+
Install Bioconductor Packages
+
To install core packages, type the following in an R command window:
+
+
+
+if (!require("BiocManager", quietly = TRUE))
+ install.packages("BiocManager")
+BiocManager::install(version = "3.17")
+
+
+
+
To install core packages, type the following in an R command window:
+
+
+
+BiocManager::install(c("GenomicFeatures", "AnnotationDbi"))
+
+
+
+
+ The install() function (in the BiocManager package) has
+ arguments that change its 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 the
+ BiocManager vignette.
+
+
+
Find Bioconductor Packages
+
+
Visit the software package list to discover available packages.
+
+ To search through available packages programmatically, use the following:
+
+
+
+
+BiocManager::available()
+
+
+
+
+ For example, using a “^org” search pattern will show all of the available
+ organism annotation packages.
+
+
+
+ Update Installed Bioconductor Packages
+
+
+
+ Bioconductor packages, especially those in the development branch, are
+ updated fairly regularly. To identify packages requiring update within your
+ version of Bioconductor, start a new session of R and enter:
+
+
+
+
+BiocManager::install()
+
+
+
+
+ Use the argument ask=FALSE to update old packages without
+ being prompted. Read the help page for ?install for additional details.
+
+
+
Updgrading Installed Bioconductor Packages
+
+
+ Due to the development cycle, all versions of R will eventually support more
+ than one version of Bioconductor. To use the latest version of Bioconductor
+ for your version of R, enter:
+
+
+
+
+if (!require("BiocManager", quietly = TRUE))
+ install.packages("BiocManager")
+BiocManager::install()
+
+
+
+
+ Remember that more recent versions of Bioconductor may be available if your
+ version of R is out-of-date. BiocManager will notify you when your version
+ of R is out-of-date.
+
+
+
+ For more details on Bioconductor approaches to versioning, see the
+ advanced section
+ in the vignette and version numbering in the
+ developer reference
+ section.
+
+
+
Recompiling Installed Bioconductor Packages
+
+
+ Rarely, underlying changes in the operating system require ALL installed
+ packages to be recompiled for source (C or Fortran) compatibility. One way
+ to address this might be to start a new R session and enter:
+
+
+
+
+if (!require("BiocManager", quietly = TRUE))
+ install.packages("BiocManager")
+pkgs <- rownames(installed.packages())
+BiocManager::install(pkgs, type = "source", checkBuilt = TRUE)
+
+
+
+
+ As this will reinstall all currently installed packages, it likely involves
+ a significant amount of network bandwidth and compilation time. All packages
+ are implicitly updated, and the cumulative effect might introduce wrinkles
+ that disrupt your work flow. It also requires that you have the necessary
+ compilers installed.
+
+
+
+ Troubleshoot Package Installations
+
+
+
Use the commands:
+
+
+
+BiocManager::valid() ## R version 3.5 or later
+
+
+
+
+ to flag packages that are either out-of-date or too new for your version of
+ Bioconductor. The output suggests ways to solve identified problems, and the
+ help page ?valid lists arguments influencing the behavior
+ of the function.
+
+
+
Troubleshoot BiocManager
+
+
+ One likely reason for BiocManager not working on your system could be that
+ your version of R is too old for BiocManager. In order
+ avoid this issue, please ensure that you have the latest version of R
+ installed in your system. BiocManager supports R versions from 3.5.0 and
+ above.
+
+
+
Why use BiocManager::install()?
+
+
+ BiocManager::install() is the recommended way to install
+ Bioconductor packages. There are several reasons for preferring this to the
+ ‘standard’ way in which R pacakges are installed via
+ install.packages().
+
+
+
+ Bioconductor has a repository and release schedule that differs from R
+ (Bioconductor has a ‘devel’ branch to which new packages and updates are
+ introduced, and a stable ‘release’ branch emitted once every 6 months to
+ which bug fixes but not new features are introduced).
+
+
+
+ A consequence of the mismatch between R and Bioconductor release schedules
+ 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 some
+ months before the next Bioc release. After the Bioc release the users of the
+ R minor version will be pointed to an out-of-date version of Bioconductor.
+
+
+
+ A consequence of the distinct ‘devel’ branch is that
+ install.packages()
+ sometimes points only to the ‘release’ repository, whereas Bioconductor
+ developers and users wanting leading-edge features wish to access the
+ Bioconductor ‘devel’ repository. For instance, the Bioconductor 3.0 release
+ is available for R.3.1.x, so Bioconductor developers and leading-edge users
+ need to be able to install the devel version of Bioconductor packages into
+ the same version (though perhaps different instance or at least library
+ location) of R that supports version 2.14 of Bioconductor.
