* using log directory 'd:/Rcompile/CRANpkg/local/4.0/BayesRGMM.Rcheck' * using R version 4.0.5 (2021-03-31) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'BayesRGMM/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'BayesRGMM' version '2.1' * package encoding: UTF-8 * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'BayesRGMM' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... 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 * loading checks for arch 'i386' ** checking whether the package can be loaded ... OK ** checking whether the package can be loaded with stated dependencies ... OK ** checking whether the package can be unloaded cleanly ... OK ** checking whether the namespace can be loaded with stated dependencies ... OK ** checking whether the namespace can be unloaded cleanly ... OK ** checking loading without being on the library search path ... OK ** checking use of S3 registration ... OK * loading checks for arch 'x64' ** checking whether the package can be loaded ... OK ** checking whether the package can be loaded with stated dependencies ... OK ** checking whether the package can be unloaded cleanly ... OK ** checking whether the namespace can be loaded with stated dependencies ... OK ** checking whether the namespace can be unloaded cleanly ... OK ** checking loading without being on the library search path ... 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 ... [12s] OK * checking Rd files ... OK * checking Rd metadata ... 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 ... 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 pragmas in C/C++ headers and code ... OK * checking compiled code ... OK * checking sizes of PDF files under 'inst/doc' ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... [4s] OK ** running examples for arch 'x64' ... [5s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... [23s] ERROR Running 'testthat.R' [23s] Running the tests in 'tests/testthat.R' failed. Complete output: > library(testthat) > library(BayesRGMM) > > > test_check("BayesRGMM") Data Descriptives: Longitudinal Data Information: Number of Observations: 815 Number of Covariates: 3 Number of subjects: 100 Start running MCMC procedure: Finish MCMC Procedure. Coefficients: PostMean StErr 2.5% 97.5% x1 -0.2 0.09 -0.9 0.82 x2 -0.5 0.06 -1.0 0.05 x3 1.0 0.03 0.7 1.18 x4 -1.1 0.03 -1.3 -0.81 AMRA parameters: PostMean StErr 2.5% 97.5% phi 1 -0.004 0.008 -0.07 0.06 psi 1 0.021 0.016 -0.08 0.14 Random effect: Variance (Intercept) 0.4 Model Information: logL AIC BIC CIC DIC MPL RJR ACC -196 604 880 9e-04 516 6 1 0.9 1 2 3 148 175 192 0% 33.33333% 66.66667% 100% -9.7060423 -1.2010528 0.1110465 6.5569038 Start reading Data End reading Data Read Hyperparameters. Start running MCMC procedure: Start running MCMC procedure: Finish MCMC Procedure. Data Descriptives: Longitudinal Data Information: Number of Observations: 354 Number of Covariates: 3 Number of subjects: 100 Coefficients: PostMean StErr 2.5% 97.5% x1 -0.2 0.04 -0.4 0.2 x2 -0.6 0.06 -1.1 -0.1 x3 0.7 0.04 0.4 0.9 x4 -0.4 0.02 -0.6 -0.2 Parameters in HSD model: PostMean StErr 2.5% 97.5% IndTime1 -0.3 0.05 -0.6 -0.01 IndTime2 -0.2 0.03 -0.4 0.08 Random effect: Variance (Intercept) 0.4 Model Information: logL AIC BIC CIC DIC MPL RJR ACC -133 479 755 0.8 383 5 1 0.9 Estimate of Ri: [,1] [,2] [,3] [,4] [,5] [1,] 1.0 0.2 0.2 0.0 0.0 [2,] 0.2 1.0 0.3 0.2 0.0 [3,] 0.2 0.3 1.0 0.3 0.1 [4,] 0.0 0.2 0.3 1.0 0.3 [5,] 0.0 0.0 0.1 0.3 1.0 [ FAIL 1 | WARN 0 | SKIP 2 | PASS 0 ] == Skipped tests =============================================================== * empty test (2) == Failed tests ================================================================ -- Error (test_BayesRGMM_CPREM.R:54:1): A simulation study of CumulativeProbit -- Error in `CumulativeProbitMCMC(num.of.iter, Data, Robustness, InitialValues, HyperPara, UpdatePara, TuningPara, Interactive)`: inv(): matrix is singular Backtrace: x 1. \-BayesRGMM::BayesCumulativeProbitHSD(...) at test_BayesRGMM_CPREM.R:54:0 2. \-BayesRGMM:::CumulativeProbitMCMC(...) [ FAIL 1 | WARN 0 | SKIP 2 | PASS 0 ] Error: Test failures Execution halted ** running tests for arch 'x64' ... [17s] ERROR Running 'testthat.R' [17s] Running the tests in 'tests/testthat.R' failed. Complete output: > library(testthat) > library(BayesRGMM) > > > test_check("BayesRGMM") Data Descriptives: Longitudinal Data Information: Number of Observations: 815 Number of Covariates: 3 Number of subjects: 100 Start running MCMC procedure: Finish MCMC Procedure. Coefficients: PostMean StErr 2.5% 97.5% x1 -0.2 0.09 -0.9 0.82 x2 -0.5 0.06 -1.0 0.05 x3 1.0 0.03 0.7 1.18 x4 -1.1 0.03 -1.3 -0.81 AMRA parameters: PostMean StErr 2.5% 97.5% phi 1 -0.004 0.008 -0.07 0.06 psi 1 0.021 0.016 -0.08 0.14 Random effect: Variance (Intercept) 0.4 Model Information: logL AIC BIC CIC DIC MPL RJR ACC -196 604 880 9e-04 516 6 1 0.9 1 2 3 148 175 192 0% 33.33333% 66.66667% 100% -9.7060423 -1.2010528 0.1110465 6.5569038 Start reading Data End reading Data Read Hyperparameters. Start running MCMC procedure: Start running MCMC procedure: Finish MCMC Procedure. Data Descriptives: Longitudinal Data Information: Number of Observations: 354 Number of Covariates: 3 Number of subjects: 100 Coefficients: PostMean StErr 2.5% 97.5% x1 -0.2 0.04 -0.4 0.2 x2 -0.6 0.06 -1.1 -0.1 x3 0.7 0.04 0.4 0.9 x4 -0.4 0.02 -0.6 -0.2 Parameters in HSD model: PostMean StErr 2.5% 97.5% IndTime1 -0.3 0.05 -0.6 -0.01 IndTime2 -0.2 0.03 -0.4 0.08 Random effect: Variance (Intercept) 0.4 Model Information: logL AIC BIC CIC DIC MPL RJR ACC -133 479 755 0.8 383 5 1 0.9 Estimate of Ri: [,1] [,2] [,3] [,4] [,5] [1,] 1.0 0.2 0.2 0.0 0.0 [2,] 0.2 1.0 0.3 0.2 0.0 [3,] 0.2 0.3 1.0 0.3 0.1 [4,] 0.0 0.2 0.3 1.0 0.3 [5,] 0.0 0.0 0.1 0.3 1.0 [ FAIL 1 | WARN 0 | SKIP 2 | PASS 0 ] == Skipped tests =============================================================== * empty test (2) == Failed tests ================================================================ -- Error (test_BayesRGMM_CPREM.R:54:1): A simulation study of CumulativeProbit -- Error in `CumulativeProbitMCMC(num.of.iter, Data, Robustness, InitialValues, HyperPara, UpdatePara, TuningPara, Interactive)`: inv(): matrix is singular Backtrace: x 1. \-BayesRGMM::BayesCumulativeProbitHSD(...) at test_BayesRGMM_CPREM.R:54:0 2. \-BayesRGMM:::CumulativeProbitMCMC(...) [ FAIL 1 | WARN 0 | SKIP 2 | PASS 0 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking re-building of vignette outputs ... [12s] WARNING Error(s) in re-building vignettes: --- re-building 'BayesRGMM.Rnw' using Sweave Error: processing vignette 'BayesRGMM.Rnw' failed with diagnostics: chunk 4 (label = Simulation: Ordinal outcome) Error in CumulativeProbitMCMC(num.of.iter, Data, Robustness, InitialValues, : inv(): matrix is singular --- failed re-building 'BayesRGMM.Rnw' SUMMARY: processing the following file failed: 'BayesRGMM.Rnw' Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 1 WARNING