R Under development (unstable) (2026-03-17 r89645 ucrt) -- "Unsuffered Consequences" 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-sva.R > ## Don't edit - it was autogenerated by inst/testme/deploy.R > futurize:::testme("futurize-sva") Test 'futurize-sva' ... chr "none" > if (requireNamespace("sva") && requireNamespace("doFuture")) { + library(futurize) + library(sva) + print(sessionInfo()) + options(f .... [TRUNCATED] Loading required namespace: sva Loading required namespace: doFuture Loading required package: future Loading required package: mgcv Loading required package: nlme This is mgcv 1.9-4. For overview type '?mgcv'. Loading required package: genefilter Loading required package: BiocParallel R Under development (unstable) (2026-03-17 r89645 ucrt) Platform: x86_64-w64-mingw32/x64 Running under: Windows Server 2022 x64 (build 20348) Matrix products: default LAPACK version 3.12.1 locale: [1] LC_COLLATE=C LC_CTYPE=German_Germany.utf8 [3] LC_MONETARY=C LC_NUMERIC=C [5] LC_TIME=C time zone: Europe/Berlin tzcode source: internal attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] sva_3.58.0 BiocParallel_1.44.0 genefilter_1.92.0 [4] mgcv_1.9-4 nlme_3.1-168 futurize_0.2.0 [7] future_1.70.0 loaded via a namespace (and not attached): [1] generics_0.1.4 RSQLite_2.4.6 lattice_0.22-9 [4] listenv_0.10.1 digest_0.6.39 grid_4.6.0 [7] iterators_1.0.14 fastmap_1.2.0 blob_1.3.0 [10] foreach_1.5.2 Matrix_1.7-4 AnnotationDbi_1.72.0 [13] DBI_1.3.0 limma_3.66.0 survival_3.8-6 [16] httr_1.4.8 XML_3.99-0.22 Biostrings_2.78.0 [19] codetools_0.2-20 cli_3.6.5 rlang_1.1.7 [22] crayon_1.5.3 XVector_0.50.0 Biobase_2.70.0 [25] parallelly_1.46.1 future.apply_1.20.2 bit64_4.6.0-1 [28] splines_4.6.0 cachem_1.1.0 tools_4.6.0 [31] parallel_4.6.0 memoise_2.0.1 annotate_1.88.0 [34] doFuture_1.2.1 locfit_1.5-9.12 globals_0.19.1 [37] BiocGenerics_0.56.0 vctrs_0.7.1 R6_2.6.1 [40] png_0.1-9 matrixStats_1.5.0 stats4_4.6.0 [43] KEGGREST_1.50.0 Seqinfo_1.0.0 S4Vectors_0.48.0 [46] edgeR_4.8.0 IRanges_2.44.0 bit_4.6.0 [49] statmod_1.5.1 MatrixGenerics_1.22.0 xtable_1.8-8 [52] compiler_4.6.0 Found2batches Adjusting for0covariate(s) or covariate level(s) Standardizing Data across genes Fitting L/S model and finding priors Finding parametric adjustments Adjusting the Data num [1:50, 1:20] 2.456 0.507 1.135 1.434 1.529 ... - attr(*, "dimnames")=List of 2 ..$ : chr [1:50] "gene1" "gene2" "gene3" "gene4" ... ..$ : chr [1:20] "sample1" "sample2" "sample3" "sample4" ... Found2batches Adjusting for0covariate(s) or covariate level(s) Standardizing Data across genes Fitting L/S model and finding priors Finding parametric adjustments Adjusting the Data Futures created: 2 num [1:50, 1:20] 2.456 0.507 1.135 1.434 1.529 ... - attr(*, "dimnames")=List of 2 ..$ : chr [1:50] "gene1" "gene2" "gene3" "gene4" ... ..$ : chr [1:20] "sample1" "sample2" "sample3" "sample4" ... Found2batches Adjusting for0covariate(s) or covariate level(s) Standardizing Data across genes Fitting L/S model and finding priors Finding parametric adjustments Adjusting the Data Futures created: 2 Found2batches Adjusting for1covariate(s) or covariate level(s) Standardizing Data across genes Fitting L/S model and finding priors Finding parametric adjustments Adjusting the Data num [1:50, 1:20] 2.417 0.481 1.148 1.409 1.561 ... - attr(*, "dimnames")=List of 2 ..$ : chr [1:50] "gene1" "gene2" "gene3" "gene4" ... ..$ : chr [1:20] "sample1" "sample2" "sample3" "sample4" ... Found2batches Adjusting for1covariate(s) or covariate level(s) Standardizing Data across genes Fitting L/S model and finding priors Finding parametric adjustments Adjusting the Data Futures created: 2 num [1:50, 1:20] 2.417 0.481 1.148 1.409 1.561 ... - attr(*, "dimnames")=List of 2 ..$ : chr [1:50] "gene1" "gene2" "gene3" "gene4" ... ..$ : chr [1:20] "sample1" "sample2" "sample3" "sample4" ... Failed to undo environment variables: - Expected environment variables: [n=218] '!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_CHECK_AUTOCONF_', '_R_CHECK_BOGUS_RETURN_', '_R_CHECK_BROWSER_NONINTERACTIVE_', 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'_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_03_18_15_25_17_31911' Test time: user.self=9s, sys.self=0.8s, elapsed=2e+01s, user.child=NAs, sys.child=NAs Test 'futurize-sva' ... success > > proc.time() user system elapsed 9.04 0.84 18.07