CRAN Package Check Results for Package pense

Last updated on 2019-03-24 07:47:21 CET.

Check Details

Version: 1.2.1
Check: top-level files
Result: WARN
     Output from running autoreconf:
     autoheader: warning: missing template: HAVE_OPENMP_C
     autoheader: Use AC_DEFINE([HAVE_OPENMP_C], [], [Description])
     autoheader: warning: missing template: HAVE_OPENMP_CXX
     autoheader: warning: missing template: RESTRICT
     autoreconf: /usr/bin/autoheader failed with exit status: 1
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

Version: 1.2.1
Check: installed package size
Result: NOTE
     installed size is 6.8Mb
     sub-directories of 1Mb or more:
     libs 6.6Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 1.2.1
Check: whether package can be installed
Result: NOTE
    Found the following notes/warnings:
     Non-staged installation was used
Flavor: r-devel-windows-ix86+x86_64

Version: 1.2.1
Check: examples
Result: ERROR
    Running examples in ‘pense-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: coef.pense
    > ### Title: Extract Model Coefficients
    > ### Aliases: coef.pense
    >
    > ### ** Examples
    >
    > # Generate data with highly correlated groups of variables and some outliers
    > set.seed(12345)
    > n <- 50
    > n_out <- 3
    > p <- 20
    > x <- 1 + matrix(rnorm(n * p), ncol = p)
    > x[, 2] <- x[, 1] + rnorm(n, sd = 0.01)
    > x[, 3] <- x[, 1] + rnorm(n, sd = 0.01)
    > x[, 5] <- x[, 4] + rnorm(n, sd = 0.01)
    > x[, 6] <- x[, 4] + rnorm(n, sd = 0.01)
    >
    > y <- x %*% c(rep(c(2, 5), each = 3), numeric(p - 6)) + rnorm(n)
    >
    > y[seq_len(n_out)] <- rnorm(n_out, -100, sd = 3)
    >
    > # Compute the PENSE estimator
    > set.seed(1234)
    > est_en <- pense(x, y, alpha = 0.5, warm_reset = 1, cv_k = 3)
    
     *** caught segfault ***
    address 0, cause 'memory not mapped'
    
    Traceback:
     1: enpy_exact(x, y, alpha, lambda, options, en_options)
     2: enpy(std_data$xs, std_data$yc, alpha, lambda, delta = pense_options$bdp, cc = pense_options$cc, options = initest_options, en_options = en_options)
     3: pense_init_cold(x = x_train, y = y_train, lambda = job$lambda, ...)
     4: FUN(X[[i]], ...)
     5: cluster$lapply(jobs_cold_est, get_cold_est, alpha = alpha, standardize = standardize, pense_options = options, initest_options = init_options, en_options = en_options)
     6: doTryCatch(return(expr), name, parentenv, handler)
     7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     8: tryCatchList(expr, classes, parentenv, handlers)
     9: tryCatch({ cold_inits <- cluster$lapply(jobs_cold_est, get_cold_est, alpha = alpha, standardize = standardize, pense_options = options, initest_options = init_options, en_options = en_options)}, error = function(e) { cluster$stopCluster() stop(e)})
    10: pense(x, y, alpha = 0.5, warm_reset = 1, cv_k = 3)
    An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86

Version: 1.2.1
Check: tests
Result: ERROR
     Running ‘testthat.R’ [18s/41s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(pense)
     Loading required package: Matrix
     >
     > test_check("pense")
    
     *** caught segfault ***
     address 0, cause 'memory not mapped'
    
     Traceback:
     1: enpy_ols(x, y, options)
     2: pense::enpy(x, y, alpha = alpha, lambda = lambda, delta = 0.5, options = initest_options(psc_method = "rr", maxit = 5, psc_keep = 0.2, resid_keep_method = "proportion", resid_keep_prop = 0.6), en_options = en_options_aug_lars())
     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("enpy", { if (requireNamespace("lars", quietly = TRUE) && requireNamespace("robustbase", quietly = TRUE)) { source("enpy.old.R", local = TRUE) n <- 500L p <- 50L set.seed(12345) x <- matrix(rnorm(n * p), ncol = p) y <- 2 + x %*% c(1, 1, 1, rep.int(0, p - 3L)) + rnorm(n) alpha <- 0 lambda <- 0 new <- pense::enpy(x, y, alpha = alpha, lambda = lambda, delta = 0.5, options = initest_options(psc_method = "rr", maxit = 5, psc_keep = 0.2, resid_keep_method = "proportion", resid_keep_prop = 0.6), en_options = en_options_aug_lars()) target <- enpy(x, y, lambda1 = alpha * lambda, lambda2 = 0.5 * (1 - alpha) * lambda, deltaesc = 0.5, cc.scale = 1.54764, psc.method = "rr", prosac = 0.8, clean.method = "proportion", prop = 0.4, py.nit = 5, en.tol = 1e-08) diffs <- apply(new$coeff, 2, function(x) { min(colSums(abs(target$coeff - x))) }) expect_lt(sum(abs(diffs)), 1e-08) }})
     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: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter, { lister$start_file(basename(path)) source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap) end_context() })
     29: FUN(X[[i]], ...)
     30: lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
     31: force(code)
     32: with_reporter(reporter = current_reporter, results <- lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap))
     33: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
     34: 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)
     35: 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)
     36: test_check("pense")
     An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86

Version: 1.2.1
Check: whether package can be installed
Result: ERROR
    Installation failed.
Flavor: r-release-linux-x86_64