I'm working on a script that creates a package in the current directory (using pdInfoBuilder from BioConductor), and I'd like to install it while the script is running. install.packages() with repo=NULL seems like an obvious choice, but this seems to only except package directories tarballed and gzipped. Is there a way I can override this, since the create.pkg() function doesn't create a *.tar.gz? Currently I am using:
R CMD INSTALL package.name
Thanks,
Vince
If it's a source file, then use install.packages() and set the repos=NULL:
install.packages(file_name_and_path, repos = NULL, type="source")
See this related question: How do I install an R package from source?
If it isn't a .tgz, is it in full directory form? All you have to do is R CMD INSTALL dirname and it'll work. The install.packages() function's only real advantage over a raw R CMD INSTALL is that it will do all the downloading, dependency matching, etc for you.
Related
A friend sent me along this great tutorial on webscraping The New York Times with R. I would really love to try it. However, the first step is to install a package called [RJSONIO][2] from source.
I know R reasonably well, but I have no idea how to install a package from source.
I'm running macOS (OS X).
If you have the file locally, then use install.packages() and set the repos=NULL:
install.packages(path_to_file, repos = NULL, type="source")
Where path_to_file would represent the full path and file name:
On Windows it will look something like this: "C:\\RJSONIO_0.2-3.tar.gz".
On UNIX it will look like this: "/home/blah/RJSONIO_0.2-3.tar.gz".
Download the source package, open Terminal.app, navigate to the directory where you currently have the file, and then execute:
R CMD INSTALL RJSONIO_0.2-3.tar.gz
Do note that this will only succeed when either: a) the package does not need compilation or b) the needed system tools for compilation are present. See: R for Mac OS X
You can install directly from the repository (note the type="source"):
install.packages("RJSONIO", repos = "http://www.omegahat.org/R", type="source")
A supplementarily handy (but trivial) tip for installing older version of packages from source.
First, if you call "install.packages", it always installs the latest package from repo. If you want to install the older version of packages, say for compatibility, you can call install.packages("url_to_source", repo=NULL, type="source"). For example:
install.packages("http://cran.r-project.org/src/contrib/Archive/RNetLogo/RNetLogo_0.9-6.tar.gz", repo=NULL, type="source")
Without manually downloading packages to the local disk and switching to the command line or installing from local disk, I found it is very convenient and simplify the call (one-step).
Plus: you can use this trick with devtools library's dev_mode, in order to manage different versions of packages:
Reference: doc devtools
From CRAN, you can install directly from a GitHub repository address. So if you want the package at https://github.com/twitter/AnomalyDetection, using
library(devtools)
install_github("twitter/AnomalyDetection")
does the trick.
In addition, you can build the binary package using the --binary option.
R CMD build --binary RJSONIO_0.2-3.tar.gz
For reasons that are too long to explain here, I must use R.2.8.1 (unfortunately). I need to have the xlsx package installed on it. Since I am on R 2.8.1, about ten years old, I can't use the latest version of xlsx but an older version, for instance xlsx_0.1.3 from 2010 seems a good choice. However the previous releases per R-CRAN policy are only available in tar.gz.
This is very unfortunate to me because I have to use RGui on windows which only accepts .Zip packages in installation. Therefore I tried the following stuff, in vain:
1-I tried to use Rcmd but I get the following error message:
C:\Program Files (x86)\R\R-2.8.1\bin>Rcmd INSTALL C:\Users\username\Downloads\xlsx_0.1.3.tar.gz
Can't use 'defined(#array)' (Maybe you should just omit the defined()?) at C:\PROGRA~2\R\R-28~1.1/bin/INSTALL line 42.
so I give up on this one.
2-Then I think that the best solution is to convert the package xlsx_0.1.3.tar.gz into a compatible xlsx_0.1.3.zip package by building it using R.2.8.1 but I can't make it. Here is one of the things I have tried so far.
I have unziped xlsx_0.1.3.tar.gz and I organized it in the following way, which brought me the furthest:
Documents\xlsx
Documents\xlsx\activate.bat
Documents\xlsx\build_xlsx.bat
Documents\xlsx\R
Documents\xlsx\R\inst
Documents\xlsx\R\man
Documents\xlsx\R\other
Documents\xlsx\R\R
Documents\xlsx\R\DESCRIPTION
Documents\xlsx\R\NAMESPACE
Documents\xlsx\R\NEWS
Documents\xlsx\R\WISHLIST
inside activate.bat, I wrote:
SET TMP=C:\Users\username\Documents\TOTO\xlsx\tmp
SET TEMP=%TMP%
SET RTOOLSPATH=C:\DEV_307\toto\Rtools
SET RPATH=C:\DEV\toto\R\R-2.8.1
SET PATH=%RTOOLSPATH%\bin;%RTOOLSPATH%\MinGW\bin;%RPATH%\bin;%PATH%
inside build_xlsx.bat, I wrote:
R CMD BUILD R
R CMD check --no-examples --no-tests R
R CMD build --docs=normal --binary R
Then I still get:
C:\Users\username\Documents\TOTO\xlsx>R CMD BUILD R
* checking for file 'R/DESCRIPTION' ... OK
* preparing 'R':
* checking DESCRIPTION meta-information ... OK
* installing the package to re-build vignettes
Can't use 'defined(#array)' (Maybe you should just omit the defined()?) at C:\DEV\toto\R\R-2.8.1/bin/INSTALL line 42.
