* using log directory ‘/data/gannet/ripley/R/packages/tests-Intel/MultiBD.Rcheck’
* using R Under development (unstable) (2024-04-23 r86471)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Intel(R) oneAPI DPC++/C++ Compiler 2024.1.0 (2024.1.0.20240308)
    ifx (IFX) 2024.1.0 20240308
* running under: Fedora Linux 36 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘MultiBD/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MultiBD’ version ‘0.2.0’
* 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 ‘MultiBD’ can be installed ... [134s/476s] OK
* used C++ compiler: ‘Intel(R) oneAPI DPC++/C++ Compiler 2024.1.0 (2024.1.0.20240308)’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* 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 ... [6s/16s] 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 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 ... NOTE
File ‘MultiBD/libs/MultiBD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘MultiBD-Ex.R’ failed
The error most likely occurred in:

> ### Name: SIR_prob
> ### Title: Transition probabilities of an SIR process
> ### Aliases: SIR_prob
> 
> ### ** Examples
> 
> data(Eyam)
> 
> loglik_sir <- function(param, data) {
+   alpha <- exp(param[1]) # Rates must be non-negative
+   beta  <- exp(param[2])
+   
+   if(length(unique(rowSums(data[, c("S", "I", "R")]))) > 1) {
+     stop ("Please make sure the data conform with a closed population")
+   }
+   
+   sum(sapply(1:(nrow(data) - 1), # Sum across all time steps k
+              function(k) {
+                log(
+                  SIR_prob(  # Compute the forward transition probability matrix
+                    t  = data$time[k + 1] - data$time[k], # Time increment
+                    alpha = alpha, beta = beta, 
+                    S0 = data$S[k], I0 = data$I[k],       # From: R(t_k), I(t_k)
+                    nSI = data$S[k] - data$S[k + 1], nIR = data$R[k + 1] - data$R[k],
+                    computeMode = 4, nblocks = 80         # Compute using 4 threads
+                  )[data$S[k] - data$S[k + 1] + 1, 
+                    data$R[k + 1] - data$R[k] + 1]        # To: R(t_(k+1)), I(t_(k+1))
+                )
+              }))
+ }
> 
> loglik_sir(log(c(3.204, 0.019)), Eyam) # Evaluate at mode

 *** caught segfault ***
address (nil), cause 'unknown'

Traceback:
 1: SIR_Cpp(t, alpha, beta, S0, I0, nSI + 1, nIR + 1, dir, nblocks,     tol, computeMode, nThreads)
 2: matrix(SIR_Cpp(t, alpha, beta, S0, I0, nSI + 1, nIR + 1, dir,     nblocks, tol, computeMode, nThreads), nrow = nSI + 1, byrow = T)
 3: SIR_prob(t = data$time[k + 1] - data$time[k], alpha = alpha,     beta = beta, S0 = data$S[k], I0 = data$I[k], nSI = data$S[k] -         data$S[k + 1], nIR = data$R[k + 1] - data$R[k], computeMode = 4,     nblocks = 80)
 4: FUN(X[[i]], ...)
 5: lapply(X = X, FUN = FUN, ...)
 6: sapply(1:(nrow(data) - 1), function(k) {    log(SIR_prob(t = data$time[k + 1] - data$time[k], alpha = alpha,         beta = beta, S0 = data$S[k], I0 = data$I[k], nSI = data$S[k] -             data$S[k + 1], nIR = data$R[k + 1] - data$R[k], computeMode = 4,         nblocks = 80)[data$S[k] - data$S[k + 1] + 1, data$R[k +         1] - data$R[k] + 1])})
 7: loglik_sir(log(c(3.204, 0.019)), Eyam)
An irrecoverable exception occurred. R is aborting now ...
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [121s/222s]
 [121s/223s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [41s/169s] OK
* checking PDF version of manual ... [7s/28s] 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, 2 NOTEs
See
  ‘/data/gannet/ripley/R/packages/tests-Intel/MultiBD.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 17:43.18, 318.97 + 26.28