Downloading older versions of r

Remember that more recent versions of Bioconductor may be available if your version of R is out-of-date. BiocManager will notify you when your version of R is out-of-date.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. 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. 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. The output suggests ways to solve identified problems, and the help page?

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.

BiocManager::install is the recommended way to install Bioconductor packages. A consequence of the mismatch between R and Bioconductor release schedules is that the Bioconductor version identified by install.

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 After the Bioc release the users of the R minor version will be pointed to an out-of-date version of Bioconductor. For instance, the Bioconductor 3. 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. Version : 9. July 13, Version : 6. October 05, Version : 2. November 26, Release notes February 24, Release notes August 04, August 04, Release notes July 16, July 16, Update 4b Size : 1. Update 4b. Release notes July 21, July 21, Release notes September 11, September 11, Update 4a Size : Update 4a.

Version : 4. Release notes July 03, July 03, February 24, Release notes March 24, March 24, Version : 1. Release notes October 09, October 09, Release notes June 04, June 04, Release notes April 02, April 02, Release notes July 24, July 24, This is not how packages are usually installed, but it is sometimes done this way on servers.

To find the libraries for your user, you can run. For example, this is what shows on Ubuntu Linux:. Renviron in their home directory. At a system level, the library path s can be set with an Renviron. See the R startup documentation page for more information. In some installations typically on Linux , R is configured to keep the same site library across R version upgrades.

The problem here is that packages that built and installed with one version of R may be incompatible with a newer version of R, at least when the major or minor version changes. Note that Subminor version upgrades of R generally do not introduce incompatibilities.

In other installations typically on Mac and Windows , R is configured to use a new library when R has a major or minor version upgrade. The drawback is that you must reinstall your packages after upgrading R. The user and site library paths can be customized. See the R startup documentation for more information.

The default library configuration differs across platforms, and so the behavior after an R version upgrade also differs across platforms. On Windows, the default user library has the major. The default site library has the major. With this configuration, user-installed packages get installed in the user library. Only R version upgrades that involve a minor version change will result in the user library changing. When this happens, you will need to reinstall all your packages.

On macOS, the default configuration does not have a user library. The site library has the major. With this configuration, user-installed packages get installed into the site library. Users on macOS usually have permission to write to the site library. R version upgrades that involve a minor version change will require the user to reinstall all packages. On Linux, the default user library has the major.

The site library is not versioned. There can be multiple site libraries, though this should not cause any differences in most use cases.

The process of upgrading R on Linux is different from upgrading it Mac and Windows. On Mac and Windows, the user usually needs to go download the new version of R and install it, so it is obvious when R is upgraded.

On Linux, R is usually upgraded in the process of a system software update, such as when you run apt-get upgrade on Debian or Ubuntu. Additionally, Linux systems often have different people administering them and using them. For these two reasons, the installed version of R can change without the user being aware of it.

User-installed packages go into the user library. After R gets a minor version upgrade, the user will find that their user-installed packages are no longer available, and will need to reinstall all of them. This may come as a surprise to users, but the solution is straightforward.

When R is upgraded, those packages will continue to be available even after a major or minor version upgrade, but they potentially could be incompatible with the new version of R. If this happens, users will experience problems like the ones described previously. In these cases, a user or system administrator should check which version of R each package was built with, and reinstall those packages that were built with an old version of R, as described above.

One risk of doing this is that this will not only reinstall those R packages, but also upgrade the versions of those packages, which could cause problems if the newer version of the package has different behavior. Because of these potential problems, administrators of Linux servers should be exercise caution when upgrading R.

On most Linux distributions, it is possible to freeze system packages like R to a specific version, and only upgrade after testing. If you have questions about this article or would like to discuss ideas presented here, please post on RStudio Community.

Our developers monitor these forums and answer questions periodically. See help for more help with all things Shiny. Shiny from. User libraries and version incompatibilities There are two possible sources of problems with R version upgrades, both of which are related to package libraries.

In both cases, the solution is to reinstall packages with the new version of R. Detecting which version of R a package was built with The following code will show which packages are installed, their version numbers, and which version of R they were built with.

Reinstalling packages with the new version of R After upgrading R, if you have any packages that were built with an older version of R, you should reinstall those packages to avoid compatibility issues. User and site libraries In all R installations, there is a site library: packages installed there are available to all users. Versioned and unversioned libraries In some installations typically on Linux , R is configured to keep the same site library across R version upgrades.

Customized library paths The user and site library paths can be customized. Platform-specific notes The default library configuration differs across platforms, and so the behavior after an R version upgrade also differs across platforms.