devtools::check fails after use_catch() without (undocumented) fix #1235
Description
I got the somewhat unexpected result after the last update of testthat to 3.0.0 that R CMD CHECK failed for my package which uses Catch due to the new test methods for compiled code and the following line in particular:
testthat/R/test-compiled-code.R
Line 34 in 45a9c70
While this can be fixed by adding Suggests: xml2 to the DESCRIPTION file of my own package, this is undocumented and can only be discovered by getting the error or looking up the code directly. I suggest to either document this dependency in run_cpp_tests and adding a message to use_catch or placing xml2 again in the imports of testthat. As a user of the Catch-feature, the first approach seems a little unnatural to me as I am not using the xml2 package directly and it seems to be more of an implementation detail of testthat, but I understand that xml2 might be an unnecessary dependency for most testthat users.
Here is a reprex using the usethis workflow:
tmp <- tempdir()
setwd(tmp)
usethis::create_package("testcatch", open=FALSE)
#> ✓ Creating 'testcatch/'
#> ✓ Setting active project to '/private/var/folders/29/_qzzdhnn75780wtf8805n85w0000gn/T/RtmpRYD114/testcatch'
#> ✓ Creating 'R/'
#> ✓ Writing 'DESCRIPTION'
#> Package: testcatch
#> Title: What the Package Does (One Line, Title Case)
#> Version: 0.0.0.9000
#> Authors@R (parsed):
#> * First Last <first.last@example.com> [aut, cre] (YOUR-ORCID-ID)
#> Description: What the package does (one paragraph).
#> License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a
#> license
#> Encoding: UTF-8
#> LazyData: true
#> Roxygen: list(markdown = TRUE)
#> RoxygenNote: 7.1.1
#> ✓ Writing 'NAMESPACE'
#> ✓ Setting active project to '<no active project>'
setwd("testcatch")
usethis::use_rcpp()
#> ✓ Setting active project to '/private/var/folders/29/_qzzdhnn75780wtf8805n85w0000gn/T/RtmpRYD114/testcatch'
#> ✓ Creating 'src/'
#> ✓ Adding '*.o', '*.so', '*.dll' to 'src/.gitignore'
#> ● Copy and paste the following lines into '/private/var/folders/29/_qzzdhnn75780wtf8805n85w0000gn/T/RtmpRYD114/testcatch/R/testcatch-package.R':
#> ## usethis namespace: start
#> #' @useDynLib testcatch, .registration = TRUE
#> ## usethis namespace: end
#> NULL
#> ✓ Adding 'Rcpp' to LinkingTo field in DESCRIPTION
#> ✓ Adding 'Rcpp' to Imports field in DESCRIPTION
#> ● Copy and paste the following lines into '/private/var/folders/29/_qzzdhnn75780wtf8805n85w0000gn/T/RtmpRYD114/testcatch/R/testcatch-package.R':
#> ## usethis namespace: start
#> #' @importFrom Rcpp sourceCpp
#> ## usethis namespace: end
#> NULL
#> ✓ Writing 'src/code.cpp'
usethis::use_testthat()
#> ✓ Adding 'testthat' to Suggests field in DESCRIPTION
#> ✓ Creating 'tests/testthat/'
#> ✓ Writing 'tests/testthat.R'
#> ● Call `use_test()` to initialize a basic test file and open it for editing.
testthat::use_catch()
#> > Added C++ unit testing infrastructure.
#> > Please ensure you have 'LinkingTo: testthat' in your DESCRIPTION.
#> > Please ensure you have 'useDynLib(testcatch, .registration = TRUE)' in your NAMESPACE.
