R version 4.6.0 alpha (2026-03-31 r89747 ucrt) Copyright (C) 2026 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > #! /usr/bin/env Rscript > ## This runs testme test script inst/testme/test-futurize-vegan.R > ## Don't edit - it was autogenerated by inst/testme/deploy.R > futurize:::testme("futurize-vegan") Test 'futurize-vegan' ... chr "none" > if (requireNamespace("vegan") && getRversion() >= + "4.4.0") { + all_equal_ignore_call <- function(a, b, ...) { + attr(a, "heading" .... [TRUNCATED] Loading required namespace: vegan Loading required package: future Loading required package: permute *** mrpp() Call: mrpp(dat = dune, grouping = dune.env$Management, permutations = 99) Dissimilarity index: euclidean Weights for groups: n Class means and counts: BF HF NM SF delta 10.03 11.08 10.66 12.27 n 3 5 6 6 Chance corrected within-group agreement A: 0.1246 Based on observed delta 11.15 and expected delta 12.74 Significance of delta: 0.01 Permutation: free Number of permutations: 99 Futures created: 2 Call: mrpp(dat = dune, grouping = dune.env$Management, permutations = 99, parallel = cl) Dissimilarity index: euclidean Weights for groups: n Class means and counts: BF HF NM SF delta 10.03 11.08 10.66 12.27 n 3 5 6 6 Chance corrected within-group agreement A: 0.1246 Based on observed delta 11.15 and expected delta 12.74 Significance of delta: 0.01 Permutation: free Number of permutations: 99 *** adonis2() Permutation test for adonis under reduced model Permutation: free Number of permutations: 99 adonis2(formula = dune ~ Management, data = dune.env, permutations = 99) Df SumOfSqs R2 F Pr(>F) Model 3 1.4686 0.34161 2.7672 0.01 ** Residual 16 2.8304 0.65839 Total 19 4.2990 1.00000 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Futures created: 2 Permutation test for adonis under reduced model Permutation: free Number of permutations: 99 adonis2(formula = dune ~ Management, data = dune.env, permutations = 99, parallel = cl) Df SumOfSqs R2 F Pr(>F) Model 3 1.4686 0.34161 2.7672 0.01 ** Residual 16 2.8304 0.65839 Total 19 4.2990 1.00000 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 *** anova() on cca object - S3 method anova.cca() Permutation test for cca under reduced model Permutation: free Number of permutations: 99 Model: cca(formula = dune ~ A1 + Management, data = dune.env) Df ChiSquare F Pr(>F) Model 4 0.77978 2.1896 0.01 ** Residual 15 1.33549 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Futures created: 2 Permutation test for cca under reduced model Permutation: free Number of permutations: 99 Model: cca(formula = dune ~ A1 + Management, data = dune.env) Df ChiSquare F Pr(>F) Model 4 0.77978 2.1896 0.01 ** Residual 15 1.33549 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 *** anosim() Call: anosim(x = dune, grouping = dune.env$Management, permutations = 99) Dissimilarity: bray ANOSIM statistic R: 0.2579 Significance: 0.03 Permutation: free Number of permutations: 99 Futures created: 2 Call: anosim(x = dune, grouping = dune.env$Management, permutations = 99, parallel = cl) Dissimilarity: bray ANOSIM