CRAN Package Check Results for Package runjags

Last updated on 2017-02-19 23:48:35.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.0.4-2 8.05 152.73 160.78 NOTE
r-devel-linux-x86_64-debian-gcc 2.0.4-2 5.97 151.48 157.45 NOTE
r-devel-linux-x86_64-fedora-clang 2.0.4-2 278.72 NOTE --no-stop-on-test-error
r-devel-linux-x86_64-fedora-gcc 2.0.4-2 266.59 NOTE --no-stop-on-test-error
r-devel-macos-x86_64-clang 2.0.4-2 190.13 NOTE --no-stop-on-test-error
r-devel-windows-ix86+x86_64 2.0.4-2 25.00 88.00 113.00 OK --no-examples --no-tests --no-vignettes
r-patched-linux-x86_64 2.0.4-2 5.28 120.30 125.58 OK
r-patched-solaris-sparc 2.0.4-2 1742.10 OK
r-patched-solaris-x86 2.0.4-2 270.10 ERROR
r-release-linux-x86_64 2.0.4-2 5.21 118.24 123.45 OK
r-release-osx-x86_64-mavericks 2.0.4-2 OK
r-release-windows-ix86+x86_64 2.0.4-2 25.00 89.00 114.00 OK --no-examples --no-tests --no-vignettes
r-oldrel-windows-ix86+x86_64 2.0.4-2 5.00 3.00 8.00 ERROR --no-examples --no-tests --no-vignettes

Memtest notes: clang-ASAN

Check Details

Version: 2.0.4-2
Check: compiled code
Result: NOTE
    File ‘runjags/libs/runjags.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.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 2.0.4-2
Flags: --no-stop-on-test-error
Check: compiled code
Result: NOTE
    File ‘runjags/libs/runjags.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.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-macos-x86_64-clang

