BiocCheck SummaryBiocCheckBiocCheck be runBiocCheckBiocCheck outputBiocCheckGitCloneBiocCheckGitCloneBiocCheckGitCloneBiocCheckGitClone outputBiocCheckBiocCheck Summarylibrary(BiocCheck)BiocCheck 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.)BiocCheckBiocCheck is meant to run within R on a directory containing an R package, or
a source tarball (.tar.gz file):
BiocCheck("<packageDirOrTarball>")BiocCheck takes options which can be seen with ?BioCheck.
Note that the --new-package option is turned on in the Single Package
Builder (SPB) during the new package submission process.
BiocCheck be runBiocCheck should always be run after 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
GitHub Actions,
a continuous integration system on GitHub. This service allows automatic
testing of R packages in a controlled build environment.
See the biocthis package for more details.
BiocCheckBiocCheck should be installed as follows:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("BiocCheck")BiocCheck outputActual BiocCheck output is shown below in bold.
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.
Checking for ‘LazyData: true’ usage…
For packages that include data, we recommend not including LazyData: TRUE.
This rarely proves to be a good thing. In our experience it only slows down
the loading of packages with large data (NOTE).
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)99 ‘y’ version in the x.y.z versioning scheme
(ERROR). Package versions starting with a non-zero value will
get flagged with a warning. Typical new package submissions
start with a zero ‘x’ version (e.g., 0.99.*; WARNING). This
is only done if the --new-package option is supplied. An ‘x’ nonzero will
only be accepted if the package was pre-released or published under such a
case.ERROR).Depends: field of your
DESCRIPTION file, BiocCheck checks to make sure that the R
version specified matches the version currently used in
Bioconductor. This helps to prevent mixing of Bioconductor release and
devel versions (esp. when R versions differ) which is a frequent source of
confusion and errors (NOTE).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. Checks inspect both
package-wide files and data files found in the data, inst/extdata, and
data-raw folders. (WARNING)
It may be necessary to remove large files from your Git history; see Remove Large Data Files and Clean Git Tree
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…
Checking for blank lines in DESCRIPTION…
Checks to make sure there are no blank lines in the DESCRIPTION
file (ERROR).
Checking if DESCRIPTION is well formatted…
Checks if the DESCRIPTION can be parsed with read.dcf (ERROR)
Checking Description: field length… Checks that the Description field in the DESCRIPTION file has a minimum
WARNING if less than 50)WARNING if less than 20)NOTE if less than 3)Checking for whitespace in DESCRIPTION field names…
Checks to make sure there is no whitespace in DESCRIPTION file field
names (ERROR).
Checking that Package field matches dir/tarball name…
Checks to make sure that Package field of DESCRIPTION file matches
directory or tarball name (ERROR).
Checking for Version field…
Checks to make sure a Version field is present in the DESCRIPTION
file (ERROR).
Checking for valid maintainer…
Checks to make sure the DESCRIPTION file has a valid Authors@R field which
resolves to a valid Maintainer (ERROR).
A valid Authors@R field consists of:
person.cre (creator) role.family or given name defined.NOTE if not.Suggests that the maintainer provide an ORCID iD in the Authors@R
field as an argument in the person function, e.g., comment = c(ORCID = ...)
(NOTE).
ERROR). Licenses are compared to the
database provided at file.path(R.home("share)", "licenses", "license.db")). Licenses not listed in the database are flagged
with a NOTE indicating that restrictive use status cannot be
determined. A NOTE is also generated if the License: field is
malformed, or the database cannot be located.== in the DESCRIPTION file (ERROR).NOTE).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).
.Rbuildignore file (ERROR).<package_name>.BiocCheck folder byproduct when running BiocCheck(".")
locally does not get included in the package directory (ERROR).R CMD build; therefore, inst/doc folder is not needed
(ERROR).Can be disabled with --no-check-vignettes.
Checking vignette directory…
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)BiocInstaller code (WARNING)sessionInfo() or session_info() for
reproducibility (NOTE).ERROR).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).
