Last updated on 2020-08-07 01:50:19 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| bigassertr | 12 | ||
| bigparallelr | 12 | ||
| bigreadr | 12 | ||
| bigsnpr | 1 | 3 | 8 |
| bigsparser | 12 | ||
| bigstatsr | 6 | 6 | |
| bigutilsr | 1 | 11 | |
| inplace | 12 | ||
| mmapcharr | 12 | ||
| pcadapt | 12 | ||
| primefactr | 12 | ||
| rmio | 12 | ||
| runonce | 5 | 7 |
Current CRAN status: OK: 12
Current CRAN status: OK: 12
Current CRAN status: OK: 12
Current CRAN status: ERROR: 1, NOTE: 3, OK: 8
Version: 1.4.4
Check: installed package size
Result: NOTE
installed size is 9.9Mb
sub-directories of 1Mb or more:
libs 8.2Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-release-macos-x86_64, r-oldrel-macos-x86_64
Version: 1.4.4
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 f80a2000, 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: 1.4.4
Check: tests
Result: ERROR
Running ‘spelling.R’
Running ‘testthat.R’ [115s/156s]
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, '-'))
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 222 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 32 | SKIPPED: 3 | WARNINGS: 0 | FAILED: 0 ]
*** caught segfault ***
address f7448000, 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())
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(200, { G5 <- snp_fastImputeSimple(G, "random") G5[c(18, 72), 400] }) abs_val <- rbinom(1e+06, size = 2, prob = mean(G[, 400], na.rm = TRUE)/2) expect_equal(table(imp_val)/length(imp_val), table(abs_val)/length(abs_val), tolerance = 0.2, check.attributes = FALSE) 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, new.env(parent = env), chdir = TRUE, wrap = wrap)
27: force(code)
28: doWithOneRestart(return(expr), restart)
29: withOneRestart(expr, restarts[[1L]])
30: withRestarts(testthat_abort_reporter = function() NULL, force(code))
31: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter, { reporter$start_file(basename(path)) lister$start_file(basename(path)) source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap) reporter$.end_context() reporter$end_file() })
32: FUN(X[[i]], ...)
33: lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
34: force(code)
35: doWithOneRestart(return(expr), restart)
36: withOneRestart(expr, restarts[[1L]])
37: withRestarts(testthat_abort_reporter = function() NULL, force(code))
38: with_reporter(reporter = current_reporter, results <- lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap))
39: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
40: test_dir(path = test_path, reporter = reporter, env = env, filter = filter, ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
41: test_package_dir(package = package, test_path = test_path, filter = filter, reporter = reporter, ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
42: test_check("bigsnpr", filter = paste0(k, "-"))
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86
Current CRAN status: OK: 12
Current CRAN status: NOTE: 6, OK: 6
Version: 1.2.3
Check: installed package size
Result: NOTE
installed size is 15.2Mb
sub-directories of 1Mb or more:
extdata 2.3Mb
libs 12.3Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64
Current CRAN status: ERROR: 1, OK: 11
Version: 0.3.2
Check: running tests for arch ‘i386’
Result: ERROR
Running 'spelling.R' [1s]
Running 'testthat.R' [150s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(bigutilsr)
>
> test_check("bigutilsr")
-- 1. Failure: covrob_ogk() is the same as rrcov::CovOgk() (@test-OGK.R#20) ---
test$cov not equal to true@cov.
100/100 mismatches (average diff: 0.95)
[1] 1315.21 - 1316.02 == -0.8078
[2] -8.54 - -8.50 == -0.0405
[3] 30.02 - 30.51 == -0.4854
[4] -6.70 - -5.24 == -1.4643
[5] -19.39 - -18.21 == -1.1785
[6] -37.21 - -37.42 == 0.2127
[7] -52.45 - -52.51 == 0.0669
[8] -1.95 - -2.47 == 0.5208
[9] 87.74 - 88.26 == -0.5157
...
-- 2. Failure: covrob_ogk() is the same as rrcov::CovOgk() (@test-OGK.R#20) ---
test$center not equal to true@center.
10/10 mismatches (average diff: 0.028)
[1] -0.933 - -0.948 == 0.01466
[2] -0.506 - -0.503 == -0.00264
[3] -0.605 - -0.580 == -0.02559
[4] 0.302 - 0.384 == -0.08161
[5] -0.889 - -0.822 == -0.06632
[6] -1.055 - -1.066 == 0.01013
[7] -0.230 - -0.231 == 0.00134
[8] -2.214 - -2.243 == 0.02883
[9] 0.359 - 0.384 == -0.02466
...
== testthat results ===========================================================
[ OK: 250 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
1. Failure: covrob_ogk() is the same as rrcov::CovOgk() (@test-OGK.R#20)
2. Failure: covrob_ogk() is the same as rrcov::CovOgk() (@test-OGK.R#20)
Error: testthat unit tests failed
Execution halted
Flavor: r-release-windows-ix86+x86_64
Current CRAN status: OK: 12
Current CRAN status: OK: 12
Current CRAN status: NOTE: 12
Version: 4.3.3
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: 'vcfR'
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, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-macos-x86_64
Version: 4.3.3
Check: installed package size
Result: NOTE
installed size is 7.1Mb
sub-directories of 1Mb or more:
extdata 2.7Mb
libs 3.6Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64
Current CRAN status: OK: 12
Current CRAN status: OK: 12
Current CRAN status: NOTE: 5, OK: 7
Version: 0.2.2
Check: dependencies in R code
Result: NOTE
Namespace in Imports field not imported from: ‘urltools’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86, r-release-macos-x86_64, r-oldrel-macos-x86_64