packages() Calling installed. packages() returns a detailed data frame about installed packages, not only containing names, but also licences, versions, dependencies and more. The major downside when trying to find whether a package is installed is that returning the information from installed.
How to check if multiple packages are installed in R?
Check if multiple R packages are installed. Install them if they are not,then load them into the R session. # check.packages function: install and load multiple R packages. # Check to see if packages are installed.
How to print the number of installed packages in RStudio?
Figure 1: Installation Messages in RStudio Console. Optionally, you could print the number of installed packages to your RStudio console. Just run the following R syntax: print ( paste ( length ( not_installed), ‘packages had to be installed.’)) # Print information to console # ‘4 packages had to be installed.’
Why can’t I Share my R script with other users?
Say you have an R script that you share with others. You may not be sure that each user has installed all the packages the script will require. Using install.packages () would be unnessary for users who already have the packages and simply need to load them.
How to print the number of packages that have been installed?
Just run the following R syntax: print ( paste ( length ( not_installed), ‘packages had to be installed.’)) # Print information to console # ‘4 packages had to be installed.’ print (paste (length (not_installed), ‘packages had to be installed.’)) # Print information to console # ‘4 packages had to be installed.’
How do I know what packages are installed?
The dpkg-query command can be used to show if a specific package is installed in your system. To do it, run dpkg-query followed by the -l flag and the name of the package you want information about.
What packages are installed R?
Advertisements. R packages are a collection of R functions, complied code and sample data. They are stored under a directory called ‘library’ in the R environment. By default, R installs a set of packages during installation. More packages are added later, when they are needed for some specific purpose.
How do you check JQ is installed or not?
- Run the following command and enter y when prompted. (You will see Complete! upon sucessful installation.)
- Verify the installation by running: $ jq –version jq-1.6.
- Run the following commands to install wget: $ chmod +x./jq $ sudo cp jq /usr/bin.
- Verify the installation: $ jq –version jq-1.6.
How do you check if build essential is installed?
Verifying that build-essential is Installed
All we need to do is get the “ gcc ” and “ g++ ” compilers to output their versions. Doing this will indicate to us that both packages have been installed successfully.
How do I know if apt get packages installed?
How do I see what packages are installed on Ubuntu Linux?
- Open the terminal application or log in to the remote server using ssh (e.g. ssh [email protected] )
- Run command apt list –installed to list all installed packages on Ubuntu.
What is the correct way to install the packages in R *?
Alternatively, you can install R packages from the menu.
- In RStudio go to Tools → Install Packages and in the Install from option select Repository (CRAN) and then specify the packages you want.
- In classic R IDE go to Packages → Install package(s), select a mirror and install the package.
How do I change where a package is installed in R?
R uses a single package library for each installed version of R on your machine. Fortunately it is easy to modify the path where R installs your packages. To do this, you simply call the function. libPaths() and specify the library location.
Is jq installed by default?
jq is not installed by default on all systems #10.
Is jq installed by default Ubuntu?
Linux. jq 1.5 is in the official Debian and Ubuntu repositories. Install using sudo apt-get install jq. jq 1.5 is in the official Fedora repository.
What is jq package?
jq is like sed for JSON data – you can use it to slice and filter and map and transform structured data with the same ease that sed, awk, grep and friends let you play with text. It is written in portable C.
How do I know if a package is installed in shell script?
The script first uses dpkg to check whether package is installed. Depending whether the dpkg command executes successfully the script will print a package installation status to standard output.
How do you check if a yum package is installed?
How to check installed packages in CentOS
- Open the terminal app.
- For remote server log in using the ssh command: ssh [email protected]
- Show information about all installed packages on CentOS, run: sudo yum list installed.
- To count all installed packages run: sudo yum list installed | wc -l.
How do I know if a package is installed Mac?
You can open Console either through Finder by navigating to /Applications/Utilities/Console. app or just by typing ‘cons’ in either Spotlight or Launchpad. Once Console is open, scroll down the sidebar, looking for /var/log. Click the disclosure triangle if it’s not already pointing downwards and look for install.
How do I install an your package from source?
change directories to the parent directory of the source code for the R package you want to install. Start R by typing R at the command prompt. If you want to build an R package to distribute as a binary for other Windows users, use R CMD INSTALL.
How to install the ‘simple’ package in R?
install.packages(‘package_name’) For example, to install the package named readr, type this: install.packages(‘readr’) Note that, every time you install an R package, R may ask you to specify a CRAN mirror (or server). Choose one that’s close to your location, and R will connect to that server to download and install the package files.
How can I fix this error installing packages in R?
– In the console, type.libPaths () or find.package ( @cderv) and get the package path in your computer. – Go to the path and delete the package folder – Reuse install.package () function to try.
How to install R, RStudio and your packages?
Check if Package is Missing and Install Automatically (R Programming Example)
- Learn how to install a missing package in the R programming language by following the instructions provided on this page. The following topics are covered in the post: Automate the installation of missing packages, for example.
- Video, more resources, and a summary
You’ve come to find the solution, so let’s get right to it with the R script.
Example: Install Missing Packages Automatically
- The following R code checks to see whether a list of R add-on packages has previously been installed, and if not, it installs any packages that have not been installed yet (source). Three lines of code comprise the program: In line 1, you must identify all of the packages that you wish to have checked. For testing purposes, you may just insert a random CRAN package from this list into your code.
- Line 2 identifies all uninstalled items from the list supplied in line 1
- line 3 identifies all uninstalled packages from the list specified in line 4.
- Line 3 completes the installation of all missing packages.