Single colon typos are checked for when a user inputs ‘package:function’
instead of using double colons (‘::’) to import a function (ERROR).
Users should not download data from external hosting platforms. This
means avoiding references to major platforms such as GitHub, GitLab,
and BitBucket. For the same reason we do not import GitHub packages,
external data can be unstable and not well maintained. Maintainers
should re-use data already available in Bioconductor or contribute
an ExperimentHub, AnnotationHub or similar package (ERROR).
A package should not download files at the time of loading or attaching
i.e., using library. Using download.file and download should be avoided
and when found, an ERROR will be emitted.
paste and paste0 function calls within signaling functions such as
message, warning, and stop are redundant and should be avoided
(NOTE). paste calls with the collapse argument are ignored.
When notifying users, message should be used. When cat and print are
used, users will get a note saying that these should only be used in show
methods for classes (NOTE).
message, warn*, and error keywords should not be included in
signal condition functions: message, warning, and stop. This is
redundant and should be avoided (NOTE).
It is favorable to use the assignment arrow (‘<-’) over the equals assignment
(‘=’) for clarity in the code and legibility. Any use of the = will be
flagged with a 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 membership checks with class() / is() and == / !=.
Developers should use is(x, 'class') for S4 classes. (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.
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).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).install() calls is bad practice. A
separation between analysis and configuration tasks keeps code
modular and reproducible (ERROR).<<- is bad practice. It can over-write
user-defined symbols, and introduces non-linear paths of evaluation
that are difficult to debug (NOTE).Sys.setenv function (ERROR).suppressWarnings and suppressMessages is
problematic as it usually indicates a larger underlying issue with
the fragility of the package codebase (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. (WARNING)
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). If exception is made the
recommended usage is to use donttest over dontrun (NOTE) as donttest
requires valid R code.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 are several helpful packages that can be used for formatting of
R code to particular coding standards such as formatR and
styler as well as the “Reformat code” button in
RStudio Desktop. Each solution has its advantages, though
styler works with roxygen2 examples and is actively
maintained. You can re-format your code using styler as shown
below:
## Install styler if necessary
if (!requireNamespace("styler", quietly = TRUE)) {
install.packages("styler")
}
## Automatically re-format the R code in your package
styler::style_pkg(transformers = styler::tidyverse_style(indent_by = 4))If you are
working with RStudio Desktop use also the “Reformat code”
button which will help you break long lines of code. Alternatively,
use formatR, though beware that it can break valid R code
involving both types of quotation marks (" and ') and does not
support re-formatting roxygen2 examples. In general,
it is best to version control your code before applying any
automatic re-formatting solutions and implement unit tests to
verify that your code runs as intended after you re-format your code.
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 on CRAN. Packages
submitted to Bioconductor must be removed from CRAN before the next
Bioconductor release (WARNING).
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 include your package name in the list of watched tags. When a question is asked and tagged with your package name, you’ll get an email.
Package name is in support site watched tags is now a requirement.
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.
BiocCheckGitCloneBiocCheckGitClone is meant to run within R on a directory containing an R package:
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 are given by this internal constant:
BiocCheck:::.HIDDEN_FILE_EXTS## [1] ".renviron" ".rprofile" ".rproj" ".rproj.user"
## [5] ".rhistory" ".rapp.history" ".o" ".sl"
## [9] ".so" ".dylib" ".a" ".dll"
## [13] ".def" ".ds_store" "unsrturl.bst" ".log"
## [17] ".aux" ".backups" ".cproject" ".directory"
## [21] ".dropbox" ".exrc" ".gdb.history" ".gitattributes"
## [25] ".gitmodules" ".hgtags" ".project" ".seed"
## [29] ".settings" ".tm_properties" ".rdata"These files may be included in your personal directories but should be added to
a .gitignore file so they are not Git tracked.
Checking DESCRIPTION
Default R CMD build behavior will format the DESCRIPTION file; After this occurs, it is hard to determine certain aspects of the original DESCRIPTION file. An example would be how the Authors and Maintainers are specified. The DESCRIPTION file is therefore checked in its raw original form.
