update test output

kingaa · May 1, 2024 · ed2d2b5 · ed2d2b5
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diff --git a/CRAN.md b/CRAN.md
@@ -31,6 +31,7 @@ git push github v4.6
 - perform extra checks:
   - `make xcheck`
   - `make ycheck`
+  - `make rchk`
   - `make vcheck` and examine `valgrind` output in `pomp-Ex.Rout` for evidence of memory leaks.
   - `make revdeps`
 
@@ -50,7 +51,7 @@ git push github v4.6
 
 ## Announcement
 
-- Prepare an announcement for the blog: `www/vignettes/_post/`
+- Prepare an announcement for the blog: `www/_posts/`
 - Update manual pages:
   - `make publish`
   - Then push changes to `kingaa.github.io`

diff --git a/tests/R_v_C.Rout b/tests/R_v_C.Rout
@@ -1,7 +1,7 @@
 
-R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+R version 4.4.0 (2024-04-24) -- "Puppy Cup"
 Copyright (C) 2024 The R Foundation for Statistical Computing
-Platform: x86_64-pc-linux-gnu (64-bit)
+Platform: x86_64-pc-linux-gnu
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.
@@ -109,16 +109,16 @@ Type 'q()' to quit R.
 > ## ----comparison----------------------------------------------------------
 > system.time(simulate(gompertz,nsim=10000,format="arrays"))
    user  system elapsed 
-  6.806   0.114   6.921 
+  5.299   0.032   5.331 
 > system.time(simulate(Gompertz,nsim=10000,format="arrays"))
    user  system elapsed 
-  0.161   0.001   0.162 
+  0.141   0.017   0.159 
 > system.time(pfilter(gompertz,Np=1000))
    user  system elapsed 
-  0.642   0.013   0.655 
+  0.541   0.000   0.540 
 > system.time(pfilter(Gompertz,Np=1000))
    user  system elapsed 
-  0.029   0.001   0.029 
+  0.028   0.000   0.028 
 > 
 > dev.off()
 null device 

diff --git a/tests/abc.Rout.save b/tests/abc.Rout.save
@@ -1,7 +1,7 @@
 
-R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+R version 4.4.0 (2024-04-24) -- "Puppy Cup"
 Copyright (C) 2024 The R Foundation for Statistical Computing
-Platform: x86_64-pc-linux-gnu (64-bit)
+Platform: x86_64-pc-linux-gnu
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.

diff --git a/tests/baddm.Rout.save b/tests/baddm.Rout.save
@@ -1,7 +1,7 @@
 
-R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+R version 4.4.0 (2024-04-24) -- "Puppy Cup"
 Copyright (C) 2024 The R Foundation for Statistical Computing
-Platform: x86_64-pc-linux-gnu (64-bit)
+Platform: x86_64-pc-linux-gnu
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.

diff --git a/tests/bake.Rout.save b/tests/bake.Rout.save
@@ -1,7 +1,7 @@
 
-R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+R version 4.4.0 (2024-04-24) -- "Puppy Cup"
 Copyright (C) 2024 The R Foundation for Statistical Computing
-Platform: x86_64-pc-linux-gnu (64-bit)
+Platform: x86_64-pc-linux-gnu
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.

diff --git a/tests/basic_probes.Rout.save b/tests/basic_probes.Rout.save
@@ -1,7 +1,7 @@
 
-R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+R version 4.4.0 (2024-04-24) -- "Puppy Cup"
 Copyright (C) 2024 The R Foundation for Statistical Computing
-Platform: x86_64-pc-linux-gnu (64-bit)
+Platform: x86_64-pc-linux-gnu
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.

diff --git a/tests/betabinom.Rout.save b/tests/betabinom.Rout.save
@@ -1,7 +1,7 @@
 
-R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+R version 4.4.0 (2024-04-24) -- "Puppy Cup"
 Copyright (C) 2024 The R Foundation for Statistical Computing
-Platform: x86_64-pc-linux-gnu (64-bit)
+Platform: x86_64-pc-linux-gnu
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.

