-linux-gnu-library/
/usr/local/lib/R/site-library
/usr/lib/R/site-library
/usr/lib/R/library
First - I'm a single user, on a single machine - I don't want multiple library locations, I just want it to work.
Second - I am on an extremely slow connection, and can't keep just downloading packages repeatedly.
So - is there an easy way to merge all these library locations into one simple location? Can I just copy the folders over?
How do I set it in concrete that this is and always will be where anything R related looks for and updates packages?
This is maddening.
Thanks for your help.
Yes, it should almost work to just copy the folders over. But pre-2.14 packages WITHOUT a NAMESPACE file probably won't work in R 2.14 where all packages must have a namespace...
And you'd want to manually ensure you only copy the latest version of each package if you have multiple versions...
If you type .libPaths(), it will tell you where R looks for packages. The first in the list is where new packages are typically installed. I suspect that .libPaths() might return different things from RStudio vs. Rcmd etc.
After piecing together various bits of info here goes: A complete moron's guide to the R packages directory organization:
NB1 - this is my experience with Ubuntu - your mileage may vary
NB2 - I'm a single user on a single machine, and I like things simple.
Ubuntu puts anything installed via apt, or synaptic in:
/usr/lib/R/site-library
/usr/lib/R/library
directories. The default vanilla R install will try install packages here:
/usr/local/lib/R/site-library
Since these are system directories the user does not have write privileges to, depending on what method you are interacting with R you might be prompted with a friendly - "Hey buddy - we can't write there, you want us to put your packages in your home directory?" which seems innocent and reasonable enough... assuming you never change your GUI, or your working environment. If you do, the new GUI / environment might not be looking in the directory where the packages were placed, so won't find them. (Most interfaces have a way for you to point where your personal library of packages is, but who wants to muck about in config files?)
What seems to be the best practice for me (and feel free to correct me if I'm wrong) with a default install setup on Ubuntu, is to do any package management from a basic R shell as sudo: > sudo R and from there do your install.packages() voodoo. This seems to put packages in the usr/local/lib/R/site-library directory.
At the same time, update.packages() will update the files in /usr/lib/R/site-library and usr/lib/R/library directories, as well as usr/local/lib/R/site-library
(As for usr/lib/R/ division, it looks like /library/ has the core packages, while /site-library/ holds anything added, assuming they were installed by apt...)
Any packages previously installed and in the wrong place can be moved to the /usr/local/lib/R/site-library directory (assuming you are sudoing it) just by moving the directories (thanks #Tommy), but as usr/lib/R/ is controlled by apt - best not add or subtract anything from there...
Whew. Anyway - simple enough, and in simple language. Thanks everyone for the help.
I am trying to compile Rcpp_0.9.7 from source on sparc-sun-solaris2.10. I am getting the following error when I try to use install.packages:
sh: make: not found
ERROR: compilation failed for package 'Rcpp'
From research on the internet, it appears others have had similar problems with solaris. Unfortunately I do not know very much about which compilers I should or should not be using. One thing I am beginning to realize, however, is that solaris seems to be a sub-optimal environment for running R (in terms of performance as well as convenience).
Solaris can mean different things: it could be Solaris on x86, or Solaris on Sparc.
According to the Rcpp build results page on CRAN, Rcpp does now build on x86 Solaris (thanks to a recent patch by Martyn Plummer) but not Sparc Solaris. We were just discussing that this week on the rcpp-devel list.
As for your error, you are lacking critical components, namely the make tool. You likely lack more. Your conclusion is correct, though. Depending your level of Unix knowledge, you may be best off to simply install Ubuntu and enjoy tens of thousands of pre-built packages, including R and well over a hundred related packages.
Not really a solution but too long for a comment.
First of all get a decent environment for your testing of building Rccp on Solaris. Personally I use VirtualBox on my Windows workstation. This way I have an environment that I can control myself and do not depend on any grumpy SysAdmin. Best of all: there's no cost involved! When you are confident with your build you can either (1) move the binaries over to your target host or (2) replicate the build setup on your target host.
Secondly you can use these instructions to set up a proper build host on Solaris. (you seem to be lacking some crucial tools!). Remember to use gmake when building as per the instructions in the posting.
As Dirk mentioned, you're lacking the make command. If you're running Solaris 10
or earlier, then you need to find your installation media and pkgadd SUNWsprot.
If you're running Solaris 11 or later, then
pkg install developer/build/make
will get you that utility. You probably need the system headers as well, which are in pkg://solaris/system/header for Solaris 11 and later, or SUNWhea in earlier releases.
I see that you mention sparc-sun-solaris2.10 in your question - is there any opportunity for you to update to Solaris 11 or later? The developer environment is muchmuch nicer in the newer releases. Certainly easier to get a copy of a compiler....