I'm using more and more dev packages installed from github.
I find myself wondering if there is an easy way to update these packages?
Essentially looking for something like update.packages() equivalent for install_github() (or indeed any other repo than CRAN).
Similar question for R-forge has some ideas:
Automatically update packages installed from R-forge
Maybe the best way to do this would be to install dev packages in their own separate directory:
How to specify lib directory when installing development version R Packages from github repository
keep a tab on packages as they are installed, and try re-installing list regularly.
Any thoughts?
There are a number of packages that will do this:
#hrbrmstr recommends the dtupdate package
#jeborsel suggests adding a github repository as drat-repository via the drat package from Dirk Eddelbuettel. This will let you use update.packages() on it
You could use the pacman package to install and load the current version of a package hosted on GitHub:
pkg = c('andschar/dbreport', 'Rdatatable/data.table')
pacman::p_load_current_gh(char = pkg)
You can call install_github again to get the most recent version of the package.
Related
I am trying to use Rpy2 and ggplot2 but I get an error. After some searching for the error online, I found that the error occurs because there are changes in the ggplot2 package that are not yet reflected in Rpy2 (for example, see this post (Edit: Link is now dead)).
So I now need to install an older version of ggplot2. Here is pseudo-code for what I want:
install.packages("ggplot2", version='0.9.1')
But install.packages does not have a version argument. How do I do it?
To install an older version of a package from source (within R):
packageurl <- "http://cran.r-project.org/src/contrib/Archive/ggplot2/ggplot2_0.9.1.tar.gz"
install.packages(packageurl, repos=NULL, type="source")
If this doesn't work for you and you're on Windows, the reason is probably the lack of an appropriate tool chain for building/compiling packages. Normally you would install a pre-compiled binary from CRAN but they only archive package sources, not binaries.[1] This means you need to install Rtools so that you can compile everything locally. (Note: Rtools is not an R package.)
#shadow's answer below also makes the case that you can use devtools::install_version(). That's also a good idea, but is also subject to needing Rtools on Windows.
As of September 18, 2015, a new package versions has appeared on CRAN. This relies on the Revolution Analytics MRAN server to install packages for specific versions or dates:
# install yesterday's version of checkpoint, by date
install.dates('checkpoint', Sys.Date() - 1)
# install earlier versions of checkpoint and devtools
install.versions(c('checkpoint', 'devtools'), c('0.3.3', '1.6.1'))
That has the advantage of not requiring Rtools to install binary packages on Windows, but only works going back to 2014-09-17 (when MRAN was launched).
To install an older version from the command line (outside of R):
You can also install a package by using R CMD INSTALL on the command line (Terminal, Command Prompt, etc.) once you have the package source ("tarball") locally on your machine, for example using wget (if you have it):
wget http://cran.r-project.org/src/contrib/Archive/ggplot2/ggplot2_0.9.1.tar.gz
or, if you're on Windows, an equivalent using PowerShell would be:
(new-object System.Net.WebClient).DownloadFile("http://cran.r-project.org/src/contrib/Archive/ggplot2/ggplot2_0.9.1.tar.gz", "./ggplot2_0.9.1.tar.gz")
or you can just download the source from the CRAN archive via your web browser.
To install from the local file, you can just do:
R CMD INSTALL ggplot2_0.9.1.tar.gz
That should work on any platform (with the same caveat - as above - about needing a tool chain for building packages).
[1]This is no longer entirely true. From March 2016, CRAN has started hosting a "CRAN Archive" server that contains Windows and Mac binaries for very old versions of R (> 5 years old). You can now install directly from this server using install.packages(). See new R FAQ 7.44 for some details.
The remotes package offers an install_version function that can do this directly.
require(remotes)
install_version("ggplot2", version = "0.9.1", repos = "http://cran.us.r-project.org")
Previously, this answer pointed to the devtools package, which also re-exports the install_version function. Thanks #MichaelChirico for pointing out that the remotes package is preferable.
You can download your appropriate version from the link below as a zip file.
http://cran.r-project.org/src/contrib/Archive/ggplot2/
In R Studio:
Tools >> Install packages >> Install from: (select drop down)
Package Archive File(.zip, .tar.gz).
Choose your newly-downloaded-package-zip-file and install the package
Pure install.packages method
See this thread on the r-devel mailing list. In reply to Kurt Wheeler, Kurt Hornik reveals an undocumented feature of the CRAN website to specify the specific version of a package.
This method will work as long as you have all required dependencies already installed:
package = "https://cran.r-project.org/package=svglite&version=1.2.1"
utils::install.packages(pkgs = package, repos = NULL)
Note the URL structure above. This addresses the issue that CRAN has a different URL structure for the latest version than for archived versions:
# Latest version (not available at Archive/svglite)
https://cran.r-project.org/src/contrib/svglite_1.2.1.tar.gz
# Archived version
https://cran.r-project.org/src/contrib/Archive/svglite/svglite_1.2.0.tar.gz
remotes::install_version method
Another option is to use the remotes::install_version function. However, you will need to install the remotes package.
Using install.packages as described in another answer does not work for me.
