Last updated on 2024-07-12 15:52:59 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.1.3 | 290.48 | 379.26 | 669.74 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 2.1.3 | 218.43 | 218.75 | 437.18 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2.1.3 | 924.83 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 2.1.3 | 963.25 | NOTE | |||
| r-devel-windows-x86_64 | 2.1.3 | 250.00 | 388.00 | 638.00 | NOTE | |
| r-patched-linux-x86_64 | 2.1.3 | 274.38 | 367.51 | 641.89 | OK | |
| r-release-linux-x86_64 | 2.1.3 | 270.39 | 367.92 | 638.31 | OK | |
| r-release-macos-arm64 | 2.1.3 | 238.00 | NOTE | |||
| r-release-macos-x86_64 | 2.1.3 | 363.00 | NOTE | |||
| r-release-windows-x86_64 | 2.1.3 | 262.00 | 385.00 | 647.00 | NOTE | |
| r-oldrel-macos-arm64 | 2.1.3 | 214.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 2.1.3 | 352.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 2.1.3 | 317.00 | 488.00 | 805.00 | NOTE |
Version: 2.1.3
Check: compiled code
Result: NOTE
File ‘rxode2/libs/rxode2.so’:
Found non-API call to R: ‘HASHTAB’
Compiled code should not call non-API entry points in R.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 2.1.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [66s/113s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(rxode2)
rxode2 2.1.3 using 3 threads (see ?getRxThreads)
no cache: create with `rxCreateCache()`
> library(testthat)
> setRxThreads(1L)
> library(data.table)
> setDTthreads(1L)
> ##test_check("rxode2", reporter = testthat::LocationReporter)
> test_check("rxode2")
using C compiler: ‘gcc-13 (Debian 13.3.0-1) 13.3.0’
using C compiler: ‘gcc-13 (Debian 13.3.0-1) 13.3.0’
using C compiler: ‘gcc-13 (Debian 13.3.0-1) 13.3.0’
using C compiler: ‘gcc-13 (Debian 13.3.0-1) 13.3.0’
using C compiler: ‘gcc-13 (Debian 13.3.0-1) 13.3.0’
using C compiler: ‘gcc-13 (Debian 13.3.0-1) 13.3.0’
udunits database from /usr/share/xml/udunits/udunits2.xml
using C compiler: ‘gcc-13 (Debian 13.3.0-1) 13.3.0’
using C compiler: ‘gcc-13 (Debian 13.3.0-1) 13.3.0’
using C compiler: ‘gcc-13 (Debian 13.3.0-1) 13.3.0’
using C compiler: ‘gcc-13 (Debian 13.3.0-1) 13.3.0’
using C compiler: ‘gcc-13 (Debian 13.3.0-1) 13.3.0’
! in order to put confidence bands around the intervals, you need at least 2500 simulations
summarizing data...done
! in order to put confidence bands around the intervals, you need at least 2500 simulations
summarizing data...done
! in order to put confidence bands around the intervals, you need at least 2500 simulations
summarizing data...done
! in order to put confidence bands around the intervals, you need at least 2500 simulations
summarizing data...done
! in order to put confidence bands around the intervals, you need at least 2500 simulations
summarizing data...done
! in order to put confidence bands around the intervals, you need at least 2500 simulations
summarizing data...done
using C compiler: ‘gcc-13 (Debian 13.3.0-1) 13.3.0’
i parameter labels from comments will be replaced by 'label()'
i add covariate `wt_cl`
i add covariate `WT`
i promote `wt_cl` to population parameter with initial estimate 0.75
i fix `wt_cl` to `0.75`
i change initial estimate of `wt_cl` to `0.75`
using C compiler: ‘gcc-13 (Debian 13.3.0-1) 13.3.0’
using C compiler: ‘gcc-13 (Debian 13.3.0-1) 13.3.0’
using C compiler: ‘gcc-13 (Debian 13.3.0-1) 13.3.0’
i change initial estimate of `b` to `1`
i change initial estimate of `h` to `1`
i change initial estimate of `h` to `3`
i convert 'lka' from population parameter to between subject variability
i convert 'lka' from between subject variability to population parameter
i convert 'lka' from between subject variability to population parameter
i convert 'lka' from between subject variability to population parameter
i convert 'lcl' from population parameter to between subject variability
i old initial estimate was negative, changing to positive
i convert 'lvc' from population parameter to between subject variability
i old initial estimate is zero, changing to 1
i convert 'lvc' from between subject variability to population parameter
i convert 'lvc' from population parameter to between subject variability
i changing between subject variability parameter 'lka' to covariate parameter
i changing between subject variability parameter 'lka' to covariate parameter
using C compiler: ‘gcc-13 (Debian 13.3.0-1) 13.3.0’
*** caught segfault ***
address (nil), cause 'memory not mapped'
Traceback:
1: rxSolveSEXP(object, .ctl, .nms, .xtra, params, events, inits, setupOnlyS = .setupOnly)
2: withCallingHandlers(expr, warning = function(w) { assign(".ws", unique(c(w$message, .ws)), .thisEnv)})
3: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning"))
4: suppressWarnings(withCallingHandlers(expr, warning = function(w) { assign(".ws", unique(c(w$message, .ws)), .thisEnv)}))
