8  Tools

The behavior of R CMD check can be controlled through a variety of command line arguments and environment variables.

There is an internal --install=value command line argument not shown by R CMD check --help, with possible values

check:file

Assume that installation was already performed with stdout/stderr to file, the contents of which need to be checked (without repeating the installation). This is useful for checks applied by repository maintainers: it reduces the check time by the installation time given that the package has already been installed. In this case, one also needs to specify where the package was installed to using command line option --library.

fake

Fake installation, and turn off the run-time tests.

skip

Skip installation, e.g., when testing recommended packages bundled with R.

no

The same as --no-install : turns off installation and the tests which require the package to be installed.

The following environment variables can be used to customize the operation of check: a convenient place to set these is the check environment file (default, ~/.R/check.Renviron).

_R_CHECK_ALL_NON_ISO_C_

If true, do not ignore compiler (typically GCC) warnings about non ISO C code in system headers. Note that this may also show additional ISO C++ warnings. Default: false.

_R_CHECK_FORCE_SUGGESTS_

If true, give an error if suggested packages are not available. Default: true (but false for CRAN submission checks).

_R_CHECK_RD_CONTENTS_

If true, check Rd files for auto-generated content which needs editing, and missing argument documentation. Default: true.

_R_CHECK_RD_LINE_WIDTHS_

If true, check Rd line widths in usage and examples sections. Default: false (but true for CRAN submission checks).

_R_CHECK_RD_STYLE_

If true, check whether Rd usage entries for S3 methods use the full function name rather than the appropriate \method markup. Default: true.

_R_CHECK_RD_XREFS_

If true, check the cross-references in .Rd files. Default: true.

_R_CHECK_SUBDIRS_NOCASE_

If true, check the case of directories such as R and man. Default: true.

_R_CHECK_SUBDIRS_STRICT_

Initial setting for --check-subdirs. Default: default (which checks only tarballs, and checks in the src only if there is no configure file).

_R_CHECK_USE_CODETOOLS_

If true, make use of the codetools package, which provides a detailed analysis of visibility of objects (but may give false positives). Default: true (if recommended packages are installed).

_R_CHECK_USE_INSTALL_LOG_

If true, record the output from installing a package as part of its check to a log file (00install.out by default), even when running interactively. Default: true.

_R_CHECK_VIGNETTES_NLINES_

Maximum number of lines to show from the bottom of the output when reporting errors in running or re-building vignettes. ( Value 0 means all lines will be shown.) Default: 10 for running, 25 for re-building.

_R_CHECK_CODOC_S4_METHODS_

Control whether codoc() testing is also performed on S4 methods. Default: true.

_R_CHECK_DOT_INTERNAL_

Control whether the package code is scanned for .Internal calls, which should only be used by base (and occasionally by recommended) packages. Default: true.

_R_CHECK_EXECUTABLES_

Control checking for executable (binary) files. Default: true.

_R_CHECK_EXECUTABLES_EXCLUSIONS_

Control whether checking for executable (binary) files ignores files listed in the package’s BinaryFiles file. Default: true (but false for CRAN submission checks). However, most likely this package-level override mechanism will be removed eventually.

_R_CHECK_PERMISSIONS_

Control whether permissions of files should be checked. Default: true iff .Platform$OS.type == "unix".

_R_CHECK_FF_CALLS_

Allows turning off checkFF() testing. If set to registration, checks the registration information (number of arguments, correct choice of .C/.Fortran/.Call/.External) for such calls provided the package is installed. Default: true.

_R_CHECK_FF_DUP_

Controls checkFF(check_DUP) Default: true (and forced to be true for CRAN submission checks).

_R_CHECK_LICENSE_

Control whether/how license checks are performed. A possible value is maybe (warn in case of problems, but not about standardizable non-standard license specs). Default: true.

_R_CHECK_RD_EXAMPLES_T_AND_F_

Control whether check_T_and_F() also looks for “bad” (global) T/F uses in examples. Off by default because this can result in false positives.

_R_CHECK_RD_CHECKRD_MINLEVEL_

Controls the minimum level for reporting warnings from checkRd. Default: -1.

_R_CHECK_XREFS_REPOSITORIES_

If set to a non-empty value, a space-separated list of repositories to use to determine known packages. Default: empty, when the CRAN and Bioconductor repositories known to R is used.

