* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/PartialNetwork.Rcheck’ * using R Under development (unstable) (2024-09-28 r87195) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 13.2.1 20240316 (Red Hat 13.2.1-7) GNU Fortran (GCC) 13.2.1 20240316 (Red Hat 13.2.1-7) * running under: Fedora Linux 38 (Workstation Edition) * using session charset: UTF-8 * checking for file ‘PartialNetwork/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PartialNetwork’ version ‘1.0.4’ * 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 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 ‘PartialNetwork’ can be installed ... [265s/213s] OK * used C++ compiler: ‘g++ (GCC) 13.2.1 20240316 (Red Hat 13.2.1-7)’ * 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 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 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 ... [13s/14s] 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 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 compilation flags used ... 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 ... OK * checking examples with --run-donttest ... [391s/276s] ERROR Running examples in ‘PartialNetwork-Ex.R’ failed The error most likely occurred in: > ### Name: mcmcSAR > ### Title: Bayesian Estimator of SAR model > ### Aliases: mcmcSAR > > ### ** Examples > > ## No test: > # We assume that the network is fully observed > # See our vignette for examples where the network is partially observed > # Number of groups > M <- 50 > # size of each group > N <- rep(30,M) > # individual effects > beta <- c(2,1,1.5) > # contextual effects > gamma <- c(5,-3) > # endogenous effects > alpha <- 0.4 > # std-dev errors > se <- 1 > # prior distribution > prior <- runif(sum(N*(N-1))) > prior <- vec.to.mat(prior, N, normalise = FALSE) > # covariates > X <- cbind(rnorm(sum(N),0,5),rpois(sum(N),7)) > # true network > G0 <- sim.network(prior) > # normalise > G0norm <- norm.network(G0) > # simulate dependent variable use an external package > y <- CDatanet::simsar(~ X, contextual = TRUE, Glist = G0norm, + theta = c(alpha, beta, gamma, se)) Error in CDatanet::simsar(~X, contextual = TRUE, Glist = G0norm, theta = c(alpha, : unused argument (contextual = TRUE) Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [33s/38s] OK * checking PDF version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * checking for new files in some other directories ... OK * DONE Status: 1 ERROR See ‘/data/blackswan/ripley/R/packages/tests-devel/PartialNetwork.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 9:43.48, 714.57 + 27.70