* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/palaeoSig.Rcheck’ * using R Under development (unstable) (2025-07-15 r88411) * using platform: x86_64-pc-linux-gnu * R was compiled by clang version 20.1.8 flang version 20.1.8 * running under: Fedora Linux 42 (Workstation Edition) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘palaeoSig/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘palaeoSig’ version ‘2.1-3’ * 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 ‘palaeoSig’ can be installed ... [21s/65s] OK See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/palaeoSig-00install.html' for details. * 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 code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [5s/11s] OK * checking whether the package can be loaded with stated dependencies ... [5s/10s] OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... [5s/13s] OK * checking whether the namespace can be unloaded cleanly ... [5s/12s] OK * checking loading without being on the library search path ... [5s/11s] 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 ... [32s/101s] OK * checking Rd files ... NOTE checkRd: (-1) jointsig.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) jointsig.Rd:44-45: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) jointsig.Rd:46-48: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) jointsig.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) jointsig.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) jointsig.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) obs.cor.Rd:114-118: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) obs.cor.Rd:119-122: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) obs.cor.Rd:123-124: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) predict.agelme.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) predict.agelme.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) predict.agelme.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) predict.agelme.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) predict.agelme.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) randomTF.Rd:97: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) randomTF.Rd:98-99: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) randomTF.Rd:100-103: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) randomTF.Rd:104-105: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) randomTF.Rd:106-107: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) randomTF.Rd:108: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) rne.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) rne.Rd:47-48: Lost braces in \itemize; \value handles \item{}{} directly * 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 data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [22s/58s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [7s/23s] OK Running ‘testthat.R’ [7s/22s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [1m/63m] ERROR Error(s) in re-building vignettes: --- re-building ‘h-block-crossvalidation.Rmd’ using rmarkdown # A tibble: 1 × 1 RMSE 1 1.28 Warning in so_squares < (min(so_squares) + 0.1 * range(so_squares)) : longer object length is not a multiple of shorter object length # A tibble: 1 × 1 h 1 900 Warning in so_squares < (min(so_squares) + 0.1 * range(so_squares)) : longer object length is not a multiple of shorter object length # A tibble: 1 × 1 h 1 900 --- finished re-building ‘h-block-crossvalidation.Rmd’ Warning: elapsed-time limit of 1 hours reached for sub-process --- re-building ‘randomTF-spatial.Rmd’ using rmarkdown OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead. OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set). SUMMARY: processing the following file failed: ‘randomTF-spatial.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [9s/19s] OK * checking HTML version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 1 NOTE