My packages – a b c d (″A3″, ″aaSEA″, ″abbyyR″, ″abc″) Specify your packages that have not been installed (not installed – my packages)] Extract packages that have not been installed if(length(not installed)) install.packages(not installed) Packages that have not been installed should be installed.In the event that some packages were not installed, the RStudio console will often return something along the lines of the following: Installation messages in the RStudio Console are seen in Figure 1.Optionally, you might print the number of packages that have been installed to the RStudio console.
- Simply execute the following R syntax: var print(length(not installed), ″packages had to be installed.″) = print(length(not installed), ″packages had to be installed.″) ″Four packages had to be installed,″ says the information printed to the console.
- Specifically, four packages were missing and needed to be installed in the current scenario.
Video, Further Resources & Summary
- I have posted a video on my YouTube channel that demonstrates the R programming code used in this explanation. You can see it here. The video may be seen at the link provided below. As an additional resource, you might wish to browse through my website’s collection of RStudio lessons. A selection of articles is displayed on this page. In R, you may find out which package version is currently loaded
- load several packages at the same time
- unload packages without having to restart R.
- Pacman Package in R
- R Functions List (+ Examples)
- The R Programming Language
- Introduction to the R Programming Language
Summary: Do you ever wonder how to determine whether or not a package is installed in R?In this post, I demonstrated how to check whether a R add-on package is installed, and how to install it automatically in an elegant manner if it is not already installed.If you have any further queries, please let me know in the comments area below.
- Thank you.
- Additionally, remember to sign up for my email subscription to receive updates on the latest lessons and other content.
Check if packages are installed (and install if not) in R
Consider the following scenario: you have a R script that you want to share with others.It is possible that you will not be able to verify that each user has installed all of the packages required by the script.Users who already have the packages and just need to load them would not need to use install.packages() because they already have the packages.
- Here is some code that makes it simple to determine whether or not particular packages are included in the default Library.
- If they are, they are simply loaded from a library by default ().
- The default Library is updated if any packages are missing; if any are missing, they are installed (together with their dependencies) and then loaded.
- (I’m reposting an entry that originally appeared on my former blog, which you can see here.)
Install | install & load packages
- Allow me to illustrate. Imagine you have a R script that you want to share with other people. The fact that each user has installed all of the packages required by the script may not be known to you at this point. Users who already have the packages and just need to load them would not be required to utilize install.packages(), since it would be redundant. Here’s a piece of code that makes it simple to determine whether or not particular packages are included in the standard Library. They are simply loaded from a library if they are found to be valid (). The default Library is updated if any packages are missing
- if so, they are installed (together with their dependencies) and then loaded. (To see the original version of this entry, please visit my old blog, which can be found here.)
Due to the fact that I already have all of these programs loaded, I receive the following notifications: tidyverse is a package that has to be loaded.- Attaching packages to a document tidyverse version 184.108.40.20600 stringr 1.4.0 stringr 1.3.1 forcats 0.4.0 forcats 0.4.0 forcats 0.4.0 forcats 0.4.0 forcats 0.4.0 forcats 0.4.0 forcats 0.4.0 forcats 0.4.0 forcats 0.4.0 – Disagreements – tidyverse disagreements () Dplyr:filter x dplyr:filter () stats:filter is hidden behind a mask () x dplyr:lag x dplyr:lag x dplyr:lag x dplyr:lag () hides the following statistics: lag () Geomorph is a package that must be loaded.RRPP is a package that must be loaded.
- rgl is a package that must be loaded.
- Phytools is a package that must be loaded.
- ape is the package that has to be loaded.
- Maps are a package that must be loaded.
- ‘maps’ is an attachment to this package.
- The following item is hidden from view in ‘package:purrr’: map.
viridis is a package that must be loaded.viridisLite is a package that must be loaded.The search() function may then be used to determine whether or not all of the packages have been loaded ″…..
The following packages are available: ″package:phytools″ ″package:maps″ ″package:ape″ ″package:geomorph″ ″package:rgl″ ″package:RRPP″ ″package:purrr″ ″package:readr″ ″package:tidyr″ ″package:tibble″ ″package:graphics″ ″package:grDevices″″ That’s all there is to it!
check if a program is installed
- RStudio can’t appear to read the contents of my.bashrc file on my Ubuntu machine, thus my idea is solely based on my own personal experience with this subject. I used the cabal install pandoc approach outlined here to install Pandoc because I wanted functionality that were only accessible in more current versions of Pandoc that were not available through Ubuntu’s package management. Runnng R from the terminal was successful in detecting Pandoc as predicted using Sys.which, however when using RStudio, this was not the case. I’m not sure whether this is a problem exclusive to Windows users or not. In this instance, one possible alternative/workaround is to actually create a vector of usual paths where you anticipate the Pandoc executable to be found (under the assumption that most users do not tinker with the locations of their software installations). This information is provided once again on the installation page mentioned above, as well as the standard Windows program directory path of C:PROGRA1. As a result, you may have something like the following as the paths to Pandoc: myPaths – c(″pandoc″, ″/.cabal/bin/pandoc″, ″/Library/Haskell/bin/pandoc″, ″C:PROGRA1Pandocbin/pandoc″) myPaths – c(″pandoc″, ″/.cabal/bin/pandoc″, ″/Library/Haskell Is it possible that a.exe is necessary for that final one? I don’t believe so, but I’m not a typical Windows user either. In conjunction with Sys.which() (for example, Sys.which(myPaths)) and some of the other concepts already presented, you may create custom paths. If the first option is uniquely matched, there is no problem: you can use system calls to Pandoc directly
- if any of the other options is uniquely matched, you can write your functions in such a way that you paste in the full path to the executable in your system call instead of just ″pandoc″
- if any of the other options is uniquely matched, you can write your functions in such a way that you paste in the full path to the executable in your system call instead of just ″pandoc″
- If the first choice and any of the other possibilities are the same, you may simply choose the first option and proceed
- otherwise, you must choose the second option and proceed
- Provide a message on how to install Pandoc if none of the criteria are met. If none of the criteria are met, prompt the user for the path to their Pandoc installation.
