To get started with R, you need to acquire your own copy. This appendix will show you how to download R as well as RStudio, a software application that makes R easier to use. You’ll go from downloading R to opening your first R session.
Name for what is sometimes called ‘Mac Roman’ encoding. 1.2 Export to text files Exporting results from R is usually a less contentious task, but there are still a number of pitfalls.
Both R and RStudio are free and easy to download.
A.1 How to Download and Install R
R is maintained by an international team of developers who make the language available through the web page of The Comprehensive R Archive Network. The top of the web page provides three links for downloading R. Follow the link that describes your operating system: Windows, Mac, or Linux.
A.1.1 Windows
To install R on Windows, click the “Download R for Windows” link. Then click the “base” link. Next, click the first link at the top of the new page. This link should say something like “Download R 3.0.3 for Windows,” except the 3.0.3 will be replaced by the most current version of R. The link downloads an installer program, which installs the most up-to-date version of R for Windows. Run this program and step through the installation wizard that appears. The wizard will install R into your program files folders and place a shortcut in your Start menu. Note that you’ll need to have all of the appropriate administration privileges to install new software on your machine.
A.1.2 Mac
To install R on a Mac, click the “Download R for Mac” link. Next, click on the
R-3.0.3 package link (or the package link for the most current release of R). An installer will download to guide you through the installation process, which is very easy. The installer lets you customize your installation, but the defaults will be suitable for most users. I’ve never found a reason to change them. If your computer requires a password before installing new progams, you’ll need it here.
Download photostream to mac without iphoto. Binaries Versus Source
R can be installed from precompiled binaries or built from source on any operating system. For Windows and Mac machines, installing R from binaries is extremely easy. The binary comes preloaded in its own installer. Although you can build R from source on these platforms, the process is much more complicated and won’t provide much benefit for most users. For Linux systems, the opposite is true. Precompiled binaries can be found for some systems, but it is much more common to build R from source files when installing on Linux. The download pages on CRAN’s website provide information about building R from source for the Windows, Mac, and Linux platforms.
A.1.3 Linux
R comes preinstalled on many Linux systems, but you’ll want the newest version of R if yours is out of date. The CRAN website provides files to build R from source on Debian, Redhat, SUSE, and Ubuntu systems under the link “Download R for Linux.” Click the link and then follow the directory trail to the version of Linux you wish to install on. The exact installation procedure will vary depending on the Linux system you use. CRAN guides the process by grouping each set of source files with documentation or README files that explain how to install on your system.
32-bit Versus 64-bit
R comes in both 32-bit and 64-bit versions. Which should you use? In most cases, it won’t matter. Both versions use 32-bit integers, which means they compute numbers to the same numerical precision. The difference occurs in the way each version manages memory. 64-bit R uses 64-bit memory pointers, and 32-bit R uses 32-bit memory pointers. Free memorex cd label maker software for mac. This means 64-bit R has a larger memory space to use (and search through).
As a rule of thumb, 32-bit builds of R are faster than 64-bit builds, though not always. On the other hand, 64-bit builds can handle larger files and data sets with fewer memory management problems. In either version, the maximum allowable vector size tops out at around 2 billion elements. If your operating system doesn’t support 64-bit programs, or your RAM is less than 4 GB, 32-bit R is for you. The Windows and Mac installers will automatically install both versions if your system supports 64-bit R.
A.2 Using R
R isn’t a program that you can open and start using, like Microsoft Word or Internet Explorer. Instead, R is a computer language, like C, C++, or UNIX. You use R by writing commands in the R language and asking your computer to interpret them. In the old days, people ran R code in a UNIX terminal window—as if they were hackers in a movie from the 1980s. Now almost everyone uses R with an application called RStudio, and I recommend that you do, too.
R and UNIX
You can still run R in a UNIX or BASH window by typing the command:
which opens an R interpreter. You can then do your work and close the interpreter by running q() when you are finished.
