CRAN Package Check Results for Package bigstatsr

Last updated on 2019-07-03 01:47:12 CEST.

Additional issues

clang-UBSAN MKL OpenBLAS

Check Details

Version: 0.9.1
Check: installed package size
Result: NOTE
     installed size is 11.2Mb
     sub-directories of 1Mb or more:
     extdata 2.3Mb
     libs 8.4Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 0.9.1
Check: examples
Result: ERROR
    Running examples in ‘bigstatsr-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: FBM.code256-class
    > ### Title: Class FBM.code256
    > ### Aliases: FBM.code256-class FBM.code256_RC FBM.code256 add_code256
    >
    > ### ** Examples
    >
    > X <- FBM(10, 10, type = "raw")
    > X[] <- sample(as.raw(0:3), size = length(X), replace = TRUE)
    > X[]
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
     [1,] 00 02 00 01 01 01 02 01 01 00
     [2,] 03 02 02 01 01 00 01 01 03 02
     [3,] 02 00 00 00 02 03 01 00 02 01
     [4,] 00 00 00 03 03 03 03 02 02 03
     [5,] 01 00 00 02 03 00 03 02 00 02
     [6,] 00 01 00 00 03 02 01 03 03 00
     [7,] 02 01 01 03 01 03 01 01 00 00
     [8,] 02 01 00 02 03 01 00 02 03 03
     [9,] 01 01 00 01 00 01 01 02 00 01
    [10,] 01 02 01 01 02 02 01 03 03 00
    >
    > code <- rep(NA_real_, 256)
    > code[1:3] <- c(1, 3, 5)
    >
    > X.code <- add_code256(X, code)
    > X.code[]
    
     *** caught segfault ***
    address fd140000, cause 'invalid permissions'
    
    Traceback:
     1: extractMat(x$address, i, j)
     2: decodeMat(extractMat(x$address, i, j), x$code256)
     3: extract_matrix(x, transform_ind(i, n), transform_ind(j, m))
     4: X.code[]
     5: X.code[]
    An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86

Version: 0.9.1
Check: tests
Result: ERROR
     Running ‘spelling.R’
     Running ‘testthat.R’ [14s/30s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(bigstatsr)
     >
     > test_check("bigstatsr")
     ========== SEED: 1 ==========
    
     *** caught segfault ***
     address fca70000, cause 'invalid permissions'
    
     Traceback:
     1: extractVec(x$address, i)
     2: decodeVec(extractVec(x$address, i), x$code256)
     3: extract_vector(x, transform_i_only(i, n, m))
     4: x[ind]
     5: x[ind]
     6: .local(x)
     7: diag(X)
     8: diag(X)
     9: eval_bare(get_expr(quo), get_env(quo))
     10: quasi_label(enquo(object), label, arg = "object")
     11: expect_equal(diag(X), diag(x))
     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())
     23: test_that("same dimensions", { expect_equal(nrow(X), nrow(x)) expect_equal(ncol(X), ncol(x)) expect_equal(dim(X), dim(x)) expect_equal(length(X), length(x)) expect_equal(diag(X), diag(x))})
     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, new.env(parent = env), chdir = TRUE, wrap = wrap)
     36: force(code)
     37: 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() })
     38: FUN(X[[i]], ...)
     39: lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
     40: force(code)
     41: with_reporter(reporter = current_reporter, results <- lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap))
     42: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
     43: 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)
     44: 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)
     45: test_check("bigstatsr")
     An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86