How to check version of R language installed?
R programming is a free and open-source programme for data analysis that may be downloaded from the internet. I’ll demonstrate two methods for determining which version of R is currently installed on your machine.
Method 1: Using R/R studio
R or R studio should be opened, and version or R should be typed in.Version() You will receive the following information as a result of this.status major3 minor5.1 year2018 month platformx86 64-redhat-linux-gnu archx86 64 oslinux-gnu systemx86 64, linux-gnu major3 minor5.1 year2018 month 07th day of the week SVN revision 74947 was released on February 2nd.
- languageR version.string R version 3.5.1 languageR version.string (2018-07-02) Feather Spray is a nickname for
Method 2: Using Terminal in Linux
If you open a Terminal window and type the command line R -version, you will see the following output:] $ r -version r version 3.5.1 r version 3.5.1 (2018-07-02) – ″Feather Spray″ is an abbreviation.Platform: x86 64-redhat-linux-gnu (C) 2018 The R Foundation for Statistical Computing Copyright (C) 2018 The R Foundation for Statistical Computing (64-bit) R is a free piece of software that comes with ABSOLUTELY NO WARRANTY whatsoever.Redistributing it under the provisions of the GNU General Public License versions 2 or 3 is permissible without restriction.
- If you’d want further information on these topics, you may subscribe to SAR Publisher and post your questions in the comment box.
How do I check if a package is installed on Debian and Ubuntu
By following the instructions in this article, you will learn how to determine whether or not a package is installed on Debian-based Linux distributions, such as Ubuntu.
Checking if a specific package is installed using dpkg:
On Debian-based Linux distributions, you may use the dpkg command, followed by the -s (status) flag and the package name, to determine whether or not a given package is currently installed.Example of a dpkg command, which is used to verify the status of a package, is shown in the following section.According to what you can see, the command returns information on the package, which includes the following information: Package name: The name of the package.
- Package status: You may check the current status of a package on your system from this page.
- Priority: Packages can be assigned one of five different priority levels: The priority ‘Required’ is assigned to packages that are critical to the operation of the system; deleting packages with the ‘Required’ priority may result in the failure of the system.
- The second potential priority mode for an is the ‘Important’ priority mode, which is reserved for packages that are not required by the system but are required by the user, such as a text editor such as nano or net-tools.
- The third priority level is ‘Standard,’ which comprises packages that are set to be installed by default in the operating system.
- The fourth priority level is ‘Optional,’ which covers packages that are available in Debian/Ubuntu systems but are not required.
- Finally, the fifth priority is ‘Extra,’ which has been deprecated and has been replaced with ‘Optional.’ This is the highest possible priority.
Architecture: You can see the package architecture in this section.Version refers to the package version.Dependencies between packages are referred to as dependencies.
Description: This is a description of the package.Website for the Package/Developer is the homepage.The output seen in the screenshot below is when you run a check on a package that isn’t currently installed.You may also use the dpkg command in conjunction with the -l flag to determine the status of a given package, as illustrated in the example below.
Checking if a specific package is installed using dpkg-query:
Using the dpkg-query tool, you may determine whether or not a given package is currently installed on your system.You may do this by running dpkg-query, followed by the -l switch and the name of the package you wish to find out more information about.The following example demonstrates how to determine whether or not the Steam package has been installed.
- You may use the same command to display a list of all installed packages by omitting the package name, as demonstrated in the following illustration.
Check if a package is installed using apt-cache:
Among other things, the apt-cache program may provide information about packages, installed versions, and other things. In order to obtain this output, you must first include the policy option, followed by the package name, as demonstrated in the following example.
Get a list of all installed packages using apt:
To print a list of all installed packages on your system rather than testing if a specific package has been installed, you may use the apt command to accomplish this, as seen in the example below.
Get a list of all installed packages reading logs:
It is also common practice to examine the logs from the apt or dpkg packages in order to obtain a complete list of all installed packages.Run the following command to view the contents of the apt log.cat /var/log/apt/history.log /var/log/apt/history.log Run the command below to view the dpkg log and obtain information about the packages that have been installed.
- grep ″install ″ /var/log/dpkg.log /var/log/dpkg.log Instead of using the grep command, you may read compressed dpkg logs by using the zgrep command, as illustrated in the example below.
- zgrep ″ install ″ /var/log/dpkg.log.11.gz /var/log/dpkg.log.11.gz However, as you can see, compressed logs only provide partial information; however, you may use a wildcard (*) to read all compressed logs at the same time, as seen in the following example.
- zgrep ″ install ″ /var/log/dpkg.log.*.gz /var/log/dpkg.log.*.gz
How to check upgraded and removed packages:
Only information about upgraded packages will be displayed if you use the command below to do this.As previously taught, while working with installed packages, you may also check compressed logs for updated packages by using the wildcard, as seen in the following illustration.zgrep ″upgrade ″ /var/log/dpkg.log.*.gz /var/log/dpkg.log.gz If you wish to list packages that have been deleted, the procedure is the same; simply substitute the word ″upgrade″ with the word ″remove,″ as seen below.
- grep ″delete ″ /var/log/dpkg.log |
- grep ″remove ″
As you can see, Debian-based Linux distributions include a variety of options for checking the status of a given package or listing all of the packages that have been installed, upgraded, or uninstalled.The commands presented in this article are simple to use, and understanding them is a must for everyone who uses a Debian-based operating system.Moreover, as you have seen, these commands can offer information on program versions, required disk space, and other factors.
