Fix more CRAN test problems

10 files changed, 121 insertions, 76 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
index a7f43ca..5f138ce 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: jagsUI
-Version: 1.6.1
-Date: 2024-01-23
+Version: 1.6.2
+Date: 2024-01-24
 Title: A Wrapper Around 'rjags' to Streamline 'JAGS' Analyses
 Authors@R: c(
     person("Ken", "Kellner", email="contact@kenkellner.com", role=c("cre","aut")),
diff --git a/Makefile b/Makefile
index 6d49f26..5f9b685 100644
--- a/Makefile
+++ b/Makefile
@@ -17,7 +17,7 @@ cran-check:
 
 test:
 	make install
-	Rscript -e "Sys.setenv("AT_HOME" = "TRUE"); tinytest::test_package('jagsUI')"
+	Rscript -e "Sys.setenv("AT_HOME" = "TRUE"); tinytest::test_package('jagsUI', color=FALSE, verbose=0)"
 
 coverage:
 	make install
diff --git a/inst/tinytest/test_autojags.R b/inst/tinytest/test_autojags.R
index e06c75e..61ff997 100644
--- a/inst/tinytest/test_autojags.R
+++ b/inst/tinytest/test_autojags.R
@@ -1,3 +1,4 @@
+at_home <- identical( Sys.getenv("AT_HOME"), "TRUE" )
 set.seed(123)
 
 data(longley)
@@ -25,11 +26,14 @@ nul <- capture.output(
             out <- autojags(data = data, inits = inits, parameters.to.save = params,
             model.file = modfile, n.chains = 3, n.adapt = 100, n.burnin=50, 
             iter.increment=10, n.thin = 2, verbose=FALSE))
-ref <- readRDS("autojags_ref.Rds")
+
 
 # Remove time/date based elements
-out$mcmc.info$elapsed.mins <- ref$mcmc.inf$elapsed.mins
-expect_equal(out[-c(17,18,21)], ref[-c(17,18,21)])
+if(at_home){
+  ref <- readRDS("autojags_ref.Rds")
+  out$mcmc.info$elapsed.mins <- ref$mcmc.inf$elapsed.mins
+  expect_equal(out[-c(17,18,21)], ref[-c(17,18,21)])
+}
 
 
 # codaOnly---------------------------------------------------------------------
@@ -37,11 +41,13 @@ nul<- capture.output(
             out <- autojags(data = data, inits = inits, parameters.to.save = params,
             model.file = modfile, n.chains = 3, n.adapt = 100, n.burnin=50, 
             iter.increment=10, n.thin = 2, verbose=FALSE, codaOnly=c("mu")))
-ref <- readRDS("autojags_ref_codaonly.Rds")
 
 # Remove time/date based elements
-out$mcmc.info$elapsed.mins <- ref$mcmc.inf$elapsed.mins
-expect_equal(out[-c(17,18,21)], ref[-c(17,18,21)])
+if(at_home){
+  ref <- readRDS("autojags_ref_codaonly.Rds")
+  out$mcmc.info$elapsed.mins <- ref$mcmc.inf$elapsed.mins
+  expect_equal(out[-c(17,18,21)], ref[-c(17,18,21)])
+}
 
 # Check recovery after process_output errors-----------------------------------
 # Setting DIC to -999 forces process_output to error for testing
@@ -69,12 +75,14 @@ expect_true(grepl("Update 3", nul[10]))
 expect_true(nul[11] == "")
 # All are combined to yield 30 total iterations in each chain
 expect_equal(coda::niter(out$samples), 30)
-ref <- readRDS("autojags_ref_alliter.Rds")
-out$mcmc.info$elapsed.mins <- ref$mcmc.inf$elapsed.mins
-expect_equal(out[-c(17,18,21)], ref[-c(17,18,21)])
+
+if(at_home){
+  ref <- readRDS("autojags_ref_alliter.Rds")
+  out$mcmc.info$elapsed.mins <- ref$mcmc.inf$elapsed.mins
+  expect_equal(out[-c(17,18,21)], ref[-c(17,18,21)])
+}
 
