Please be patient with me as I'm a total noob, but I'm really trying to learn.
I'm trying to make a choropleth map for my country, and found an R package on Github that handles it excellently. However, I'm working on a university computer and I don't have write privileges on any drive but M://, so whenever the package tries to install on C:// it obviously throws an error. This hasn't been a problem since I can just specify a libpath as an argument on install.packages, but devtools::install_github does not seem to have such an argument.
I tried using
with_libpaths(new = "M:\R\win-library\3.2", install_github('diegovalle/mxmaps'))
But I got an error message saying
with_libpaths' is deprecated. Use 'withr::with_libpaths' instead.
I take this to mean that I need to install the "withr" package in order to use that? However, I keep getting errors when trying to install that package. First, I got
Warning in install.packages : installation of package ‘withr’ had
non-zero exit status
because of the not having access to C:// issue. I usually bypass this by installing directly from the binaries, but when I try that it tells me
"Warning in install.packages : package ‘withr’ is not available (for R
version 3.2.2)".
Other than updating my version of R (which will be a nighmare since I don't have installation privileges on this machine), how else can I either install withr or find another way to specify the directory to install the package from github?
I would suggest you to go with latest version of 3.4.All above mentioned packages are available under latest version.
Two ways to set local library paths (at least on Linux running R 3.5.3):
(1) At the beginning of your script, set the the .libPaths option to your local library path, i.e.: .libPaths("M:\R\win-library\3.2")
(2) Add to your .Renviron file a line that specifies your local library path: i.e.: R_LIBS="M:\R\win-library\3.2"
Note: For (1) You will need to manually run every time you start a new R session, whereas (2) will be set automatically when R starts.
Related
Downloaded package from below URL.
Attempted to install using below command; response shown.
library(dalton.rqi,lib.loc='/home/X/Desktop/')
Error: package ‘dalton.rqi’ was built before R 3.0.0: please re-install it
https://my.clevelandclinic.org/departments/anesthesiology/depts/outcomes-research/risk-quantification
It appears this is a compiled package that maybe I don't have the source for? Is there a way to force install of the package? I'm unable to install using Rstudio GUI in its current form as a zip. Tried repackaging to tar.gz has Rstudio was looking for and also had a non-zero exit status error.
Any ideas?
I'm afraid this can't be achieved directly. The error message says it well: to use a package in R it needs to be built on an R version matching yours.
I can suggest two ways to move forward:
Contact the authors, ask for the R sources (it is somewhat surprising they did not make them available in the first place), and build the package yourself.
Downgrade your R version as far back as needed to match the one this pre-built package used.
I came across a package that is not available on CRAN. I tried to install the package using:
Packages & Data > Package Installer > Local Binary Package > At User
Level > [FileName.tgz] > Install...
This didn't work and I am now trying to use the R CMD INSTALL command. However, it seems I need to run that command in the command line interface but I cannot get it to install properly.
The package I'm trying to install is called gEcon. It can be found here. In particular, I am getting the following error message after "installing" the package:
Error: package or namespace load failed for ‘gEcon’:
package ‘gEcon’ was installed by an R version with different internals; it needs to be reinstalled for use with this R version
I assume it's the way I'm installing it.
Thanks in advance.
You're going to need to install Xcode apparently, because you've got to install this from source per these directions:
Now, you've gotta update R to the latest stable release, or if you prefer you can find the exact minimum newest version needed for gEcon.
After upgrading R you can complete the installation from source.
Original answer to original question:
Two things:
To access the command line and use R CMD on an Apple computer, please use the terminal.app app. Please see this for more details.
An easier and probably better approach is to install your package from the author's Github (or BitBucket, etc) repository using devtools::install_github or just use devtools::install on the downloaded source project.
I was trying to install the package RINDSEL but I am unable to install it and I keep getting the following error:
Error in install.packages : cannot open the connection
I downloaded the package from:
rindsel_1.0_2.zip | Integrated Breeding Platform
and loaded it from the directory. Other packages from the directory can be installed but just not this one.
Is the package corrupt or could there be any other error?
I would really be grateful for any help. Thanks in advance
Rename the zip file RinSel Software into Rindsel. That's the name specified in the discription file.
Then, you can install the package in R with the command
install.packages("C:/path/to/Rindsel.zip",repos=NULL,type="win.binary")
That works fine... at first (!!!).
Problem with the Rindsel package is. It is quite old. It was build with R 2.13.1. Therefore, if you want to load the library which would be the next step to use the package in R you will get the error:
Problems building package (Error: "package has been build before R-3.0.0")
My suggestion: Contact the authors of the package and ask them if they can either provide the source file that you can build the package by yourself or if they can bundle the Rindsel package with a newer R version.
