Last updated on 2021-05-24 07:49:42 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.6.1 | 215.70 | 247.58 | 463.28 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.6.1 | 137.62 | 185.53 | 323.15 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.6.1 | 603.38 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 1.6.1 | 550.27 | OK | |||
| r-devel-windows-x86_64 | 1.6.1 | 409.00 | 497.00 | 906.00 | ERROR | |
| r-devel-windows-x86_64-gcc10-UCRT | 1.6.1 | OK | ||||
| r-patched-linux-x86_64 | 1.6.1 | 163.60 | 237.78 | 401.38 | OK | |
| r-patched-solaris-x86 | 1.6.1 | 516.60 | ERROR | |||
| r-release-linux-x86_64 | 1.6.1 | 151.30 | 236.00 | 387.30 | OK | |
| r-release-windows-ix86+x86_64 | 1.6.1 | 409.00 | 497.00 | 906.00 | ERROR | |
| r-oldrel-macos-x86_64 | 1.6.1 | NOTE | ||||
| r-oldrel-windows-ix86+x86_64 | 1.6.1 | 425.00 | 369.00 | 794.00 | OK |
Version: 1.6.1
Check: installed package size
Result: NOTE
installed size is 8.3Mb
sub-directories of 1Mb or more:
libs 6.6Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-oldrel-macos-x86_64
Version: 1.6.1
Check: running tests for arch ‘i386’
Result: ERROR
Running 'spelling.R' [0s]
Running 'testthat.R' [114s]
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, '-'))
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 224 ]
== Skipped tests ===============================================================
* is_cran is TRUE (3)
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 32 ]
== Skipped tests ===============================================================
* .Machine$sizeof.pointer == 8 is not TRUE (1)
* is_cran is TRUE (1)
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 14 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 28 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 104 ]
== Skipped tests ===============================================================
* is_cran is TRUE (1)
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 24 ]
== Skipped tests ===============================================================
* is_cran is TRUE (1)
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 0 ]
== Skipped tests ===============================================================
* On CRAN (1)
* is_cran is TRUE (1)
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 100 ]
== Skipped tests ===============================================================
* is_cran is TRUE (1)
== Failed tests ================================================================
-- Failure (test-9-Fst.R:25:3): snp_fst() works --------------------------------
snp_fst(list_df_af[pop_grps]) not equal to `all_fst`.
4087/4542 mismatches (average diff: 0.0169)
[1] 0.00948 - 0.01541 == -0.00593
[3] 0.10615 - 0.07539 == 0.03076
[4] 0.04337 - 0.02001 == 0.02336
[5] 0.00266 - 0.01332 == -0.01066
[6] 0.01582 - 0.01287 == 0.00295
[8] 0.00673 - 0.02882 == -0.02209
[9] 0.02507 - 0.01304 == 0.01203
[10] -0.00319 - 0.01005 == -0.01325
[11] 0.00438 - 0.00119 == 0.00319
...
Backtrace:
x
1. \-base::lapply(...) test-9-Fst.R:25:2
2. \-bigsnpr:::FUN(X[[i]], ...)
3. \-testthat::expect_equal(...) test-9-Fst.R:40:4
-- Failure (test-9-Fst.R:25:3): snp_fst() works --------------------------------
snp_fst(list_df_af[pop_grps], overall = TRUE) not equal to `fst`.
Lengths differ: 1 is not 0
Backtrace:
x
1. \-base::lapply(...) test-9-Fst.R:25:2
2. \-bigsnpr:::FUN(X[[i]], ...)
3. \-testthat::expect_equal(...) test-9-Fst.R:41:4
[ FAIL 2 | WARN 0 | SKIP 1 | PASS 13 ]
Error: Test failures
Execution halted
Flavors: r-devel-windows-x86_64, r-release-windows-ix86+x86_64
Version: 1.6.1
Check: running tests for arch ‘x64’
Result: ERROR
Running 'spelling.R' [0s]
Running 'testthat.R' [104s]
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, '-'))
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 224 ]
== Skipped tests ===============================================================
* is_cran is TRUE (3)
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 32 ]
== Skipped tests ===============================================================
* is_cran is TRUE (1)
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 25 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 28 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 104 ]
== Skipped tests ===============================================================
* is_cran is TRUE (1)
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 24 ]
== Skipped tests ===============================================================
* is_cran is TRUE (1)
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 0 ]
== Skipped tests ===============================================================
* On CRAN (1)
* is_cran is TRUE (1)
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 100 ]
== Skipped tests ===============================================================
* is_cran is TRUE (1)
== Failed tests ================================================================
-- Failure (test-9-Fst.R:25:3): snp_fst() works --------------------------------
snp_fst(list_df_af[pop_grps], overall = TRUE) not equal to `fst`.
Lengths differ: 1 is not 0
Backtrace:
x
1. \-base::lapply(...) test-9-Fst.R:25:2
2. \-bigsnpr:::FUN(X[[i]], ...)
