Test Summary Report R-Paket VCA V1.5.0 ------------------------------------- 1) Package Description: ----------------------- Package: VCA Version: 1.5.0 Date: 2024-01-18 Title: Variance Component Analysis Author: Andre Schuetzenmeister [aut, cre], Florian Dufey [aut] Maintainer: Andre Schuetzenmeister Depends: R (>= 3.0.0) Imports: stats, graphics, grDevices, lme4, Matrix, methods, numDeriv Suggests: VFP, STB, knitr, rmarkdown, prettydoc, RUnit Description: ANOVA and REML estimation of linear mixed models is implemented, once following Searle et al. (1991, ANOVA for unbalanced data), once making use of the 'lme4' package. The primary objective of this package is to perform a variance component analysis (VCA) according to CLSI EP05-A3 guideline "Evaluation of Precision of Quantitative Measurement Procedures" (2014). There are plotting methods for visualization of an experimental design, plotting random effects and residuals. For ANOVA type estimation two methods for computing ANOVA mean squares are implemented (SWEEP and quadratic forms). The covariance matrix of variance components can be derived, which is used in estimating confidence intervals. Linear hypotheses of fixed effects and LS means can be computed. LS means can be computed at specific values of covariables and with custom weighting schemes for factor variables. See ?VCA for a more comprehensive description of the features. License: GPL (>= 3) VignetteBuilder: knitr, rmarkdown RoxygenNote: 7.2.3 NeedsCompilation: yes Packaged: 2024-01-18 09:59:40 UTC; schueta6 Built: R 4.4.0; x86_64-w64-mingw32; 2024-01-18 10:30:07 UTC; windows Archs: x64 -- File: D:/RCompile/CRANincoming/R-devel/lib/VCA/Meta/package.rds 2) Test Environment: -------------------- sysname : Windows release : Server x64 version : build 20348 nodename : CRANWIN3 machine : x86-64 login : CRAN user : CRAN effective_user : CRAN 3) Test Protocol: ----------------- RUNIT TEST PROTOCOL -- Thu Jan 18 11:34:46 2024 *********************************************** Number of test functions: 176 Number of errors: 0 Number of failures: 3 1 Test Suite : VCA - 176 test functions, 0 errors, 3 failures FAILURE in TF043.LSMeans.atCovarLevel: Error in checkEquals(as.numeric(round(lsm[-c(1, 2), "Estimate"], 2)), : Numeric: lengths (0, 8) differ FAILURE in TF044.LSMeans.atCovarLevel: Error in checkEquals(nrow(lsm), 2) : Mean relative difference: 1 FAILURE in TF045.LSMeans.atCovarLevel: Error in checkEquals(nrow(lsm1), 2) : Mean relative difference: 1 Details *************************** Test Suite: VCA Test function regexp: ^TF[[:digit:]]{3}.+ Test file regexp: runit.*\.R$ Involved directory: d:/RCompile/CRANincoming/R-devel/VCA.Rcheck/tests/runit/UnitTests --------------------------- Test file: d:/RCompile/CRANincoming/R-devel/VCA.Rcheck/tests/runit/UnitTests/runit.VCAinference.R TF001.VCAinference.constrained_CIs.balanced: (6 checks) ... OK (0.95 seconds) TF002.VCAinference.unconstrained_CIs.balanced: (6 checks) ... OK (1.23 seconds) TF003.VCAinference.negative_VC.balanced: (4 checks) ... OK (1.14 seconds) TF004.VCAinference.VC_CI.balanced: (6 checks) ... OK (1.21 seconds) TF005.VCAinference.WinCAEv_PrecPerf.SD_CI: (2 checks) ... OK (0.43 seconds) TF006.VCAinference.WinCAEv_PrecPerf.SD_CI: (2 checks) ... OK (0.39 seconds) TF007.VCAinference.CrossedNested.VC_CI.balanced: (5 checks) ... OK (0.33 seconds) TF008.VCAinference.CrossedNested.VC_CI.unbalanced: (1 checks) ... OK (0.32 seconds) TF009.VCAinference.CrossedNested.VC_CI.balanced: (5 checks) ... OK (0.31 seconds) TF010.VCAinference.CrossedNested.VC_CI.unbalanced: (1 checks) ... OK (0.29 seconds) TF011.VCAinference.CrossedNested.VC_CI.balanced: (5 checks) ... OK (0.35 seconds) TF012.VCAinference.CrossedNested.VC_CI.unbalanced: (1 checks) ... OK (0.33 seconds) TF013.anovaVCA.Satt_methodology_for_CI.balanced: (2 checks) ... OK (0.34 seconds) TF014.anovaVCA.Satt_methodology_for_CI.balanced: (2 checks) ... OK (0.27 seconds) TF015.anovaMM.Satt_methodology.balanced: (2 checks) ... OK (0.17 seconds) TF016.anovaMM.Satt_methodology.balanced: (2 checks) ... OK (0.17 seconds) TF017.anovaVCA.Est_outsided_CI: (4 checks) ... OK (0.31 seconds) TF018.VCAinference.constrained_CIs.balanced: (6 checks) ... OK (0.41 seconds) TF019.VCAinference.unconstrained_CIs.balanced: (4 checks) ... OK (0.23 seconds) TF020.VCAinference.balanced.REML.satterthwaite: (4 checks) ... OK (0.21 seconds) TF021.VCAinference.VC_CI.balanced.REML: (6 checks) ... OK (0.2 seconds) --------------------------- Test file: d:/RCompile/CRANincoming/R-devel/VCA.Rcheck/tests/runit/UnitTests/runit.anovaMM.R TF001.anovaMM.balanced1: (2 checks) ... OK (0.23 seconds) TF002.anovaMM.NegVC.balanced: (2 checks) ... OK (0.89 seconds) TF003.anovaMM.NegVC.unbalanced: (2 checks) ... OK (0.89 seconds) TF004.anovaMM.ProcMixed.balanced1: (2 checks) ... OK (0.15 seconds) TF005.anovaMM.ProcMixed.unbalanced1: (2 checks) ... OK (0.16 seconds) TF006.anovaDF.balanced: (1 checks) ... OK (0.17 seconds) TF007.anovaDF.unbalanced: (1 checks) ... OK (0.21 seconds) TF008.anovaDF.balanced: (1 checks) ... OK (0.18 seconds) TF009.anovaDF.unbalanced: (1 checks) ... OK (0.28 seconds) TF010.anovaMM.exception_handling: (6 checks) ... OK (0.02 seconds) TF011.anovaMM.SD_results: (3 checks) ... OK (0.73 seconds) TF012.anovaMM.CV_perc_results: (3 checks) ... OK (0.52 seconds) TF013.anovaMM.Percent_Total_results: (3 checks) ... OK (0.48 seconds) TF014.anovaMM.missing_value_handling: (4 checks) ... OK (0.35 seconds) TF015.anovaMM.sleepstudy: (1 checks) ... OK (0.17 seconds) TF016.anovaMM.error.chol2inv: (1 checks) ... OK (0.19 seconds) TF017.anovaMM.zeroVariance: (3 checks) ... OK (0.48 seconds) TF018.anovaMM.byProcessing: (2 checks) ... OK (0.46 seconds) --------------------------- Test file: d:/RCompile/CRANincoming/R-devel/VCA.Rcheck/tests/runit/UnitTests/runit.anovaVCA.R TF001.anovaVCA.exception: (6 checks) ... OK (0 seconds) TF002.anovaVCA.EP05_A2_intermediate_precision.balanced: (3 checks) ... OK (1.06 seconds) TF003.anovaVCA.EP05_A2_intermediate_precision.unbalanced: (3 checks) ... OK (0.91 seconds) TF004.anovaVCA.SD_results: (3 checks) ... OK (1 seconds) TF005.anovaVCA.CV_perc_results: (3 checks) ... OK (0.89 seconds) TF006.anovaVCA.Percent_Total_results: (3 checks) ... OK (0.92 seconds) TF007.anovaVCA.EP05_A3_Reproducibility.balanced: (3 checks) ... OK (0.94 seconds) TF008.anovaVCA.EP05_A3_Reproducibility.unbalanced: (3 checks) ... OK (1.06 seconds) TF009.anovaVCA.WRI: (3 checks) ... OK (1.07 seconds) TF010.anovaVCA.BDI.external_labs.balanced: (3 checks) ... OK (0.95 seconds) TF011.anovaVCA.BDI.external_labs.unbalanced: (3 checks) ... OK (1.06 seconds) TF012.anovaVCA.variable_conversion: (1 checks) ... OK (0.95 seconds) TF013.anovaVCA.missing_value_handling: (4 checks) ... OK (0.61 seconds) TF014.anovaVCA.crossed_nested.balanced: (5 checks) ... OK (0.33 seconds) TF015.anovaVCA.crossed_nested.unbalanced: (5 checks) ... OK (0.31 seconds) TF016.anovaVCA.crossed_nested.balanced: (5 checks) ... OK (0.43 seconds) TF017.anovaVCA.crossed_nested.unbalanced: (5 checks) ... OK (0.32 seconds) TF018.anovaDF.balanced: (1 checks) ... OK (0.29 seconds) TF019.anovaDF.unbalanced: (1 checks) ... OK (0.28 seconds) TF020.anovaDF.balanced: (1 checks) ... OK (0.29 seconds) TF021.anovaDF.unbalanced: (1 checks) ... OK (0.32 seconds) TF022.anovaDF.balanced: (1 checks) ... OK (0.36 seconds) TF023.anovaDF.unbalanced: (1 checks) ... OK (0.42 seconds) TF024.anovaDF.balanced: (1 checks) ... OK (0.31 seconds) TF025.anovaDF.unbalanced: (1 checks) ... OK (0.34 seconds) TF026.anovaDF.balanced.ordering: (2 checks) ... OK (0.64 seconds) TF027.check.sweep_vs_SAS_computation: (1 checks) ... OK (0.44 seconds) TF034.anovaVCA.zeroVariance: (2 checks) ... OK (0.58 seconds) TF035.anovaVCA.MisspecifiedModel: (1 checks) ... OK (0.02 seconds) TF036.anovaVCA.byProcessing: (2 checks) ... OK (0.71 seconds) --------------------------- Test file: d:/RCompile/CRANincoming/R-devel/VCA.Rcheck/tests/runit/UnitTests/runit.misc.R TF001.CovarianceMatrix: (5 checks) ... OK (0.31 seconds) TF002.marginal_residuals: (3 checks) ... OK (0.19 seconds) TF003.conditional_residuals: (3 checks) ... OK (0.17 seconds) TF004.ddfm.LMM.unbalanced: (3 checks) ... OK (0.32 seconds) TF005.ddfm.LMM.unbalanced: (3 checks) ... OK (0.34 seconds) TF006.stepwiseVCA.fully_nested: (6 checks) ... OK (0.3 seconds) TF007.getL.simple_contrasts: (2 checks) ... OK (0.23 seconds) TF008.getL.complex_contrasts: (1 checks) ... OK (0.28 seconds) TF009.getL.complex_contrasts: (1 checks) ... OK (0.27 seconds) TF010.ranef.balanced.nested: (1 checks) ... OK (0.29 seconds) TF011.ranef.balanced.nested: (1 checks) ... OK (0.3 seconds) TF012.ranef.balanced.nested: (1 checks) ... OK (0.29 seconds) TF013.ranef.unbalanced.nested: (1 checks) ... OK (0.28 seconds) TF014.ranef.unbalanced.nested: (1 checks) ... OK (0.3 seconds) TF015.ranef.unbalanced.nested: (1 checks) ... OK (0.3 seconds) TF016.as.matrix.anovaVCA: (1 checks) ... OK (0.3 seconds) TF017.as.matrix.anovaMM: (1 checks) ... OK (0.17 seconds) TF018.SattDF_total_vs_Neter_Wasserman: (1 checks) ... OK (0.28 seconds) TF019.SattDF_total_vs_Neter_Wasserman: (1 checks) ... OK (0.34 seconds) TF020.SattDF_total_vs_Neter_Wasserman: (1 checks) ... OK (0.33 seconds) TF021.lsmeans.balanced: (4 checks) ... OK (0.22 seconds) TF022.lsmeans.unbalanced: (2 checks) ... OK (0.19 seconds) TF023.ddfm_fixef.all_methods.Orthodont.balanced: (3 checks) ... OK (0.18 seconds) TF024.ddfm_lsmeans.all_methods.Orthodont.unbalanced: (3 checks) ... OK (0.24 seconds) TF025.lsmeans.including_covariate: (1 checks) ... OK (0.22 seconds) TF026.lsmeans.complex_model.including_covariate: (1 checks) ... OK (0.28 seconds) TF027.anovaVCA.by_processing: (6 checks) ... OK (3.89 seconds) TF028.anovaMM.by_processing: (6 checks) ... OK (1.94 seconds) TF029.anovaVCA.by_processing: (12 checks) ... OK (4.23 seconds) TF030.anovaVCA.by_processing: (6 checks) ... OK (3.59 seconds) TF031.test.lsmeans: (1 checks) ... OK (0.24 seconds) TF032.ANOVA_vs_REML.residuals.raw: (4 checks) ... OK (1.39 seconds) TF033.ANOVA_vs_REML.residuals.studentized: (4 checks) ... OK (1.45 seconds) TF034.ANOVA_vs_REML.residuals.pearson: (4 checks) ... OK (1.6 seconds) TF035.ANOVA_vs_REML.residuals.standardized: (4 checks) ... OK (1.43 seconds) TF036.ANOVA_vs_REML.ranef.raw: (4 checks) ... OK (1.47 seconds) TF037.ANOVA_vs_REML.ranef.studentized: (4 checks) ... OK (1.6 seconds) TF038.ANOVA_vs_REML.ranef.standardized: (4 checks) ... OK (1.42 seconds) TF039.remlVCA.by_processing: (12 checks) ... OK (1.03 seconds) TF040.remlMM.by_processing: (12 checks) ... OK (0.87 seconds) TF041.REML.test.lsmeans: (1 checks) ... OK (0.11 seconds) TF042.balancedness.ordered_vs_unordered: (4 checks) ... OK (0.97 seconds) TF043.LSMeans.atCovarLevel: FAILURE !! (check number 1) Error in checkEquals(as.numeric(round(lsm[-c(1, 2), "Estimate"], 2)), : Numeric: lengths (0, 8) differ TF044.LSMeans.atCovarLevel: FAILURE !! (check number 1) Error in checkEquals(nrow(lsm), 2) : Mean relative difference: 1 TF045.LSMeans.atCovarLevel: FAILURE !! (check number 1) Error in checkEquals(nrow(lsm1), 2) : Mean relative difference: 1 TF046.model.terms: (6 checks) ... OK (1.15 seconds) TF047.as.matrix.VCA.REML: (12 checks) ... OK (0.25 seconds) TF048.as.matrix.VCAinference.REML: (18 checks) ... OK (0.16 seconds) TF049.as.matrix.VCAinference.ANOVA: (30 checks) ... OK (0.39 seconds) TF050.lmerSummary: (4 checks) ... OK (0.47 seconds) TF051.Scale.reScale.anovaVCA: (20 checks) ... OK (7.58 seconds) TF052.Scale.reScale.anovaMM: (20 checks) ... OK (4.39 seconds) TF053.Scale.reScale.remlVCA: (20 checks) ... OK (7.22 seconds) TF054.Scale.reScale.remlMM: (20 checks) ... OK (7.29 seconds) TF055.fitVCA.anovaVCA.remlVCA: (20 checks) ... OK (15.21 seconds) TF056.orderData.remlVCA: (1 checks) ... OK (4 seconds) TF057.orderData.remlMM: (1 checks) ... OK (3.9 seconds) TF058.predict.anovaMM: (1 checks) ... OK (0.35 seconds) TF059.predict.remlMM.newdata: (1 checks) ... OK (0.14 seconds) TF060.predict.remlMM.newdata: (1 checks) ... OK (0.08 seconds) TF061.predict.remlMM.restriction: (1 checks) ... OK (0.1 seconds) TF062.comparison.fitLMM.REML: (1 checks) ... OK (0.17 seconds) TF063.comparison.fitLMM.ANOVA: (1 checks) ... OK (0.37 seconds) TF064.Scale.reScale.response: (1 checks) ... OK (0.47 