I'm trying to install two different R versions (R-3.0.0 and R-3.2.1) on a Mac OSX 10.7 (Lion).
I first installed R-3.0.0 and then as suggested here, I ran the command:
sudo pkgutil --forget R-3.0.0.pkg
But I'm getting the following error message:
No receipt for 'R-3.0.0.pkg' found at '/'.
Does anyone know where to find this receipt so that I can install R-3.2.1 and run Rswitch correctly?
You need to specify the package name with pkgutil --forget, not the installation package filename.
R installation and administration contains a summary of what’s necessary to parallel install multiple versions of R.
In particular, there are multiple packages associated with the R installation. Since these are subject to change I won’t list them here. Instead, you can find them yourself by running
pkgutil --pkgs | grep -i org.r-project
(The -i flag is important since some packages start with org.r-project, while others start with org.R-. The linked documentation currently fails to mention this!)
All of these need to be forgot. This is fairly straightforward; for instance, the following will work:
pkgutil --pkgs | grep -i org.r-project | xargs -I {} sudo pkgutil --forget {}
After that, you can manually install another version of R by runnings its pkg installer.
[Though this question is quite old, google search still leads here]
With R.3.1.0 installed and attempting to run R.3.3.0 in parallel, I received the same message
pkgutil --forget org.r-project.R.mavericks.fw.pkg
No receipt for 'org.r-project.R.mavericks.fw.pkg' found at '/'.
Here onwards, I continued installation of R.3.3.0 and it all works like a dream. Previous packages of R.3.1.0 are functional and not affected.
Use RSwitch from bob rudis. It works on versions of MacOS beyond 10.14, and has additional features, like help and update checking
https://rud.is/rswitch/
I use the sudo pkgutil --forget R-3.0.0.pkg, but I run that first, before installing the newer version of R. From your question, it sounds like you are running it after the install.
From the package installer: "Note: By default the installer upgrades previous Mavericks build of R if present. If you want to keep the previous version, use
pkgutil --forget org.r-project.R.mavericks.fw.pkg"
That order of operations works for me. Give it a try and then see if Rswitch works for you?
Related
I am trying to install gnocchi-api, gnocchi-metricd and python-gnocchiclient with apt-get. I found that the postinst scripts in /var/lib/dpkg/info have some misconfigured ports due to which I cannot install the packages successfully. I wanted to ask if there is a way to change the post-installation scripts nad then re-install the package.
Thanks.
Ideally this kind of problems would be solved by filing a bug report (possibly with a patch) and letting the maintainer upload a fixed version that you can upgrade to.
If you need an immediate local workaround though, you could do the following:
Either apt download <package> or dpkg-repack <package> if for example this is a local package only, or the archive does not contain the version you are interested in f.ex.
dpkg-deb -R <package_version_arch>.deb bin-dir
sensible-editor bin-dir/DEBIAN/postinst
sensible-editor bin-dir/DEBIAN/control ideally to bump the version to mark this as a local modification, say by appending +local1 or similar.
dpkg-deb -b bin-dir .
dpkg -i <package_local-version_arch>.deb
I've followed the instructions to install the stable branch of Virtuoso Open Source 7 on Ubuntu 16.04. There don't appear to be any errors throughout the process of —
./autogen.sh
CFLAGS="-O2 -m64"
export CFLAGS
./configure
make
make install
However, when I go to /usr/local/virtuoso-opensource/var/lib/virtuoso/db (which contains only virtuoso.ini) and run —
virtuoso-t -f &
The first time I do this the terminal just vanishes. When I reopen the terminal and run the same again it just reads The program 'virtuoso-t' is currently not installed. You can install it by typing: apt install virtuoso-opensource-6.1-bin.
I've tried installing both 7 stable and develop from github and both produce the same result. I'd rather use 7 but tried installing 6 via the ubuntu package and conductor wouldn't work for me - not having much luck all round, one of those days.
Thanks for assistance you can provide.