_R_CHECK_SRC_MINUS_W_IMPLICIT_

Control whether installation output is checked for compilation warnings about implicit function declarations (as spotted by GCC with command line option -Wimplicit-function-declaration, which is implied by -Wall). NB: implicit function declarations are errors in some recent C compilers, including Apple clang. Default: true from R 4.2.0, previously false.

_R_CHECK_SRC_MINUS_W_UNUSED_

Control whether installation output is checked for compilation warnings about unused code constituents (as spotted by GCC with command line option -Wunused, which is implied by -Wall). Default: true.

_R_CHECK_WALL_FORTRAN_

Control whether gfortran 4.0 or later -Wall warnings are used in the analysis of installation output. Default: false, even though the warnings are justifiable.

_R_CHECK_ASCII_CODE_

If true, check R code for non-ascii characters. Default: true.

_R_CHECK_ASCII_DATA_

If true, check data for non-ascii characters. En route, checks that all the datasets can be loaded and that their components can be accessed. Default: true.

_R_CHECK_COMPACT_DATA_

If true, check data for ascii and uncompressed saves, and also check if using bzip2 or xz compression would be significantly better. Default: true.

_R_CHECK_SKIP_ARCH_

Comma-separated list of architectures that will be omitted from checking in a multi-arch setup. Default: none.

_R_CHECK_SKIP_TESTS_ARCH_

Comma-separated list of architectures that will be omitted from running tests in a multi-arch setup. Default: none.

_R_CHECK_SKIP_EXAMPLES_ARCH_

Comma-separated list of architectures that will be omitted from running examples in a multi-arch setup. Default: none.

_R_CHECK_VC_DIRS_

Should the unpacked package directory be checked for version-control directories (CVS, .svn …)? Default: true for tarballs.

_R_CHECK_PKG_SIZES_

Should du be used to find the installed sizes of packages? R CMD check does check for the availability of du. but this option allows the check to be overruled if an unsuitable command is found (including one that does not respect the -k flag to report in units of 1Kb, or reports in a different format – the GNU, macOS and Solaris du commands have been tested). Default: true if du is found.

_R_CHECK_PKG_SIZES_THRESHOLD_

Threshold used for _R_CHECK_PKG_SIZES_ (in Mb). Default: 5

_R_CHECK_DOC_SIZES_

Should qpdf be used to check the installed sizes of PDFs? Default: true if qpdf is found.

_R_CHECK_DOC_SIZES2_

Should gs be used to check the installed sizes of PDFs? This is slower than (and in addition to) the previous check, but does detect figures with excessive detail (often hidden by over-plotting) or bitmap figures with too high a resolution. Requires that R_GSCMD is set to a valid program, or gs (or on Windows, gswin32.exe or gswin64c.exe) is on the path. Default: false (but true for CRAN submission checks).

_R_CHECK_ALWAYS_LOG_VIGNETTE_OUTPUT_

By default the output from running the R code in the vignettes is kept only if there is an error. This also applies to the build_vignettes.log log from the re-building of vignettes. Default: false.

_R_CHECK_CLEAN_VIGN_TEST_

Should the vign_test directory be removed if the test is successful? Default: true.

_R_CHECK_REPLACING_IMPORTS_

Should warnings about replacing imports be reported? These sometimes come from auto-generated NAMESPACE files in other packages, but most often from importing the whole of a namespace rather than using importFrom. Default: true.

_R_CHECK_UNSAFE_CALLS_

Check for calls that appear to tamper with (or allow tampering with) already loaded code not from the current package: such calls may well contravene CRAN policies. Default: true.

_R_CHECK_TIMINGS_

Optionally report timings for installation, examples, tests and running/re-building vignettes as part of the check log. The format is [as/bs] for the total CPU time (including child processes) a and elapsed time b, except on Windows, when it is [bs]. In most cases timings are only given for OK checks. Times with an elapsed component over 10 mins are reported in minutes (with abbreviation m). The value is the smallest numerical value in elapsed seconds that should be reported: non-numerical values indicate that no report is required, a value of 0 that a report is always required. Default: "". (10 for CRAN checks unless set in the environment.)