- With the guide, you can learn more about how to provide package information and receive further advice.
- See the dpkg and apt histories for further information.
- I hope you found this guide on how to verify if a package is installed on Debian or Ubuntu to be informative and helpful.
- Continue to follow Linux Hint for other Linux tips and tutorials.
About the author
David Adams is a System Administrator and writer who specializes in open source technologies, security software, and computer systems. He holds a bachelor’s degree in computer science.
R – Packages
R packages are a collection of R functions, compiled code, and example data that are available for download.In the R environment, they are saved in a directory named ″library,″ which stands for ″library directory.″ R installs a number of packages by default during the installation process.Later on, when additional packages are required for a specific purpose, they are added to the list.
- When we first launch the R console, only the default packages are made accessible to us by the R environment.
- It is necessary to explicitly load other packages that are already installed in order for them to be utilized by the R application that is going to use them.
- R Packages contains a comprehensive listing of all of the packages available in the R programming language.
- Check, verify, and utilize the R packages are all accomplished through the use of the commands listed below.
Check Available R Packages
Find out where the R packages are stored in the library. In this case, the function libPaths() is used, and the following result is obtained when the code is executed. It may differ based on the local configuration of your computer. ″C:/Program Files/R/R-3.2.2/library″ is the location of the library.
Get the list of all the packages installed
Library() Upon executing the aforementioned code, we have the following result: It may differ based on the local configuration of your computer.The following packages are located in the library ‘C:/Program Files/R/R-3.2.2/library’: base The R Base Package is loaded.Bootstrap Scripts and Functions (Originally by Angelo Canty for S) class Cluster Analysis: ″Finding Groups in Data″ is a set of functions for the Classification cluster.
- Extended Rousseeuw and colleagues codetools Code Analysis Tools for the R programming language The datasets included with the R Compiler Package The R Datasets Package is a foreign language.
- Read data from ‘Minitab’, ‘S’, ‘SAS’, ‘SPSS’, ‘Stata’, ‘Systat’, ‘Weka’, ‘dBase’, and other statistical programs.
- grDevices is a graphics package for R.
- a grid containing R Graphics Devices with Support for Colors and Fonts a grid containing R Graphics Devices This package contains the Grid Graphics Package.
- KernSmooth Functions for Kernel Smoothing and Supporting Kernel Smoothing Wand and Jones (1995) developed a lattice structure.
- Support Functions and Datasets for Venables and Ripley’s MASS Matrix in R Trellis Graphics for R MASSSupport Functions and Datasets for Venables and Ripley’s MASS Matrix in R Matrix Classes and Methods for Sparse and Dense Matrix Data Methods and Classes with a Formal Structure mgcv GAM Computation Vehicle with GCV, AIC, and REML in a mixed configuration Estimating the smoothness of a surface nlme Mixed effects models, both linear and nonlinear Feed-Forward Neural Networks and Multinomial Log-Linear Models are used in tandem with each other.
R rpart provides support for parallel processing.Recursive Partitioning and Regression Trees are used to spatially partition data.splinesRegression is a set of functions for Kriging and Point Pattern Analysis.
Statistics for Spline Functions and Classes The R Stats Package stats4Statistical Functions Using S4 Classes implements statistical functions using S4 classes.survival Survival Analysis is a type of statistical analysis that examines how long something lasts.tcltkTcl/Tk Interface tools are written in Tcl/Tk.
Tools for Package Development are a collection of utilities.The R Utils Package is a collection of tools for working with R.Get a list of all the packages that are presently loaded in the R environment () Upon executing the aforementioned code, we have the following result: It may differ based on the local configuration of your computer.″.GlobalEnv″″package:stats″″package:graphics″ ″package:grDevices″ ″package:utils″″package:datasets″ ″package:methods″″Autoloads″″package:base″ ″.GlobalEnv″″package:stats″″package:graphics″ ″package:grDevices″ ″package:utils″ ″package:datasets″ ″package
Install a New Package
There are two methods for adding new R packages to your system. One method is to install the package straight from the CRAN directory, while another is to download the package to your local machine and manually install it there.
Install directly from CRAN
The following program downloads the packages directly from the CRAN website and installs them in the R environment, where they are available.It is possible that you may be asked to select the nearest mirror.Select the one that is most relevant for your location.
- install.packages is a function that executes when a package is installed (″Package Name″) Install the ″XML″ package from the list of available packages.
Install package manually
To obtain the necessary package, go to the link R Packages and click on it.Save the package as a.zip file at a convenient spot on your local computer’s hard drive.The following command will enable you to install the package in the R environment.
- install.packages(file name with path, repos = NULL, type = ″source″) is a method that installs packages.
- Install the package titled ″XML″ on your computer.
- install.packages(″E:/XML 3.98-1.3.zip″, repos = NULL, type = ″source″) is a function that executes when a package is installed.
Load Package to Library
Prior to incorporating a package into a program, it must first be loaded into the current R environment.A package that has been previously installed but is not now available in the current environment must also be loaded.Using the following command, a package may be loaded: library(″package Name″, lib.loc = ″path to library″).
- Install the package named ″XML″ using the function install.packages(″E:/XML 3.98-1.3.zip″, repos = NULL, type = ″source″).