seconds) TF065.comparison.fitVCA.REML: (1 checks) ... OK (0.2 seconds) TF066.comparison.fitVCA.ANOVA: (1 checks) ... OK (0.71 seconds) TF067.checkException.NoReScaling: (2 checks) ... OK (0.31 seconds) TF068.check.Scale.reScale.anovaVCA: (10 checks) ... OK (1.38 seconds) TF069.check.Scale.reScale.remlVCA: (10 checks) ... OK (1.12 seconds) TF070.check.Scale.reScale.anovaMM: (10 checks) ... OK (0.72 seconds) TF071.check.Scale.reScale.remlMM: (10 checks) ... OK (0.74 seconds) TF072.getMM.multi.covariables: (2 checks) ... OK (0.01 seconds) TF073.fitVCA_ANOVA_VarVC_TRUE: (1 checks) ... OK (0.68 seconds) TF074.fitVCA_REML_VarVC_TRUE: (1 checks) ... OK (0.17 seconds) TF075.protectedCall.anovaVCA: (1 checks) ... OK (0.01 seconds) TF076.protectedCall.remlVCA: (1 checks) ... OK (0.21 seconds) TF077.protectedCall.remlMM: (1 checks) ... OK (0.17 seconds) TF078.protectedCall.anovaMM: (1 checks) ... OK (0.01 seconds) TF079.protectedCall.fitVCA.anova: (1 checks) ... OK (0.04 seconds) TF080.protectedCall.fitVCA.reml: (1 checks) ... OK (0.15 seconds) TF081.protectedCall.fitLMM.anova: (1 checks) ... OK (0.03 seconds) TF082.protectedCall.fitLMM.reml: (1 checks) ... OK (0.14 seconds) --------------------------- Test file: d:/RCompile/CRANincoming/R-devel/VCA.Rcheck/tests/runit/UnitTests/runit.remlMM.R TF001.anovaVCA_vs_remlMM: (2 checks) ... OK (0.36 seconds) TF002.anovaMM.balanced1: (2 checks) ... OK (0.21 seconds) TF003.anovaMM.NegVC.balanced: (1 checks) ... OK (0.22 seconds) TF004.anovaMM.ProcMixed.balanced1: (2 checks) ... OK (0.11 seconds) TF005.anova_vs_reml.balanced: (4 checks) ... OK (0.57 seconds) TF006.anova_vs_reml.balanced: (2 checks) ... OK (0.28 seconds) TF007.anova_vs_reml.regression.balanced: (4 checks) ... OK (0.25 seconds) TF008.remlMM.exception_handling: (6 checks) ... OK (0.01 seconds) TF009.remlMM.Percent_Total_results: (3 checks) ... OK (0.31 seconds) TF010.remlMM.regression.sleepstudy: (1 checks) ... OK (0.1 seconds) TF011.remlMM.zeroVariance: (3 checks) ... OK (0.33 seconds) TF012.remlMM.byProcessing: (2 checks) ... OK (0.12 seconds) --------------------------- Test file: d:/RCompile/CRANincoming/R-devel/VCA.Rcheck/tests/runit/UnitTests/runit.remlVCA.R TF001.remlVCA.exception: (6 checks) ... OK (0 seconds) TF002.remlVCA.EP05_A2_intermediate_precision.balanced: (6 checks) ... OK (1.64 seconds) TF003.remlVCA.EP05_A2_intermediate_precision.unbalanced: (3 checks) ... OK (0.31 seconds) TF004.remlVCA.EP05_A3_Reproducibility.balanced: (3 checks) ... OK (0.21 seconds) TF005.remlVCA.WRI: (3 checks) ... OK (0.92 seconds) TF006.remlVCA.BDI.external_labs.balanced: (3 checks) ... OK (0.15 seconds) TF007.remlVCA.crossed_nested.balanced: (5 checks) ... OK (0.49 seconds) TF008.remlVCA.crossed_nested.balanced: (5 checks) ... OK (0.37 seconds) TF009.remlVCA.zeroVariance: (2 checks) ... OK (0.19 seconds) TF010.remlVCA.byProcessing: (2 checks) ... OK (0.13 seconds) TF011.remlVCA.VCAinference: (1 checks) ... OK (0.11 seconds) TF012.remlVCA.VCAinference: (24 checks) ... OK (0.21 seconds) TF013.remlVCA.VCAinference: (1 checks) ... OK (0.11 seconds)