_R_CHECK_EXAMPLE_TIMING_THRESHOLD_

If timings are being recorded, set the threshold in seconds for reporting long-running examples (either user+system CPU time or elapsed time). Default: "5".

_R_CHECK_EXAMPLE_TIMING_CPU_TO_ELAPSED_THRESHOLD_

For checks with timings enabled, report examples where the ratio of CPU time to elapsed time exceeds this threshold (and the CPU time is at least one second). This can help detect the simultaneous use of multiple CPU cores. Default: NA.

_R_CHECK_TEST_TIMING_CPU_TO_ELAPSED_THRESHOLD_

Report for running an individual test if the ratio of CPU time to elapsed time exceeds this threshold (and the CPU time is at least one second). Not supported on Windows. Default: NA.

_R_CHECK_VIGNETTE_TIMING_CPU_TO_ELAPSED_THRESHOLD_

Report if when running/re-building vignettes (individually or in aggregate) the ratio of CPU time to elapsed time exceeds this threshold (and the CPU time is at least one second). Not supported on Windows. Default: NA.

_R_CHECK_CODETOOLS_PROFILE_

A string with comma-separated name=value pairs (with value a logical constant) giving additional arguments for the codetools functions used for analyzing package code. E.g., use _R_CHECK_CODETOOLS_PROFILE_="suppressLocalUnused=FALSE" to turn off suppressing warnings about unused local variables. Default: no additional arguments, corresponding to using skipWith = TRUE, suppressPartialMatchArgs = FALSE and suppressLocalUnused = TRUE.

_R_CHECK_CRAN_INCOMING_

Check whether package is suitable for publication on CRAN. Default: false, except for CRAN submission checks.

_R_CHECK_CRAN_INCOMING_REMOTE_

Include checks that require remote access among the above. Default: same as _R_CHECK_CRAN_INCOMING_

_R_CHECK_XREFS_USE_ALIASES_FROM_CRAN_

When checking anchored Rd xrefs, use Rd aliases from the CRAN package web areas in addition to those in the packages installed locally. Default: false.

_R_SHLIB_BUILD_OBJECTS_SYMBOL_TABLES_

Make the checks of compiled code more accurate by recording the symbol tables for objects (.o files) at installation in a file symbols.rds. (Only currently supported on Linux, Solaris, macOS, Windows and FreeBSD.) Default: true.

_R_CHECK_CODE_ASSIGN_TO_GLOBALENV_

Should the package code be checked for assignments to the global environment? Default: false (but true for CRAN submission checks).

_R_CHECK_CODE_ATTACH_

Should the package code be checked for calls to attach()? Default: false (but true for CRAN submission checks).

_R_CHECK_CODE_DATA_INTO_GLOBALENV_

Should the package code be checked for calls to data() which load into the global environment? Default: false (but true for CRAN submission checks).

_R_CHECK_DOT_FIRSTLIB_

Should the package code be checked for the presence of the obsolete function .First.lib()? Default: false (but true for CRAN submission checks).

_R_CHECK_DEPRECATED_DEFUNCT_

Should the package code be checked for the presence of recently deprecated or defunct functions (including completely removed functions). Also for platform-specific graphics devices. Default: false (but true for CRAN submission checks).

_R_CHECK_SCREEN_DEVICE_

If set to warn, give a warning if examples etc open a screen device. If set to stop, give an error. Default: empty (but stop for CRAN submission checks).

_R_CHECK_WINDOWS_DEVICE_

If set to stop, give an error if a Windows-only device is used in example etc. This is only useful on Windows: the devices do not exist elsewhere. Default: empty (but stop for CRAN submission checks on Windows).

_R_CHECK_TOPLEVEL_FILES_

Report on top-level files in the package sources that are not described in ‘Writing R Extensions’ nor are commonly understood (like ChangeLog). Variations on standard names (e.g. COPYRIGHT) are also reported. Default: false (but true for CRAN submission checks).

_R_CHECK_GCT_N_

Should the --use-gct use gctorture2(n) rather than gctorture(TRUE)? Use a positive integer to enable this. Default: 0.