Checking if DESCRIPTION is well formatted
The DESCRIPTION file must be properly formatted and able to be read in with
read.dcf() in order to function properly on the Bioconductor build
machines. This check attempts to read.dcf("DESCRIPTION") and throws an ERROR
if mal-formatted. (ERROR)
Checking for valid maintainer
While in the past using the Author and Maintainer fields were acceptable, R
has moved towards using the Authors@R standard for listing package
contributors. This checks that Authors@R is utilized and that there are no
instances of Author or Maintainer in the DESCRIPTION (ERROR)
Checking that CITATION file is correctly formatted
BiocCheck tries to read the provided CITATION file (i.e. not the one
automatically generated by each package) with readCitationFile() - this is
expected to be in the INST folder (NOTE). readCitationFile() needs to work
properly without the package being installed. Most common causes of failure
occur when trying to use helper functions like packageVersion() or packageDate()
instead of using meta\(Version or meta\)Date. See R documentation for more
information.
Here is an example of a formatted CITATION file. See the GenomicRanges
package CITATION file for details.
library(utils)
readCitationFile(
system.file("CITATION", package = "GenomicRanges")
)## Lawrence M, Huber W, Pag\`es H, Aboyoun P, Carlson M, et al. (2013)
## Software for Computing and Annotating Genomic Ranges. PLoS Comput Biol
## 9(8): e1003118. doi:10.1371/journal.pcbi.1003118
##
## A BibTeX entry for LaTeX users is
##
## @Article{,
## title = {Software for Computing and Annotating Genomic Ranges},
## author = {Michael Lawrence and Wolfgang Huber and Herv\'e Pag\`es and Patrick Aboyoun and Marc Carlson and Robert Gentleman and Martin Morgan and Vincent Carey},
## year = {2013},
## journal = {{PLoS} Computational Biology},
## volume = {9},
## issue = {8},
## doi = {10.1371/journal.pcbi.1003118},
## url = {http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003118},
## }BiocCheckContributions to BiocCheck are welcome and encouraged through pull requests.
Please adhere to the Pull Request template when submitting your contributions.
sessionInfo()## R version 4.3.2 Patched (2023-11-13 r85521)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.3 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.18-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: America/New_York
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] BiocCheck_1.38.2 BiocStyle_2.30.0
##
## loaded via a namespace (and not attached):
## [1] rappdirs_0.3.3 sass_0.4.8 utf8_1.2.4
## [4] generics_0.1.3 bitops_1.0-7 RSQLite_2.3.5
## [7] digest_0.6.34 magrittr_2.0.3 evaluate_0.23
## [10] bookdown_0.37 fastmap_1.1.1 blob_1.2.4
## [13] jsonlite_1.8.8 graph_1.80.0 DBI_1.2.1
## [16] BiocManager_1.30.22 httr_1.4.7 fansi_1.0.6
## [19] stringdist_0.9.12 XML_3.99-0.16.1 httr2_1.0.0
## [22] codetools_0.2-19 jquerylib_0.1.4 cli_3.6.2
## [25] rlang_1.1.3 dbplyr_2.4.0 Biobase_2.62.0
## [28] bit64_4.0.5 cachem_1.0.8 yaml_2.3.8
## [31] BiocBaseUtils_1.4.0 parallel_4.3.2 tools_4.3.2
## [34] memoise_2.0.1 dplyr_1.1.4 filelock_1.0.3
## [37] BiocGenerics_0.48.1 RUnit_0.4.32 curl_5.2.0
## [40] vctrs_0.6.5 R6_2.5.1 stats4_4.3.2
## [43] biocViews_1.70.0 BiocFileCache_2.10.1 lifecycle_1.0.4
## [46] RBGL_1.78.0 bit_4.0.5 pkgconfig_2.0.3
## [49] bslib_0.6.1 pillar_1.9.0 glue_1.7.0
## [52] xfun_0.41 tibble_3.2.1 tidyselect_1.2.0
## [55] knitr_1.45 htmltools_0.5.7 rmarkdown_2.25
## [58] compiler_4.3.2 RCurl_1.98-1.14