A.3 RStudio
RStudio is an application like Microsoft Word—except that instead of helping you write in English, RStudio helps you write in R. I use RStudio throughout the book because it makes using R much easier. Also, the RStudio interface looks the same for Windows, Mac OS, and Linux. That will help me match the book to your personal experience.
You can download RStudio for free. Just click the “Download RStudio” button and follow the simple instructions that follow. Once you’ve installed RStudio, you can open it like any other program on your computer—usually by clicking an icon on your desktop.
The R GUIs
Windows and Mac users usually do not program from a terminal window, so the Windows and Mac downloads for R come with a simple program that opens a terminal-like window for you to run R code in. This is what opens when you click the R icon on your Windows or Mac computer. These programs do a little more than the basic terminal window, but not much. You may hear people refer to them as the Windows or Mac R GUIs.
Microsoft office standard mac. When you open RStudio, a window appears with three panes in it, as in Figure A.1. The largest pane is a console window. This is where you’ll run your R code and see results. The console window is exactly what you’d see if you ran R from a UNIX console or the Windows or Mac GUIs. Everything else you see is unique to RStudio. Hidden in the other panes are a text editor, a graphics window, a debugger, a file manager, and much more. You’ll learn about these panes as they become useful throughout the course of this book.
Do I still need to download R?
Even if you use RStudio, you’ll still need to download R to your computer. RStudio helps you use the version of R that lives on your computer, but it doesn’t comewith a version of R on its own.
A.4 Opening R
Now that you have both R and RStudio on your computer, you can begin using R by opening the RStudio program. https://corpsburn.weebly.com/blog/photoshop-atlental-download-for-mac. Open RStudio just as you would any program, by clicking on its icon or by typing “RStudio” at the Windows Run prompt.
Using Bioconductor
The current release of Bioconductor is version3.11; it works with R version4.0.0. Users of older R andBioconductor must update their installation to take advantageof new features and to access packages that have been added toBioconductor since the last release.
The development version of Bioconductor is version3.12; it works with R version4.0.0. More recent ‘devel’versions of R (if available) will be supported during the nextBioconductor release cycle.
Install the latest release of R, then get the latest version ofBioconductor by starting R and entering the commands
It may be possible to change the Bioconductor version of an existinginstallation; see the ‘Changing version’ section of the BiocManagervignette.
Details, including instructions toinstall additional packages and toupdate,find, andtroubleshoot are providedbelow. A devel version ofBioconductor is available. There are goodreasons for using
BiocManager::install() formanaging Bioconductor resources.
Install R
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Install Bioconductor Packages
To install core packages, type the following in an R command window:
Install specific packages, e.g., “GenomicFeatures” and “AnnotationDbi”, with
The
install() function (in the BiocManager package) has arguments that changeits default behavior; type ?install for further help.
For a more detailed explanation on using BiocManager and its advanced usage,such as version switching, please refer to theBiocManager vignette.
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Find Bioconductor Packages
Visit the software package listto discover available packages.
To search through available packages programmatically, use the following:
For example, using a “^org” search pattern will show all of the availableorganism annotation packages.
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Update Installed Bioconductor Packages
Bioconductor packages, especially those in the development branch, areupdated fairly regularly. To identify packages requiring update withinyour version of Bioconductor, start a new session of R and enter
Use the argument
ask=FALSE to update old packages without beingprompted. Read the help page for ?install for additional details.
Upgrading installed Bioconductor packages
Some versions of R support more than one version of Bioconductor. Touse the latest version of Bioconductor for your version of R, enter
Remember that more recent versions of Bioconductor may be available if yourversion of R is out-of-date.
For more details on Bioconductor approaches to versioning, seethe advanced sectionin the vignette and version numbering in the developer reference section.
Recompiling installed Bioconductor packages
Rarely, underlying changes in the operating system require ALLinstalled packages to be recompiled for source (C or Fortran)compatibility. One way to address this might be to start a new Rsession and enter
As this will reinstall all currently installed packages, it likelyinvolves a significant amount of network bandwidth and compilationtime. All packages are implicitly updated, and the cumulative effectmight introduce wrinkles that disrupt your work flow. It also requiresthat you have the necessary compilers installed.
