BiocCheckBiocCheckBiocCheck be runBiocCheckBiocCheck outputBiocCheckGitCloneBiocCheckGitCloneBiocCheckGitCloneBiocCheckGitClone outputBiocCheckBiocCheck encapsulates Bioconductor package guidelines and best
practices, analyzing packages and reporting three categories of
issues:
BiocCheck will continue past an ERROR, thus it is
possible to have more than one, but it will exit with an error code
if run from the OS command line.)BiocCheckMost commonly you will use BiocCheck from your operating system command line, as
R CMD BiocCheck packageWhere package is either a directory containing an R package, or a source
tarball (.tar.gz file).
BiocCheck can also be run interactively:
library(BiocCheck)
BiocCheck("packageDirOrTarball")R CMD BiocCheck takes options which can be seen by running
R CMD BiocCheck --help## Usage: R CMD BiocCheck [options] package
##
##
## Options:
## --new-package
## enable checks specific to new packages
##
## --no-check-dependencies
## disable check for bad dependencies
##
## --no-check-deprecated
## disable check for usage of deprecated packages
##
## --no-check-remotes
## disable check for usage of remote packages other than those hosted on CRAN or Bioconductor
##
## --no-check-version-num
## disable check for valid version number
##
## --no-check-R-ver
## disable check for valid R version
##
## --no-check-pkg-size
## disable check for package tarball size
##
## --no-check-file-size
## disable check for individual file size
##
## --no-check-bioc-views
## disable biocViews-specific checks (for non-BioC packages)
##
## --no-check-bbs
## disable BBS-specific checks (for non-BioC packages). Valid DESCRIPTION
##
## --no-check-namespace
## disable namespace checks
##
## --no-check-vignettes
## disable vignette checks
##
## --no-check-library-calls
## disable check usage of functions that install or update packages
##
## --no-check-install-self
## disable check for require or library of itself
##
## --no-check-coding-practices
## disable check for some common best coding practices
##
## --no-check-function-len
## disable check for function length
##
## --no-check-man-doc
## disable checks for man page documentation
##
## --no-check-news
## disable checks for NEWS file
##
## --no-check-unit-tests
## disable checks for unit tests
##
## --no-check-skip-bioc-tests
## disable check for tests that skip when on bioc
##
## --no-check-formatting
## disable checks for file formatting
##
## --no-check-CRAN
## disable check for if package exists in CRAN
##
## --no-check-bioc-help
## disable check for registration on Bioconductor mailing list and support site
##
## --build-output-file=BUILD-OUTPUT-FILE
## file containing R CMD build output, for additional analysis
##
## --quit-with-status
## enable exit code option when performing check
##
## -h, --help
## Show this help message and exitNote that the --new-package option is turned on in the package
builder attached to the Bioconductor package tracker, since this is
almost always used to build new packages that have been submitted.
BiocCheck be runRun BiocCheck after running R CMD check.
Note that BiocCheck is not a replacement for R CMD check; it is
complementary. It should be run after R CMD check completes
successfully.
BiocCheck can also be run via the Travis-CI
(continuous integration) system. This service allows automatic testing of R
packages in a controlled build environment.
Simply add the following line to your package’s .travis.yml file:
bioc_check: trueBiocCheckBiocCheck should be installed as follows:
if (!"BiocManager" %in% rownames(installed.packages()))
install.packages("BiocManager")
BiocManager::install("BiocCheck")The package loading process attempts to install a script called
BiocCheck (BiocCheck.bat on Windows) into the bin directory of
your R installation. If it fails to do that (most likely due to
insufficient permissions), it will tell you, saying something like:
Failed to copy the "script/BiocCheck" script to
/Library/Frameworks/R.framework/Resources/bin. If you want to be
able to run 'R CMD BiocCheck' you'll need to copy it yourself to a
directory on your PATH, making sure it is executable. See the
BiocCheck vignette for more information.You can fix the problem by following these instructions (noting that
R may live in a different directory on your system than what is
shown above).
If you don’t have permission to copy this file to the bin directory
of your R installation, you can, as noted, copy it to any directory
that’s in your PATH. For assistance modifying your PATH, see this link
(Windows) or this
one (Mac/Unix).