diff --git a/tests/blowflies.Rout.save b/tests/blowflies.Rout.save
@@ -1,7 +1,7 @@
 
-R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+R version 4.4.0 (2024-04-24) -- "Puppy Cup"
 Copyright (C) 2024 The R Foundation for Statistical Computing
-Platform: x86_64-pc-linux-gnu (64-bit)
+Platform: x86_64-pc-linux-gnu
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.

diff --git a/tests/bsmc2-01.png b/tests/bsmc2-01.png
diff --git a/tests/bsmc2-02.png b/tests/bsmc2-02.png
diff --git a/tests/bsmc2-03.png b/tests/bsmc2-03.png
diff --git a/tests/bsmc2-04.png b/tests/bsmc2-04.png
diff --git a/tests/bsmc2.Rout.save b/tests/bsmc2.Rout.save
@@ -1,7 +1,7 @@
 
-R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+R version 4.4.0 (2024-04-24) -- "Puppy Cup"
 Copyright (C) 2024 The R Foundation for Statistical Computing
-Platform: x86_64-pc-linux-gnu (64-bit)
+Platform: x86_64-pc-linux-gnu
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.

diff --git a/tests/bsplines1.Rout.save b/tests/bsplines1.Rout.save
@@ -1,7 +1,7 @@
 
-R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+R version 4.4.0 (2024-04-24) -- "Puppy Cup"
 Copyright (C) 2024 The R Foundation for Statistical Computing
-Platform: x86_64-pc-linux-gnu (64-bit)
+Platform: x86_64-pc-linux-gnu
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.

diff --git a/tests/bsplines2.Rout.save b/tests/bsplines2.Rout.save
@@ -1,7 +1,7 @@
 
-R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+R version 4.4.0 (2024-04-24) -- "Puppy Cup"
 Copyright (C) 2024 The R Foundation for Statistical Computing
-Platform: x86_64-pc-linux-gnu (64-bit)
+Platform: x86_64-pc-linux-gnu
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.

diff --git a/tests/concat.Rout.save b/tests/concat.Rout.save
@@ -1,7 +1,7 @@
 
-R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+R version 4.4.0 (2024-04-24) -- "Puppy Cup"
 Copyright (C) 2024 The R Foundation for Statistical Computing
-Platform: x86_64-pc-linux-gnu (64-bit)
+Platform: x86_64-pc-linux-gnu
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.

diff --git a/tests/covmat.Rout.save b/tests/covmat.Rout.save
@@ -1,7 +1,7 @@
 
-R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+R version 4.4.0 (2024-04-24) -- "Puppy Cup"
 Copyright (C) 2024 The R Foundation for Statistical Computing
-Platform: x86_64-pc-linux-gnu (64-bit)
+Platform: x86_64-pc-linux-gnu
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.

diff --git a/tests/csnippet.Rout.save b/tests/csnippet.Rout.save
@@ -1,7 +1,7 @@
 
-R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+R version 4.4.0 (2024-04-24) -- "Puppy Cup"
 Copyright (C) 2024 The R Foundation for Statistical Computing
-Platform: x86_64-pc-linux-gnu (64-bit)
+Platform: x86_64-pc-linux-gnu
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.

diff --git a/tests/dacca.Rout.save b/tests/dacca.Rout.save
@@ -1,7 +1,7 @@
 
-R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+R version 4.4.0 (2024-04-24) -- "Puppy Cup"
 Copyright (C) 2024 The R Foundation for Statistical Computing
-Platform: x86_64-pc-linux-gnu (64-bit)
+Platform: x86_64-pc-linux-gnu
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.

