• using R Under development (unstable) (2026-03-06 r89549)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)     GNU Fortran (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8 * current time: 2026-03-06 09:24:34 UTC
• using option ‘--no-stop-on-test-error’
• checking for file ‘spStack/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘spStack’ version ‘1.1.2’
• 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 ‘spStack’ can be installed ... [64s/75s] OK See the install log for details.
• used C++ compiler: ‘g++ (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’
• 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 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 ... [27s/28s] 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 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 $(LAPACK_LIBS) ... OK
• checking use of PKG_*FLAGS in Makefiles ... OK
• checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
• checking pragmas in C/C++ headers and code ... OK
• checking compilation flags used ... OK
• checking compiled code ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... ERROR Running examples in ‘spStack-Ex.R’ failed The error most likely occurred in: > ### Name: get_stacking_weights > ### Title: Optimal stacking weights > ### Aliases: get_stacking_weights > > ### ** Examples > > set.seed(1234) > data(simGaussian) > dat <- simGaussian[1:100, ] > > mod1 <- spLMstack(y ~ x1, data = dat, + coords = as.matrix(dat[, c("s1", "s2")]), + cor.fn = "matern", + params.list = list(phi = c(1.5, 3), + nu = c(0.5, 1), + noise_sp_ratio = c(1)), + n.samples = 1000, loopd.method = "exact", + parallel = FALSE, solver = "ECOS", verbose = TRUE) Error in result$getValue : $ operator is invalid for atomic vectors Calls: spLMstack -> get_stacking_weights Execution halted
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... OK   Running ‘testthat.R’
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [57s/57s] ERROR Error(s) in re-building vignettes: --- re-building ‘posterior-predictive.Rmd’ using rmarkdown Quitting from posterior-predictive.Rmd:42-59 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `result$getValue`: ! $ operator is invalid for atomic vectors --- Backtrace:     ▆  1. └─spStack::spLMstack(...)  2. └─spStack::get_stacking_weights(loopd_mat, solver = solver) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'posterior-predictive.Rmd' failed with diagnostics: $ operator is invalid for atomic vectors --- failed re-building ‘posterior-predictive.Rmd’ --- re-building ‘spStack.Rmd’ using rmarkdown Quitting from spStack.Rmd:50-59 [unnamed-chunk-4] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `result$getValue`: ! $ operator is invalid for atomic vectors --- Backtrace:     ▆  1. └─spStack::spLMstack(...)  2. └─spStack::get_stacking_weights(loopd_mat, solver = solver) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'spStack.Rmd' failed with diagnostics: $ operator is invalid for atomic vectors --- failed re-building ‘spStack.Rmd’ --- re-building ‘spatial-temporal.Rmd’ using rmarkdown Quitting from spatial-temporal.Rmd:203-213 [unnamed-chunk-14] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `result$getValue`: ! $ operator is invalid for atomic vectors --- Backtrace:     ▆  1. └─spStack::stvcGLMstack(...)  2. └─spStack::get_stacking_weights(loopd_mat, solver = solver) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'spatial-temporal.Rmd' failed with diagnostics: $ operator is invalid for atomic vectors --- failed re-building ‘spatial-temporal.Rmd’ --- re-building ‘spatial.Rmd’ using rmarkdown Quitting from spatial.Rmd:128-138 [spLMstack] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `result$getValue`: ! $ operator is invalid for atomic vectors --- Backtrace:     ▆  1. └─spStack::spLMstack(...)  2. └─spStack::get_stacking_weights(loopd_mat, solver = solver) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'spatial.Rmd' failed with diagnostics: $ operator is invalid for atomic vectors --- failed re-building ‘spatial.Rmd’ --- re-building ‘technical_overview.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘technical_overview.Rmd’ SUMMARY: processing the following files failed:   ‘posterior-predictive.Rmd’ ‘spStack.Rmd’ ‘spatial-temporal.Rmd’   ‘spatial.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... 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: 2 ERRORs