writeLines("## usethis namespace: start\n#' @useDynLib testcatch, .registration = TRUE\n#' @importFrom Rcpp sourceCpp\n## usethis namespace: end\nNULL", con = "R/testcatch-package.R")
usethis::use_package("testthat", type = "LinkingTo")
#> ✓ Adding 'testthat' to LinkingTo field in DESCRIPTION
#> ● Possible includes are:
#> #include <testthat.h>
devtools::check(document=TRUE)
#> Updating testcatch documentation
#> Loading testcatch
#> Re-compiling testcatch
#> ─ installing *source* package ‘testcatch’ ... (470ms)
#> ** using staged installation
#> ** libs
#> clang++ -std=gnu++11 -I"/usr/local/Cellar/r/4.0.3/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/4.0/site-library/Rcpp/include' -I'/usr/local/lib/R/4.0/site-library/testthat/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include -O3 -Wall -pedantic -pipe -Weffc++ -fPIC -g -O2 -c code.cpp -o code.o
#> clang++ -std=gnu++11 -I"/usr/local/Cellar/r/4.0.3/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/4.0/site-library/Rcpp/include' -I'/usr/local/lib/R/4.0/site-library/testthat/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include -O3 -Wall -pedantic -pipe -Weffc++ -fPIC -g -O2 -c test-example.cpp -o test-example.o
#> clang++ -std=gnu++11 -I"/usr/local/Cellar/r/4.0.3/lib/R/include" -DNDEBUG -I'/usr/local/lib/R/4.0/site-library/Rcpp/include' -I'/usr/local/lib/R/4.0/site-library/testthat/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include -O3 -Wall -pedantic -pipe -Weffc++ -fPIC -g -O2 -c test-runner.cpp -o test-runner.o
#> clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/Cellar/r/4.0.3/lib/R/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/readline/lib -L/usr/local/lib -o testcatch.so code.o test-example.o test-runner.o -L/usr/local/Cellar/r/4.0.3/lib/R/lib -lR -lintl -Wl,-framework -Wl,CoreFoundation
#> installing to /private/var/folders/29/_qzzdhnn75780wtf8805n85w0000gn/T/RtmpRYD114/devtools_install_32da458875bd/00LOCK-testcatch/00new/testcatch/libs
#> ** checking absolute paths in shared objects and dynamic libraries
#> ─ DONE (testcatch) (529ms)
#> Writing NAMESPACE
#> ── Building ─────────────────────────────────────────────────────── testcatch ──
#> Setting env vars:
#> ● CFLAGS : -Wall -pedantic
#> ● CXXFLAGS : -Wall -pedantic
#> ● CXX11FLAGS: -Wall -pedantic
#> ────────────────────────────────────────────────────────────────────────────────
#> checking for file ‘/private/var/folders/29/_qzzdhnn75780wtf8805n85w0000gn/T/RtmpRYD114/testcatch/DESCRIPTION’ ... ✓ checking for file ‘/private/var/folders/29/_qzzdhnn75780wtf8805n85w0000gn/T/RtmpRYD114/testcatch/DESCRIPTION’ (616ms)
#> ─ preparing ‘testcatch’:
#> checking DESCRIPTION meta-information ... ✓ checking DESCRIPTION meta-information
#> ─ cleaning src
#> ─ checking for LF line-endings in source and make files and shell scripts
#> ─ checking for empty or unneeded directories
#> Removed empty directory ‘testcatch/man’
#> ─ building ‘testcatch_0.0.0.9000.tar.gz’
#>
#> ── Checking ─────────────────────────────────────────────────────── testcatch ──
#> Setting env vars:
#> ● _R_CHECK_CRAN_INCOMING_USE_ASPELL_: TRUE
#> ● _R_CHECK_CRAN_INCOMING_REMOTE_ : FALSE
#> ● _R_CHECK_CRAN_INCOMING_ : FALSE
#> ● _R_CHECK_FORCE_SUGGESTS_ : FALSE
#> ● NOT_CRAN : true
#> ── R CMD check ─────────────────────────────────────────────────────────────────
#> * using log directory ‘/private/var/folders/29/_qzzdhnn75780wtf8805n85w0000gn/T/RtmpRYD114/testcatch.Rcheck’
#> * using R version 4.0.3 (2020-10-10)
#> * using platform: x86_64-apple-darwin19.6.0 (64-bit)
#> * using session charset: UTF-8
#> * using options ‘--no-manual --as-cran’
#> * checking for file ‘testcatch/DESCRIPTION’ ... OK
#> * this is package ‘testcatch’ version ‘0.0.0.9000’
#> * package encoding: UTF-8
#> * checking package namespace information ... OK
#> * checking package dependencies ... OK
#> * checking if this is a source package ... OK
#> * checking if there is a namespace ... OK
#> * checking for executable files ... OK
#> * checking for hidden files and directories ... OK
#> * checking for portable file names ... OK
#> * checking for sufficient/correct file permissions ... OK
#> * checking serialization versions ... OK
#> * checking whether package ‘testcatch’ can be installed ... OK
#> * checking installed package size ... OK
#> * checking package directory ... OK
#> * checking for future file timestamps ... NOTE
#> unable to verify current time
#> * checking DESCRIPTION meta-information ... WARNING
#> Non-standard license specification:
#> `use_mit_license()`, `use_gpl3_license()` or friends to pick a
#> license
#> Standardizable: FALSE
#> * checking top-level files ... OK
#> * checking for left-over files ... OK
#> * checking index information ... OK
#> * checking package subdirectories ... OK
#> * checking R files for non-ASCII characters ... OK
#> * checking R files for syntax errors ... OK
#> * checking whether the package can be loaded ... OK
#> * checking whether the package can be loaded with stated dependencies ... OK
#> * checking whether the package can be unloaded cleanly ... OK
#> * checking whether the namespace can be loaded with stated dependencies ... OK
#> * checking whether the namespace can be unloaded cleanly ... OK
#> * checking loading without being on the library search path ... OK
#> * checking dependencies in R code ... OK
#> * checking S3 generic/method consistency ... OK
#> * checking replacement functions ... OK
#> * checking foreign function calls ... OK
#> * checking R code for possible problems ... OK
#> * checking for missing documentation entries ... OK
#> * checking line endings in C/C++/Fortran sources/headers ... OK
#> * checking pragmas in C/C++ headers and code ... OK
#> * checking compilation flags used ... NOTE
#> Compilation used the following non-portable flag(s):
#> ‘-Weffc++’
#> * checking compiled code ... NOTE
#> File ‘testcatch/libs/testcatch.so’:
#> Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
#>
#> It is good practice to register native routines and to disable symbol
#> search.