 # Parallel----------------------------------------------------------
-at_home <- identical( Sys.getenv("AT_HOME"), "TRUE" )
 if(at_home){
   set.seed(123)
   nul <- capture.output(
diff --git a/inst/tinytest/test_input_processing.R b/inst/tinytest/test_input_processing.R
index 18affd0..e6ffc27 100644
--- a/inst/tinytest/test_input_processing.R
+++ b/inst/tinytest/test_input_processing.R
@@ -15,7 +15,7 @@ data1 <- list(a=1, b=c(1,2), c=matrix(rnorm(4), 2,2),
               d=array(rnorm(8), c(2,2,2)), e=c(NA, 1))
 test <- process_input(data1, params="a", NULL, 2, 1, 100, 50, 2, 
                       NULL, DIC=TRUE, quiet=TRUE, parallel=FALSE)
-expect_identical(test$data, data1)
+expect_equal(test$data, data1)
 
 # Data frame handling
 data2 <- list(a=data.frame(v1=c(1,2)), b=data.frame(v1=c(0,1), v2=c(2,3)))
@@ -143,7 +143,7 @@ set.seed(123)
 test <- check_inits(inits1, n_chains=2)
 ref <- list(list(.RNG.name = "base::Mersenne-Twister", .RNG.seed = 28758),
     list(.RNG.name = "base::Mersenne-Twister", .RNG.seed = 78830))
-expect_identical(test, ref)
+expect_equal(test, ref)
 
 # A list of lists
 set.seed(123)
@@ -151,7 +151,7 @@ test <- check_inits(inits2, n_chains=2)
 ref <- list(list(a = 1, b = 2, .RNG.name = "base::Mersenne-Twister",
     .RNG.seed = 28758), list(a = 3, b = 4, .RNG.name = "base::Mersenne-Twister",
     .RNG.seed = 78830))
-expect_identical(test, ref)
+expect_equal(test, ref)
 # Wrong number of list elements for number of chains
 expect_error(check_inits(inits2, n_chains=3))
 
@@ -164,14 +164,14 @@ test <- check_inits(inits4, n_chains=2)
 ref <- list(list(a = 1, b = 2, .RNG.name = "base::Mersenne-Twister",
     .RNG.seed = 28758), list(a = 1, b = 2, .RNG.name = "base::Mersenne-Twister",
     .RNG.seed = 78830))
-expect_identical(test, ref)
+expect_equal(test, ref)
 
 # An empty list
 set.seed(123)
 test <- check_inits(inits5, n_chains=2)
 ref <- list(list(.RNG.name = "base::Mersenne-Twister", .RNG.seed = 28758),
     list(.RNG.name = "base::Mersenne-Twister", .RNG.seed = 78830))
-expect_identical(test, ref)
+expect_equal(test, ref)
 
 # Function but doesn't return list
 expect_error(check_inits(inits6, n_chains=2))
diff --git a/inst/tinytest/test_jags.R b/inst/tinytest/test_jags.R
index 6d57a6a..fab9e35 100644
--- a/inst/tinytest/test_jags.R
+++ b/inst/tinytest/test_jags.R
@@ -1,3 +1,4 @@
+at_home <- identical( Sys.getenv("AT_HOME"), "TRUE" )
 set.seed(123)
 
 data(longley)
@@ -32,7 +33,10 @@ ref <- readRDS("longley_reference_fit.Rds")
 
 # Remove time/date based elements
 out$mcmc.info$elapsed.mins <- ref$mcmc.inf$elapsed.mins
-expect_equal(out[-c(17,18,21)], ref[-c(17,18,21)])
+
+if(at_home){
+  expect_equal(out[-c(17,18,21)], ref[-c(17,18,21)])
+}
 
 # Plots
 pdf(NULL)
@@ -69,13 +73,15 @@ expect_equal(out$summary[,"sd"], coda_sum$statistics[,"SD"])
 expect_equal(out$summary[,"50%"], coda_sum$quantiles[,"50%"])
 