+
+
+
+ An indirect consequence of Bioconductor’s structured release is that
+ packages generally have more extensive dependencies with one another, both
+ explicitly via the usual package mechanisms and implicitly because the
+ repository, release structure, and Bioconductor community interactions favor
+ re-use of data representations and analysis concepts across packages. There
+ is thus a higher premium on knowing that packages are from the same release,
+ and that all packages are current within the release.
+
+
+
+ The BiocManager package serves as the primary way to ensure that the
+ appropriate Bioconductor installation is used with respect to the version of
+ R in use regardless of the R and Bioconductor release cycles.
+
+
+
+
+> library(BiocManager)
+Bioconductor version 3.9 (BiocManager 1.30.4), ?BiocManager::install
+for help
+
+
+
+
+ The install() function is provided by BiocManager. This is
+ a wrapper around install.packages, but with the repository chosen according
+ to the version of Bioconductor in use, rather than to the version relevant
+ at the time of the release of R.
+
+
+
+ install() also nudges users to remain current within a
+ release, by default checking for out-of-date packages and asking if the user
+ would like to update.
+
+
+
+
+> BiocManager::install()
+Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 Patched
+(2019-05-02 r76454)
+Update old packages: 'BBmisc', 'genefilter', 'GenomicAlignments',
+ 'GenomicRanges', 'IRanges', 'MASS', 'reshape2', 'Rgraphviz',
+ 'RJSONIO', 'rtracklayer'
+Update all/some/none? [a/s/n]:
+
+
+
+
+ The BiocManager package provides facilities for switching to the ‘devel’
+ version of Bioconductor.
+
+
+
+
+> BiocManager::install(version = "devel")
+Upgrade 89 packages to Bioconductor version '3.10'? [y/n]: y
+Installing package(s) 'BiocVersion'
+trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/BiocVersion_3.10.0.tar.gz'
+Content type 'application/x-gzip' length 987 bytes
+==================================================
+downloaded 987 bytes
+
+* installing *source* package 'BiocVersion' ...
+** help
+*** installing help indices
+** building package indices
+** testing if installed package can be loaded
+* DONE (BiocVersion)
+
+...
+Bioconductor version 3.10 (BiocManager 1.30.4), ?BiocManager::install for
+help
+
+
+
+
+ (at some points in the R / Bioconductor release cycle use of ‘devel’
+ requires use of a different version of R itself, in which case the attempt
+ to install devel fails with an appropriate message).
+
+
+
+ The BiocManager package also provides valid() to test that
+ the installed packages are not a hodgepodge from different Bioconductor
+ releases (the ‘too new’ packages have been installed from source rather than
+ a repository; regular users would seldom have these).
+
+
+
+
+> BiocManager::valid()
+
+* sessionInfo()
+
+R version 3.6.0 Patched (2019-05-02 r76454)
+Platform: x86_64-pc-linux-gnu (64-bit)
+...
+
+Bioconductor version '3.9'
+
+ * 2 packages out-of-date
+ * 0 package too new
+...
+create a valid installation with
+
+ BiocManager::install(c(
+ "GenomicFeatures", "AnnotationDbi"
+ ), update = TRUE, ask = FALSE)
+
+more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date
+
+Warning message:
+2 packages out-of-date; 0 packages too new
+
+
+
+
+ For users who spend a lot of time in Bioconductor, the features outlined
+ above become increasingly important and install() is much
+ preferred to install.packages().
+
+
+
Pre-configured Bioconductor
+
+
+ Bioconductor is also available as
+ Docker images or available for use in the
+ AnVIL.
+
+
+
Legacy and Older R Versions
+
+
+ is always recommended to update to the most current version of R and
+ Bioconductor. If this is not possible and R < 3.5.0 ,
+ please use the following for installing Bioconductor packages.
+
+
+
To install core packages, type the following in an R command window:
+
+
+
+source("https://bioconductor.org/biocLite.R")
+
+
+
+
+ Install specific packages, e.g., “GenomicFeatures” and “AnnotationDbi”,
+ with:
+
+
+
+
+BiocInstaller::biocLite(c("GenomicFeatures", "AnnotationDbi"))
+
+
+
+ 
+ 
+