Version: 2.0.4-2
Check: tests
Result: ERROR
     Running ‘checkinputs.R’ [1m/23m]
    Running the tests in ‘tests/checkinputs.R’ failed.
    Complete output:
     > # First load runjags and verify that the options can be set:
     > library('runjags')
     > runjags.options(inits.warning=FALSE, rng.warning=FALSE, silent.jags=TRUE)
     > newopts <- runjags.options()
     > stopifnot(newopts$inits.warning==FALSE)
     > stopifnot(newopts$rng.warning==FALSE)
     > stopifnot(newopts$silent.jags==TRUE)
     >
     >
     > # Test some runjags inputs with the rjags method:
     >
     > testnum <- 1
     > if(require("rjags")){
     +
     + # Required for nvar etc:
     + library("coda")
     +
     + model <- "model {
     + for(i in 1 : N){ #data# N
     + Y[i] ~ dnorm(true.y[i], precision); #data# Y
     + true.y[i] <- (m * X[i]) + c; #data# X
     + }
     + m ~ dunif(-1000,1000); #inits# m
     + c ~ dunif(-1000,1000);
     + precision ~ dexp(1);
     + #monitor# m, c, precision
     + }"
     +
     + # Simulate the data
     + X <- 1:100
     + Y <- rnorm(length(X), 2*X + 10, 1)
     + N <- length(X)
     +
     + initfunction <- function(chain) return(switch(chain, "1"=list(m=-10), "2"=list(m=10)))
     + initfunction2 <- function() return(switch(sample(c(1,2),1), "1"=list(m=-10), "2"=list(m=10)))
     +
     + datalist <- list(X=X, Y=Y, N=N)
     +
     + cat('Running input test number', testnum, '\n'); testnum <- testnum+1
     + results <- run.jags(model, n.chains=2, sample=1000, burnin=1000, inits=initfunction, method='rjags')
     + cat('Running input test number', testnum, '\n'); testnum <- testnum+1
     + results <- run.jags(model, n.chains=2, sample=1000, burnin=1000, inits=initfunction2, method='rjags')
     + cat('Running input test number', testnum, '\n'); testnum <- testnum+1
     + results <- run.jags(model, n.chains=2, sample=1000, burnin=1000, inits=lapply(1:2,initfunction), method='rjags')
     + cat('Running input test number', testnum, '\n'); testnum <- testnum+1
     + results <- run.jags(model, n.chains=2, sample=1000, burnin=1000, inits=initfunction(1), method='rjags')
     +
     + cat('Running input test number', testnum, '\n'); testnum <- testnum+1
     + results <- run.jags(model, n.chains=2, sample=1000, burnin=1000, data=datalist, inits=initfunction, method='rjags')
     + cat('Running input test number', testnum, '\n'); testnum <- testnum+1
     + results <- run.jags(model, n.chains=2, sample=1000, burnin=1000, data=datalist, inits=initfunction2, method='rjags')
     + cat('Running input test number', testnum, '\n'); testnum <- testnum+1
     + results <- run.jags(model, n.chains=2, sample=1000, burnin=1000, data=datalist, inits=lapply(1:2,initfunction), method='rjags')
     + cat('Running input test number', testnum, '\n'); testnum <- testnum+1
     + results <- run.jags(model, n.chains=2, sample=1000, burnin=1000, data=datalist, inits=initfunction(1), method='rjags')
     + stopifnot(nvar(as.mcmc.list(results))==(3))
     + stopifnot(all(varnames(as.mcmc.list(results))==c('m','c','precision')))
     +
     + cat('Running input test number', testnum, '\n'); testnum <- testnum+1
     + results <- extend.jags(results,sample=1000)
     + stopifnot(niter(as.mcmc.list(results))==2000)
     + stopifnot(nvar(as.mcmc.list(results))==3)
     +
     + cat('Running input test number', testnum, '\n'); testnum <- testnum+1
     + results2 <- extend.jags(results, sample=1000, drop.chain=1, summarise=FALSE)
     + stopifnot(nchain(as.mcmc.list(results2))==1)
     + stopifnot(identical(list.format(results$end.state[[2]])$.RNG.name, list.format(results2$end.state[[1]])$.RNG.name))
     +
     + cat('Running input test number', testnum, '\n'); testnum <- testnum+1
     + results2 <- extend.jags(results, sample=1000, drop.monitor="precision", summarise=FALSE)
     + stopifnot(nvar(as.mcmc.list(results2))==2)
     +
     + cat('Running input test number', testnum, '\n'); testnum <- testnum+1
     + results2 <- extend.jags(results, sample=1000, add.monitor="true.y", summarise=FALSE)
     + stopifnot(nvar(as.mcmc.list(results2))==(3+N))
     + stopifnot(varnames(as.mcmc.list(results2))[1]=='m' && varnames(as.mcmc.list(results2))[103]=='true.y[100]')
     +
     + cat('Running input test number', testnum, '\n'); testnum <- testnum+1
     + results2 <- extend.jags(results, sample=1000, add.monitor=c("true.y", "dic"), summarise=FALSE)
     + stopifnot(nvar(as.mcmc.list(results2))==(3+N))
     + stopifnot(varnames(as.mcmc.list(results2))[1]=='m' && varnames(as.mcmc.list(results2))[103]=='true.y[100]')
     +
     + cat('Running input test number', testnum, '\n'); testnum <- testnum+1
     + results2 <- extend.jags(results, sample=1000, add.monitor=c("true.y", "deviance"), summarise=FALSE)
     + stopifnot(nvar(as.mcmc.list(results2))==(4+N))
     + stopifnot(varnames(as.mcmc.list(results2))[1]=='m' && varnames(as.mcmc.list(results2))[104]=='deviance')
     +
     + cat('Running input test number', testnum, '\n'); testnum <- testnum+1
     + results <- run.jags(model, n.chains=2, sample=1000, burnin=1000, data=datalist, inits=initfunction, method='rjparallel')
     + stopifnot(nvar(as.mcmc.list(results))==(3))
     + stopifnot(all(varnames(as.mcmc.list(results))==c('m','c','precision')))
     +
     + cat('Running input test number', testnum, '\n'); testnum <- testnum+1
     + results2 <- extend.jags(results, sample=1000, add.monitor="true.y", summarise=FALSE, method='rjp')
     + stopifnot(nvar(as.mcmc.list(results2))==(3+N))
     + stopifnot(varnames(as.mcmc.list(results2))[1]=='m' && varnames(as.mcmc.list(results2))[103]=='true.y[100]')
     +
     + cat('Running input test number', testnum, '\n'); testnum <- testnum+1
     + results2 <- extend.jags(results, sample=1000, add.monitor=c("true.y", "deviance"), summarise=FALSE, method='rjp')
     + stopifnot(nvar(as.mcmc.list(results2))==(4+N))
     + stopifnot(varnames(as.mcmc.list(results2))[1]=='m' && varnames(as.mcmc.list(results2))[104]=='deviance')
     +
     + cat("All input checks passed\n")
     +
     + }else{
     + cat("The input checks were not performed as rjags is not installed\n")
     + }
     Loading required package: rjags
     Loading required package: coda
     Linked to JAGS 4.2.0
     Loaded modules: basemod,bugs
     Running input test number 1
     Finished running the simulation
     Running input test number 2
     Finished running the simulation
     Running input test number 3
     Finished running the simulation
     Running input test number 4
     Finished running the simulation
     Running input test number 5
     Finished running the simulation
     Running input test number 6
     Finished running the simulation
     Running input test number 7
     Finished running the simulation
     Running input test number 8
     Finished running the simulation
     Running input test number 9
     Finished running the simulation
     Running input test number 10
     Finished running the simulation
     Running input test number 11
     Finished running the simulation
     Running input test number 12
     Finished running the simulation
     Running input test number 13
     module dic loaded
     Finished running the simulation
     Running input test number 14
     Finished running the simulation
     Running input test number 15
Flavor: r-patched-solaris-x86

Version: 2.0.4-2
Flags: --no-examples --no-tests --no-vignettes
Check: whether package can be installed
Result: ERROR
    Installation failed.
Flavor: r-oldrel-windows-ix86+x86_64