If you manually copy this file to a directory in your PATH that is not
your R bin directory, you’ll continue to see the above message when
(re-)installing BiocCheck but you can safely ignore it.
BiocCheck outputActual BiocCheck output is shown below in bold.
Checking Package Dependencies…
Can be disabled with --no-check-dependencies.
Checking if other packages can import this one…
ERROR).Checking to see if we understand object initialization….
NOTE).Checking for deprecated package usage…
Can be disabled with --no-check-deprecated.
At present, this looks to see whether your package has a dependency on
the multicore package (ERROR).
Our recommendation is to use BiocParallel. Note that ‘fork’ clusters do not rpovide any gain from parallelizing code on Windows. Socket clusters work on all operating systems.
Also checks Deprecated Packages currently specified in release and devel
versions of Bioconductor (ERROR).
Checking for remote package usage…
Can be disabled with --no-check-remotes
Bioconductor only allows dependencies that are hosted on CRAN or
Bioconductor. The use of Remotes: in the DESCRIPTION to specify a unique
remote location is not allowed.
Can be disabled with --no-check-version-num and --no-check-R-ver.
Checking version number…
Version:
field in your DESCRIPTION file. If it doesn’t, it usually means
you did not build the tarball with R CMD build. (ERROR)--new-package option is
supplied (ERROR).ERROR).Depends: field of your
DESCRIPTION file, BiocCheck checks to make sure that the R
version specified matches the version currently used by
Bioconductor. This prevents the package from being used in earlier
versions of R, which is not recommended and is a frequent cause of
user confusion (WARNING).For more information on package versions, see the Version Numbering HOWTO.
Can be disabled with --no-check-pkg-size and --no-check-file-size.
Checking package size Checks that the package size meets Bioconductor requirements. The current package size limit is 5 MB for Software packages. Experiment Data and Annotation packages are excluded from this check. This check is only run if checking a source tarball. (ERROR)
Checking individual file sizes The current size limit for all individual files is 5 MB. (WARNING)
These can be disabled with the --no-check-bioc-views option, which
might be useful when checking non-Bioconductor packages (since
biocViews is a concept unique to Bioconductor).
Checking biocViews…
Can be disabled with --no-check-bioc-views
biocViews field is present in the DESCRIPTION file
(ERROR).ERROR).WARNING).WARNING).recommendBiocViews() function from biocViews to
automatically suggest some biocViews for your package.More information about biocViews is available in the Using biocViews HOWTO.
The Bioconductor Build System (BBS) is our nightly build system and it has certain requirements. Packages which don’t meet these requirements can be silently skipped by BBS, so it’s important to make sure that every package meets the requirements.
Can be disabled with --no-check-bbs
Checking build system compatibility…
ERROR).ERROR).Package field of DESCRIPTION file matches
directory or tarball name (ERROR).Version field is present in the DESCRIPTION
file (ERROR).Checking for valid maintainer…
Checks to make sure the DESCRIPTION file has either a Maintainer
field, or a valid Authors@R field which resolves to a valid
Maintainer (ERROR).
Authors@R field consists of:
person.cre (creator) role.family or given name defined.Can be disabled with --no-check-namespace
Checking DESCRIPTION/NAMESPACE consistency…
BiocCheck detects packages that are imported in NAMESPACE but not
DESCRIPTION, or vice versa, and provides an explanation of how to fix
this (ERROR).
Checking for namespace import suggestions…
If the package codetoolsBioC is installed, BiocCheck will run it
to see if it has suggestions for the “Imports” section of your package
NAMESPACE.
codetoolsBioC is an experimental package that is not presently
available via BiocManager::install(). It is available from our
Subversion repository with the credentials readonly/readonly.
Output of codetoolsBioC is printed to the screen but BiocCheck does
not label it ERROR, WARNING, or NOTE.
Can be disabled with --no-check-vignettes.
Checking vignette directory…
Only run if your package is a software package (as determined by your biocViews), or if package type cannot be determined.
vignettes directory exists (ERROR).vignettes directory only contains vignette sources
(.Rmd, .Rnw, .Rrst, .Rhtml, *.Rtex) (ERROR).ERROR).WARNING)ERROR)WARNING)eval=FALSE chunks is more than 50% of
the total (WARNING).eval=FALSE.
The majority of vignette code is expected to be evaluated (WARNING)Checking whether vignette is built with ‘R CMD build’…
Only run when --build-output-file is specified.