5: .collectWarnings(rxSolveSEXP(object, .ctl, .nms, .xtra, params, events, inits, setupOnlyS = .setupOnly), lst = TRUE)
6: doTryCatch(return(expr), name, parentenv, handler)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: tryCatchList(expr, classes, parentenv, handlers)
9: tryCatch({ .envReset$ret <- .collectWarnings(rxSolveSEXP(object, .ctl, .nms, .xtra, params, events, inits, setupOnlyS = .setupOnly), lst = TRUE)}, error = function(e) { if (regexpr("not provided by package", e$message) != -1) { if (.envReset$cacheReset) { .malert("unsuccessful cache reset; try manual reset with 'rxClean()'") stop(e) } else { gc() .minfo("try resetting cache") rxode2::rxClean() .envReset$cacheReset <- TRUE .envReset$reset <- TRUE .msuccess("done") } } else if (regexpr("maximal number of DLLs reached", e$message) != -1) { if (.envReset$unload) { .malert("Could not unload rxode2 models, try restarting R") stop(e) } else { gc() .minfo("try resetting cache and unloading all rxode2 models") try(rxode2::rxUnloadAll()) rxode2::rxClean() .envReset$unload <- TRUE .envReset$reset <- TRUE .msuccess("done") } } else { stop(e) }})
10: rxSolve.default(.args.object, events = .et, updateObject = TRUE)
11: rxSolve(.args.object, events = .et, updateObject = TRUE)
12: o1$add.sampling(0)
13: eval(code, test_env)
14: eval(code, test_env)
15: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
16: doTryCatch(return(expr), name, parentenv, handler)
17: tryCatchOne(expr, names, parentenv, handlers[[1L]])
18: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
19: doTryCatch(return(expr), name, parentenv, handler)
20: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
21: tryCatchList(expr, classes, parentenv, handlers)
22: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
23: test_code(desc, code, env = parent.frame(), default_reporter = local_interactive_reporter())
24: test_that("rxSolve produces the correct results for rhs", { expect_warning(o1 <- rxSolve(orhs, et)) expect_equal(round(as.data.frame(o1), 4), structure(list(time = c(0.4, 4, 40, 400, 4000, 40000, 4e+05, 4e+06, 4e+07, 4e+08, 4e+09, 4e+10), x = c(1, 0.9117, 0.7168, 0.4506, 0.1832, 0.039, 0.0049, -832.9988, -18106.8843, -190902.2423, -1918897.229, -19198891.1895), z = c(0, 0.0882, 0.2831, 0.5494, 0.8168, 0.961, 0.9951, 833.9988, 18107.8843, 190903.2423, 1918898.229, 19198892.1895), y = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0)), row.names = c(NA, -12L), class = "data.frame"), tolerance = 1e-04) o1$add.sampling(0) expect_equal(round(as.data.frame(o1), 4), structure(list(time = c(0, 0.4, 4, 40, 400, 4000, 40000, 4e+05, 4e+06, 4e+07, 4e+08, 4e+09, 4e+10), x = c(1, 0.9852, 0.9055, 0.7158, 0.4505, 0.1832, 0.039, 0.0049, -832.9941, -18106.8732, -190902.279, -1918898.6518, -19198893.9661), z = c(0, 0.0148, 0.0945, 0.2842, 0.5495, 0.8168, 0.961, 0.9951, 833.9941, 18107.8732, 190903.279, 1918899.6518, 19198894.9661), y = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0)), row.names = c(NA, 13L), class = "data.frame"), tolerance = 1e-04)})
25: eval(code, test_env)
26: eval(code, test_env)
27: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
28: doTryCatch(return(expr), name, parentenv, handler)
29: tryCatchOne(expr, names, parentenv, handlers[[1L]])
30: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
31: doTryCatch(return(expr), name, parentenv, handler)
32: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
33: tryCatchList(expr, classes, parentenv, handlers)
34: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
35: test_code(test = NULL, code = exprs, env = env, default_reporter = StopReporter$new())
36: source_file(path, env = env(env), desc = desc, error_call = error_call)
37: FUN(X[[i]], ...)
38: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
39: doTryCatch(return(expr), name, parentenv, handler)
40: tryCatchOne(expr, names, parentenv, handlers[[1L]])
41: tryCatchList(expr, classes, parentenv, handlers)
42: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
43: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call))
44: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, error_call = error_call)
45: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel)
46: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
47: test_check("rxode2")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.1.3
Check: installed package size
Result: NOTE
installed size is 5.3Mb
sub-directories of 1Mb or more:
R 1.0Mb
libs 2.6Mb
Flavors: r-devel-windows-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 2.1.3
Check: compiled code
Result: NOTE
File 'rxode2/libs/x64/rxode2.dll':
Found non-API call to R: 'HASHTAB'
Compiled code should not call non-API entry points in R.
See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Flavor: r-devel-windows-x86_64