statistic R: 0.2579 Significance: 0.03 Permutation: free Number of permutations: 99 *** mantel() Mantel statistic based on Pearson's product-moment correlation Call: mantel(xdis = veg.dist, ydis = env.dist, permutations = 99) Mantel statistic r: 0.2379 Significance: 0.05 Upper quantiles of permutations (null model): 90% 95% 97.5% 99% 0.165 0.208 0.258 0.274 Permutation: free Number of permutations: 99 Futures created: 2 Mantel statistic based on Pearson's product-moment correlation Call: mantel(xdis = veg.dist, ydis = env.dist, permutations = 99, parallel = cl) Mantel statistic r: 0.2379 Significance: 0.05 Upper quantiles of permutations (null model): 90% 95% 97.5% 99% 0.165 0.208 0.258 0.274 Permutation: free Number of permutations: 99 *** mantel.partial() Partial Mantel statistic based on Pearson's product-moment correlation Call: mantel.partial(xdis = xdis, ydis = ydis, zdis = zdis, permutations = 99) Mantel statistic r: -1 Significance: 1 Upper quantiles of permutations (null model): 90% 95% 97.5% 99% 0.110 0.146 0.167 0.180 Permutation: free Number of permutations: 99 Futures created: 2 Partial Mantel statistic based on Pearson's product-moment correlation Call: mantel.partial(xdis = xdis, ydis = ydis, zdis = zdis, permutations = 99, parallel = cl) Mantel statistic r: -1 Significance: 1 Upper quantiles of permutations (null model): 90% 95% 97.5% 99% 0.110 0.146 0.167 0.180 Permutation: free Number of permutations: 99 *** cascadeKM() Futures created: 2 *** estaccumR() N S Chao ACE 1 10.00000 10.00000 10.18109 2 15.66667 15.66667 15.81514 3 18.44444 18.44444 18.59696 4 20.00000 20.00000 20.17422 5 23.44444 23.44444 23.62628 6 24.77778 24.77778 24.95719 7 26.00000 26.00000 26.21889 8 26.77778 26.80556 27.00645 9 27.33333 27.36111 27.56753 10 27.88889 27.94444 28.17613 11 28.11111 28.16111 28.38441 12 28.11111 28.11111 28.23687 13 28.44444 28.44444 28.60885 14 29.00000 29.00000 29.20141 15 29.22222 29.22222 29.48022 16 29.55556 29.55556 29.88228 17 29.66667 29.66667 30.03390 18 29.66667 29.66667 30.03847 19 29.88889 29.88889 30.36386 20 30.00000 30.00000 30.45896 Futures created: 2 N S Chao ACE 1 10.00000 10.00000 10.18109 2 15.66667 15.66667 15.81514 3 18.44444 18.44444 18.59696 4 20.00000 20.00000 20.17422 5 23.44444 23.44444 23.62628 6 24.77778 24.77778 24.95719 7 26.00000 26.00000 26.21889 8 26.77778 26.80556 27.00645 9 27.33333 27.36111 27.56753 10 27.88889 27.94444 28.17613 11 28.11111 28.16111 28.38441 12 28.11111 28.11111 28.23687 13 28.44444 28.44444 28.60885 14 29.00000 29.00000 29.20141 15 29.22222 29.22222 29.48022 16 29.55556 29.55556 29.88228 17 29.66667 29.66667 30.03390 18 29.66667 29.66667 30.03847 19 29.88889 29.88889 30.36386 20 30.00000 30.00000 30.45896 *** oecosimu() oecosimu object Call: oecosimu(comm = sipoo, nestfun = nestedchecker, method = "r0") nullmodel method 'r0' with 99 simulations alternative hypothesis: statistic is less or greater than simulated values Checkerboard Units : 2767 C-score (species mean): 2.258776 statistic SES mean 2.5% 50% 97.5% Pr(sim.) checkerboards 2767 -18.913 8031.6 7444.4 8042.0 