_R_CHECK_LIMIT_CORES_

If set, check the usage of too many cores in package parallel. If set to warn gives a warning, to false or FALSE the check is skipped, and any other non-empty value gives an error when more than 2 children are spawned. Default: unset (but TRUE for CRAN submission checks).

_R_CHECK_CODE_USAGE_VIA_NAMESPACES_

If set, check code usage (via codetools) directly on the package namespace without loading and attaching the package and its suggests and enhances. Default: true (and true for CRAN submission checks).

_R_CHECK_CODE_USAGE_WITH_ONLY_BASE_ATTACHED_

If set, check code usage (via codetools) with only the base package attached. Default: true.

_R_CHECK_EXIT_ON_FIRST_ERROR_

If set to a true value, the check will exit on the first error. Default: false.

_R_CHECK_S3_METHODS_NOT_REGISTERED_

If set to a true value, report (apparent) S3 methods exported but not registered. Default: true.

_R_CHECK_OVERWRITE_REGISTERED_S3_METHODS_

If set to a true value, report already registered S3 methods in base/recommended packages which are overwritten when this package’s namespace is loaded. Default: false (but true for CRAN submission checks).

_R_CHECK_TESTS_NLINES_

Number of trailing lines of test output to reproduce in the log. If 0 all lines except the R preamble are reproduced. Default: 13.

_R_CHECK_NATIVE_ROUTINE_REGISTRATION_

If set to a true value, report if the entry points to register native routines and to suppress dynamic search are not found in a package’s DLL. (NB: this requires system command nm to be on the PATH. On Windows, objdump.exe is first searched for in compiler toolchain specified via Makeconf (can be customized by environment variable BINPREF). If not found there, it must be on the PATH. On Unix this would be normal when using a package with compiled code (which are the only ones this checks), but Windows’ users should check. Default: false (but true for CRAN submission checks).

_R_CHECK_NO_STOP_ON_TEST_ERROR_

If set to a true value, do not stop running tests after first error (as if command line option --no-stop-on-test-error had been given). Default: false (but true for CRAN submission checks).

_R_CHECK_PRAGMAS_

Run additional checks on the pragmas in C/C++ source code and headers. Default: false (but true for CRAN submission checks).

_R_CHECK_COMPILATION_FLAGS_

If the package is installed and has C/C++/Fortran code, check the install log for non-portable flags (for example those added to src/Makevars during configuration). Currently -W flags are reported, except -Wall, -Wextra and -Weverything, and flags which appear to be attempts to suppress warnings are highlighted. See ‘Writing R Extensions’ for the rationale of this check (and why even -Werror is unsafe).

Environment variable _R_CHECK_COMPILATION_FLAGS_KNOWN_ can be set to a space-separated set of flags which come from the R build used for testing (flags such as -Wall and -Wextra are already known). For example, for CRAN builds of R >= 4.0.0 on macOS one could use

_R_CHECK_COMPILATION_FLAGS_KNOWN_="-mmacosx-version-min=10.13" 

Default: unset.

_R_CHECK_R_DEPENDS_

Check that any dependence on R is not on a recent patch-level version such as R (>= 3.3.3) since blocking installation of a package will also block its reverse dependencies. Possible values "note", "warn" and logical values (where currently true values are equivalent to "note"). Default: false (but "warn" for --as-cran).

_R_CHECK_SERIALIZATION_

Check that serialized R objects in the package sources were serialized with version 2 and there is no dependence on R >= 3.5.0. (Version 3 is in use as from R 3.5.0 but should only be used when necessary.) Default: false (but true for CRAN submission checks).

_R_CHECK_R_ON_PATH_

This checks if the package attempts to use R or Rscript from the path rather than that under test. It does so by putting scripts at the head of the path which print a message and fail. Default: false (but true for CRAN submission checks).

_R_CHECK_PACKAGES_USED_IN_TESTS_USE_SUBDIRS_

If set to a true value, also check the R code in common unit test subdirectories of tests for undeclared package dependencies. Default: false (but true for CRAN submission checks).

_R_CHECK_SHLIB_OPENMP_FLAGS_

Check correct and portable use of SHLIB_OPENMP_*FLAGS in src/Makevars (and similar). Default: false (but true for CRAN submission checks).

