* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/INLAMSM.Rcheck’
* using R Under development (unstable) (2021-06-19 r80532)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘INLAMSM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘INLAMSM’ version ‘0.2-3’
* 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 ‘INLAMSM’ can be installed ... [15s/16s] 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 R 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 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 ... [20s/20s] 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 examples ... OK
* checking examples with --run-donttest ... [11s/11s] ERROR
Running examples in ‘INLAMSM-Ex.R’ failed
The error most likely occurred in:

> ### Name: CV
> ### Title: Multivariate mortality data from Comunidad Valenciana (Spain)
> ### Aliases: CV
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> ## No test: 
> if(require(INLA, quietly = TRUE)) {
+ require(sp)
+ require(spdep)
+ data(CV)
+ W <- as(nb2mat(CV.nb, style = "B"), "Matrix")
+ 
+ #Data (two diseases only)
+ d <- list(OBS = c(CV$Obs.Cirrhosis, CV$Obs.Lung),
+  EXP = c(CV$Exp.Cirrhosis, CV$Exp.Lung))
+ 
+  # Index for latent effect
+ d$idx <- 1:length(d$OBS)
+ 
+ k <- 2  #Number of diseases
+ 
+ # Linear constraint for models
+ A <- kronecker(Diagonal(k, 1), Matrix(1, ncol = nrow(W), nrow = 1))
+ e = rep(0, k)
+ 
+ # Two independent ICAR models
+ #model <- inla.rgeneric.define(inla.rgeneric.indep.IMCAR.model,
+ #  k = k, W = W)
+ model <- inla.INDIMCAR.model(k = k, W = W)
+ r.simcar <- try(
+   inla(OBS ~ 1 + f(idx, model = model, extraconstr = list(A = as.matrix(A), e = e)),
+     data = d, E = EXP, family = "poisson",
+      # To run faster, REMOVE in real applications
+      control.mode = list(theta = c(1.4, 2.1), restart = TRUE),
+     control.predictor = list(compute = TRUE))
+ )
+ summary(r.simcar)
+ 
+ # IMCAR model
+ #model <- inla.rgeneric.define(inla.rgeneric.IMCAR.model,
+ #  k = k, W = W, alpha.min = 0, alpha.max = 1)
+ model <- inla.IMCAR.model(k = k, W = W)
+ r.imcar <- try(
+   inla(OBS ~ 1 + f(idx, model = model, extraconstr = list(A = as.matrix(A), e = e)),
+     data = d, E = EXP, family = "poisson",
+      # To run faster, REMOVE in real applications
+      control.mode = list(theta = c(1.77, 2.01, 0.93),
+        restart = TRUE),
+     control.compute = list(config = TRUE),
+     control.predictor = list(compute = TRUE))
+ )
+ summary(r.imcar)
+ 
+ # Transform parameters
+ summary.post <- inla.MCAR.transform(r.imcar, k = k)
+ 
+ # Posterior of variance matrix
+ summary.post$VAR.p # Using point estimates
+ summary.post$VAR.m # Using posterior sampling
+ 
+ } #if(require(INLA))
This is INLA_21.02.23 built 2021-06-15 08:32:26 UTC.
 - See www.r-inla.org/contact-us for how to get help.
 - To enable PARDISO sparse library; see inla.pardiso()
 - Save 273.9Mb of storage running 'inla.prune()'
Warning in inla.model.properties.generic(inla.trim.family(model), mm[names(mm) ==  :
  Model 'rgeneric' in section 'latent' is marked as 'experimental'; changes may appear at any time.
  Use this model with extra care!!! Further warnings are disabled.
Error in `::`(base, quote) : could not find function "::"
Error in `::`(base, quote) : could not find function "::"
Error in `::`(base, quote) : could not find function "::"
Error in `:::`(compiler, checkCompilerOptions) : 
  could not find function ":::"
Fatal error: unable to initialize the JIT

Error in inla.inlaprogram.has.crashed() : 
  The inla-program exited with an error. Unless you interupted it yourself, please rerun with verbose=TRUE and check the output carefully.
  If this does not help, please contact the developers at <help@r-inla.org>.
Error in `::`(base, quote) : could not find function "::"
Error in `::`(base, quote) : could not find function "::"
Error in `::`(base, quote) : could not find function "::"
Error in `:::`(compiler, checkCompilerOptions) : 
  could not find function ":::"
Fatal error: unable to initialize the JIT

Error in inla.inlaprogram.has.crashed() : 
  The inla-program exited with an error. Unless you interupted it yourself, please rerun with verbose=TRUE and check the output carefully.
  If this does not help, please contact the developers at <help@r-inla.org>.
Error: $ operator is invalid for atomic vectors
Execution halted
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* checking for new files in some other directories ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/blackswan/ripley/R/packages/tests-devel/INLAMSM.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 2:09.17, 117.59 + 11.00