 # codaOnly---------------------------------------------------------------------
-out <- jags(data = data, inits = inits, parameters.to.save = params,
+if(at_home){
+  out <- jags(data = data, inits = inits, parameters.to.save = params,
             model.file = modfile, n.chains = 3, n.adapt = 100, n.iter = 100,
             n.burnin = 50, n.thin = 1, codaOnly=c("mu", "sigma"), verbose=FALSE)
-ref <- readRDS("reference_codaOnly.Rds")
+  ref <- readRDS("reference_codaOnly.Rds")
 
-out$mcmc.info$elapsed.mins <- ref$mcmc.inf$elapsed.mins
-expect_equal(out[-c(17,18,21)], ref[-c(17,18,21)])
+  out$mcmc.info$elapsed.mins <- ref$mcmc.inf$elapsed.mins
+  expect_equal(out[-c(17,18,21)], ref[-c(17,18,21)])
+}
 
 # DIC = FALSE------------------------------------------------------------------
 out <- jags(data = data, inits = inits, parameters.to.save = params,
@@ -83,32 +89,41 @@ out <- jags(data = data, inits = inits, parameters.to.save = params,
             n.burnin = 50, n.thin = 1, DIC=FALSE, verbose=FALSE)
 expect_false(out$calc.DIC)
 
-ref <- readRDS("reference_noDIC.Rds")
-out$mcmc.info$elapsed.mins <- ref$mcmc.inf$elapsed.mins
-expect_equal(out[-c(15,16,19)], ref[-c(15,16,19)])
+if(at_home){
+  ref <- readRDS("reference_noDIC.Rds")
+  out$mcmc.info$elapsed.mins <- ref$mcmc.inf$elapsed.mins
+  expect_equal(out[-c(15,16,19)], ref[-c(15,16,19)])
+}
 
 # Reordered parameter names----------------------------------------------------
 pars_new <- c("mu", "sigma", "alpha", "beta")
 out <- jags(data = data, inits = inits, parameters.to.save = pars_new,
             model.file = modfile, n.chains = 3, n.adapt = 100, n.iter = 100,
             n.burnin = 50, n.thin = 1, verbose=FALSE)
-ref <- readRDS("reference_parsorder.Rds")
+expect_equal(c(paste0("mu[",1:16,"]"), "sigma","alpha","beta","deviance"), 
+             colnames(out$samples[[1]]))
 
-out$mcmc.info$elapsed.mins <- ref$mcmc.inf$elapsed.mins
-expect_equal(out[-c(17,18,21)], ref[-c(17,18,21)])
+if(at_home){
+  ref <- readRDS("reference_parsorder.Rds")
+  out$mcmc.info$elapsed.mins <- ref$mcmc.inf$elapsed.mins
+  expect_equal(out[-c(17,18,21)], ref[-c(17,18,21)])
+}
 
 # Reordered parameter names and no DIC-----------------------------------------
 pars_new <- c("mu", "sigma", "alpha", "beta")
 out <- jags(data = data, inits = inits, parameters.to.save = pars_new,
             model.file = modfile, n.chains = 3, n.adapt = 100, n.iter = 100,
             n.burnin = 50, n.thin = 1, DIC = FALSE, verbose=FALSE)
-ref <- readRDS("reference_parsorder_noDIC.Rds")
+expect_equal(c(paste0("mu[",1:16,"]"), "sigma","alpha","beta"), 
+             colnames(out$samples[[1]]))
 
-out$mcmc.info$elapsed.mins <- ref$mcmc.inf$elapsed.mins
-expect_equal(out[-c(15,16,19)], ref[-c(15,16,19)])
+if(at_home){
+  ref <- readRDS("reference_parsorder_noDIC.Rds")
+  out$mcmc.info$elapsed.mins <- ref$mcmc.inf$elapsed.mins
+  expect_equal(out[-c(15,16,19)], ref[-c(15,16,19)])
+}
 