_R_CHECK_CONNECTIONS_LEFT_OPEN_

When checking examples, check for each example if connections are left open: if any are found, this is reported with a fatal error. NB: ‘connections’ includes most use of files and any parallel clusters which have not be stopped by stopCluster(). Default: false (but true for CRAN submission checks).

_R_CHECK_FUTURE_FILE_TIMESTAMPS_

Check if any of the input files has a timestamp in the future (and to do so, checks that the system clock is correct to within 5 minutes). Default: false (but true for CRAN submission checks).

_R_CHECK_LENGTH_1_CONDITION_

No longer in use: conditions of length greater than one in if or while statements are now an error.

_R_CHECK_VIGNETTES_SKIP_RUN_MAYBE_

Should running the R code in the vignettes be skipped if vignette outputs are to be rebuilt (which will involve running that code). Default: false (but true for CRAN checking)

_R_CHECK_BUILD_VIGNETTES_SEPARATELY_

Prior to R 3.6.0, re-building the vignette outputs was done in a single R session which allowed accidental reliance of one vignette on another (for example, in the loading of packages). The current default is to use a separate session for each vignette; this option allows testing the older behaviour, Default: true

_R_CHECK_SYSTEM_CLOCK_

As part of the ‘checking for future file timestamps’ enabled by --as-cran, check the system clock against an external clock to catch errors such as the wrong day or even year. Not necessary on systems doing repeated checks. Default: true (but false for CRAN checking)

_R_CHECK_AUTOCONF_

For packages with a configure file generated by GNU autoconf and either configure.ac or configure,.in, check that autoreconf can, if available, be run in a copy of the sources (this will detect missing source files and report autoconf warnings). Environment variable AUTORECONf controls the command used: it can give the full path to autoreconf (without spaces) and can include flags such as --warnings=obsolete (which is added for autoreconf version 2.68 or 2.69 and is the default for later versions). Default: false (but true for CRAN submission checks).

_R_CHECK_DATALIST_

Check whether file data/datalist is out-of-date. Default: false (but true for CRAN submission checks).

_R_CHECK_THINGS_IN_CHECK_DIR_

Check and report at the end of the check run if files have been left in the check directory. Default: false (but true for CRAN submission checks).

_R_CHECK_THINGS_IN_TEMP_DIR_

Check and report at the end of tthe check run if files would have been left in the temporary directory (usually /tmp on a Unix-alike). It does this by setting the environment variable TEMPDIR to a subdirectory of the R session directory for the check process: if any files or directories are left there they are removed. Since some of these might be out of the user’s control, environment variable _R_CHECK_THINGS_IN_TEMP_DIR_EXCLUDE_ can specify an (extended regex) pattern of file paths not to be reported – CRAN uses ^ompi. for directories left behind by OpenMPI. There are rare instances where TEMPDIR is not respected and so files are left in /tmp (and not reported, but see the next item): one example is /tmp/boost_interprocess on some OSes. Default: false (but true for CRAN submission checks).

_R_CHECK_THINGS_IN_OTHER_DIRS_

Check and report at the end of the check run if new files or directories are created in a selected set of directories during the check run. (This is confined to files owned by the user running the check process.) Currently the directories monitored are the home directory, /tmp (excluding RtmpXXXXXX dirs), /dav/shm, ~/.cache (recursively) and ~/.local/share (recursively) or their equivalents on Windows and macOS (the directories in which the default settings for tools::R_user_dir() use a R subdirectory). Additional directories can be specified in environment variable _R_CHECK_THINGS_IN_OTHER_DIRS_XTRA_, separated by semicolons. Directories are reported with a trailing / on all platforms.

Environment variable _R_CHECK_THINGS_IN_OTHER_DIRS_EXCLUDE_ can specify an (extended regex) pattern of file paths not to be reported – this should match absolute file paths with home represented by ~. For example, on a Linux system

'^~/.cache/(mozilla/firefox|mesa_shader_cache)/'

matches cache directories used by Firefox and OpenGL (and their content). If the value starts with @ it is considered as a filepath which is read with each line treated as a pattern to be matched.