#>
#> See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
#> * checking examples ... NONE
#> * checking for unstated dependencies in ‘tests’ ... OK
#> * checking tests ...
#> Running ‘testthat.R’
#> ERROR
#> Running the tests in ‘tests/testthat.R’ failed.
#> Last 13 lines of output:
#> > test_check("testcatch")
#> ── �[38;5;214mError�[39m (test-cpp.R:1:1): (code run outside of `test_that()`) ─────────────────
#> Error: The xml2 package must be installed in order to use `run_cpp_tests()`
#> �[34mℹ�[39m Do you need to run `install.packages('xml2')`?
#> �[1mBacktrace:�[22m
#> �[90m �[39m█
#> �[90m 1. �[39m└─testthat::run_cpp_tests("testcatch") �[90mtest-cpp.R:1:0�[39m
#> �[90m 2. �[39m └─testthat:::check_installed("xml2", "run_cpp_tests()")
#>
#> ══ testthat results ═══════════════════════════════════════════════════════════
#> �[38;5;214mError�[39m (test-cpp.R:1:1): (code run outside of `test_that()`)
#>
#> [ �[38;5;214mFAIL�[39m 1 | �[35mWARN�[39m 0 | �[34mSKIP�[39m 0 | �[32mPASS�[39m 0 ]
#> Error: Test failures
#> Execution halted
#> * checking for non-standard things in the check directory ... OK
#> * checking for detritus in the temp directory ... OK
#> * DONE
#>
#> Status: 1 ERROR, 1 WARNING, 3 NOTEs
#> See
#> ‘/private/var/folders/29/_qzzdhnn75780wtf8805n85w0000gn/T/RtmpRYD114/testcatch.Rcheck/00check.log’
#> for details.
#>
#> ── R CMD check results ─────────────────────────────── testcatch 0.0.0.9000 ────
#> Duration: 49s
#>
#> > checking tests ...
#> See below...
#>
#> > checking DESCRIPTION meta-information ... WARNING
#> Non-standard license specification:
#> `use_mit_license()`, `use_gpl3_license()` or friends to pick a
#> license
#> Standardizable: FALSE
#>
#> > checking for future file timestamps ... NOTE
#> unable to verify current time
#>
#> > checking compilation flags used ... NOTE
#> Compilation used the following non-portable flag(s):
#> ‘-Weffc++’
#>
#> > checking compiled code ... NOTE
#> File ‘testcatch/libs/testcatch.so’:
#> Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
#>
#> It is good practice to register native routines and to disable symbol
#> search.
#>
#> See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
#>
#> ── Test failures ───────────────────────────────────────────────── testthat ────
#>
#> > library(testthat)
#> > library(testcatch)
#> >
#> > test_check("testcatch")
#> ── �[38;5;214mError�[39m (test-cpp.R:1:1): (code run outside of `test_that()`) ─────────────────
#> Error: The xml2 package must be installed in order to use `run_cpp_tests()`
#> �[34mℹ�[39m Do you need to run `install.packages('xml2')`?