 # Run in parallel--------------------------------------------------------------
-at_home <- identical( Sys.getenv("AT_HOME"), "TRUE" )
 if(parallel::detectCores() > 1 & at_home){
   set.seed(123)
   params <- c('alpha','beta','sigma', 'mu')     
diff --git a/inst/tinytest/test_jagsbasic.R b/inst/tinytest/test_jagsbasic.R
index d1c2f95..2ed54c9 100644
--- a/inst/tinytest/test_jagsbasic.R
+++ b/inst/tinytest/test_jagsbasic.R
@@ -1,3 +1,4 @@
+at_home <- identical( Sys.getenv("AT_HOME"), "TRUE" )
 set.seed(123)
 
 data(longley)
@@ -25,9 +26,10 @@ out <- jags.basic(data = data, inits = inits, parameters.to.save = params,
             model.file = modfile, n.chains = 3, n.adapt = 100, n.iter = 100,
             n.burnin = 50, n.thin = 2, verbose=FALSE)
 
-ref <- readRDS("jagsbasic_reference_fit.Rds")
-
-expect_equal(out, ref)
+if(at_home){
+  ref <- readRDS("jagsbasic_reference_fit.Rds")
+  expect_equal(out, ref)
+}
 
 # Saved model and reordered parameter names------------------------------------
 set.seed(123)
@@ -39,7 +41,10 @@ ref <- readRDS("jagsbasic_ref_saved.Rds")
 
 expect_equal(names(out), names(ref))
 out$model <- ref$model
-expect_equal(out, ref)
+
+if(at_home){
+  expect_equal(out, ref)
+}
 
 # Update-----------------------------------------------------------------------
 out2 <- update(out, n.iter=100, n.thin = 2, verbose=FALSE)
@@ -47,7 +52,10 @@ expect_equal(nrow(out2$samples[[1]]), 50)
 ref <- readRDS('jagsbasic_ref_update.Rds')
 expect_equal(names(out2), names(ref))
 out2$model <- ref$model
-expect_equal(out2, ref)
+
+if(at_home){
+  expect_equal(out2, ref)
+}
 
 # Error if seed is set---------------------------------------------------------
 expect_error(jags.basic(data = data, inits = inits, parameters.to.save = params,
@@ -55,7 +63,6 @@ expect_error(jags.basic(data = data, inits = inits, parameters.to.save = params,
             n.burnin = 50, n.thin = 2, verbose=FALSE, save.model=TRUE, seed=123))
 
 # Parallel---------------------------------------------------------------------
-at_home <- identical( Sys.getenv("AT_HOME"), "TRUE" )
 if(parallel::detectCores() > 1 & at_home){
   set.seed(123)
   params <- c('beta', 'alpha', 'sigma', 'mu')     
diff --git a/inst/tinytest/test_mcmc_tools.R b/inst/tinytest/test_mcmc_tools.R
index 73871f9..31db316 100644
--- a/inst/tinytest/test_mcmc_tools.R
+++ b/inst/tinytest/test_mcmc_tools.R
@@ -106,4 +106,4 @@ comb <- rbind(
   rbind(as.matrix(cs1[[2]]), as.matrix(cs2[[2]])),
   rbind(as.matrix(cs1[[3]]), as.matrix(cs2[[3]]))
 )
-expect_identical(comb, as.matrix(test))
+expect_equal(comb, as.matrix(test))
diff --git a/inst/tinytest/test_process_output.R b/inst/tinytest/test_process_output.R
index edc4de5..e0a2729 100644
--- a/inst/tinytest/test_process_output.R
+++ b/inst/tinytest/test_process_output.R
@@ -1,3 +1,5 @@
+at_home <- identical( Sys.getenv("AT_HOME"), "TRUE" )
+
 process_output <- jagsUI:::process_output
 calc_stats <- jagsUI:::calc_stats
 fill_array <- jagsUI:::fill_array
@@ -44,14 +46,14 @@ expect_true(is.null(out2$pD))
 