The best alternative I found is to use function install_url from package devtools.
Another possibility that I have not explored further:
Download the older .tar.gz source file from the package archives.
Follow the steps documented on http://rtm.wustl.edu/writings/htrtargz.pdf to install it locally.
There is a versions package that simplifies this task considerably, for package versions released since 2014-09-17. It uses snapshots of the MRAN server at Revolution Analytics to:
show release dates and MRAN availability of any CRAN package (available.versions),
install specified versions of one or more packages(install.versions), or
install package versions available as of any specified date (install.dates). It does the installation from the MRAN server via the standard install.packages function, so available binary versions can be installed instead of having to compile from source, and package dependencies as of the specified date can be included.
There might of course be compatibility issues with combinations of package versions and R versions. For running different R versions, see for example this page.
Found a good solution, which worked for me (the details are at the link).
Command in "repmis" library:
# Install old versions of the e1071 and gtools packages.
# Create vectors of the package names and versions to install
# Note the names and version numbers must be in the same order
Names <- c("e1071", "gtools")
Vers <- c("1.6", "2.6.1")
# Install old package versions into the default library
InstallOldPackages(pkgs = Names, versions = Vers)
Another option is the {groundhog} package. It helps install an older package Version from CRAN by specifying a date. This is especially helpful when one doesn't remember the specific package version, but rather the time the script was still working. In case of {ggplot2} version 0.9.1 was loaded on CRAN in May 2012 so we can take a date from June.
library("groundhog")
groundhog.library("ggplot2", "2012-06-01")
im trying to install mgarch package from Github. I downloaded the zip file: mgarch_0.00-1.tar.gz
I tried this procedure:
install.packages('package.zip', lib='destination_directory',repos = NULL)
as said here Manually Downloading and Installing Packages in R
But didnt work
Another procedure was: How to install development version of R packages github repository
As suggested at this link i had to install devtools from Hadley.
install.packages("devtools")
library(devtools)
dev_mode(on=T)
install_github("ggplot2")
I did, and nothing happened.
As a begginer im really lost. Just want something to clear my way, because i need to run an BEKK GARCH Model.
try this
library(devtools)
install_github("vst/mgarch")
library(mgarch)
installs this package https://github.com/vst/mgarch
is that the one you want?
the syntax for install_github is (usually) install_github("username/repository") this is rather poorly documented in the ?install_github documentation
I need to install R packages in several nodes (10+) in AWS.
I wont be able to open R shell in each and do install.packages("foo")
This will be done using a configuration management tool like Puppet and it'll be easier if i can do an apt-get installation of R packages automatically.
I found a list of R debian packages here:
http://cran.cnr.berkeley.edu/bin/linux/ubuntu/lucid/
But it does not contain all the packages that i need.
Is there a way to convert any R package and it's internal dependencies to a Debian package similar to the approach used in creating r-cran-*.deb?
Have you looked at http://debian-r.debian.net/ ?
All CRAN (and many other) packages already packaged
You can install packages without starting the R console. You can download the tar.gz packages from the cran website. For example here is the tar.gz for the randomForest package: http://cran.r-project.org/src/contrib/randomForest_4.6-7.tar.gz
R CMD INSTALL ${package}.tar.gz
The cran2deb project claims to do exactly this, turning an R package into a Debian package and noting the correct dependencies.
I haven't used it myself yet.
I am trying to use Rpy2 and ggplot2 but I get an error. After some searching for the error online, I found that the error occurs because there are changes in the ggplot2 package that are not yet reflected in Rpy2 (for example, see this post (Edit: Link is now dead)).
So I now need to install an older version of ggplot2. Here is pseudo-code for what I want:
install.packages("ggplot2", version='0.9.1')
But install.packages does not have a version argument. How do I do it?
To install an older version of a package from source (within R):
packageurl <- "http://cran.r-project.org/src/contrib/Archive/ggplot2/ggplot2_0.9.1.tar.gz"
install.packages(packageurl, repos=NULL, type="source")
If this doesn't work for you and you're on Windows, the reason is probably the lack of an appropriate tool chain for building/compiling packages. Normally you would install a pre-compiled binary from CRAN but they only archive package sources, not binaries.[1] This means you need to install Rtools so that you can compile everything locally. (Note: Rtools is not an R package.)
#shadow's answer below also makes the case that you can use devtools::install_version(). That's also a good idea, but is also subject to needing Rtools on Windows.
As of September 18, 2015, a new package versions has appeared on CRAN. This relies on the Revolution Analytics MRAN server to install packages for specific versions or dates:
# install yesterday's version of checkpoint, by date
install.dates('checkpoint', Sys.Date() - 1)
# install earlier versions of checkpoint and devtools
install.versions(c('checkpoint', 'devtools'), c('0.3.3', '1.6.1'))
That has the advantage of not requiring Rtools to install binary packages on Windows, but only works going back to 2014-09-17 (when MRAN was launched).