#> �[1mBacktrace:�[22m
#> �[90m �[39m█
#> �[90m 1. �[39m└─testthat::run_cpp_tests("testcatch") �[90mtest-cpp.R:1:0�[39m
#> �[90m 2. �[39m └─testthat:::check_installed("xml2", "run_cpp_tests()")
#>
#> ══ testthat results ═══════════════════════════════════════════════════════════
#> �[38;5;214mError�[39m (test-cpp.R:1:1): (code run outside of `test_that()`)
#>
#> [ �[38;5;214mFAIL�[39m 1 | �[35mWARN�[39m 0 | �[34mSKIP�[39m 0 | �[32mPASS�[39m 0 ]
#> Error: Test failures
#> Execution halted
#>
#> 1 error x | 1 warning x | 3 notes x
#> Error: R CMD check found ERRORsCreated on 2020-11-16 by the reprex package (v0.3.0)
Session info
devtools::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.0.3 (2020-10-10)
#> os macOS Catalina 10.15.7
#> system x86_64, darwin19.6.0
#> ui unknown
#> language (EN)
#> collate de_DE.UTF-8
#> ctype de_DE.UTF-8
#> tz Europe/Berlin
#> date 2020-11-16
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> ! package * version date lib source
#> assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.0)
#> backports 1.2.0 2020-11-02 [1] CRAN (R 4.0.3)
#> callr 3.5.1 2020-10-13 [1] CRAN (R 4.0.3)
#> cli 2.1.0 2020-10-12 [1] CRAN (R 4.0.3)
#> crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.0)
#> desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.0)
#> devtools 2.3.2 2020-09-18 [1] CRAN (R 4.0.2)
#> digest 0.6.27 2020-10-24 [1] CRAN (R 4.0.3)
#> ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.0)
#> evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.0)
#> fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.0)
#> fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.2)
#> git2r 0.27.1 2020-05-03 [1] CRAN (R 4.0.0)
#> glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2)
#> highr 0.8 2019-03-20 [1] CRAN (R 4.0.0)
#> htmltools 0.5.0 2020-06-16 [1] CRAN (R 4.0.2)
#> knitr 1.30 2020-09-22 [1] CRAN (R 4.0.3)
#> lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.0)
#> magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.0)
#> memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.0)
#> pillar 1.4.6 2020-07-10 [1] CRAN (R 4.0.2)
#> pkgbuild 1.1.0 2020-07-13 [1] CRAN (R 4.0.2)
#> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.0)
#> pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.1)
#> prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.0)
#> processx 3.4.4 2020-09-03 [1] CRAN (R 4.0.2)
#> ps 1.4.0 2020-10-07 [1] CRAN (R 4.0.3)
#> purrr 0.3.4 2020-04-17 [1] CRAN (R 4.0.0)
#> R6 2.5.0 2020-10-28 [1] CRAN (R 4.0.3)
#> rcmdcheck 1.3.3 2019-05-07 [1] CRAN (R 4.0.0)
#> Rcpp 1.0.5 2020-07-06 [1] CRAN (R 4.0.2)
#> remotes 2.2.0 2020-07-21 [1] CRAN (R 4.0.2)
#> rlang 0.4.8 2020-10-08 [1] CRAN (R 4.0.3)
#> rmarkdown 2.5 2020-10-21 [1] CRAN (R 4.0.3)
#> roxygen2 7.1.1 2020-06-27 [1] CRAN (R 4.0.2)
#> rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.0)
#> rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.0.3)
#> sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.0)
#> stringi 1.5.3 2020-09-09 [1] CRAN (R 4.0.2)
#> stringr 1.4.0 2019-02-10 [1] CRAN (R 4.0.0)
#> R testcatch * 0.0.0.9000 <NA> [?] <NA>
#> testthat 3.0.0 2020-10-31 [1] CRAN (R 4.0.3)
#> tibble 3.0.4 2020-10-12 [1] CRAN (R 4.0.3)
#> usethis 1.6.3 2020-09-17 [1] CRAN (R 4.0.2)
#> vctrs 0.3.4 2020-08-29 [1] CRAN (R 4.0.2)
#> whisker 0.4 2019-08-28 [1] CRAN (R 4.0.0)
#> withr 2.3.0 2020-09-22 [1] CRAN (R 4.0.3)
#> xfun 0.19 2020-10-30 [1] CRAN (R 4.0.3)
#> xml2 1.3.2 2020-04-23 [1] CRAN (R 4.0.3)
#> xopen 1.0.0 2018-09-17 [1] CRAN (R 4.0.0)
#> yaml 2.2.1 2020-02-01 [1] CRAN (R 4.0.0)
#>
#> [1] /usr/local/lib/R/4.0/site-library
#> [2] /usr/local/Cellar/r/4.0.3/lib/R/library
#>
#> R ── Package was removed from disk.