 #Exclude parameters
 out3 <- process_output(samples, coda_only=c("alpha","kappa", "mu"), DIC=TRUE, quiet=TRUE)
-expect_identical(names(out3$sims.list), names(out$sims.list))
-expect_identical(names(out3$mean), names(out$mean))
+expect_equal(names(out3$sims.list), names(out$sims.list))
+expect_equal(names(out3$mean), names(out$mean))
 expect_false(any(is.na(unlist(out3$mean))))
-expect_identical(rownames(out3$summary), c("beta", "sigma", "deviance"))
+expect_equal(rownames(out3$summary), c("beta", "sigma", "deviance"))
 
 # Check progress messages
 co <- capture.output(out <- process_output(samples, DIC=TRUE, quiet=FALSE))
-expect_identical(co, c("Calculating statistics....... ", "", "Done. "))
+expect_equal(co, c("Calculating statistics....... ", "", "Done. "))
                 
 
 # Unexpected error happens during process_output-------------------------------
@@ -61,12 +63,14 @@ expect_message(out_fail <- process_output(samples, quiet=TRUE))
 expect_true(is.null(out_fail)) # result is NULL
 
 #test that process_output matches old jagsUI process.output--------------------
-old_all <- readRDS("old_jagsUI_output.Rds")
-new_po <- process_output(old_all$samples, DIC=TRUE, quiet=TRUE)
-old_po <- readRDS("old_process_output.Rds")  
-expect_identical(new_po$summary, old_all$summary)
-new_po$summary <- NULL
-expect_identical(new_po, old_po)
+if(at_home){
+  old_all <- readRDS("old_jagsUI_output.Rds")
+  new_po <- process_output(old_all$samples, DIC=TRUE, quiet=TRUE)
+  old_po <- readRDS("old_process_output.Rds")  
+  expect_equal(new_po$summary, old_all$summary)
+  new_po$summary <- NULL
+  expect_equal(new_po, old_po)
+}
 
 # test that fill_array works properly------------------------------------------
 dat <- 1:10
@@ -229,22 +233,26 @@ expect_true(length(out) == 11)
 
 
 # test that stats for all parameters are calculated by calc_stats--------------
-samples <- readRDS('coda_samples.Rds')
-st <- calc_stats(samples)
-expect_equal(dim(st), c(length(param_names(samples)), 11))
-expect_equal(rownames(st), param_names(samples))
-expect_equal(colnames(st), c('mean','sd','q2.5','q25','q50','q75','q97.5',
+if(at_home){
+  samples <- readRDS('coda_samples.Rds')
+  st <- calc_stats(samples)
+  expect_equal(dim(st), c(length(param_names(samples)), 11))
+  expect_equal(rownames(st), param_names(samples))
+  expect_equal(colnames(st), c('mean','sd','q2.5','q25','q50','q75','q97.5',
                              'overlap0','f','Rhat','n.eff'))
-ref_output <- readRDS('calc_stats_output.Rds')
-expect_equal(st, ref_output)
+  ref_output <- readRDS('calc_stats_output.Rds')
+  expect_equal(st, ref_output)
+}
 
 
 # test that calculating stats for a subset of parameters works-----------------
-samples <- readRDS('coda_samples.Rds') 
-ref_output <- readRDS('calc_stats_output.Rds')
-ref_output[c(1,4:19),2:11] <- NA
-st_sub <- calc_stats(samples, coda_only=c('alpha','mu'))
-expect_identical(ref_output, st_sub)
+if(at_home){
+  samples <- readRDS('coda_samples.Rds') 
+  ref_output <- readRDS('calc_stats_output.Rds')
+  ref_output[c(1,4:19),2:11] <- NA
+  st_sub <- calc_stats(samples, coda_only=c('alpha','mu'))
+  expect_equal(ref_output, st_sub)
+}
 
