* using log directory ‘/srv/hornik/tmp/CRAN/VCA.Rcheck’ * using R Under development (unstable) (2024-01-07 r85787) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 17.0.6 (3) Debian flang-new version 17.0.6 (3) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘VCA/DESCRIPTION’ ... OK * this is package ‘VCA’ version ‘1.4.6’ * checking CRAN incoming feasibility ... [4s/4s] NOTE Maintainer: ‘Andre Schuetzenmeister ’ Package has a VignetteBuilder field but no prebuilt vignette index. * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘VCA’ can be installed ... [8s/8s] OK * used C compiler: ‘Debian clang version 17.0.6 (3)’ * used Fortran compiler: ‘Debian flang-new version 17.0.6 (3)’ * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] OK * checking whether startup messages can be suppressed ... [1s/1s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [14s/14s] OK * checking Rd files ... [0s/0s] NOTE checkRd: (-1) Fsweep.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Fsweep.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Fsweep.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Fsweep.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Fsweep.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Fsweep.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Fsweep.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) Fsweep.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) VCAinference.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) VCAinference.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) VCAinference.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) anovaMM.Rd:59: Lost braces; missing escapes or markup? 59 | A Linear Mixed Model, noted in standard matrix notation, can be written as {y = Xb + Zg + e}, where | ^ checkRd: (-1) getSSQsweep.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) getSSQsweep.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... [0s/0s] OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking usage of KIND in Fortran files ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [7s/7s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [35s/35s] ERROR Running ‘RunAllTests.R’ [35s/35s] Running the tests in ‘tests/RunAllTests.R’ failed. Complete output: > # Run all unit tests, i.e. all checks of all test-functions > # > # Author: Andre Schuetzenmeister > ############################################################################### > > library(VCA) > library(RUnit) > > # enable/disable time-consuming model 1 and model 2 testcases with real-world data > # see file "runit.VCAinference.R" > > realWorldModel2 <- FALSE > realWorldModel1 <- FALSE > > options(warn=1) > > # current working directory > wd <- getwd() > > # set path from wd, where RunAllTests.R resided to RUnit test-scripts (scripts directory) > sd <- "./runit/UnitTests" > tc.path <- sub("\\./", "/", paste0(wd, sd)) > > # test function regexpr fits to string "TFxyz" which are used as identifiers for easier referencing > > testSuite <- defineTestSuite(name="VCA", dirs=tc.path, + testFileRegexp="runit.*\\.R$", + testFuncRegexp = "^TF[[:digit:]]{3}.+", # use custom regexpr for test functions + rngKind="default", + rngNormalKind="default") > > > testData <- runTestSuite(testSuite, verbose=0L) *************************************************************************** Variance Component Analysis (VCA) - test cases for function 'VCAinference'. *************************************************************************** Mixed model equations solved locally. Results could not be assigned to object! Mixed model equations solved locally. Results could not be assigned to object! Mixed model equations solved locally. Results could not be assigned to object! Mixed model equations solved locally. Results could not be assigned to object! Mixed model equations solved locally. Results could not be assigned to object! Mixed model equations solved locally. Results could not be assigned to object! Mixed model equations solved locally. Results could not be assigned to object! Mixed model equations