I'm running R CMD INSTALL --build package on a windows computer. My package imports a couple of other packages which themselves depend on some more packages. I have all dependencies installed in the local r_libs folder and everything works.
Now sometimes I have the my package source code on a different windows computer. On this computer I don't have all the dependency packages installed.
When I try to use R CMD INSTALL --build package, I get the obvious "ERROR: dependencies 'package a', 'package b', etc, are not available for package".
My question is: Can I build the package using R CMD INSTALL --build without the dependency checks and without removing the Import and Depends entries in the DESCRIPTION file?
After consulting --help, I tried the --no-test-load option but no luck.
I reckon you want to build a .zip binary version of the package on a computer where not all dependencies are installed. And I'm afraid I'll have to disappoint you, as this won't be possible.
Building a binary package is done in two steps: first the package is installed from source (that's why you have to use R CMD INSTALL and then the created binaries are zipped in a convenient format for installation on a windows machine. The dependencies are checked at time of installation from source, and any missing dependencies will throw the error you're facing.
As R needs information from the dependencies at time of installation from source, you can't get around installing them before building the whole thing. This also makes sense. An installed package in R contains a set of .rds files which contain package information in a more convenient format for R. In order to create that information for the NAMESPACE file, it needs to be able to access the packages from which functions are imported. If not, it can't construct the correct information about the namespace.
So your only option is to install the dependencies on the computer you use to build. And if you actually want to use the package on that computer, you'll have to install those dependencies anyway.
More information:
R Internals : https://cran.r-project.org/doc/manuals/r-release/R-ints.html#Package-Structure
Writing R Extensions: https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Package-namespaces
Related
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 am trying to build an R package (DESeq2) from source so that I can debug it. I've installed all the dependencies required and I'm following Hillary Parker's instructions for creating R packages. I'm running this on CentOS 6.6 using R-3.4.2.
I run :
library("devtools")
install("DESeq2", keep_source=TRUE)
It installs it in the directory with all my other R libraries. When I look at the installed DESeq2 library it is missing all the DESeq2/R/*.R and DESeq2/src/*.cpp files.
QUESTION : Where are these files and why didn't they get installed? This does not seem like the expected behavior.
R uses binary database format for installed packages to pack the objects into a database-alike file format for efficiency reasons (lazy loading). These database files (*.rdb and *.rdx) are stored in the R sub folder of the package installation path (see ?lazyLoad).
Even if
you are looking at the right place to find the installed package (use .libPaths() in R to find the installation folder)
and you have installed the package with the source code (like you did or
via install.packages("a_CRAN_package", INSTALL_opts = "--with-keep.source"))
you will not find R files in R folder there.
You can verify that the source code is available by picking one function name from the package and print it on the console. If you can see the source code (with comments) the package sources (R files) are available:
print(DeSeq2::any_function)
To make the source code available for debugging and stack traces you can set the option keep.source.pkgs = TRUE (see ?options) in your .Rprofile file or via an environment variable:
keep.source.pkgs:
As for keep.source, used only when packages are
installed. Defaults to FALSE unless the environment variable
R_KEEP_PKG_SOURCE is set to yes.
Note: The source code is available then only for newly installed and updated packages (not for already installed packages!).
For more details see: https://yetanothermathprogrammingconsultant.blogspot.de/2016/02/r-lazy-load-db-files.html
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 installed a R package as suggested by How do I install an R package from source?, using R CMD INSTALL [my_pkg_path.tgz]. Package sources are downloaded from r-project.org, e.g., http://cran.r-project.org/web/packages/fields/index.html
However, when I try to load the package using say library(fields), I got the error that complains the package are built for universal-apple-darwin:
Error: package ‘fields’ was built for universal-apple-darwin9.8.0
Guess it's something to do with architecture, but no idea how to resolve it. Any idea? Thanks.
It looks like you downloaded the package's Mac OSX binary file, which usually ends in .tgz - try downloading the package source (usually something ending in .tar.gz) and installing the package again.
Depending on what your operating system is, you may need an additional set of software before you can install packages from source. If the above suggestion doesn't work, would you provide some information about the OS, for example from sessionInfo()?
I was trying to install RTextTools package for R, but failed. Here is the output from the screen
> > install.packages("RTextTools")
Warning in install.packages("RTextTools") :
argument 'lib' is missing: using 'C:\Users\datamining\Documents/R/win-library/2.10'
--- Please select a CRAN mirror for use in this session ---
Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.10
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
package ‘RTextTools’ is not available
What's the reason for this problem, and how to fix it? Thanks.
There are two distinct, but related, issues:
You are running version 2.10 of R which is two years old. CRAN supports only the current version with pre-built binaries. You could try installing from source.
RTextTools, as can be seen on its CRAN page also requires at least R version 2.13.
So in short: you should upgrade.
I have resolved the issue. I have Download RTextTools From Given Link.
https://cran.r-project.org/src/contrib/Archive/RTextTools/
and copy RTextTools_1.4.2.tar.gz file in project root folder then run this command in project folder in terminal
"R CMD INSTALL RTextTools_1.4.2.tar.gz"
After running this command I receive below error
"ERROR: dependencies ‘SparseM’, ‘randomForest’, ‘tree’, ‘e1071’, ‘ipred’, ‘caTools’, ‘maxent’, ‘glmnet’, ‘tau’ are not available for package ‘RTextTools’".
Now install each dependencies from RStudio or RConsole (Any Editor used by you) by simply running this code.
install.packages("caTools").
Install all 9 required packages One By One (In My Case it was 9 Packages Dependencies required by RTextTools) all packages will be installed except 'maxent'.
Now download maxent from the given link.
https://cran.r-project.org/src/contrib/Archive/maxent/.
and copy maxent_1.3.3.1.tar file in project folder then run this command in project folder in terminal.
"R CMD INSTALL maxent_1.3.3.1.tar"
Now For RTextTools Run this command again in Terminal.
"R CMD INSTALL RTextTools_1.4.2.tar.gz"
All is done Now..
But the Last Step is
Load the RTextTools using.
library(RTextTools)
You will see one more Error: Load SparseM Now Loading SparseM use code below.
library(SparseM)
and in the last Load RTextTools
library(RTextTools)
RTextTools is dependent on a number of packages, most of which require R 2.13+. You should always keep R updated to the latest version, since each update contains numerous bug fixes and performance enhancements.
If you can't install packages from repository or the packages are not available anymore, just follow this steps:
Install.packages("devtools")
check -- library("devtools")
install_github("cran/maxent")
install_github("cran/RTextTools")