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Troubleshoot Package Installations
Use the commands
to flag packages that are either out-of-date or too new for yourversion of Bioconductor. The output suggests ways to solve identifiedproblems, and the help page
?valid lists arguments influencingthe behavior of the function.
Troubleshoot BiocManager
One likely reason for BiocManager not working on your system couldbe that your version of R is too old for
BiocManager . In orderavoid this issue, please ensure that you have the latest version of Rinstalled in your system. BiocManager supports R versions from 3.5.0and above.
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Why use BiocManager::install()?BiocManager::install() is the recommended way to install Bioconductorpackages. There are several reasons for preferring this to the‘standard’ way in which R pacakges are installed viainstall.packages() .
Bioconductor has a repository and release schedule that differs from R(Bioconductor has a ‘devel’ branch to which new packages and updatesare introduced, and a stable ‘release’ branch emitted once every 6months to which bug fixes but not new features are introduced). Pro tools ultimate free download mac.
A consequence of the mismatch between R and Bioconductor releaseschedules is that the Bioconductor version identified by
install.packages() is sometimes not the most recent ‘release’available. For instance, an R minor version may be introduced somemonths before the next Bioc release. After the Bioc release the usersof the R minor version will be pointed to an out-of-date version ofBioconductor.
A consequence of the distinct ‘devel’ branch is that
install.packages() sometimes points only to the ‘release’repository, whereas Bioconductor developers and users wantingleading-edge features wish to access the Bioconductor ‘devel’repository. For instance, the Bioconductor 3.0 release is availablefor R.3.1.x, so Bioconductor developers and leading-edge users need tobe able to install the devel version of Bioconductor packages into thesame version (though perhaps different instance or at least librarylocation) of R that supports version 2.14 of Bioconductor.
Persian font for mac download. An indirect consequence of Bioconductor’s structured release is thatpackages generally have more extensive dependencies with one another,both explicitly via the usual package mechanisms and implicitlybecause the repository, release structure, and Bioconductor communityinteractions favor re-use of data representations and analysisconcepts across packages. There is thus a higher premium on knowingthat packages are from the same release, and that all packages arecurrent within the release.
The BiocManager package serves as the primary way to ensure thatthe appropriate Bioconductor installation is used with respectto the version of R in use regardless of the R and Bioconductorrelease cycles.
The
install() Fast lane bad meets evil mp3 download. function is provided by BiocManager. This is awrapper around install.packages , but with the repository chosenaccording to the version of Bioconductor in use, rather than to theversion relevant at the time of the release of R.
Latest Mac Versioninstall() also nudges users to remain current within a release, bydefault checking for out-of-date packages and asking if the user wouldlike to update
The BiocManager package provides facilities for switching to the‘devel’ version of Bioconductor
(at some points in the R / Bioconductor release cycle use of ‘devel’requires use of a different version of R itself, in which case theattempt to install devel fails with an appropriate message).
The BiocManager package also provides
valid() to test that theinstalled packages are not a hodgepodge from different Bioconductorreleases (the ‘too new’ packages have been installed from sourcerather than a repository; regular users would seldom have these).
For users who spend a lot of time in Bioconductor, the featuresoutlined above become increasingly important and
install() is muchpreferred to install.packages() .
Mac Os X Version Names
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Pre-configured Bioconductor
Bioconductor is also available as a set ofAmazon Machine Images (AMIs) andDocker images.
Legacy and Older R Versions
It is always recommended to update to the most current version of R andBioconductor. If this is not possible and
R < 3.5.0 , please use the followingfor installing Bioconductor packages
Mac Version 10.7 Free Download
To install core packages, type the following in an R command window:
Install specific packages, e.g., “GenomicFeatures” and “AnnotationDbi”, with
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