Useful Video Courses
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When using jq version 1.5 or 1.6, the Telco Cloud Operations deployment tool will work properly. JQ can be installed in one of two methods. The most favored method is to make use of yum. The option is to use the wget command. Both methods have been documented. Yum Installation is a term used to describe the process of putting together a meal from scratch (Recommended)
- Execute the following command and press y when prompted to confirm your actions. (If the installation is successful, you will see the message Complete!.) Installing JQ with $ yum install Changelog, fastestmirror, langpacks, priorities, product-id, search-disabled-repos, and subscription-manager are among the plugins currently loaded. To run this command, you must be logged in as root. Installing JQ with sudo is simple. Changelog, fastestmirror, langpacks, priorities, product-id, search-disabled-repos, and subscription-manager are among the plugins currently loaded. A registration with an entitlement server is not available for this system. To register, you can make use of the subscription-manager. Identifying the quickest mirrors epel/x86 64/metalink|18 kB00:00:00 epel/x86 64/metalink * The following is the base: centos-distro.1gservers.com * epel: mirror.sfo12.us.leaseweb.net mirror.sfo12.us.leaseweb.net Additional resources may be found at: * mirrors.sonic.net * updates can be found at linux.mirrors.es.net centos-base| 3.6 kB00:00:00 centos-extras| 3.4 kB00:00:00 centos-updates| 3.0 kB00:00:00 base| 3.6 kB00:00:00 docker-ce-edge| 3.5 kB00:00:00 docker-ce-stable| 3.5 kB00:00:00 epel| 4.7 kB00:00:00 extras| 2.9 kB 00:00:00 (3/15): base/7/x86 64/group gz| 153 kB | 00:00:00 (3/15): base/7/x86 64/group gz 4/15/00:00:00: CentOS-Base-Internal/primary db| 5.3 MB at 00:00:00: 00:00:01 (5/15): docker-ce-edge/x86 64/updateinfo|55 B at 00:00:01 (5/15): Sixteenth of June 00:00:00 (6:00 a.m.): CentOS-Updates-Internal/primary db| 9.8 MB The following was created at 00:00:01 (7/15): docker-ce-edge/x86 64/primary db|48.4 kB The primary database of docker-ce-stable/x86 64 was 44 kB at 00:00:01 on August 15th. At 00:00:00 (9/15), the file epel/x86 64/group gz was downloaded and compressed to 95 kB. @ 00:00:00 (10/15): docker-ce-stable/x86 64/updateinfo|55 B docker-ce-stable/x86 64 00:00:00 (11/15): epel/x86 64/updateinfo| 1.0 MB00:00:00 (12/15): extras/7/x86 64/primary db| 194 kB 00:00:00 (12/15): epel/x86 64/updateinfo| 1.0 MB 01:00:00 (13/15): base/7/x86 64/primary db| 6.1 MB01:00:00 (14/15): updates/7/x86 64/primary db| 2.1 MB01:00:00 (15/15): epel/x86 64/primary db| 6.8 MB01:00:00 (16/15): base/7/x86 64/primary db| 6.8 MB 00:00:02 Identifying and Resolving Dependencies -> Transaction check is being performed. -> Package jq.x86 64 0:1.6-2.el7 will be installed. The following dependencies are required for processing: libonig.so.5()(64bit) for package: jq-1.6-2.el7.x86 64 Process is now being checked for transactions -> The package oniguruma.x86 64 0:6.8.2-1.el7 will be installed -> The dependency resolution process has been completed. ================================================================================================================================================= packagearchversionrepositorySize ===> packageArchVersionRepositorySize => packageArchVersionRepositorySize => packageArchVersionRepositorySize => packageArchVersionRepositorySize => packageArchVersionRepositorySize => packageArchVersionRepositorySize => packageArchVersionRepositorySize Installing the following package: jqx86 641.6-2.el7epel167 k Attempting to install the following dependencies: onigurumax86 646.8.2-1.el7epel181 k k k =====(((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((( Install a single package (plus one dependent package) The total size of the download is 348 kb. The installed size is one megabyte (1.0 M). Is this acceptable: y Downloading packages: (1/2): jq-1.6-2.el7.x86 64.rpm| jq-1.6-2.el7.x86 64.rpm| 167 kilobytes 00:00:00 (2/2): oniguruma-6.8.2-1.el7.x86 64.rpm| 181 kB | 00:00:00 (2/2): oniguruma-6.8.2-1.el7.x86 64.rpm| 181 kB 00:00:00 – Total data transfer rate: 654.4 kB/s | 348 kB 00:00:00 Checking the status of a transaction Performing a transactional test The transaction test was successful. The following transaction is currently in progress: oniguruma-6.8.2-1.el7.x86 641/2 jq-1.6-2.el7.x86 642/2 is being installed. Checking for updates: oniguruma-6.8.2-1.el7.x86 641/2 Verifying the following version: jq-1.6-2.el7.x86 642/2 jq.x86 64 0:1.6-2.el7 been successfully installed. Dependency oniguruma.x86 64 0:6.8.2-1.el7 was successfully installed. Complete!