diff --git a/tests/defunct.Rout.save b/tests/defunct.Rout.save
@@ -1,7 +1,7 @@
 
-R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+R version 4.4.0 (2024-04-24) -- "Puppy Cup"
 Copyright (C) 2024 The R Foundation for Statistical Computing
-Platform: x86_64-pc-linux-gnu (64-bit)
+Platform: x86_64-pc-linux-gnu
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.
@@ -20,91 +20,91 @@ Type 'q()' to quit R.
 > library(pomp)
 > 
 > try(as.pomp())
-Error : 'as.pomp' is defunct.
+Error in as.pomp() : 'as.pomp' is defunct.
 Use 'as_pomp' instead.
 See help("Defunct")
 > try(bspline.basis())
-Error : 'bspline.basis' is defunct.
+Error in bspline.basis() : 'bspline.basis' is defunct.
 Use 'bspline_basis' instead.
 See help("Defunct")
 > try(cond.logLik())
-Error : 'cond.logLik' is defunct.
+Error in cond.logLik() : 'cond.logLik' is defunct.
 Use 'cond_logLik' instead.
 See help("Defunct")
 > try(eff.sample.size())
-Error : 'eff.sample.size' is defunct.
+Error in eff.sample.size() : 'eff.sample.size' is defunct.
 Use 'eff_sample_size' instead.
 See help("Defunct")
 > try(mvn.diag.rw())
-Error : 'mvn.diag.rw' is defunct.
+Error in mvn.diag.rw() : 'mvn.diag.rw' is defunct.
 Use 'mvn_diag_rw' instead.
 See help("Defunct")
 > try(mvn.rw())
-Error : 'mvn.rw' is defunct.
+Error in mvn.rw() : 'mvn.rw' is defunct.
 Use 'mvn_rw' instead.
 See help("Defunct")
 > try(mvn.rw.adaptive())
-Error : 'mvn.rw.adaptive' is defunct.
+Error in mvn.rw.adaptive() : 'mvn.rw.adaptive' is defunct.
 Use 'mvn_rw_adaptive' instead.
 See help("Defunct")
 > try(periodic.bspline.basis())
-Error : 'periodic.bspline.basis' is defunct.
+Error in periodic.bspline.basis() : 'periodic.bspline.basis' is defunct.
 Use 'periodic_bspline_basis' instead.
 See help("Defunct")
 > try(pred.mean())
-Error : 'pred.mean' is defunct.
+Error in pred.mean() : 'pred.mean' is defunct.
 Use 'pred_mean' instead.
 See help("Defunct")
 > try(pred.var())
-Error : 'pred.var' is defunct.
+Error in pred.var() : 'pred.var' is defunct.
 Use 'pred_var' instead.
 See help("Defunct")
 > try(probe.acf())
-Error : 'probe.acf' is defunct.
+Error in probe.acf() : 'probe.acf' is defunct.
 Use 'probe_acf' instead.
 See help("Defunct")
 > try(probe.ccf())
-Error : 'probe.ccf' is defunct.
+Error in probe.ccf() : 'probe.ccf' is defunct.
 Use 'probe_ccf' instead.
 See help("Defunct")
 > try(probe.marginal())
-Error : 'probe.marginal' is defunct.
+Error in probe.marginal() : 'probe.marginal' is defunct.
 Use 'probe_marginal' instead.
 See help("Defunct")
 > try(probe.mean())
-Error : 'probe.mean' is defunct.
+Error in probe.mean() : 'probe.mean' is defunct.
 Use 'probe_mean' instead.
 See help("Defunct")
 > try(probe.median())
-Error : 'probe.median' is defunct.
+Error in probe.median() : 'probe.median' is defunct.
 Use 'probe_median' instead.
 See help("Defunct")
 > try(probe.nlar())
-Error : 'probe.nlar' is defunct.
+Error in probe.nlar() : 'probe.nlar' is defunct.
 Use 'probe_nlar' instead.
 See help("Defunct")
 > try(probe.period())
-Error : 'probe.period' is defunct.
+Error in probe.period() : 'probe.period' is defunct.
 Use 'probe_period' instead.
 See help("Defunct")
 > try(probe.quantile())
-Error : 'probe.quantile' is defunct.
+Error in probe.quantile() : 'probe.quantile' is defunct.
 Use 'probe_quantile' instead.
 See help("Defunct")
 > try(probe.sd())
-Error : 'probe.sd' is defunct.
+Error in probe.sd() : 'probe.sd' is defunct.
 Use 'probe_sd' instead.
 See help("Defunct")
 > try(probe.var())
-Error : 'probe.var' is defunct.
+Error in probe.var() : 'probe.var' is defunct.
 Use 'probe_var' instead.
 See help("Defunct")
 > try(rw.sd())
-Error : 'rw.sd' is defunct.
+Error in rw.sd() : 'rw.sd' is defunct.
 Use 'rw_sd' instead.
 See help("Defunct")
 > try(saved.states())
-Error : 'saved.states' is defunct.
+Error in saved.states() : 'saved.states' is defunct.
 Use 'saved_states' instead.
 See help("Defunct")
 > 
diff --git a/tests/dinit.Rout.save b/tests/dinit.Rout.save
@@ -1,7 +1,7 @@
 