solved locally. Results could not be assigned to object! Mixed model equations solved locally. Results could not be assigned to object! Mixed model equations solved locally. Results could not be assigned to object! Mixed model equations solved locally. Results could not be assigned to object! Mixed model equations solved locally. Results could not be assigned to object! Mixed model equations solved locally. Results could not be assigned to object! Mixed model equations solved locally. Results could not be assigned to object! Mixed model equations solved locally. Results could not be assigned to object! SAS PROC MIXED uses the inverse of the Fisher-Information Matrix as approximation of Covariance-Matrix of Variance Components. This is equal to the one obtained via ANOVA-approach stated in "Variance Components" (Searle et al. 1991) in case of balanced designs, otherwise Var(VC) of both results may differ: SAS_Est R_Est SAS_LCL R_LCL SAS_UCL R_UCL lot 0.01377 0.01377 -0.013750 -0.016870 0.041280 0.044400 device 0.06190 0.06190 -0.062340 -0.063040 0.186100 0.186800 lot:device:day 0.01235 0.01235 -0.004180 -0.004480 0.028870 0.029180 lot:device:day:run 0.05125 0.05125 0.033110 0.032950 0.069400 0.069560 error 0.00118 0.00118 0.000932 0.000932 0.001543 0.001543 Est_Diff LCL_Diff UCL_Diff lot 0 0.00312 -0.00312 device 0 0.00070 -0.00070 lot:device:day 0 0.00030 -0.00031 lot:device:day:run 0 0.00016 -0.00016 error 0 0.00000 0.00000 Mixed model equations solved locally. Results could not be assigned to object! Mixed model equations solved locally. Results could not be assigned to object! SAS PROC MIXED uses the inverse of the Fisher-Information Matrix as approximation of Covariance-Matrix of Variance Components. This is equal to the one obtained via ANOVA-approach stated in "Variance Components" (Searle et al. 1991) in case of balanced designs, otherwise Var(VC) of both results may differ: SAS_Est R_Est SAS_LCL R_LCL SAS_UCL R_UCL Est_Diff lot 0.18920 0.18920 -0.19090 -0.21540 0.56920 0.59380 0 device 0.43590 0.43590 -0.46080 -0.45200 1.33260 1.32380 0 lot:device:day 0.31780 0.31780 0.18600 0.18680 0.44960 0.44870 0 lot:device:day:run 0.05724 0.05724 0.02931 0.02931 0.08517 0.08517 0 error 0.04108 0.04108 0.03241 0.03241 0.05376 0.05376 0 LCL_Diff UCL_Diff lot 0.0245 -0.0246 device -0.0088 0.0088 lot:device:day -0.0008 0.0009 lot:device:day:run 0.0000 0.0000 error 0.0000 0.0000 Mixed model equations solved locally. Results could not be assigned to object! Mixed model equations solved locally. Results could not be assigned to object! SAS PROC MIXED uses the inverse of the Fisher-Information Matrix as approximation of Covariance-Matrix of Variance Components. This is equal to the one obtained via ANOVA-approach stated in "Variance Components" (Searle et al. 1991) in case of balanced designs, otherwise Var(VC) of both results may differ: SAS_Est R_Est SAS_LCL R_LCL SAS_UCL lot -0.000850 -0.000850 -0.001540 -0.001690 -1.700e-04 device 0.058040 0.058040 -0.057620 -0.058080 1.737e-01 lot:device:day -0.017410 -0.017410 -0.034820 -0.035110 -3.250e-06 lot:device:day:run 0.084000 0.084000 0.053940 0.054130 1.141e-01 error 0.000337 0.000337 0.000266 0.000266 4.400e-04 R_UCL Est_Diff LCL_Diff UCL_Diff lot -0.00002000 0 0.00015 -0.00015000 device 0.17420000 0 0.00046 -0.00050000 lot:device:day 0.00028594 0 0.00029 -0.00028919 lot:device:day:run 0.11390000 0 -0.00019 0.00020000 error 0.00044000 0 0.00000 0.00000000 Mixed model equations solved locally. Results could not be assigned to object! Mixed model equations solved locally. Results could not be assigned to object! Mixed model equations solved locally. Results could not be assigned to object! Mixed model equations solved locally. Results could not be assigned to object! Warning in VCAinference(fit, ci.method = "satterthwaite") : Point estimate(s) of VC(s) 'Site:Day:Run' found outside of confidence interval, CI was set to 'NA'! Inference from (V)ariance (C)omponent (A)nalysis ------------------------------------------------ > VC: ----- Estimate DF CI LCL CI UCL One-Sided LCL One-Sided UCL total 0.3405 15.5385 0.1875 0.8005 0.2059 0.6927 Site 0.1381 2.6726 0.0423 2.4767 0.0510 1.4414 Site:Day 0.0084 0.4506 0.0012 36811.9725 0.0017 1697.8716 Site:Day:Run 0.0004 0.0005 Inf error 0.1936 80.0000 0.1452 0.2710 0.1520 0.2564 95% Confidence Level Satterthwaite methodology used for computing CIs boundary (singular) fit: see help('isSingular') boundary (singular) fit: see help('isSingular') ************************************************************************** Variance Component Analysis (VCA) - test cases defined in runit.anovaMM.R. ************************************************************************** Error in anovaMM() : argument "form" is missing, with no default Error in anovaMM(Data = 1) : argument "form" is missing, with no default Error in anovaMM(Data = data.frame()) : argument "form" is missing, with no default Error in anovaMM(Data = data.frame(y = 1:10)) : argument "form" is missing, with no default Error in orderData(Data, tobj, quiet = quiet, order.data = order.data) : all(vars %in% colnames(Data)) is not TRUE Error in orderData(Data, tobj, quiet = quiet, order.data = order.data) : all(vars %in% colnames(Data)) is not TRUE There are 3 missing values for the response variable (obs: 43, 57, 66)! Variable 'run' has 3 missing values (obs: 19, 38, 50)! Variable 'day' has 3 missing values (obs: 78, 79, 80)! Convert variable Site from "character" to "factor"! Convert variable ID from "character" to "factor"! Warning in anovaMM(y ~ day + cov + day:(run), dat1) : All values of response variable 'y' are equal! Warning in anovaMM(y ~ day/(run), dat1) : All values of response variable 'y' are equal! Warning in anovaMM(y ~ (day)/(run), dat1) : All values of response variable 'y' are equal! *********************************************************************** Variance Component Analysis (VCA) - test cases for function 'anovaVCA'. *********************************************************************** Error in anovaVCA() : argument "form" is missing, with no default Error in anovaVCA(Data = 1) : argument "form" is missing, with no default Error in anovaVCA(Data = data.frame()) : argument "form" is missing, with no default Error in anovaVCA(Data = data.frame(y = 1:10)) : argument "form" is missing, with no default Error in orderData(Data, tobj, quiet = quiet, exclude.numeric = FALSE, : all(vars %in% colnames(Data)) is not TRUE Error in orderData(Data, tobj, quiet = quiet, exclude.numeric = FALSE, : all(vars %in% colnames(Data)) is not TRUE There are 3 missing values for the response variable (obs: 43, 57, 66)! Variable 'day' has 3 missing values (obs: 78, 79, 80)! Variable 'run' has 3 missing values (obs: 19, 38, 50)! Warning in asMethod(object) : sparse->dense coercion: allocating vector of size 1.9 GiB *** caught segfault *** address 0x7ffd00ae0b08, cause 'memory not mapped' Traceback: 1: Fsweep(M, asgn = asgn) 2: getSSQsweep(Data, tobj) 3: anovaVCA(y ~ VC1/VC2, HugeData) 4: doTryCatch(return(expr), name, parentenv, handler) 5: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 6: tryCatchList(expr, classes, parentenv, handlers) 7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))}) 8: try(fit <- anovaVCA(y ~ VC1/VC2, HugeData), silent = TRUE) 9: func() 10: system.time(func(), gcFirst = RUnitEnv$.gcBeforeTest) 11: doTryCatch(return(expr), name, parentenv, handler) 12: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 13: tryCatchList(expr, classes, parentenv, handlers) 14: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))}) 15: try(system.time(func(), gcFirst = RUnitEnv$.gcBeforeTest)) 16: .executeTestCase(funcName, envir = sandbox, setUpFunc = .setUp, tearDownFunc = .tearDown) 17: .sourceTestFile(testFile, testSuite$testFuncRegexp) 18: runTestSuite(testSuite, verbose = 0L) An irrecoverable exception occurred. R is aborting now ... Segmentation fault * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... [9s/9s] OK * checking PDF version of manual ... [4s/4s] OK * checking HTML version of manual ... [2s/2s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 2 NOTEs