 
 # test that calculation of pD/DIC works----------------------------------------
diff --git a/inst/tinytest/test_update.R b/inst/tinytest/test_update.R
index cb3613b..80485ea 100644
--- a/inst/tinytest/test_update.R
+++ b/inst/tinytest/test_update.R
@@ -1,3 +1,4 @@
+at_home <- identical( Sys.getenv("AT_HOME"), "TRUE" )
 set.seed(123)
 
 data(longley)
@@ -32,33 +33,40 @@ expect_equal(out2$mcmc.info$n.samples, 150)
 expect_equal(nrow(out2$samples[[1]]), 50)
 
 # Remove time/date based elements
-out2$mcmc.info$elapsed.mins <- ref$mcmc.inf$elapsed.mins
-expect_equal(out2[-c(17,19,21)], ref[-c(17,19,21)])
+if(at_home){
+  out2$mcmc.info$elapsed.mins <- ref$mcmc.inf$elapsed.mins
+  expect_equal(out2[-c(17,19,21)], ref[-c(17,19,21)])
+}
 
 # codaOnly---------------------------------------------------------------------
 out2 <- update(out, n.iter=100, n.thin=2, verbose=FALSE, codaOnly='mu')
-ref <- readRDS("update_ref_codaonly.Rds")
 
-out2$mcmc.info$elapsed.mins <- ref$mcmc.inf$elapsed.mins
-expect_equal(out2[-c(17,19,21)], ref[-c(17,19,21)])
+if(at_home){
+  ref <- readRDS("update_ref_codaonly.Rds")
+  out2$mcmc.info$elapsed.mins <- ref$mcmc.inf$elapsed.mins
+  expect_equal(out2[-c(17,19,21)], ref[-c(17,19,21)])
+}
 
 # Different saved parameters---------------------------------------------------
 out2 <- update(out, n.iter=100, n.thin=2, verbose=FALSE, 
                parameters.to.save=c('beta', 'alpha'))
-ref <- readRDS("update_ref_diffsaved.Rds")
 
-out2$mcmc.info$elapsed.mins <- ref$mcmc.inf$elapsed.mins
-expect_equal(out2[-c(17,19,21)], ref[-c(17,19,21)])
+if(at_home){
+  ref <- readRDS("update_ref_diffsaved.Rds")
+  out2$mcmc.info$elapsed.mins <- ref$mcmc.inf$elapsed.mins
+  expect_equal(out2[-c(17,19,21)], ref[-c(17,19,21)])
+}
 
 # DIC = FALSE------------------------------------------------------------------
 out2 <- update(out, n.iter=100, n.thin=2, verbose=FALSE, 
                parameters.to.save=c('alpha'), DIC=FALSE)
-ref <- readRDS("update_ref_noDIC.Rds")
-
 expect_false(out2$calc.DIC)
 
-out2$mcmc.info$elapsed.mins <- ref$mcmc.inf$elapsed.mins
-expect_equal(out2[-c(15,17,19)], ref[-c(15,17,19)])
+if(at_home){
+  ref <- readRDS("update_ref_noDIC.Rds")
+  out2$mcmc.info$elapsed.mins <- ref$mcmc.inf$elapsed.mins
+  expect_equal(out2[-c(15,17,19)], ref[-c(15,17,19)])
+}
 
 # Check recovery after process_output errors-----------------------------------
 # Setting DIC to -999 forces process_output to error for testing
@@ -69,7 +77,6 @@ expect_equal(coda::varnames(out2$samples), c("alpha","deviance"))
 expect_equal(names(out2), c("samples", "model"))
 
 # Parallel---------------------------------------------------------------------
-at_home <- identical( Sys.getenv("AT_HOME"), "TRUE" )
 if(parallel::detectCores() > 1 & at_home){
   set.seed(123)
   out <- jags(data = data, inits = inits, parameters.to.save = params,
diff --git a/tests/tinytest.R b/tests/tinytest.R
index 6c6da60..1fcd6d0 100644
--- a/tests/tinytest.R
+++ b/tests/tinytest.R
@@ -1,4 +1,4 @@
 if ( requireNamespace("tinytest", quietly=TRUE) ){
-	tinytest::test_package("jagsUI")
+	tinytest::test_package("jagsUI", color=FALSE, verbose=0)
 }