* using log directory 'd:/Rcompile/CRANpkg/local/3.5/basket.Rcheck' * using R version 3.5.3 (2019-03-11) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'basket/DESCRIPTION' ... OK * this is package 'basket' version '0.10.2' * 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 'basket' 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 * 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 ... [9s] 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 installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... [3s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... [176s] ERROR Running 'testthat.R' [176s] Running the tests in 'tests/testthat.R' failed. Complete output: > library(testthat) > library(basket) > > test_check("basket") -- The MEM Model Call ---------------------------------------------------------- mem_exact(responses = vemu_wide1$responders, size = vemu_wide1$evaluable, name = vemu_wide1$baskets, p0 = 0.25, cluster_analysis = TRUE) -- The Basket Summary ---------------------------------------------------------- The Null Response Rates (alternative is greater): NSCLC CRC (vemu) CRC (vemu+cetu) Null 0.250 0.250 0.25 Posterior Prob 0.951 0.002 0.00 Posterior Mean and Median Response Rates: NSCLC CRC (vemu) CRC (vemu+cetu) Mean 0.425 0.041 0.042 Median 0.422 0.032 0.033 Highest Posterior Density Interval with Coverage Probability 0.95: NSCLC CRC (vemu) CRC (vemu+cetu) lower 0.208 0.000 0.000 upper 0.628 0.105 0.109 Posterior Effective Sample Size: [,1] [,2] [,3] 19.93 55.647 50.867 -- The Cluster Summary --------------------------------------------------------- Cluster 1 "NSCLC" Cluster 2 "CRC (vemu)" "CRC (vemu+cetu)" The Null Response Rates (alternative is greater): Cluster 1 Cluster 2 Null 0.250 0.250 Posterior Prob 0.951 0.001 Posterior Mean and Median Response Rates: Cluster 1 Cluster 2 Mean 0.425 0.041 Median 0.422 0.033 Highest Posterior Density Interval with Coverage Probability 0.95: Cluster 1 Cluster 2 Lower Bound 0.214 0.000 Upper Bound 0.631 0.107 Posterior Effective Sample Size: Cluster 1 Cluster 2 20.28 52.91 The Null Response Rates (alternative is greater): NSCLC CRC (vemu) CRC (vemu+cetu) Null 0.250 0.250 0.25 Posterior Prob 0.951 0.002 0.00 Posterior Mean and Median Response Rates: NSCLC CRC (vemu) CRC (vemu+cetu) Mean 0.425 0.041 0.042 Median 0.422 0.032 0.033 Highest Posterior Density Interval with Coverage Probability 0.95: NSCLC CRC (vemu) CRC (vemu+cetu) lower 0.208 0.000 0.000 upper 0.628 0.105 0.109 Posterior Effective Sample Size: [,1] [,2] [,3] 19.93 55.647 50.867 Cluster 1 "NSCLC" Cluster 2 "CRC (vemu)" "CRC (vemu+cetu)" The Null Response Rates (alternative is greater): Cluster 1 Cluster 2 Null 0.250 0.250 Posterior Prob 0.951 0.001 Posterior Mean and Median Response Rates: Cluster 1 Cluster 2 Mean 0.425 0.041 Median 0.422 0.033 Highest Posterior Density Interval with Coverage Probability 0.95: Cluster 1 Cluster 2 Lower Bound 0.214 0.000 Upper Bound 0.631 0.107 Posterior Effective Sample Size: Cluster 1 Cluster 2 20.28 52.91 -- 1. Failure: (unknown) (@test-mcmc.r#87) ------------------------------------ mcmc_res1$basket$ess not equivalent to mcmc_ref2$ESS. 3/3 mismatches (average diff: 1.97) [1] 38.8 - 37.5 == 1.323 [2] 38.5 - 37.9 == 0.574 [3] 30.9 - 34.9 == -4.001 == testthat results =========================================================== [ OK: 49 | SKIPPED: 2 | WARNINGS: 0 | FAILED: 1 ] 1. Failure: (unknown) (@test-mcmc.r#87) Error: testthat unit tests failed Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking re-building of vignette outputs ... [7s] OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR