Last updated on 2021-11-01 00:49:32 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.8.1 | 227.48 | 242.24 | 469.72 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.8.1 | 159.24 | 198.51 | 357.75 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.8.1 | 660.27 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 1.8.1 | 599.75 | OK | |||
| r-devel-windows-x86_64 | 1.8.1 | 340.00 | 298.00 | 638.00 | OK | |
| r-devel-windows-x86_64-gcc10-UCRT | 1.8.1 | OK | ||||
| r-patched-linux-x86_64 | 1.8.1 | 202.28 | 229.91 | 432.19 | OK | |
| r-patched-solaris-x86 | 1.8.1 | 560.50 | ERROR | |||
| r-release-linux-x86_64 | 1.8.1 | 178.66 | 229.46 | 408.12 | OK | |
| r-release-macos-arm64 | 1.8.1 | NOTE | ||||
| r-release-macos-x86_64 | 1.8.1 | NOTE | ||||
| r-release-windows-ix86+x86_64 | 1.8.1 | 471.00 | 373.00 | 844.00 | OK | |
| r-oldrel-macos-x86_64 | 1.8.1 | NOTE | ||||
| r-oldrel-windows-ix86+x86_64 | 1.8.1 | 465.00 | 490.00 | 955.00 | OK |
Version: 1.8.1
Check: installed package size
Result: NOTE
installed size is 8.5Mb
sub-directories of 1Mb or more:
libs 6.7Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-x86_64
Version: 1.8.1
Check: examples
Result: ERROR
Running examples in ‘bigsnpr-Ex.R’ failed
The error most likely occurred in:
> ### Name: snp_fastImputeSimple
> ### Title: Fast imputation
> ### Aliases: snp_fastImputeSimple
>
> ### ** Examples
>
> bigsnp <- snp_attachExtdata("example-missing.bed")
> G <- bigsnp$genotypes
> G[, 2] # some missing values
[1] NA NA 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 1 0
[26] 0 0 0 0 1 0 1 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 1 0
[51] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[76] 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 NA
[101] 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 NA 0 0 0 0 0
[126] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 NA 0
[151] 1 0 0 0 0 0 0 0 0 0 0 NA 0 0 0 0 0 0 0 0 0 0 1 0 0
[176] 0 0 0 0 0 0 NA 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0
> G2 <- snp_fastImputeSimple(G)
*** caught segfault ***
address f8252000, cause 'invalid permissions'
Traceback:
1: impute(Gna, method, ncores)
2: snp_fastImputeSimple(G)
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86
Version: 1.8.1
Check: tests
Result: ERROR
Running ‘spelling.R’
Running ‘testthat.R’ [111s/173s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(bigsnpr)
Loading required package: bigstatsr
>
> for (k in 1:9)
+ test_check("bigsnpr", filter = paste0(k, '-'))
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Solaris (1)
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 227 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• is_cran is TRUE (3)
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 35 ]
*** caught segfault ***
address f7084000, cause 'invalid permissions'
Traceback:
1: impute(Gna, method, ncores)
2: snp_fastImputeSimple(G, "mean0")
3: eval(code, test_env)
4: eval(code, test_env)
5: 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)
6: doTryCatch(return(expr), name, parentenv, handler)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
9: doTryCatch(return(expr), name, parentenv, handler)
10: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
11: tryCatchList(expr, classes, parentenv, handlers)
12: 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) { })
13: test_code(desc, code, env = parent.frame(), reporter = reporter)
14: test_that("fast imputation (simple) works", { G <- snp_attachExtdata("example-missing.bed")$genotypes expect_error(snp_fastImputeSimple(G, "mean"), "should be one of") expect_warning(G1 <- snp_fastImputeSimple(G, "zero"), "deprecated") expect_equal(G[c(18, 72), 400], rep(NA_real_, 2)) expect_equal(G1[c(18, 72), 400], rep(0, 2)) G2 <- snp_fastImputeSimple(G, "mean0") expect_equal(G[c(18, 72), 400], rep(NA_real_, 2)) expect_equal(G2[c(18, 72), 400], rep(1, 2)) G3 <- snp_fastImputeSimple(G, "mean2") expect_equal(G3[c(18, 72), 400], rep(1.01, 2)) G4 <- snp_fastImputeSimple(G, "mode") expect_equal(G4[c(4, 12), 1], rep(0, 2)) expect_equal(G4[c(18, 72), 400], rep(1, 2)) imp_val <- replicate(500, { G5 <- snp_fastImputeSimple(G, "random") G5[c(18, 72), 400] }) p <- mean(G[, 400], na.rm = TRUE)/2 prob <- c((1 - p)^2, 2 * p * (1 - p), p^2) expect_gt(stats::chisq.test(table(imp_val), p = prob)$p.value, 1e-04) expect_equal(snp_fastImputeSimple(G, method = "mean2")[], snp_fastImputeSimple(G, method = "mean2", ncores = 2)[])})
15: eval(code, test_env)
16: eval(code, test_env)
17: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
18: doTryCatch(return(expr), name, parentenv, handler)
19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
20: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
25: test_code(NULL, exprs, env)
26: source_file(path, child_env(env), wrap = wrap)
27: FUN(X[[i]], ...)
28: lapply(test_paths, test_one_file, env = env, wrap = wrap)
29: doTryCatch(return(expr), name, parentenv, handler)
30: tryCatchOne(expr, names, parentenv, handlers[[1L]])
31: tryCatchList(expr, classes, parentenv, handlers)
32: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
33: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, wrap = wrap))
34: test_files(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, wrap = wrap, load_package = load_package)
35: 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, wrap = wrap, load_package = load_package, parallel = parallel)
36: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
37: test_check("bigsnpr", filter = paste0(k, "-"))
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86