* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/bayesGAM.Rcheck’ * using R Under development (unstable) (2024-04-24 r86484) * using platform: x86_64-pc-linux-gnu * R was compiled by clang version 18.1.4 flang-new version 18.1.4 * running under: Fedora Linux 36 (Workstation Edition) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘bayesGAM/DESCRIPTION’ ... OK * this is package ‘bayesGAM’ version ‘0.0.2’ * 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 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 ‘bayesGAM’ can be installed ... [16m/21m] OK See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/bayesGAM-00install.html' for details. * used C++ compiler: ‘clang version 18.1.4’ * checking C++ specification ... OK Not all R platforms support C++17 * checking installed package size ... NOTE installed size is 8.9Mb sub-directories of 1Mb or more: libs 7.8Mb * checking package 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 ... [14s/16s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘MASS’ ‘RcppParallel’ ‘mlbench’ ‘rstantools’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [46s/59s] OK * checking Rd files ... NOTE checkRd: (-1) mcmc_plots.Rd:204-206: Lost braces in \itemize; meant \describe ? checkRd: (-1) mcmc_plots.Rd:207-209: Lost braces in \itemize; meant \describe ? checkRd: (-1) mcmc_plots.Rd:210-212: Lost braces in \itemize; meant \describe ? checkRd: (-1) mcmc_plots.Rd:213-216: Lost braces in \itemize; meant \describe ? checkRd: (-1) mcmc_plots.Rd:217-220: Lost braces in \itemize; meant \describe ? checkRd: (-1) mcmc_plots.Rd:221-226: Lost braces in \itemize; meant \describe ? checkRd: (-1) mcmc_plots.Rd:227-230: Lost braces in \itemize; meant \describe ? checkRd: (-1) mcmc_plots.Rd:231-234: Lost braces in \itemize; meant \describe ? checkRd: (-1) mcmc_plots.Rd:235-239: Lost braces in \itemize; meant \describe ? checkRd: (-1) mcmc_plots.Rd:240-244: Lost braces in \itemize; meant \describe ? checkRd: (-1) mcmc_plots.Rd:245-254: Lost braces in \itemize; meant \describe ? checkRd: (-1) mcmc_plots.Rd:255-279: Lost braces in \itemize; meant \describe ? checkRd: (-1) mcmc_plots.Rd:264: Lost braces 264 | \item{\code{mcmc_neff(object, ...)}, \code{mcmc_neff_hist(object, ...)}}{ | ^ checkRd: (-1) mcmc_plots.Rd:264-272: Lost braces 264 | \item{\code{mcmc_neff(object, ...)}, \code{mcmc_neff_hist(object, ...)}}{ | ^ checkRd: (-1) mcmc_plots.Rd:273: Lost braces 273 | \item{\code{mcmc_acf(object, ...)}, \code{mcmc_acf_bar(object, ...)}}{ | ^ checkRd: (-1) mcmc_plots.Rd:273-278: Lost braces 273 | \item{\code{mcmc_acf(object, ...)}, \code{mcmc_acf_bar(object, ...)}}{ | ^ checkRd: (-1) ppc_plots.Rd:78-80: Lost braces in \itemize; meant \describe ? checkRd: (-1) ppc_plots.Rd:81-83: Lost braces in \itemize; meant \describe ? checkRd: (-1) ppc_plots.Rd:84-86: Lost braces in \itemize; meant \describe ? checkRd: (-1) ppc_plots.Rd:87-89: Lost braces in \itemize; meant \describe ? checkRd: (-1) ppc_plots.Rd:90-92: Lost braces in \itemize; meant \describe ? checkRd: (-1) ppc_plots.Rd:93-95: Lost braces in \itemize; meant \describe ? * 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 shell scripts ... 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 ... NOTE GNU make is a SystemRequirements. * 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 pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking examples ... [48s/63s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [85s/118s] OK Running ‘testthat.R’ [85s/117s] * checking PDF version of manual ... [9s/16s] OK * checking HTML version of manual ... NOTE Found the following HTML validation problems: getSamples.html:74:1 (getSamples.Rd:35): Warning: trimming empty

* checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 5 NOTEs