Note that other processes (include check runs in parallel) may create new files in these directories which will get reported. However, this optional check is very useful for narrowing down possible packages which are leaving behind unexpected files. Default: false

_R_CHECK_BASHISMS_

Check the top-level scripts configure (unless generated by autoconf) and cleanup for non-Bourne-shell code, using the Perl script checkbashisms if available. This includes reporting scripts using the non-portable #! /bin/bash. (Script checkbashisms is available in most Linux distributions in a package named either devscripts or devscripts-checkbashisms and from https://sourceforge.net/projects/checkbaskisms/files.) Default: false (but true for CRAN submission checks except on Windows).

_R_CHECK_ORPHANED_

Check if dependencies are orphaned packages. As from R 4.1.0 this checks strict dependencies recursively, so will report any orphaned packages which are needed to attach the package by library() as well as any orphaned packages which are suggested. Default: false (but true for CRAN submission checks).

_R_CHECK_EXCESSIVE_IMPORTS_

A positive integer. If set, give a NOTE if the number of imports from non-base packages exceed this threshold. Large numbers of imports make a package vulnerable to any of them becoming unavailable. Default: unset (but 20 for CRAN submission checks)

_R_CHECK_DONTTEST_EXAMPLES_

If true and examples are found with \donttest sections, the tests are run in one pass with these commented out and then in a second pass including the \donttest sections, (for the main architecture only). Only for the first pass are the results compared to any .Rout.save file and timings analysed. Overridden by --run-donttest. Default: false unless --as-cran is specified (which can be overridden by setting _R_CHECK_DONTTEST_EXAMPLES_=false).

_R_CHECK_XREFS_PKGS_ARE_DECLARED_

Check if packages used in ‘anchored’ cross-references in .Rd files (those of the form \link[pkg]{foo} and \link[pkg:bar]{foo}) are declared in the DESCRIPTION file and so these links can be checked. Default: false.

_R_CHECK_XREFS_MIND_SUSPECT_ANCHORS_

Check if package-anchored Rd cross-references are to files (and not aliases). Default: false.

_R_CHECK_BOGUS_RETURN_

If true and _R_CHECK_USE_CODETOOLS_ is also true, functions are scanned for use of return rather than return(). Default: false (but true for CRAN submission checks).

_R_CHECK_MATRIX_DATA_

By default, the check for a mismatch between the data length and the dimensions in a call to matrix gives a warning: setting this to a true value gives an error with a compact traceback. Default: false (but true for CRAN submission checks).

_R_CHECK_CODE_CLASS_IS_STRING_

Check if package code has if() condition which compare the class of an object to a string. See https://blog.r-project.org/2019/11/09/when-you-think-class.-think-again/ why this is a bad idea. Default: false (but true for CRAN submission checks).

_R_CHECK_RD_VALIDATE_RD2HTML_

Check the validity of the package HTML help pages using HTML Tidy (https://www.html-tidy.org/) (if a suitable version is available on the system path for executables or its path is specified by environment variable R_TIDYCMD). macOS users are advised to install 5.8.0 or later from https://binaries.html-tidy.org/. Default: false (but true for CRAN submission checks). --as-cran can be overridden by setting this variable to a false value.

_R_CHECK_RD_MATH_RENDERING_

Check whether HTML math rendering via KaTeX works (if package V8 is available). See https://blog.r-project.org/2022/04/08/enhancements-to-html-documentation/. Default: false (but true for CRAN submission checks).

_R_CHECK_NEWS_IN_PLAIN_TEXT_

Check whether news() can successfully read package news in plain text (file NEWS) format. Default: false (but true for CRAN submission checks).

_R_WIN_CHECK_INVALID_PARAMETERS_

Check whether arguments passed to the Windows C runtime are valid. When enabled and a C runtime function is called with an invalid parameter, R prints diagnostic information and unconditionally terminates. By default, R for Windows following MinGW-W64 default causes UCRT to ignore invalid parameters, but they may cause R to abort e.g. when R is embedded into applications built with a different compiler toolchain. One may set the value to "watson" for interactive debugging on Windows via _invoke_watson. Default: disabled.

_R_CHECK_BROWSER_NONINTERACTIVE_

If set to a true value, trap non-interactive debugger invocations. These are most likely caused by leftover browser() statements in package code. Default: unset (but true for CRAN submission checks).