3. \-testthat::expect_equal(...) test-9-Fst.R:41:4
[ FAIL 1 | WARN 0 | SKIP 1 | PASS 14 ]
Error: Test failures
Execution halted
Flavors: r-devel-windows-x86_64, r-release-windows-ix86+x86_64
Version: 1.6.1
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 f81bc000, 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: 1.6.1
Check: tests
Result: ERROR
Running ‘spelling.R’
Running ‘testthat.R’ [71s/116s]
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 223 ]
*** caught segfault ***
address f824013c, cause 'invalid permissions'
Traceback:
1: bed_clumping_chr(obj.bed, keep, ind_row = ind.row, ind_col = ind.chr, center = center, scale = scale, ordInd = ord, rankInd = match(seq_along(ord), ord), pos = pos.chr, size = size * 1000, thr = thr.r2, ncores = ncores)
2: bedClumpingChr(obj.bed, S, ind.chr, ind.row, size, infos.pos, thr.r2, ncores)
3: FUN(X[[i]], ...)
4: lapply(split(ind.noexcl, infos.chr[ind.noexcl]), function(ind.chr) { bedClumpingChr(obj.bed, S, ind.chr, ind.row, size, infos.pos, thr.r2, ncores)})
5: unlist(lapply(split(ind.noexcl, infos.chr[ind.noexcl]), function(ind.chr) { bedClumpingChr(obj.bed, S, ind.chr, ind.row, size, infos.pos, thr.r2, ncores)}), use.names = FALSE)
6: sort(unlist(lapply(split(ind.noexcl, infos.chr[ind.noexcl]), function(ind.chr) { bedClumpingChr(obj.bed, S, ind.chr, ind.row, size, infos.pos, thr.r2, ncores) }), use.names = FALSE))
7: bed_clumping(obj.bed, ind.row = ind.row, exclude = setdiff(cols_along(obj.bed), ind.col), thr.r2 = thr.r2, size = size, ncores = ncores)
8: bed_autoSVD(obj.bed, verbose = FALSE)
9: eval_bare(expr, quo_get_env(quo))
10: quasi_label(enquo(object), label, arg = "object")
11: expect_is(obj.svd <- bed_autoSVD(obj.bed, verbose = FALSE), "big_SVD")
12: eval(code, test_env)
13: eval(code, test_env)
14: 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)
15: doTryCatch(return(expr), name, parentenv, handler)
16: tryCatchOne(expr, names, parentenv, handlers[[1L]])
17: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
18: doTryCatch(return(expr), name, parentenv, handler)
19: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
20: tryCatchList(expr, classes, parentenv, handlers)
21: 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) { })
22: test_code(desc, code, env = parent.frame(), reporter = reporter)
23: test_that("bed_autoSVD() works", { obj.bed <- bed(snp_writeBed(test, bedfile = tempfile(fileext = ".bed"))) expect_output(bed_autoSVD(obj.bed, thr.r2 = NA), "Skipping clumping.") expect_is(obj.svd <- bed_autoSVD(obj.bed, verbose = FALSE), "big_SVD") expect_identical(attr(obj.svd, "lrldr"), LD.wiki34[0, 1:3]) skip_if(is_cran) obj.svd2 <- bed_autoSVD(obj.bed, size = 5, verbose = FALSE) expect_gt(length(attr(obj.svd2, "subset")), length(attr(obj.svd, "subset"))) obj.svd4 <- bed_autoSVD(obj.bed, roll.size = 0, verbose = FALSE) expect_lt(length(attr(obj.svd4, "subset")), length(attr(obj.svd, "subset"))) obj.svd5 <- bed_autoSVD(obj.bed, thr.r2 = 1, roll.size = 0, verbose = FALSE) expect_gt(min(diag(cor(obj.svd5$u, obj.svd$u))[1:3]^2), 0.98) obj.svd6 <- bed_autoSVD(obj.bed, thr.r2 = NA, roll.size = 0, verbose = FALSE) expect_equal(obj.svd6, obj.svd5) obj.svd7 <- bed_autoSVD(obj.bed, alpha.tukey = 0.999, roll.size = 0, verbose = FALSE) expect_lt(length(attr(obj.svd7, "subset")), length(attr(obj.svd6, "subset"))) expect_output(bed_autoSVD(obj.bed, alpha.tukey = 0.999999999, roll.size = 0, verbose = TRUE), "Maximum number of iterations reached.")})
24: eval(code, test_env)
25: eval(code, test_env)
26: 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)
27: doTryCatch(return(expr), name, parentenv, handler)
28: tryCatchOne(expr, names, parentenv, handlers[[1L]])
29: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
30: doTryCatch(return(expr), name, parentenv, handler)
31: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
32: tryCatchList(expr, classes, parentenv, handlers)
33: 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) { })
34: test_code(NULL, exprs, env)
35: source_file(path, child_env(env), wrap = wrap)
36: FUN(X[[i]], ...)
37: lapply(test_paths, test_one_file, env = env, wrap = wrap)
38: force(code)
39: doWithOneRestart(return(expr), restart)
40: withOneRestart(expr, restarts[[1L]])
41: withRestarts(testthat_abort_reporter = function() NULL, force(code))
42: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, wrap = wrap))
43: 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)
44: 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)
45: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
46: test_check("bigsnpr", filter = paste0(k, "-"))
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86