Analyzes the output of R CMD build to see if vignettes are built.
It simply looks for a line that starts:
* creating vignettes ...If this line is not present, it means R has not detected that a
vignette needs to be built (ERROR).
If you have vignette sources yet still get this message, there could be several causes:
VignetteBuilder line in the DESCRIPTION file.VignetteEngine line in the vignette source.See knitr’s package vignette page, or the
Non-Sweave vignettes section of “Writing R Extensions” for more
information.
Can be disabled with --no-check-library-calls and --no-check-install-self.
NOTE)
Check for use of functions that install or update packages. This list
currently includes the use of install, install.packages, update.packages
or biocLite.ERROR)
It is not necessary to call library() or require() on your own
package within code in the R directory or in man page examples. In
these contexts, your package is already loaded.Can be disabled with --no-check-coding-practices.
Checking coding practices…
Checks to see whether certain programming practices are found in the R directory.
We recommend that vapply() be used instead of sapply(). Problems
arise when the X argument to sapply() has length 0; the return
type is then a list() rather than a vector or array. (NOTE)
We recommend that seq_len() or seq_along() be used instead of
1:.... This is because the case 1:0 creates the sequence c(1, 0)
which may be an unexpected or unwanted result (NOTE).
Checking for T… Checking for F…
It is bad practice to use T and F for TRUE and FALSE. This
is because T and F are ordinary variables whose value can be
altered, leading to unexpected results, whereas the value of TRUE
and FALSE cannot be changed (WARNING).
Avoid class() == and class() != instead use is(). (WARNING)
Use system2() over system(). ‘system2’ is a more portable and
flexible interface than ‘system’.(NOTE)
Use of set.seed() in R code. The set.seed should not be set in
R functions directly. The user should always have the option for
the set.seed and know when it is being invoked. (WARNING)
Checking parsed R code in R directory, examples, vignettes…
BiocCheck parses the code in your package’s R directory, and in
evaluated man page and vignette examples to look for various symbols,
which result in issues of varying severity.
browser() causes the command-line R debugger to be invoked, and
should not be used in production code (though it’s OK to wrap such
calls in a conditional that evaluates to TRUE if some debugging
option is set) (WARNING).<<- is bad practice. It can over-write
user-defined symbols, and introduces non-linear paths of evaluation
that are difficult to debug (NOTE).BiocCheck checks for direct slot access (via @ or slot()) to
S4 objects in vignette and example code. This code should always
use accessors to interact with S4 classes. Since you may be using S4
classes (which don’t provide accessors) from another package, the
severity is only NOTE. But if the S4 object is defined in your
package, it’s mandatory to write accessors for it and to use
them (instead of direct slot access) in all vignette and example
code (NOTE).Can be disabled with --no-check-function-len.
Checking function lengths…
BiocCheck prints an informative message about the length (in lines)
of your five longest functions (this includes functions in your R
directory and in evaluated man page and vignette examples).
If there are functions longer than 50 lines, BiocCheck outputs (NOTE).
You may want to consider breaking up long functions into smaller ones. This is
a basic refactoring technique that results in code that’s easier to
read, debug, test, reuse, and maintain.
Can be disabled with --no-check-man-doc.
Checking man page documentation…
It can be handy to generate man page skeletons with prompt() and/or
RStudio. These skeletons contain comments that look like this:
%% ~~ A concise (1-5 lines) description of the dataset. ~~BiocCheck asks you to remove such comments (NOTE).
Every man page must have a non-empty \value section. (ERROR)
man page examples examples
Checking exported objects have runnable examples…
BiocCheck looks at all man pages which document exported objects and
lists the ones that don’t contain runnable examples (either because
there is no examples section or because its examples are tagged with
dontrun or donttest). Runnable examples are a key part of literate
programming and help ensure that your code does what you say it does.
ERROR).BiocCheck lists the missing
ones and asks you to add runnable examples to them (NOTE).dontrun or donttest. Use of these functions is not
recommended and shoud be justified (NOTE).Can be disabled with --no-check-news.
Checking package NEWS…
BiocCheck looks to see if there is a valid NEWS file either in the ‘inst’
directory or in the top-level directory of your package, and checks whether it
is properly formatted (NOTE).
