CRAN Package Check Results for Package bigsnpr

Last updated on 2020-08-07 01:49:35 CEST.

Check Details

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