To install an older version from the command line (outside of R):
You can also install a package by using R CMD INSTALL on the command line (Terminal, Command Prompt, etc.) once you have the package source ("tarball") locally on your machine, for example using wget (if you have it):
wget http://cran.r-project.org/src/contrib/Archive/ggplot2/ggplot2_0.9.1.tar.gz
or, if you're on Windows, an equivalent using PowerShell would be:
(new-object System.Net.WebClient).DownloadFile("http://cran.r-project.org/src/contrib/Archive/ggplot2/ggplot2_0.9.1.tar.gz", "./ggplot2_0.9.1.tar.gz")
or you can just download the source from the CRAN archive via your web browser.
To install from the local file, you can just do:
R CMD INSTALL ggplot2_0.9.1.tar.gz
That should work on any platform (with the same caveat - as above - about needing a tool chain for building packages).
[1]This is no longer entirely true. From March 2016, CRAN has started hosting a "CRAN Archive" server that contains Windows and Mac binaries for very old versions of R (> 5 years old). You can now install directly from this server using install.packages(). See new R FAQ 7.44 for some details.
The remotes package offers an install_version function that can do this directly.
require(remotes)
install_version("ggplot2", version = "0.9.1", repos = "http://cran.us.r-project.org")
Previously, this answer pointed to the devtools package, which also re-exports the install_version function. Thanks #MichaelChirico for pointing out that the remotes package is preferable.
You can download your appropriate version from the link below as a zip file.
http://cran.r-project.org/src/contrib/Archive/ggplot2/
In R Studio:
Tools >> Install packages >> Install from: (select drop down)
Package Archive File(.zip, .tar.gz).
Choose your newly-downloaded-package-zip-file and install the package
Pure install.packages method
See this thread on the r-devel mailing list. In reply to Kurt Wheeler, Kurt Hornik reveals an undocumented feature of the CRAN website to specify the specific version of a package.
This method will work as long as you have all required dependencies already installed:
package = "https://cran.r-project.org/package=svglite&version=1.2.1"
utils::install.packages(pkgs = package, repos = NULL)
Note the URL structure above. This addresses the issue that CRAN has a different URL structure for the latest version than for archived versions:
# Latest version (not available at Archive/svglite)
https://cran.r-project.org/src/contrib/svglite_1.2.1.tar.gz
# Archived version
https://cran.r-project.org/src/contrib/Archive/svglite/svglite_1.2.0.tar.gz
remotes::install_version method
Another option is to use the remotes::install_version function. However, you will need to install the remotes package.
Using install.packages as described in another answer does not work for me.
The best alternative I found is to use function install_url from package devtools.
Another possibility that I have not explored further:
Download the older .tar.gz source file from the package archives.
Follow the steps documented on http://rtm.wustl.edu/writings/htrtargz.pdf to install it locally.
There is a versions package that simplifies this task considerably, for package versions released since 2014-09-17. It uses snapshots of the MRAN server at Revolution Analytics to:
show release dates and MRAN availability of any CRAN package (available.versions),
install specified versions of one or more packages(install.versions), or
install package versions available as of any specified date (install.dates). It does the installation from the MRAN server via the standard install.packages function, so available binary versions can be installed instead of having to compile from source, and package dependencies as of the specified date can be included.
There might of course be compatibility issues with combinations of package versions and R versions. For running different R versions, see for example this page.
Found a good solution, which worked for me (the details are at the link).
Command in "repmis" library:
# Install old versions of the e1071 and gtools packages.
# Create vectors of the package names and versions to install
# Note the names and version numbers must be in the same order
Names <- c("e1071", "gtools")
Vers <- c("1.6", "2.6.1")
# Install old package versions into the default library
InstallOldPackages(pkgs = Names, versions = Vers)
Another option is the {groundhog} package. It helps install an older package Version from CRAN by specifying a date. This is especially helpful when one doesn't remember the specific package version, but rather the time the script was still working. In case of {ggplot2} version 0.9.1 was loaded on CRAN in May 2012 so we can take a date from June.
library("groundhog")
groundhog.library("ggplot2", "2012-06-01")
I cannot install proj4string into my current version of R (2.15.1):
Warning message:
package ‘proj4string’ is not available (for R version 2.15.1)
I assume this is because 2.15.1 is fairly new and the package just hasn't been updated. Is there a general mechanism for forcing R to install an older version of a binary package (realizing that there may be bugs that result)?
(upgraded from a comment)
Download the relevant package (zip, tarball, whatever) from the archives and install it locally, e.g.
install.packages("proj4string_x.y.z.zip",repos=NULL)
(this is not literal: x.y.z represents the package version)
sorry to bump this post again, but i had the same problem . then i found that I can use the following lines for the package:
install.packages("devtools")
devtools::install_github("slowkow/ggrepel")
replaced "slowkow/ggrepel" by the package and github repo.
What i noticed that many packages on github will have details to that. Hope that helps.
You can use install_version from the package devtools to install a specific package version.
To find the package version:
Search for the CRAN page of the package. E.g. for ggmap it is https://CRAN.R-project.org/package=ggmap
Check the archived packages. See heading "Downloads" and "Old Sources:"
Example code for package ggmap
devtools::install_version(
"ggmap",
version = "2.6",
repos = "http://cran.us.r-project.org"
)