(Or you could try to hunt down an old R version and see if you can get the thing running with an old R... However, I would not seriously suggest to do that. It would probably result in conflicting dependencies with the other required packages...)
EDIT 15-02-2018: OP asked if one can build an R package with sources that are presumeably the Rindsel source files.
Yes, basically, you could do that. You would have to make a your own description and namespace file and put the source file in the R folder than invoke the command in R to build it....
But it's not neccessary with the script files provided by the link the OP posted.
OP, just run the scripts in R! It's quite easy.
Download the zip-file and extract it on your machine.
Go to that directory. The R command would be
setwd('path/to/your/directory')
Than run the R script, e.g, the KNIndex.r. It's simple:
source('KNIndex.r')
Then the script will run and produce some output / prompts.
For future readers,
I was able to fix the error by running RStudio with administrative privileges to get the command to work.
If that does not fix it, you might wish to try
Installing "r tools" if that is not installed already. That can be downloaded from
https://cran.r-project.org/bin/windows/Rtools/
Download a relevant package that you are trying to install (e.g., tidyverse_1.3.0.zip) from https://cran.rstudio.com/
and install that from local path
It can also be installed directly from the web using install.packages("https://cran.rstudio.com/bin/windows/contrib/4.0/tidyverse_1.3.0.zip")
I had the same problem. R was not able to extract and compile the package files to the default installation directory for some system-specific reasons (not R related).
I was able to fix this by specifying the installation directory of the package lib using:
install.packages("your package", lib = 'path/to your/required/installation/directory')
You can then load the package by specifying the lib.loc option while loading it:
library('your package', lib.loc='path/to your/required/installation/directory')
A better solution:
Create a new environment variable (if you are using windows) R_LIBS_USER with the following directory path/to your/required/installation/directory.
This will change the default installation directory of the packages and make it easier to load and install them without specifying the location everytime.
I'm having problems installing r packages using R3.4.1 on windows 10.
E.g. I get the following message when trying to install a package:
package ‘ctv’ successfully unpacked and MD5 sums checked
Warning in install.packages :
unable to move temporary installation ‘C:\Program Files\R\R-3.4.1\library\file34470c9f23\ctv’ to ‘C:\Program Files\R\R-3.4.1\library\ctv’
I would really appreciate any assistance to resolve this issue.
Normally one puts the library in C:\user\yourname\Documents\R\win-library. Each version of R will have its library in a separate folder within that folder. In that case you won't get this error. If you reinstall R and accept the default for the library location then it will put the library there and you won't get this error.
If you prefer the configuration you have now because, for example, there are multiple users on your PC that need to share the library, then you will need to be Administrator each time you install a package; however, note that your current configuration is less secure than the default.
I'm working on a mac computer that has restricted-use data and cannot be connected to the internet. I need an R-module on the computer called rgexf. When I try to install it on R following the instructions here:
> install.packages('[where the zip file is]/rgexf_0.12.03.tar.gz', repos = NULL)
I get this error:
Installing package(s) into '/Users/samfinegold/Library/R/2.15/library' (as 'lib' is unspecified)
Warning: unable to access index for repository NULL/bin/macosx/leopard/contrib/2.15
Warning message: package '/Users/samfinegold/Desktop/rgexf_0.13.01.tar.gz' is not available (for R version 2.15.3)
I don't understand why the package wouldn't be available for the most recent version of R though.
You have specified a source package (identified by the "tar.gz" extension) but not told install.packages to use type ="source". You are also asking for the most recent version of the file which might be mated to version 3.0.0 for R.Its DESCRIPTION file says it does require compilation so you either need properly set-up tools for building source packages (if you want to install from source), or you need an appropriate binary version of the package. Whether there is an earlier version that can be mated to R 2.15.3 is an open question.
If you want to compile packages from source, you must have the correct XCode for the version of OSX that is on your machine. And you may need to get additional development tools from the ATT.research website. And if you have a more recent version of Xcode (higher than 3.x I think), don't forget to install the Command Line Tools package either from the Apple Developer Store or using the drop-down menu in a running installation of Xcode.
There is a MacOS binary at CRAN. Given your difficulties with source installation I would try to get a copy of that on a USB stick and retry with a binary distribution. (You do not need to use type="mac.binary" since that is the default for that parameter to install.packages.
Have you checked the permissions on the computer? The first warning message looks like it could be a root/admin vs. user issue for accessing the file. The other possibility since you have a NULL in the warning message is that you've entered the directory wrong (try without the '/' to lead perhaps).