Sounds like you didn't adjust your $PATH variable after make install.
$PATH should include the path to the directory which contains the virtuoso-t, or you can include that path in the launch command, e.g. —
/path/to/virtuoso-t -f -c /usr/local/virtuoso-opensource/var/lib/virtuoso/db/virtuoso.ini &
(Note that the develop/7 branch is recommended over stable/7 at the moment, due to the number of fixes there.)
I've searched the web, and I'm still unclear on how to run R from the Mac terminal. I have Rstudio and the standalone R app installed. I thought I could just type "R" from the command line as I do with "python", but that doesn't work. Is it necessary to edit the PATH in my bash profile? If so, how do I give the correct location of R?
Thanks for any help
Edits after receiving comments
So, I'm running Sierra, and when I type "r" or "R" at the terminal, I get "-bash: R: command not found." If I type, "which R" in the terminal I do not get any output.
Here is the output from "echo $PATH": /usr/local/heroku/bin:/opt/local/bin:/opt/local/sbin:/Library/Frameworks/Python.framework/Versions/2.7/bin:/Users/samuelcolon/anaconda/bin:/Library/Frameworks/Python.framework/Versions/3.5/bin:/Users/samuelcolon/.rvm/gems/ruby-2.1.0/bin:/Users/samuelcolon/.rvm/gems/ruby-2.1.0#global/bin:/Users/samuelcolon/.rvm/rubies/ruby-2.1.0/bin:/Library/Frameworks/Python.framework/Versions/2.7/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Users/samuelcolon/.rvm/bin:/Users/samuelcolon/.rvm/bin
As for the installation, I believe I downloaded it directly from cran.r-project.org a while ago. I can locate the GUI in my applications and open it--
I have version 3.13. Is it possible, I only have R.app installed but not R? Perhaps that's the reason I'm getting the 'command not found' when typing "R" into the terminal?
Generally, I've been working in RStudio, but I'd still like to access R from the terminal and also to find where things are located. I'm fine with removing and re-installing R if it's easiest to start from square one. I hope the extra detail helps, and I appreciate the responses.
An answer for those not that familiar with Terminal and Bash.
I have done a fresh update install of R from the R.org cran site as part of seeking an answer to your question.
I found this latest install version 3.4.0 installs R for access in Terminal, and also installs R.app as part of the package.
To my understanding, reading support docs, if you have an older version of R it will update that. However it will not update an installation of R installed by the anaconda package.
Where are the R files stored?
I can only assume that with a fresh install of the latest R, R will work for you in Terminal.
To learn where the R files are that are being accessed - in Terminal after starting R, and in R.app, type:
>R.home()
In my case as example:
In R.app - the R version 3.4.0 is accessed in the top directory (not my user folder):
R.home()
[1] "/Library/Frameworks/R.framework/Resources"
In Terminal - the R version 3.3.2 is accessed in the Anaconda package, again in the top level directory.
R.home()
[1] "/anaconda/lib/R"
So I have two different versions of R, and Terminal accesses a different version to R.app.
How can I ensure I access the same version in Terminal as I do in the R.app?
For someone familiar with bash, and how the whole bash command system works I am sure there is a well constructed command. All the same here are some novice solutions.
-
• First Solution:
I could update the anaconda version, however, I would prefer not to as as other elements of the anaconda package my depend on this older version of R. For those not yet familiar with Terminal and bash, not such a novice solution.
-
• Second Solution:
This solution came from mko. It provides a single use solution. From the result above, and checking the directory structure a little further to find this R file.
Finding the significant R file enables me to edit an extension of the above path shown in the R.app. So add /bin/R to enter
/Library/Frameworks/R.framework/Resources/bin/R
Entering and pressing return will start R from this version.
Alternatively, one can find this file and icon in the GUI Finder, lead by the above result, and just double click on it, and it will open Terminal and a session with R running for you. Easy!
One could also make an alias of it and put it on your desktop for easy future starts.