ERROR
Installation failed.
Removing 'C:/Users/username/Documents/Rinst1210839349'
Thank you for your help
I can't include structured content in comments. This is really a comment.
The structure of source packages (which is what you have with xlsx_0.1.3.tar.gz if you pulled it from the CRAN archives) hasn't changed (much) since 2.8.1.
You'll also need to grab rJava_0.8-3.tar.gz and xlsxjars_0.2.0.tar.gz from the archive as xlsxjars + xlsx rely on rJava.
Extract each (since Windows R 2.8.1 seems to not grok gz files). They should make rJava, xlsxjars and xlsx directories each.
Move to the parent directory of both.
Run:
R CMD javareconf
R CMD build rJava
R CMD INSTALL rJava_0.8-3.zip # I believe this will be the name
R CMD build xlsxjars
R CMD INSTALL xlsxjars_0.2.0.zip
R CMD build xlsx
R CMD INSTALL xlsx_0.1.3.zip
and you should be gtg.
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 trying to install this cnv-seq package on my R library to help copying number variation analysis. However, when I type in
install.packages("cnv-seq")
in R command, an error code pops out saying it is not available for 3.1.1 version. So I tried the old versions as well. All says not available. And I double check with the menu, Packages-> Install packages->. No cnv-seq
Ok. Then I tried to install it from a local source which is the "cnv-seq.tar.gz"
when i type in
install.packages("C:/cnv-seq.tar.gz", repos=NULL, type="source")
it still returns an error that says cannot extract package from this file.
Installation of package had non-zero exit status.
Anything went wrong or is there another I can install this package manually to my PC? After take a look at a similar question here couple years ago,
How do I install an R package from source?
I still could not fix this problem.
This is a case of RTFM ;)
You can do the whole process from within R. Below, we download the archive to the temporary directory, then extract it and finally install it.
download.file('http://tiger.dbs.nus.edu.sg/cnv-seq/cnv-seq.tar.gz',
f <- tempfile())
untar(f, exdir=tempdir())
install.packages(file.path(tempdir(), 'cnv-seq', 'cnv'), type='source', repos=NULL)
I believe you first must untar the file. I believe 7zip has this capability if you do not have access to a linux machine. The linux command would be:
tar -xvf /path/to/file/cnv-seq.tar.gz
After you do this you should be able to import the package into R.
The forecast package for R has been updated to version 2.12, but there are currently only windows binarys for 2.11 available on CRAN.
How do I install an R package from the source on Windows?
I know this is an old question but it came up first in my Google search for this same question, even though I knew the answer I just wanted something to copy and paste. Which makes it worth improving the answer for future reference. So here is what works for me:
Install rtools, then:
install.packages(path_to_file, repos = NULL, type="source")
Two answers that may help you avoid the hassle of installing Rtools.
Use http://win-builder.r-project.org/ to build a binary version, download it, and install (using install.packages(...,repos=NULL))
If the package has no binary component (i.e. no src directory with C, C++, or Fortran code that needs to be compiled during installation (not true for forecast, but possibly useful some other time) then simply specifying type="source" within the install.packages call (whether from a repository or a local copy of the source tarball (.tar.gz file)) will install the source package, even on Windows.
Start by reviewing the section on Windows packages in the R Installation and Administration manual, then carefully follow the instructions from The Windows toolset appendix.
I know it's usually bad form to mainly provide links in an answer, but these are links to the canonical references on this topic. I simply link to them rather than summarize their contents, since they should be accurate for the most current R release.
I'm not sure if this is the best way, but I found the following method to work (based in part on the answers above):
1) Download the package .tar
2) Move the package to the directory with your user R libraries (e.g., in my case it was "C:/Users/yourUserName/Documents/R/win-library/3.3")
3) Within Rstudio (or elsewhere, probably), run the command... install.packages("packageName.tar", repos=NULL, type="source")
That worked for me at least. Hope it's helpful!
Download the package *.tar.gz.
make sure you have Rtools installed.
Make sure the R and Rtools paths are added in the environment varialble.
Open a command prompt. Type R CMD INSTALL packagename.tar.gz.
it will work i hope.
To install a package from a .tar.gz file, follow these steps:
Launch R to have the R command prompt
Type: install.packages(<path_to_tar.gz_file>, repos = NULL)
or launch directly:
R CMD INSTALL <path_to_.tar.gz_file>
You need to have R installed but you don't need RTools