* using log directory 'd:/RCompile/CRANincoming/R-devel/o2geosocial.Rcheck' * using R Under development (unstable) (2024-03-21 r86166 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'o2geosocial/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'o2geosocial' version '1.1.2' * package encoding: UTF-8 * checking CRAN incoming feasibility ... [12s] NOTE Maintainer: 'Alexis Robert ' New submission Package was archived on CRAN Possibly misspelled words in DESCRIPTION: AJ (12:287) Gastanaduy (12:291) Kucharski (12:277) genotype (12:164) CRAN repository db overrides: X-CRAN-Comment: Archived on 2024-01-11 as issues were not corrected in time. * 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 'o2geosocial' can be installed ... OK * used C++ compiler: 'g++.exe (GCC) 13.2.0' * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... 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 code 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 whether startup messages can be suppressed ... 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 ... [10s] OK * checking Rd files ... OK * 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 ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... [66s] ERROR Running 'testthat.R' [66s] Running the tests in 'tests/testthat.R' failed. Complete output: > library(testthat) > library(o2geosocial) Registered S3 methods overwritten by 'o2geosocial': method from plot.outbreaker_chains outbreaker2 print.custom_likelihoods outbreaker2 print.custom_priors outbreaker2 print.outbreaker_chains outbreaker2 summary.outbreaker_chains outbreaker2 > > test_check("o2geosocial") ///// outbreaker custom likelihoods /// class: custom_likelihoods list number of items: 5 /// custom likelihoods set to NULL (default used) // $reporting NULL $timing_infections NULL $timing_sampling NULL $space NULL $age NULL ///// outbreaker custom likelihoods /// class: custom_likelihoods list number of items: 5 /// custom likelihoods // $reporting function(data, param, i) cpp_ll_reporting(data, param, i) $timing_infections function(data, param, i) cpp_ll_timing_infections(data, param, i) $timing_sampling function(data, param, i) cpp_ll_timing_sampling(data, param, i) $space function(data, config, param, i) cpp_ll_space(data, config, param, i) $age function(data, param, i) cpp_ll_age(data, param, i) ///// outbreaker results /// class: outbreaker_chains data.frame dimensions 21 rows, 22 columns ancestries not shown: alpha_2 - alpha_5 infection dates not shown: t_inf_1 - t_inf_5 intermediate generations not shown: kappa_1 - kappa_5 /// head // step post like prior a b pi alpha_1 1 1 -32.88389 -33.28774 0.4038415 0.7 0.1 0.9103669 NA 2 50 -39.51264 -38.91464 -0.5980045 0.7 0.1 0.8051902 2 3 100 -34.21771 -35.52312 1.3054073 0.7 0.1 0.9948269 2 ... /// tail // step post like prior a b pi alpha_1 19 900 -32.02185 -33.24110 1.2192534 0.7 0.1 0.9853492 5 20 950 -33.65435 -34.66317 1.0088272 0.7 0.1 0.9625783 2 21 1000 -35.73840 -36.49890 0.7604945 0.7 0.1 0.9363814 2 ///// outbreaker results /// class: outbreaker_chains data.frame dimensions 21 rows, 22 columns ancestries not shown: alpha_2 - alpha_5 infection dates not shown: t_inf_1 - t_inf_5 intermediate generations not shown: kappa_1 - kappa_5 /// head // step post like prior a b pi alpha_1 1 1 -32.88389 -33.28774 0.4038415 0.7 0.1 0.9103669 NA 2 50 -39.51264 -38.91464 -0.5980045 0.7 0.1 0.8051902 2 ... /// tail // step post like prior a b pi alpha_1 20 950 -33.65435 -34.66317 1.0088272 0.7 0.1 0.9625783 2 21 1000 -35.73840 -36.49890 0.7604945 0.7 0.1 0.9363814 2 ///// outbreaker results /// class: outbreaker_chains data.frame dimensions 21 rows, 22 columns ancestries not shown: alpha_1 - alpha_5 infection dates not shown: t_inf_1 - t_inf_5 intermediate generations not shown: kappa_1 - kappa_5 /// head // step post like prior 1 1 -32.88389 -33.28774 0.4038415 2 50 -39.51264 -38.91464 -0.5980045 3 100 -34.21771 -35.52312 1.3054073 ... /// tail // step post like prior 19 900 -32.02185 -33.24110 1.2192534 20 950 -33.65435 -34.66317 1.0088272 21 1000 -35.73840 -36.49890 0.7604945 /// head // 1 2 3 4 5 1 0 0 0 0 1 2 0 0 0 0 1 3 0 0 0 0 1 ... /// tail // 1 2 3 4 5 19 0 0 0 0 1 20 0 0 0 0 1 21 0 0 0 0 1 Biggest cluster: 5 Cluster not shown: 2 to 5 /// head // 1 2 1 0 0 2 0 0 3 0 0 ... /// tail // 1 2 19 0 0 20 0 0 21 0 0 /// head // 1 2 3 4 5 1 0 0 0 0 1 2 0 0 0 0 1 3 0 0 0 0 1 ... /// tail // 1 2 3 4 5 19 0 0 0 0 1 20 0 0 0 0 1 21 0 0 0 0 1 ///// outbreaker custom priors /// class: custom_priors list number of items: 3 /// custom priors set to NULL (default used) // $pi NULL $a NULL $b NULL ///// outbreaker custom priors /// class: custom_priors list number of items: 3 /// custom priors // $pi function(param){ return(dnorm(x = param$pi, mean = config$prior_pi[1], sd = config$prior_pi[2], log = T)) } $a function(param){ return(dnorm(x = param$a, mean = config$prior_a[1], sd = config$prior_a[2], log = T)) } $b function(param){ return(dnorm(x = param$b, mean = config$prior_b[1], sd = config$prior_b[2], log = T)) } [ FAIL 0 | WARN 35 | SKIP 0 | PASS 197 ] [ FAIL 0 | WARN 35 | SKIP 0 | PASS 197 ] > > proc.time() user system elapsed 8.17 0.70 8.81 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [155s] OK * checking PDF version of manual ... [17s] OK * checking HTML version of manual ... OK * DONE Status: 1 ERROR, 1 NOTE