The following variables control checks for undeclared/unconditional use of other packages. They work by setting up a temporary library directory and setting .libPaths() to just that and .Library, so are only effective if additional packages are installed somewhere other than .Library. The temporary library is populated by symbolic links1 to installed packages not also in .Library.

  • 1 under Windows, junction points, or copies if environment variable R_WIN_NO_JUNCTIONS has a non-empty value.

  • _R_CHECK_INSTALL_DEPENDS_

    If set to a true value and a test installation is to be done, this is done with a temporary library populated by all the Depends/Imports/LinkingTo packages. Default: false (but true for CRAN submission checks).

    Note that this is actually implemented in R CMD INSTALL, so it is available to those who first install recording to a log, then call R CMD check.

    _R_CHECK_SUGGESTS_ONLY_

    If set to a true value, running examples, tests and vignettes is done with a temporary library directory populated by all the Depends/Imports/Suggests packages. (As exceptions, packages in a VignetteBuilder field are always made available.) Default: false (but true for CRAN submission checks: some of the regular checks use true and some use false).

    _R_CHECK_DEPENDS_ONLY_

    As for _R_CHECK_SUGGESTS_ONLY_ but using only Depends/Imports (and the exceptions, including test-suite managers in Suggests). Default: false

    _R_CHECK_DEPENDS_ONLY_DATA_

    Apply _R_CHECK_DEPENDS_ONLY_ only to the check of loading from the data directory, so checks if any dataset depends on packages which are in Suggests or undeclared. Default: false (but true for CRAN submission checks)

    _R_CHECK_DEPENDS_ONLY_EXAMPLES_
    _R_CHECK_DEPENDS_ONLY_TESTS_
    _R_CHECK_DEPENDS_ONLY_VIGNETTES_

    : Apply _R_CHECK_DEPENDS_ONLY_ only to the checking of examples, tests or vignettes. These can be used on their own, or with a false value to override _R_CHECK_DEPENDS_ONLY_. Default: the value of _R_CHECK_DEPENDS_ONLY_ or false if that is unset.

    _R_CHECK_NO_RECOMMENDED_

    If set to a true value, augment the previous checks to make recommended packages unavailable unless declared (even if installed in .library). Default: false (but true for CRAN submission checks).

    This may give false positives on code which uses grDevices::densCols and stats:::.asSparse / stats:::.Diag as these invoke KernSmooth and Matrix respectively. (Those in stats are called from various contrasts functions if sparse = TRUE is used.)

    CRAN’s submission checks use something like

    _R_CHECK_CRAN_INCOMING_=TRUE
    _R_CHECK_CRAN_INCOMING_REMOTE_=TRUE
    _R_CHECK_VC_DIRS_=TRUE
    _R_CHECK_TIMINGS_=10
    _R_CHECK_INSTALL_DEPENDS_=TRUE
    _R_CHECK_SUGGESTS_ONLY_=TRUE
    _R_CHECK_NO_RECOMMENDED_=TRUE
    _R_CHECK_EXECUTABLES_EXCLUSIONS_=FALSE
    _R_CHECK_DOC_SIZES2_=TRUE
    _R_CHECK_CODE_ASSIGN_TO_GLOBALENV_=TRUE
    _R_CHECK_CODE_ATTACH_=TRUE
    _R_CHECK_CODE_DATA_INTO_GLOBALENV_=TRUE
    _R_CHECK_CODE_USAGE_VIA_NAMESPACES_=TRUE
    _R_CHECK_DOT_FIRSTLIB_=TRUE
    _R_CHECK_DEPRECATED_DEFUNCT_=TRUE
    _R_CHECK_REPLACING_IMPORTS_=TRUE
    _R_CHECK_SCREEN_DEVICE_=stop
    _R_CHECK_TOPLEVEL_FILES_=TRUE
    _R_CHECK_S3_METHODS_NOT_REGISTERED_=TRUE
    _R_CHECK_OVERWRITE_REGISTERED_S3_METHODS_=TRUE
    _R_CHECK_PRAGMAS_=TRUE
    _R_CHECK_COMPILATION_FLAGS_=TRUE
    _R_CHECK_R_DEPENDS_=warn
    _R_CHECK_SERIALIZATION_=TRUE
    _R_CHECK_R_ON_PATH_=TRUE
    _R_CHECK_PACKAGES_USED_IN_TESTS_USE_SUBDIRS_=TRUE
    _R_CHECK_SHLIB_OPENMP_FLAGS_=TRUE
    _R_CHECK_CONNECTIONS_LEFT_OPEN_=TRUE
    _R_CHECK_FUTURE_FILE_TIMESTAMPS_=TRUE
    _R_CHECK_LENGTH_1_CONDITION_=package:_R_CHECK_PACKAGE_NAME_,abort,verbose
    _R_CHECK_LENGTH_1_LOGIC2_=package:_R_CHECK_PACKAGE_NAME_,abort,verbose
    _R_CHECK_AUTOCONF_=true
    _R_CHECK_DATALIST_=true
    _R_CHECK_THINGS_IN_CHECK_DIR_=true
    _R_CHECK_THINGS_IN_TEMP_DIR_=true
    _R_CHECK_BASHISMS_=true
    _R_CLASS_MATRIX_ARRARY_=true
    _R_CHECK_ORPHANED_=true
    _R_CHECK_BOGUS_RETURN_=true
    _R_CHECK_MATRIX_DATA_=TRUE
    _R_CHECK_CODE_CLASS_IS_STRING_=true
    _R_CHECK_RD_VALIDATE_RD2HTML_=true
    _R_CHECK_RD_MATH_RENDERING_=true
    _R_CHECK_NEWS_IN_PLAIN_TEXT_=true
    _R_CHECK_BROWSER_NONINTERACTIVE_=true

