Last updated on 2023-11-27 19:52:51 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.2.5 | 197.36 | 356.70 | 554.06 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.2.6 | 165.77 | 274.95 | 440.72 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 1.2.6 | 672.04 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 1.2.6 | 747.99 | NOTE | |||
| r-devel-windows-x86_64 | 1.2.6 | 124.00 | 302.00 | 426.00 | NOTE | |
| r-patched-linux-x86_64 | 1.2.5 | 141.09 | 351.69 | 492.78 | NOTE | |
| r-release-linux-x86_64 | 1.2.6 | 135.13 | 356.00 | 491.13 | NOTE | |
| r-release-macos-arm64 | 1.2.6 | 178.00 | NOTE | |||
| r-release-macos-x86_64 | 1.2.6 | 491.00 | NOTE | |||
| r-release-windows-x86_64 | 1.2.6 | 124.00 | 336.00 | 460.00 | NOTE | |
| r-oldrel-macos-arm64 | 1.2.6 | 176.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 1.2.5 | 307.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 1.2.6 | 115.00 | 313.00 | 428.00 | NOTE |
Version: 1.2.5
Check: for GNU extensions in Makefiles
Result: NOTE
GNU make is a SystemRequirements.
Flavors: r-devel-linux-x86_64-debian-clang, r-patched-linux-x86_64, r-oldrel-macos-x86_64
Version: 1.2.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [146s/230s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(rbmi)
>
> test_check("rbmi")
mmrm() registered as emmeans extension
[ FAIL 1 | WARN 0 | SKIP 13 | PASS 1015 ]
══ Skipped tests (13) ══════════════════════════════════════════════════════════
• On CRAN (1): 'test-mmrm.R:337:5'
• is_full_test() is not TRUE (12): 'test-draws.R:115:5',
'test-fullusage.R:44:5', 'test-fullusage.R:118:5', 'test-fullusage.R:210:5',
'test-fullusage.R:301:5', 'test-fullusage.R:432:5', 'test-fullusage.R:521:5',
'test-fullusage.R:681:5', 'test-mcmc.R:327:5', 'test-mcmc.R:503:5',
'test-parallel.R:8:5', 'test-reproducibility.R:9:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-fullusage.R:926:5'): Three arms trial runs smoothly and gives expected results ──
Error in `(function (longdata, method, sample_stack, n_target_samples,
first_sample_orig, use_samp_ids, failure_limit = 0, ncores = 1,
quiet = FALSE)
{
max_sample_attempts <- n_target_samples + failure_limit
assert_that(length(sample_stack$stack) >= max_sample_attempts,
msg = sprintf("Only %s samples in the sample_stack, %s are required",
length(sample_stack$stack), max_sample_attempts))
time_taken <- system.time({
initial_sample <- get_mmrm_sample(ids = longdata$ids,
longdata = longdata, method = method)
})
if (initial_sample$failed) {
stop("Fitting MMRM to original dataset failed")
}
if (!quiet) {
cat(sprintf("\nEstimated running time (assuming single core) is %s seconds\n\n",
round(time_taken[[3]] * n_target_samples, 2)))
}
cl <- get_cluster(ncores)
mmrm_sample <- encap_get_mmrm_sample(cl, longdata, method)
samples <- list()
n_failed_samples <- 0
logger <- progressLogger$new(n_target_samples, quiet = quiet)
while (length(samples) < n_target_samples) {
ids <- sample_stack$pop(min(ncores, n_target_samples -
length(samples)))
new_samples <- mmrm_sample(ids)
isfailure <- vapply(new_samples, function(x) x$failed,
logical(1))
new_samples_keep <- new_samples[!isfailure]
n_failed_samples <- n_failed_samples + sum(isfailure)
if (n_failed_samples > failure_limit) {
if (!is.null(cl))
parallel::stopCluster(cl)
if (!is.null(method$type)) {
if (method$type == "jackknife") {
ids_fail <- ids[isfailure][[1]]
ids_jack <- longdata$ids[!longdata$ids %in%
ids_fail][[1]]
msg <- "MMRM failed to fit to the data after removing subject '%s'"
stop(sprintf(msg, ids_jack))
}
}
msg <- "More than %s failed fits. Try using a simpler covariance structure"
stop(sprintf(msg, failure_limit))
}
logger$add(length(new_samples_keep))
samples <- append(samples, new_samples_keep)
}
if (!is.null(cl))
parallel::stopCluster(cl)
assert_that(length(samples) == n_target_samples, msg = "Incorrect number of samples were produced")
if (first_sample_orig) {
samples <- append(list(initial_sample), samples)
}
if (!use_samp_ids) {
for (i in seq_along(samples)) {
samples[[i]]$ids <- longdata$ids
}
}
ret <- as_draws(method = method, samples = sample_list(samples),
data = longdata, formula = longdata$formula, n_failures = n_failed_samples)
return(ret)
})(longdata = <environment>, method = structure(list(covariance = "us",
threshold = 0.01, same_cov = FALSE, REML = TRUE, type = "bootstrap",
n_samples = 0), class = c("method", "condmean")), ncores = 1,
first_sample_orig = TRUE, use_samp_ids = TRUE, quiet = TRUE,
n_target_samples = 0, failure_limit = 0, sample_stack = <environment>)`: Fitting MMRM to original dataset failed
Backtrace:
▆
1. ├─rbmi::draws(...) at test-fullusage.R:926:5
2. └─rbmi:::draws.condmean(...)
3. ├─base::do.call(get_draws_mle, sample_opts)
4. └─rbmi (local) `<fn>`(...)
[ FAIL 1 | WARN 0 | SKIP 13 | PASS 1015 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.2.6
Check: for GNU extensions in Makefiles
Result: NOTE
GNU make is a SystemRequirements.
Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-windows-x86_64
Version: 1.2.6
Check: installed package size
Result: NOTE
installed size is 44.2Mb
sub-directories of 1Mb or more:
libs 42.9Mb
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64
Version: 1.2.5
Check: installed package size
Result: NOTE
installed size is 48.5Mb
sub-directories of 1Mb or more:
libs 47.3Mb
Flavor: r-oldrel-macos-x86_64