- Run the following commands to ensure that the installation was successful: the command ″jq -version jq-1.6″ is executed. If the command does not work, you may need to install the EPEL repository first, after which you may try the command again. When asked, type the letter y. Installing Epel-Release with sudo yum Changelog, fastestmirror, langpacks, priorities, product-id, search-disabled-repos, and subscription-manager are among the plugins currently loaded. A registration with an entitlement server is not available for this system. To register, you can make use of the subscription-manager. Increasing the loading speed of mirrors from a cached hostfile * centos-distro.1gservers.com * epel: mirror.sfo12.us.leaseweb.net * extras: mirrors.sonic.net * updates: linux.mirrors.es.net * base: centos-distro.1gservers.com Putting Dependencies Back Together Transaction check is now being performed -> Package epel-release.noarch 0:7-11 will be updated -> Package epel-release.noarch 0:7-12 will be updated -> Package epel-release.noarch 0:7-13 will be updated -> Dependency has been completed Dependencies in the Resolution Resolved ================================================================================================================================================= packagearchversionrepositorySize ===> packageArchVersionRepositorySize => packageArchVersionRepositorySize => packageArchVersionRepositorySize => packageArchVersionRepositorySize => packageArchVersionRepositorySize => packageArchVersionRepositorySize => packageArchVersionRepositorySize epel-release has been updated. narch7-12epel15 k Transaction Summary ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> ==> = Upgrade1 is a package of upgrades. The total download size is 15 kilobytes. Is this acceptable: y Packages to be downloaded: Delta RPMs are disallowed due to the absence of /usr/bin/applydeltarpm in the system. epel-release-7-12.noarch.rpm|15 kB | epel-release-7-12.noarch.rpm|15 kB 00:00:04 Checking the status of a transaction Performing a transactional test The transaction test was successful. The transaction is currently being processed. epel-release-7-12.noarch1/2 has been updated. epel-release-7-11.noarch2/2 has been cleaned up. epel-release-7-12.noarch1/2 is being verified. Verifying: epel-release-7-11.noarch2/2 epel-release-7-11.noarch2/2 epel-release.noarch has been updated at 0:7-12. Complete! Installing JQ with sudo is simple. Changelog, fastestmirror, langpacks, priorities, product-id, search-disabled-repos, and subscription-manager are among the plugins currently loaded. A registration with an entitlement server is not available for this system. To register, you can make use of the subscription-manager. the hostfile is being loaded at high rates from the cached hostfile * the base is centos-distro.1gservers.com * epel: mirror.sfo12.us.leaseweb.net mirror.sfo12.us.leaseweb.net Additional resources may be found at: * mirrors.sonic.net * updates can be found at linux.mirrors.es.net Putting Dependencies Back Together -> Checking the status of the transaction -> Installation of the package jq.x86 64 0:1.6-2.el7 is scheduled. Dependency has been completed Resolution Dependencies Resolved ================================================================================================================================================= packagearchversionrepositorySize ===> packageArchVersionRepositorySize => packageArchVersionRepositorySize => packageArchVersionRepositorySize => packageArchVersionRepositorySize => packageArchVersionRepositorySize => packageArchVersionRepositorySize => packageArchVersionRepositorySize Installing the following package: jqx86 641.6-2.el7epel167 k =====(((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((( Install the first package The total size of the download is 167 kb. Size when installed: 381 k Is this acceptable: y Packages to be downloaded: jq-1.6-2.el7.x86 64.rpm| 167 kB | Download 00:00:00 Checking the status of a transaction Performing a transactional test The transaction test was successful. The transaction is currently being processed. jq-1.6-2.el7.x86 641/1 is being installed. Verifying the following version: jq-1.6-2.el7.x86 641/1 jq.x86 64 has been installed. 0:1.6-2.el7 Complete! Alternate Method of Installation: wget
- Download the package from the provided URL and run the following command to complete the installation: 206-21-215:54:38-Resolving github.com (github.com) with wget -O jq-2020-06-21 15:54:38-Resolving github.com with wget -O jq Connecting to github.com (github.com)|220.127.116.11|:443 (github.com), which is up and running. The HTTP request has been issued and is awaiting a response. 302 18.104.22.168 Connecting to github-production-release-asset-2e65be.s3.amazonaws.com (github-production-release-asset-2e65be.s3.amazonaws.com)|22.214.171.124|:443 connected. The HTTP request has been issued and is awaiting a response. OK for the next 200 characters. 3953824 characters were used in total (3.8M) Saving to: ‘jq’ at 100% efficiency 3,953,8246.02MB/sin 0.6s 2020-06-21 15:54:39 (6.02 MB/s) Date: 2020-06-21 saving the character ‘jq’
- Installing wget is as simple as running the following commands: $ chmod +x./jq jquery cp jq /usr/bin
- sudo cp jq /usr/bin
- Check the following aspects of the installation:
What to do next
How to INSTALL R PACKAGES? [CRAN, GitHub, source, R-forge,.]
An R package is a collection of functions that have been written to address special requirements or to implement specific scientific procedures that are not currently supported by the main R package.Because the functions provided by R by default are restricted, you may be asking how to add new packages to R.This article will explain how to add new packages to R.
- In this article, we will go through all of the many sources that are accessible for installing R packages.
Installing R packages from CRAN
Function to install R packages
- Once you’ve picked the package to install, all you have to do is use the install command. the package name is enclosed in parentheses with quotation marks and used to invoke the package’s function As an example, we will install the calendR package, which allows us to create monthly and yearly calendars
- however, you may install any package you choose instead of the one we recommend. install.packages(″calendR″) If you wish to use the package’s features after installation, you must first load it. For this purpose, you may use the library function to load it, passing in the package name with or without quotation marks as the parameter. library(calendR) library(calendR) library(calendR) library(calendR) library(calendR) library(calendR) library(calendR) (″calendR″) Equivalent Once the documentation has been loaded, you may access it by calling the? or the help function with the package name or the name of any function. Also included are relevant examples to help you learn how the package operates. help(″calendR″) help(calendR)Equivalent to help(″calendR″). calendREquivalent assistance with the primary function help(calendR) It is also possible to determine the location of installation of the packages by using the. libPaths() is a function that returns a list of paths. libPaths() returns the path to the libraries’ installation directory. Alternatives to this include R packages, which may be installed from the menu. Select Tools Install Packages from the menu bar in RStudio, then select Install from Repository (CRAN) and then identify the packages you wish to install.