8541.2 0.01 ** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Futures created: 2 oecosimu object Call: oecosimu(comm = sipoo, nestfun = nestedchecker, method = "r0", parallel = cl) nullmodel method 'r0' with 99 simulations alternative hypothesis: statistic is less or greater than simulated values Checkerboard Units : 2767 C-score (species mean): 2.258776 statistic SES mean 2.5% 50% 97.5% Pr(sim.) checkerboards 2767 -18.913 8031.6 7444.4 8042.0 8541.2 0.01 ** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Failed to undo environment variables: - Expected environment variables: [n=219] '!ExitCode', 'ALLUSERSPROFILE', 'APPDATA', 'BIBINPUTS', 'BINDIR', 'BSTINPUTS', 'COMMONPROGRAMFILES', 'COMPUTERNAME', 'COMSPEC', 'CURL_CA_BUNDLE', 'CV_Instance001', 'CYGWIN', 'CommonProgramFiles(x86)', 'CommonProgramW6432', 'DriverData', 'HOME', 'HOMEDRIVE', 'HOMEPATH', 'JAGS_ROOT', 'JAVA_HOME', 'LANGUAGE', 'LC_COLLATE', 'LC_MONETARY', 'LC_TIME', 'LOCALAPPDATA', 'LOGONSERVER', 'LS_HOME', 'LS_LICENSE_PATH', 'MAKE', 'MAKEFLAGS', 'MAKELEVEL', 'MFLAGS', 'MSMPI_BENCHMARKS', 'MSMPI_BIN', 'MSYS2_ENV_CONV_EXCL', 'NUMBER_OF_PROCESSORS', 'OCL', 'OMP_THREAD_LIMIT', 'OS', 'PATH', 'PATHEXT', 'PROCESSOR_ARCHITECTURE', 'PROCESSOR_IDENTIFIER', 'PROCESSOR_LEVEL', 'PROCESSOR_REVISION', 'PROGRAMFILES', 'PROMPT', 'PSModulePath', 'PUBLIC', 'PWD', 'ProgramData', 'ProgramFiles(x86)', 'ProgramW6432', 'RTOOLS44_HOME', 'RTOOLS45_HOME', 'R_ARCH', 'R_BROWSER', 'R_BZIPCMD', 'R_CMD', 'R_COMPILED_BY', 'R_CRAN_WEB', 'R_CUSTOM_TOOLS_PATH', 'R_CUSTOM_TOOLS_SOFT', 'R_DOC_DIR', 'R_ENVIRON_USER', 'R_GSCMD', 'R_GZIPCMD', 'R_HOME', 'R_INCLUDE_DIR', 'R_INSTALL_TAR', 'R_LIBS', 'R_LIBS_SITE', 'R_LIBS_USER', 'R_MAX_NUM_DLLS', 'R_OSTYPE', 'R_PAPERSIZE', 'R_PAPERSIZE_USER', 'R_PARALLELLY_MAKENODEPSOCK_AUTOKILL', 'R_PARALLELLY_MAKENODEPSOCK_CONNECTTIMEOUT', 'R_PARALLELLY_MAKENODEPSOCK_RSCRIPT_LABEL', 'R_PARALLELLY_MAKENODEPSOCK_SESSIONINFO_PKGS', 'R_PARALLELLY_MAKENODEPSOCK_TIMEOUT', 'R_PARALLELLY_RANDOM_PORTS', 'R_PARALLEL_PORT', 'R_RD4PDF', 'R_RTOOLS45_PATH', 'R_SCRIPT_LEGACY', 'R_SHARE_DIR', 'R_TESTME_NAME', 'R_TESTME_PACKAGE', 'R_TESTME_PATH', 'R_TESTS', 'R_UNZIPCMD', 'R_USER', 'R_VERSION', 'R_ZIPCMD', 'SED', 'SHLVL', 'SYSTEMDRIVE', 'SYSTEMROOT', 'TAR', 'TAR_OPTIONS', 'TEMP', 'TERM', 'TETRAD_DIR', 'TEXINPUTS', 'TMP', 'TMPDIR', 'USERDOMAIN', 'USERDOMAIN_ROAMINGPROFILE', 'USERNAME', 'USERPROFILE', 'WINDIR', '_', '_R_BIBTOOLS_CACHE_BIBENTRIES_', '_R_CHECK_AUTOCONF_', '_R_CHECK_BOGUS_RETURN_', '_R_CHECK_BROWSER_NONINTERACTIVE_', '_R_CHECK_BUILD_VIGNETTES_SEPARATELY_', '_R_CHECK_CODETOOLS_PROFILE_', '_R_CHECK_CODE_ASSIGN_TO_GLOBALENV_', '_R_CHECK_CODE_ATTACH_', '_R_CHECK_CODE_CLASS_IS_STRING_', '_R_CHECK_CODE_DATA_INTO_GLOBALENV_', '_R_CHECK_CODE_USAGE_VIA_NAMESPACES_', '_R_CHECK_CODE_USAGE_WITHOUT_LOADING_', '_R_CHECK_CODE_USAGE_WITH_ONLY_BASE_ATTACHED_', '_R_CHECK_CODOC_VARIABLES_IN_USAGES_', '_R_CHECK_COMPACT_DATA2_', '_R_CHECK_COMPILATION_FLAGS_', '_R_CHECK_CONNECTIONS_LEFT_OPEN_', '_R_CHECK_CRAN_INCOMING_', '_R_CHECK_CRAN_INCOMING_ASPELL_RECHECK_MAYBE_', '_R_CHECK_CRAN_INCOMING_ASPELL_