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FAQ

• Package Installation
  • Package Not Available
  • Fails To Install
  • Install From Devel
• Package Use
  • Find A Package or Package Information
  • ERROR: No Package Called
• Annotations
  • Annotations Disagree
• Developing Packages
  • Guidelines To Follow
  • How To Declare Dependencies
  • Troubleshooting Build Report
• Citation
  • How To Cite Bioconductor
• Connecting
  • Where to Ask Help
  • Connect With Community

Package Installation

BiocManager::install() warns that a package is not available

Bioconductor has a ‘release’ and a ‘devel’ branch. The ‘release’branch is intended for most users, and is available using thecurrent version ofR. New packages are first added to the‘devel’ branch, and then become available after the nextBioconductor release, typically in April and October. SeeWhy use BiocManager::install()? for more information about our releasepolicy, andthese instructions if you wish to use the develbranch.

Most Bioconductor packages are available for Windows, Mac OS, andLinux operating systems. A few packages are not available on one ormore platforms. This usually occurs because the package relies onadditional software that is not available for the operatingsystem. For instance, a user trying to installRcollectlencountered this message:

    > BiocManager::install("Rcollectl")    Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.2 Patched (2023-11-07      r85494)    Installing package(s) 'Rcollectl'    Warning message:    package 'Rcollectl' is not available (for R version 4.3.2 Patched)

Visiting the list ofpackage home pagesshows that the package was not available on Windows or Mac OS, the platform onwhich the user was trying to install the package. If the packageDescription does not indicate why the package is not available, pleasefeel free to ask on theBioconductor supportsite. You can also see if any platform isnot supported on thepackage build reportpages

It’s useful to check that the package name is spelt correctly, withcorrect capitalization!

Package XXX fails to install

A common reason for a package to fail to install is thatR orBioconductor software dependencies are not satisfied, as shown herefrom a user trying to install theaffyPLM package:

    ...    ** inst    ** preparing package for lazy loading    Error: package 'affy' required by 'affyPLM' could not be found    Execution halted    ERROR: lazy loading failed for package 'affyPLM'

Be sure to useBiocManager::install toinstall packages that areappropriate for your system and version ofR. Be sure that yourinstalled packages are up-to-date by followingupdate packages.

Less commonly, packages may install but then fail to load, as herewith theRsamtools package:

    Error in dyn.load(file, DLLpath = DLLpath, ...) :    unable to load shared library    '/usr/local/lib64/R/library/Rsamtools/libs/Rsamtools.so':      /usr/local/lib64/R/library/Rsamtools/libs/Rsamtools.so: undefined symbol: ecrc32

This is likely a system configuration issue, e.g., a WindowsPATHenvironment variable is not set correctly, or the Linuxldconfigprogram orLD_LIBRARY_PATH environment variable is incorrect.

Packages may also fail to install because third party software is notavailable. This often happens during theconfigure part of thepackage installation process, as illustrated here with theXMLpackage:

    * Installing *source* package 'XML' ...    ...    checking for xml2-config... no    Cannot find xml2-config    ERROR: configuration failed for package 'XML'

These types of errors can sometimes be easily solved (installingnecessary libraries or other software, perhaps referenced on thepackage home page). It will often be necessary tounderstand your system more thoroughly than you’d like, perhaps withthe assistance of the Bioconductorsupport site.

Installing packages from the development repository

To install a package from the development version of the Bioconductor repository,install and use the development version of R andBiocManager::install(version='devel'). SeeUsing ‘Devel’ Versionof Bioconductor

Package Use

How can I find information about using a package?

There are three main steps to using a package. (1) Identify anappropriate package. Do this usingbiocViews to browseavailable software. (2) Explore overall package functionality and workflows. Do this by reading the package vignettes, listed on the pagedescribing the package and available from biocViews. For instance,locateIRanges vignettes. (3) Find help onparticular functions, e.g.,

    library(IRanges)    help(package="IRanges")  ## overview    ?findOverlaps            ## specific function

For a more exploratory interface to the help system, try

    help.start()

If you are new toR, then it will help to enter into the processknowing that some basic R skills are assumed by the vignettes and helppages; spend some time learningR itself.

Library ERROR: No Package Called xxx

A package must beinstalled before it can be loaded withlibrary(). Also all package dependencies should be installed. If apackage or package dependency is not installed you may often see somethingsimilar to the following

library(BiocFileCache)Error in library(BiocFileCache) : there is no package called 'BiocFileCache'

You must first install the package with BiocManager

BiocManager::install("BiocFileCache")library(BiocFileCache)

It’s useful to check that the package name is spelt correctly, withcorrect capitalization! Remember R is case sensitive! If ERROR persists, reachout on theBioconductor support site

Annotations

Different sources (e.g., annotation packages,biomaRt, manufacturer, UCSC, GO) disagree. Why?

Different sources take different approaches to managingannotations. The annotation packages in Bioconductor are based ondownloads obtained shortly before each Bioconductor release, and socan lag by six months (at the end of the release cycle) compared toon-line resources. The advantage of this approach is that theannotations do not change unexpectedly during development of ananalysis, while the disadvantage is that the resource is not quiteup-to-date with current understanding. To find out information aboutdata sources used for each annotation package, try a command analogousto

library(org.Hs.eg.db)org.Hs.eg_dbInfo()

Bioconductor packages can help further investigate discrepancies,e.g., AnnotationDbi, rtracklayer, Biostrings, and BSgenome (e.g.,BSgenome.Hsapiens.UCSC.hg17).

Developing Packages

Bioconductor Package Development Guidelines

See theguidelines for Bioconductor package development, maintenance, and peerreview.

What packages belong in the Depends:, Imports:, or Suggests: fields?

Two relevant mailing list posts(a,b)address this. Generally, packages whose code you use in your ownpackage should where ever possible be Import:’ed. Packages requiredfor vignettes are often Suggest:’ed. Depends: is appropriate forpackages that cannot be Import:’ed (e.g., because they do not have aNAMESPACE) or for packages that provide essential functionality neededby the user of your package, e.g., your functions always returnGRanges objects, so the user will necessarily needGenomicRangeson their search path.

Troubleshooting the Build Report

Package maintainers are expected to monitor their packages. If a package startsfailing on theBioconductor build system, it is a maintainersresponsibility to investigate and push any changes to the Bioconductor packagerepository to ensure a clean build report. Some tips on reproducing ERRORs andcommonly known issues can be found on theTroubleshooting BuildReportsection of the contributions guidelines.

Citation

How do I cite Bioconductor?

Many packages provide a citation available from within R. Try the following onany installed package:

    citation('DESeq')

To cite the project as a whole, use

    citation('Biobase')

Connecting With Bioconductor Community

Where To Ask Questions

Most questions are appropriate to ask on theBioconductor supportsite. Package development questions are best asked on thebioc-develmailing list. TheBioconductor chat also has specializedchannels for areas of research that may be helpful.

Connect With Bioconductor Community

SeeSupport Forums for a listing of ways to connect with thecommunity.