- using R Under development (unstable) (2026-10-01 r90606)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
clang version 23.1.2
flang version 23.1.2
- running under: Fedora Linux 44 (Server Edition)
- using session charset: UTF-8
* current time: 2026-10-01 10:57:46 UTC
- using option ‘--no-stop-on-test-error’
- checking for file ‘hobbs/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘hobbs’ version ‘0.4.4’
- 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 ‘hobbs’ can be installed ... [20s/58s] OK
See the install log for details.
- used C compiler: ‘clang version 23.1.2’
- checking installed package size ... OK
- 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 ... 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 ... [9s/26s] 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 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 ... 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 Rust compilation ... OK
- checking examples ... ERROR
Running examples in ‘hobbs-Ex.R’ failed
The error most likely occurred in:
> ### Name: hobbs
> ### Title: Compile and sample a hobbs Bayesian model
> ### Aliases: hobbs
>
> ### ** Examples
>
> library(hobbs)
>
> set.seed(1)
> n <- 200L
> p <- 4L
> X <- cbind(1, matrix(rnorm(n * (p - 1L)), nrow = n))
> beta_true <- c(0.5, 1, -0.75, 0.25)
> sigma_true <- 0.75
> y <- as.numeric(X %*% beta_true + rnorm(n, sd = sigma_true))
>
> dat <- list(n = n, p = p, X = X, y = y)
>
> model <- '
+ param beta(p);
+ param logsigma(1);
+
+ func llk() {
+ double sigma = exp(logsigma(1));
+ for (i = 1:n) {
+ y(i) ~ dnorm(mu(i), sigma);
+ }
+ }
+
+ block beta(j) {
+ beta(j) ~ dnorm(0, 10);
+ llk();
+ } cache mu(n) {
+ for (i = 1:n) {
+ for (k = 1:p) {
+ mu(i) += beta(k) * X(i, k);
+ }
+ }
+ } update mu(n) {
+ for (i = 1:n) {
+ mu(i) += (proposal(beta(j)) - current(beta(j))) * X(i, j);
+ }
+ }
+
+ block logsigma(1) {
+ logsigma(1) ~ dnorm(0, 2);
+ llk();
+ }
+ '
>
> out <- tempfile("regression", fileext = ".bin")
>
> fit <- hobbs(
+ model = model,
+ data = dat,
+ samples = 2000,
+ burnin = 1000,
+ seed = 123,
+ out = out
+ )
/usr/bin/ld.bfd: /usr/local/clang23/bin/../lib/LLVMgold.so: error loading plugin: /usr/local/clang23/bin/../lib/LLVMgold.so: cannot open shared object file: No such file or directory
clang-23: error: linker command failed with exit code 1 (use -v to see invocation)
Error: C model compilation failed
Execution halted
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... OK
Running ‘testthat.R’
- checking PDF version of manual ... [4s/11s] 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