The location and format of the NEWS file must be consistent with
?news. Meaning the file can be one of the following four options:
inst/NEWS.Rd./NEWS.md./NEWSinst/NEWSNEWS files are a good way to keep users up-to-date on changes to your
package. Excerpts from properly formatted NEWS files will be included
in Bioconductor release announcements to tell users what has changed
in your package in the last release. In order for this to happen, your
NEWS file must be formatted in a specific way; you may want to
consider using an inst/NEWS.Rd file instead as the format is more
well-defined. Malformatted NEWS file outputs WARNING.
More information on NEWS files is available in the help topic ?news.
Can be disabled with --no-check-unit-tests.
Checking unit tests…
We strongly recommend unit tests, though we do not at present require them. For more on what unit tests are, why they are helpful, and how to implement them, read our Unit Testing HOWTO.
At present we just check to see whether unit tests are present, and if not,
urge you to add them (NOTE).
Checking skip_on_bioc() in tests…
Can be disabled with --no-check-skip-bioc-tests.
Finds flag for skipping tests in the bioconductor environment (NOTE)
Can be disabled with --no-check-formatting.
Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and vignette source…
There is no 100% correct way to format code. These checks adhere to the
Bioconductor Style Guide (NOTE).
We think it’s important to avoid very long lines in code. Note that some text editors do not wrap text automatically, requiring horizontal scrolling in order to read it. Also note that R syntax is very flexible and whitespace can be inserted almost anywhere in an expression, making it easy to break up long lines.
These checks are run against not just R code, but the DESCRIPTION and NAMESPACE files as well as man pages and vignette source files. All of these files allow long lines to be broken up.
The output of this check includes the first 6 offending lines of code;
see more with BiocCheck:::checkFormatting("path/to/YourPackage", nlines=Inf).
There is a helpful package formatR that can be used for formatting of R code to particular coding standards.
Checking if package already exists in CRAN…
This can be disabled with the --no-check-CRAN option. A package with the same
name (case differences are ignored) cannot exist in CRAN (ERROR).
Checking if new package already exists in Bioconductor…
Only run if the --new-package flag is turned on. A package
with the same name (case differences are ignored) cannot exist in
Bioconductor (ERROR).
Checking for bioc-devel mailing list subscription…
This only applies if BiocCheck is run on the Bioconductor build
machines, because this step requires special authorization. This can be disabled
with the --no-check-bioc-help option.
Checking for support site registration…
Check that the package maintainer is register at our
support site using the same email address that is in the
Maintainer field of their package DESCRIPTION file (ERROR).
This can be disabled with the --no-check-bioc-help option.
The main place people ask questions about Bioconductor packages is the support site. Please register and then optionally include your (lowercased) package name in the list of watched tags. When a question is asked and tagged with your package name, you’ll get an email. (If you don’t add your package to the list of watched tags, this will be automatically done for you).
BiocCheckGitCloneBiocCheckGitClone provides a few additional Bioconductor package checks that
can only should be run on a open source directory (raw git clone) NOT a
tarball. Reporting similarly in three categories as discussed above:
ERROR.
WARNING.
NOTE.
BiocCheckGitCloneMost commonly you will use BiocCheckGitClone from your operating system command line, as
R CMD BiocCheckGitClone packageWhere package is a directory containing an R package.
BiocCheckGitClone can also be run interactively:
library(BiocCheck)
BiocCheckGitClone("packageDir")BiocCheckGitClonePlease see previous Installing BiocCheck section.
BiocCheckGitClone outputActual BiocCheckGitClone output is shown below in bold.
Checking valid files
There are a number of files that should not be git tracked. This check notifies
if any of these files are present (ERROR)
The current list of files checked is as follows:
hidden_file_ext = c(".renviron", ".rprofile", ".rproj", ".rproj.user",
".rhistory", ".rapp.history",
".o", ".sl", ".so", ".dylib",
".a", ".dll", ".def",
".ds_store", "unsrturl.bst",
".log", ".aux",
".backups", ".cproject", ".directory",
".dropbox", ".exrc", ".gdb.history",
".gitattributes", ".gitmodules",
".hgtags",
".project", ".seed", ".settings", ".tm_properties")These files may be included in your personal directories but should be added to
a .gitignore file so they are not git tracked.