- When using the old R IDE, navigate to Packages Install package(s), choose a mirror, and then install the package.
Installing packages in R from zip source
It’s possible that you’ve downloaded a package in the zip or tar.gz format.For example, you might use the install.packages method with the arguments repos = NULL and type = ″source″ to install the package from a local zip file.It is important to note that the file path cannot contain any spaces.
- install.packages(″file pathpackage file name.extension″, repos = NULL, type = ″source″) is a function that installs packages.
- If you like, you may first adjust your working environment by using the setwd function to the location where you have obtained the package file, and then install it by supplying the name of the zip or tar.gz file you downloaded earlier.
- setwd(″file path″) install.packages(″package file name.extension″, repos = NULL, type = ″source″) is a function that installs packages.
- The final option is to select something from the menu.
- Navigate to Tools Install Packages and, under the Install from option, pick Package Archive File (.zip;.tar.gz) and then the file you want to use as an example.
- If you have the zip file hosted at a URL, you may use the install.packages.zip function from the installr package to install the packages.zip file.
It should be noted that you may also install packages from CRAN (including older versions) in this manner.install.packages(″installr″) library(installr) install.packages.zip(″installr″) install.packages.zip(″installr″) install.packages.zip(″installr″) install.packages.zip(″installr″)
Install multiple packages at once
Install R packages from GitHub or GitLab
GitHub is a well-known tool for collaborating on code.If you go to the website, you may search for R packages by typing something in the search field, such as plot package language:R in the case that you want to hunt for graphics packages, or by going to the page and searching for R packages by name.It should be noted that the search query ″language: R″ on the website is being used to limit the results to only R code repositories.
- Consider the following scenario: you wish to get the development version of the ggplot2 package from the GitHub repository.
- The URL might look something like this: The first step is to download and install the devtools package, which can be found on CRAN.
- If you get an issue, it signifies that you also need to install the RTools.
- install.packages(devtools) library is a good place to start (devtools) Then you can use the install github function with the arguments ″account name/repository name″ and ″account name/repository name″ to download and install the R package from GitHub.
- Installing ggplot2 from GitHub is as simple as installing github(″tidyverse/ggplot2″) and calling tidyverse/ggplot2.
- GitHub packages may be installed using the devtools:install github(account name /repository name) function.
This is useful if you don’t want to have to load the devtools every time you want to install a GitHub package.The: operator enables you to invoke functions from a package without first having to load it into your program.
Install R packages from R-Forge
The R Forge project is a web-based platform that includes package development tools and repository management.When installing the MPAgenomics package, you must include the package name in the repos option of the install command, as an example.The URL of the R Forge project is sent to the packages function.
- When the repository parameter is not NULL, the dependencies argument is used to define whether or not the package’s dependencies that have not been installed must also be installed.
- install.packages(″MPAgenomics″, repos = ″dependencies = TRUE″) is a function that executes when a package is installed.
Install bioconductor packages in R
An other project, Bioconductor, is dedicated to the development of tools and R packages for the analysis of biological data.First and foremost, you must install the BiocManager package.install.packages(″BiocManager″) Second, you may make advantage of the package’s install function to get everything up and running.
- Installing the nanotatoR package in BiocManager is straightforward.
- install(″nanotatoR″) It should be noted that you can install many packages at the same time.
- Installing both the NBSplice and the ncdfFlow packages at the same time BiocManager:inst (″NBSplice″, ″ncdfFlow″) It is worth mentioning that the whole list of Bioconductor packages may be viewed in R by using BiocManager:available in the command line ().
- Visit the Bioconductor R packages website for further information on the installation process and the Bioconductor R packages themselves.
Install R package in Jupyter Notebook
If you are using R in the conda environment with Jupyter Notebook and you want additional packages in addition to those that are already included, such as ‘Essentials,’ you must supply the repos parameter in the following way: install.packages(″ggplot2″, repos = ″″) is a function that installs packages.
Update R packages
List functions in R package
Upon installation, you will be able to see a list of all of the features contained inside the package.Using the help function, you may view this documentation in HTML format if the package is available on CRAN.If the package is available on CRAN, all functions included inside a page such asRecall can be found in PDF format.
- help (package = ggplot2) is a graphing package.
- Additionally, the lsf.str and ls commands may be used to enumerate all of the functions included within an attached (loaded) package.
- the string ″package:ggplot2″ lsf.str() ls (″package:ggplot2″) Another option is to write: package name: as an alternative.
- and a dropdown menu will appear in RStudio as a result of this.
- In basic R, you will need to click the tab key to display the functions on the screen; however, it should be noted that if a package has several functions, not all of them will be displayed, as is the case with the ggplot2 package, which contains the following functions: > ggplot2: ggplot2:scale fill brewerggplot2:scale size ggplot2:scale fill brewerggplot2:scale size ggplot2:Geom Lineggplot2:ScaleContinuousIdentity ggplot2:geom boxplot ggplot2:guide legend ggplot2:ScaleDiscreteIdentity ggplot2:ScaleDiscreteIdentity The ggplot2:Layout function, the ggplot2:scale color ordinal function, the ggplot2:geom hex function, and the ggplot2:Geom function are all available.
- RasterAnnggplot2:panel cols ggplot2:scale color date ggplot2:scale color date ggplot2:StatYdensity ggplot2:stat bin 2dggplot2:scale y sqrt ggplot2:aes allggplot2:alpha ggplot2:scale shape ggplot2:position dodge2
View the source code of R package functions
- It might be fascinating to look at the source code of a function every now and then. There are various alternatives available to you for this purpose: To call a function, type its name in the console.