    These are turned on by R CMD check --as-cran: the incoming checks also use

    _R_CHECK_FORCE_SUGGESTS_=FALSE

    since some packages do suggest other packages not available on CRAN or other commonly-used repositories.

    Several environment variables can be used to set ‘timeouts’: limits for the elapsed time taken by the sub-processes used for parts of the checks. A value of 0 indicates no limit, and is the default. Character strings ending in s, m or h indicate a number of seconds, minutes or hours respectively: other values are interpreted as a whole number of seconds (with invalid inputs being treated as no limit).

    _R_CHECK_ELAPSED_TIMEOUT_

    The default timeout for sub-processes not otherwise mentioned, and the default value for all except _R_CHECK_ONE_TEST_ELAPSED_TIMEOUT_. (This is also used by tools::check_packages_in_dir.)

    _R_CHECK_INSTALL_ELAPSED_TIMEOUT_

    Limit for when R CMD INSTALL is run by check.

    _R_CHECK_EXAMPLES_ELAPSED_TIMEOUT_

    Limit for running all the examples for one sub-architecture.

    _R_CHECK_ONE_TEST_ELAPSED_TIMEOUT_

    Limit for running one test for one sub-architecture. Default _R_CHECK_TESTS_ELAPSED_TIMEOUT_.

    _R_CHECK_TESTS_ELAPSED_TIMEOUT_

    Limit for running all the tests for one sub-architecture (and the default limit for running one test).

    _R_CHECK_ONE_VIGNETTE_ELAPSED_TIMEOUT_

    Limit for running the R code in one vignette, including for re-building each vignette separately.

    _R_CHECK_BUILD_VIGNETTES_ELAPSED_TIMEOUT_

    Limit for re-building all vignettes.

    _R_CHECK_PKGMAN_ELAPSED_TIMEOUT_

    Limit for each attempt at building the PDF package manual.

    Another variable which enables stricter checks is to set R_CHECK_CONSTANTS to 5. This checks that nothing2 changes the values of ‘constants’3 in R code. This is best used in conjunction with setting R_JIT_STRATEGY to 3, which checks code on first use (by default most code is only checked after byte-compilation on second use). Unfortunately these checks slow down checking of examples, tests and vignettes, typically two-fold but in the worst cases at least a hundred-fold.

  • 2 The usual culprits are calls to compiled code via .Call or .External which alter their arguments.

  • 3 things which the byte compiler assumes do not change, e.g. function bodies.

  • The following environment variables can be used to customize the operation of INSTALL.

    _R_INSTALL_LIBS_ONLY_FORCE_DEPENDS_IMPORTS_

    If true, give an error if installing only package libraries via --libs-only and some package imported or depended on is not available. Default: true (false only for special applications, which analyze native code of packages).

    Footnotes