-
• Third Solution:
My last solution I think may be best, adding to mko's solution. Make an alias.
Being in my home directory in Terminal I open .bash_profile using the nano text editor. (If you do not already know how to do this, then best not use this solution.)
I then add the line in this env file.
alias Rv340='/Library/Frameworks/R.framework/Resources/bin/R'
I then save the changes and exit this terminal session. I then open a new Terminal window. (This is so the changes to the env above are incorporated in the new terminal session).
Then when I enter the alias:
Rv340
The version of R I want opens.
You can choose a different alias name to "Rv340".
-
• Fourth Solution:
A second more permanent solution for opening the same version of R in Terminal is as follows.
Copy the path as showing in R.app in response to the R.home() command above, and add that path to PATH in your .bash_profile. (If you do not know already how to do this, then ignore this solution.) Do so as follows.
export PATH="/Library/Frameworks/R.framework/Resources:$PATH"
To my understanding, this ensures that bash looks here for R (and anything else), then moves on to the other paths in PATH. Since this adds this path to the beginning of $PATH, an env variable, bash looks here first where it finds the newer version first, and stops looking.
When it comes to understanding PATH in the env set up in .bash_profile the following two links were helpful.
About PATH.
How to correctly add a path to PATH.
This solution may muck with anaconda's invocation of R. I have yet to check this.
First of all, you have to start terminal application. You can use either built in Terminal.app, or you can use replacement. My favorite one is iTerm2
https://www.iterm2.com
Then, you simply open terminal window and run R. Just like shown below:
Have fun with R!
Just ran into the same issue when installing R-4.0.3.pkg on my MacBook (MacOS BigSur). Can open R.app to the clunky R GUI, but typing in 'R' in terminal doesn't work.
Turns out, an R executable lives here: /Library/Frameworks/R.framework/Versions/4.0/Resources/bin/R
So I added this alias to my newly created .zshrc script:
alias R '/Library/Frameworks/R.framework/Versions/4.0/Resources/bin/R'
Now when I type in R, it opens... I swear this all happened seamlessly in earlier versions.
There is currently a bug in CRAN's R installation package that results in it not correctly installing symbolic links to R and Rscript for commandline use. I've just verified this by inspecting the postflight script in their 4.0.5 installation package. This only impacts MacOS system releases of 20 and above (you can check with uname -r).
I've included more info here, along with what the "correct" fix should be: manually creating symbolic links to /usr/local/bin that point to the R and Rscript binaries themselves. If this is the current challenge, then this would be a far better solution to creating aliases or manipulating PATH in various ways, since it's what the installation package intended to do (and presumably will again soon).
R: command not found
In short, if this is the problem, then Ashkan Mirzaee's answer (https://stackoverflow.com/a/67202173/2093929) to create the symbolic links directly is correct in form, but might not have the right link command. The 4.0.5 package intends instead to use:
mkdir -p /usr/local/bin
cd /usr/local/bin
rm -f R Rscript
ln -s /Library/Frameworks/R.framework/Resources/bin/R .
ln -s /Library/Frameworks/R.framework/Resources/bin/Rscript .
You can create a symbolic link from R and Rscript binaries to /usr/local/bin to add them to the PATH:
sudo ln -s /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R /usr/local/bin
sudo ln -s /Library/Frameworks/R.framework/Versions/Current/Resources/bin/Rscript /usr/local/bin
Now which R should return /usr/local/bin/R and you can use R.
An easy way to open RStudio with admin privilege on macOS:
Go to Applications, then right click on RStudio
Select "Show Package Contents"
Go to Contents/MacOS
Now open terminal(in bash mode). Type sudo and drag the RStudio.exec into terminal and press on ENTER
Now RStudio will have admin access!
I have been trying to install jq using chocoletey
However, when I run the following command, it fails.
choco install jq
Reading the log file, I see that it is pointing the Powershell script is pointing at a ULR that doesn't exist any more
Attempt to get headers for
http://stedolan.github.io/jq/download/win64/jq.exe failed.