- Press the Ctrl + Left Click or the Cmd + Left Click keyboard shortcuts. When using RStudio, enter the name of the function (which is printed on the script)
- Go to the package’s CRAN (or GitHub, R-forge, etc.) page and download the package file in order to manually check the source code
Check for installed packages
In certain cases, it’s difficult to recall whether or not a package has been installed, and you don’t want to waste time reinstalling it.It is possible to avoid this by use the need function.Notably, the primary difference between need and library is that the first provides a true or false value, whereas the second returns an error if the package is not available for installation.
- The need function is intended to be used within other functions rather than on its own.
- Installation of the package if (require(″ggplot2″)) install.packages returns FALSE (″ggplot2″) In addition, the following line of code will return TRUE if the package has been installed, and FALSE if it has not.
- ″ggplot2″ percent in percent rownames(installed.packages()) in ″ggplot2″ percent in percent
Error: Cannot remove prior installation of package
- The possibility that you were using various versions of R on the same machine is a possibility if you experienced this problem. The solutions are as follows: Close all current R sessions and reopen R to complete the installation of the package.
- Look at the error and go to the directory where the 00LOCK file is located and delete it
- if it didn’t work, look at the error and go to where the 00LOCK file is located and remove it
- Another alternative is to utilize the.libPaths() function, which returns the path where the libraries are located, and then remove the troublesome package from the system.
Are you unable to install packages in R?
- There are a variety of reasons why you may be unable to install any package: You are no longer connected to the internet, and the package is no longer accessible for download. Look for older versions of the software whose name has been misspelled. The case of package names is important
- Rtools is necessary for the package to be built, thus you must have it installed on your computer.
If nothing else works, try closing and re-opening R, or test the program on a different machine to see if the problem remains.
Best practices for handling packages in R projects
Andrie de Vries contributed to this article.For the majority of my data science work, I like to use the most recent package available from CRAN or github.However, once any work makes its way into the production server (where it is scheduled to execute on a regular basis), I want to ensure that my environment remains stable.
- Most essential, I want to make sure that the results of these initiatives are repeatable in the future.
- This is because I want to separate the packages I use and avoid ″polluting″ my library with the most recent package versions, which is why I isolate the packages I use.
- Here are some suggestions for keeping my library clean, which I hope you will find useful.
- R makes use of a single package library for each version of R that is installed on your computer.
- Fortunately, changing the path to where R installs your packages is a simple process.
- To do this, just use the function.libPaths() and indicate the path of the library to be used.
Changing your library location
You may alter the location of the library by calling the function.libPaths ().In R, a library is the area on your computer’s hard drive where you store your packages.R produces a separate library for each dot-version of the R programming language.
- For example, the libraries for R-3.0.x and R-3.1.x are located in distinct places.
- In contrast, R-3.2.0 and R-3.2.1 share the same storage space.
- For example, to use the path /R/win-library/3.1-mran-2015-06-20 as your library location, use the following code: >.libPaths(″/R/win-library/3.1-mran-2015-06-20″) >.libPaths() ″C:/Users/adevries/Documents/R/win-library/3.1-mran-2015-06-20″ ″C:/R/R-3.1.3/library″
The initialization sequence of R
- When R starts, it goes through a number of steps to get the session up and running. You may change the contents of a number of different sections of the starting sequence to customize it. The following is a simplified version of the sequence: R begins by reading the file Rprofile.site, which is located in the R Home/etc folder, where R HOME is the directory in which R was installed. If the file is located at C:RR-3.2.2etcRprofile.site, for example, it is considered to be valid.
- Making changes to this file will have an impact on all R sessions that use this version of R
- for example, here may be a good place to specify your preferred CRAN mirror location.
- Following that, R reads the file /.Rprofile in the user’s home directory
- Last but not least, R reads the file.
- Rprofile may be found in the project folder. Some project-specific options might be defined here, which could be useful in the future.
As a result, in order to set a custom library path for a given project, you may create an a.Rprofile file at the root of your project and make the necessary adjustments there.
Contents of the.Rprofile in the project root
One of the projects on which I am now working is the extraction of data from AzureML Studio and the subsequent manipulation of this data in R.For the time being, AzureML is still running R-3.1.0, which means I must test locally using R-3.1.x instead.On the other hand, I’d want to utilize a list of packages that is as near as possible to the real set of R packages that are installed on AzureML.
- For this, I am use the CRAN time machine, which was developed by MRAN researchers.
- I’d want to utilize a picture taken on June 20th, 2015, in particular.
- As a result, the contents of my project are unique.
- This is what Rprofile looks like: options(repos = c(CRAN = ″.libPaths(″/R/win-library/3.1-mran-2015-06-20″) message(″Using library: ″,.libPaths()) options(repos = c(CRAN = ″.libPaths(″/R/win-library/3.1-mran-2015-06-20″) As a result of running this code, my CRAN mirror has been changed, and the library’s location has been changed to /R/win/library/3.1-mran-2015-06-20.
- Finally, it sends a useful message to the console when the program is first launched: The R session has been restarted.
- Revolution R Enterprise version 7.4 (64-bit) provides an improved distribution of R Revolution Analytics packages, as well as new features.
Revolution Analytics, Inc.retains ownership of the copyright.’revo()’ will take you directly to the newest Revolution R news, ‘forum()’ will take you directly to the community forum, and’readme() will take you directly to the release notes.
R/win-library/3.1-mran-2015-06-20 is being used in this program.
What else is in my project folder?
The project folder in which I’m now working is a very conventional package folder that is managed via version control.″azureml″ is the name of the package on which I’m now working.So in the screenshot below you can see my RStudio project file, the git artifacts, and the tarball for