RECHECK_START_', '_R_CHECK_CRAN_INCOMING_CHECK_FILE_URIS_', '_R_CHECK_CRAN_INCOMING_CHECK_URLS_IN_PARALLEL_', '_R_CHECK_CRAN_INCOMING_NOTE_GNU_MAKE_', '_R_CHECK_CRAN_INCOMING_REMOTE_', '_R_CHECK_CRAN_INCOMING_USE_ASPELL_', '_R_CHECK_DATALIST_', '_R_CHECK_DEPRECATED_DEFUNCT_', '_R_CHECK_DOC_SIZES2_', '_R_CHECK_DOT_FIRSTLIB_', '_R_CHECK_DOT_INTERNAL_', '_R_CHECK_EXAMPLE_TIMING_THRESHOLD_', '_R_CHECK_EXECUTABLES_', '_R_CHECK_EXECUTABLES_EXCLUSIONS_', '_R_CHECK_FF_CALLS_', '_R_CHECK_FF_DUP_', '_R_CHECK_FORCE_SUGGESTS_', '_R_CHECK_FUTURE_FILE_TIMESTAMPS_', '_R_CHECK_FUTURE_FILE_TIMESTAMPS_LEEWAY_', '_R_CHECK_HAVE_MYSQL_', '_R_CHECK_HAVE_ODBC_', '_R_CHECK_HAVE_PERL_', '_R_CHECK_HAVE_POSTGRES_', '_R_CHECK_INSTALL_DEPENDS_', '_R_CHECK_INTERNALS2_', '_R_CHECK_LENGTH_1_CONDITION_', '_R_CHECK_LICENSE_', '_R_CHECK_LIMIT_CORES_', '_R_CHECK_LOG_USE_INFO_', '_R_CHECK_MATRIX_DATA_', '_R_CHECK_MBCS_CONVERSION_FAILURE_', '_R_CHECK_NATIVE_ROUTINE_REGISTRATION_', '_R_CHECK_NEWS_IN_PLAIN_TEXT_', '_R_CHECK_NO_RECOMMENDED_', '_R_CHECK_NO_STOP_ON_TEST_ERROR_', '_R_CHECK_ORPHANED_', '_R_CHECK_OVERWRITE_REGISTERED_S3_METHODS_', '_R_CHECK_PACKAGES_USED_IGNORE_UNUSED_IMPORTS_', '_R_CHECK_PACKAGES_USED_IN_TESTS_USE_SUBDIRS_', '_R_CHECK_PACKAGE_DATASETS_SUPPRESS_NOTES_', '_R_CHECK_PACKAGE_NAME_', '_R_CHECK_PKG_SIZES_', '_R_CHECK_PKG_SIZES_THRESHOLD_', '_R_CHECK_PRAGMAS_', '_R_CHECK_RCPP_NOT_NEEDED_', '_R_CHECK_RD_BIBENTRIES_CITED_NOT_SHOWN_', '_R_CHECK_RD_EXAMPLES_T_AND_F_', '_R_CHECK_RD_LINE_WIDTHS_', '_R_CHECK_RD_MATH_RENDERING_', '_R_CHECK_RD_NOTE_LOST_BRACES_', '_R_CHECK_RD_VALIDATE_RD2HTML_', '_R_CHECK_REPLACING_IMPORTS_', '_R_CHECK_R_DEPENDS_', '_R_CHECK_S3_METHODS_SHOW_POSSIBLE_ISSUES_', '_R_CHECK_SCREEN_DEVICE_', '_R_CHECK_SERIALIZATION_', '_R_CHECK_SHLIB_OPENMP_FLAGS_', '_R_CHECK_SRC_MINUS_W_IMPLICIT_', '_R_CHECK_SUBDIRS_NOCASE_', '_R_CHECK_SUGGESTS_ONLY_', '_R_CHECK_SYSTEM_CLOCK_', '_R_CHECK_TESTS_NLINES_', '_R_CHECK_TEST_TIMING_', '_R_CHECK_TIMINGS_', '_R_CHECK_TOPLEVEL_FILES_', '_R_CHECK_UNDOC_USE_ALL_NAMES_', '_R_CHECK_UNSAFE_CALLS_', '_R_CHECK_URLS_RELATIVE_PATHS_', '_R_CHECK_URLS_SHOW_301_STATUS_', '_R_CHECK_VC_DIRS_', '_R_CHECK_VIGNETTES_NLINES_', '_R_CHECK_VIGNETTES_SKIP_RUN_MAYBE_', '_R_CHECK_VIGNETTE_TIMING_', '_R_CHECK_VIGNETTE_TITLES_', '_R_CHECK_WINDOWS_DEVICE_', '_R_CHECK_XREFS_NOTE_MISSING_PACKAGE_ANCHORS_', '_R_CHECK_XREFS_USE_ALIASES_FROM_CRAN_', '_R_CLASS_MATRIX_ARRAY_', '_R_DEPRECATED_IS_R_', '_R_S3_METHOD_LOOKUP_BASEENV_AFTER_GLOBALENV_', '_R_SHLIB_BUILD_OBJECTS_SYMBOL_TABLES_', '_R_USE_STRICT_R_HEADERS_', '__R_CHECK_DOC_FILES_NOTE_IF_ALL_INTERNAL__', 'maj.version', 'nextArg--timingsnextArg--install', 'tempdirname' - Environment variables still there: [n=0] - Environment variables missing: [n=1] 'MAKEFLAGS' Differences environment variable by environment variable: Skipping, because path appears not to be an 'R CMD check' folder: 'D:/temp/2026_04_01_06_55_16_3646' Test time: user.self=7s, sys.self=0.4s, elapsed=3e+01s, user.child=NAs, sys.child=NAs Test 'futurize-vegan' ... success > > proc.time() user system elapsed 7.28 0.46 25.70