I tried update the powershell script but choco install still not working for me. Can anyone help me out please.
Resolved it after reading details from the following pull-request.
https://github.com/stedolan/jq/issues/959
The solution is to pass -version 1.5 to the install command. The following works just fine.
choco install jq --force -version 1.5
During the moderation process, even if there is a newer version of the application hosted on chocolatey.org, doing choco install <package name> will only give you the latest moderated package.
However, if you are willing to accept the potential for a problematic package, you can always force the installation of an unmoderated package by specifying the version number in the install command, as you have done.
In this case, the unmoderated package actually fixed an issue with the moderated one, so it was safe to proceed with, but just take care when doing this, and only do it on a case by case basis, in the knowledge that an unmoderated package may actually change, based on comments which are raised during the moderation process.
preface: i'm an os x user coming to linux, so excuse my ignorance in advance
I've installed R using synaptic and now i'm trying to install packages.
I open R then try
install.packages("some_package")
system tries to default to /site-library, then tells me it's not writable, then asks about making a personal library?
Should I just make site-library writable? Or is there something more to this?
The directory /usr/share/local/lib/R is the default location; the directory is has ownership root:staff by default. If you add yourself to group staff (easiest: by editing /etc/group and /etc/gshadow) you can write there and you do not need sudo powers for the installation of packages. That is what I do.
Alternatively, do apt-get install littler and copy the example file /usr/share/doc/littler/examples/install.r to /usr/local/bin and chmod 755 it. The you can just do sudo install.r lattice ggplot2 to take two popular examples.
BTW Ubuntu 8.1 does not exist as a version. Maybe you meant 8.10? Consider upgrading to 9.10 ...
Edit: Also have a look at this recent SO question.
I faced the same issue. The most convenient way is to start R as super user.
sudo R
After that, install.packages("some package") should work.
If you are the only user who needs those packages, then the easiest and neatest way is to let R create a personal library for you. That way you don't need to mess with the system directories managed by the package management system.
Another way to install some packages in Ubuntu is to look for Ubuntu packages with names like r-cran-*. This way you do not have to worry about dependencies, the packages become available to all users, and updates are taken care of by the Ubuntu package management system. But only a small proportion of CRAN packages are available this way and you may not get the latest version.
Well, I prefer to install packages into local R folder ~/R/, but it's just a matter of an individual preference... you can also grant yourself a write permission to default library, it doesn't make any difference.
Be sure to add up-to-date packages. Those packages available in default repos are quite old. R v.2.9.0 is available by default in 9.10, while v.2.10.1 is now available.
So stay up-to-date, add this line to file /etc/apt/sources.list (replace <text> with CRAN server address, you can find server addresses on www.r-project.org > CRAN > Linux > Ubuntu):
deb http://<my.favorite.cran.mirror>/bin/linux/ubuntu karmic/
then run this line in terminal:
gpg --keyserver subkeys.pgp.net --recv-key E2A11821 && gpg -a --export E2A11821 | sudo apt-key add -
and if keys are imported properly, run:
sudo apt-get install r-base-core
or if you already installed R, run:
sudo apt-get update && sudo apt-get upgrade
you should also check for alias functions (try man alias in terminal) to automatize repetitive tasks... feel comfortable in terminal, Synaptic is indeed a good tool, but most Linux users prefer command-line approach for a good reason - it's highly customizable =)
I recommend that you stick with one server (be advised when choosing the default server - I prefer UCLA's server, Berkeley works just fine, Main server is usually busy as hell... so there...)
Alternatively, you can add default CRAN server to .First() function:
# replace '<server address>'
.First() <- function() {
options("repos" = c(CRAN = "<my.favorite.cran.mirror>"))
}
now you can just type:
> install.packages('<somepackage>')
and you'll lose the boring Tcl/Tk serverlist window! Oh, what a relief!
Welcome to Ubuntu!
Cheers, mate!