-R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+R version 4.4.0 (2024-04-24) -- "Puppy Cup"
 Copyright (C) 2024 The R Foundation for Statistical Computing
-Platform: x86_64-pc-linux-gnu (64-bit)
+Platform: x86_64-pc-linux-gnu
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.

diff --git a/tests/dp-01.png b/tests/dp-01.png
diff --git a/tests/dp-02.png b/tests/dp-02.png
diff --git a/tests/dp-03.png b/tests/dp-03.png
diff --git a/tests/dp.Rout.save b/tests/dp.Rout.save
@@ -1,7 +1,7 @@
 
-R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+R version 4.4.0 (2024-04-24) -- "Puppy Cup"
 Copyright (C) 2024 The R Foundation for Statistical Computing
-Platform: x86_64-pc-linux-gnu (64-bit)
+Platform: x86_64-pc-linux-gnu
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.

diff --git a/tests/dprocess.Rout.save b/tests/dprocess.Rout.save
@@ -1,7 +1,7 @@
 
-R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+R version 4.4.0 (2024-04-24) -- "Puppy Cup"
 Copyright (C) 2024 The R Foundation for Statistical Computing
-Platform: x86_64-pc-linux-gnu (64-bit)
+Platform: x86_64-pc-linux-gnu
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.

diff --git a/tests/ebola.Rout.save b/tests/ebola.Rout.save
@@ -1,7 +1,7 @@
 
-R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+R version 4.4.0 (2024-04-24) -- "Puppy Cup"
 Copyright (C) 2024 The R Foundation for Statistical Computing
-Platform: x86_64-pc-linux-gnu (64-bit)
+Platform: x86_64-pc-linux-gnu
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.

diff --git a/tests/emeasure.Rout.save b/tests/emeasure.Rout.save
@@ -1,7 +1,7 @@
 
-R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+R version 4.4.0 (2024-04-24) -- "Puppy Cup"
 Copyright (C) 2024 The R Foundation for Statistical Computing
-Platform: x86_64-pc-linux-gnu (64-bit)
+Platform: x86_64-pc-linux-gnu
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.

diff --git a/tests/eulermultinom.Rout.save b/tests/eulermultinom.Rout.save
@@ -1,7 +1,7 @@
 
-R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+R version 4.4.0 (2024-04-24) -- "Puppy Cup"
 Copyright (C) 2024 The R Foundation for Statistical Computing
-Platform: x86_64-pc-linux-gnu (64-bit)
+Platform: x86_64-pc-linux-gnu
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.

diff --git a/tests/flow.Rout.save b/tests/flow.Rout.save
@@ -1,7 +1,7 @@
 
-R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+R version 4.4.0 (2024-04-24) -- "Puppy Cup"
 Copyright (C) 2024 The R Foundation for Statistical Computing
-Platform: x86_64-pc-linux-gnu (64-bit)
+Platform: x86_64-pc-linux-gnu
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.

diff --git a/tests/gillespie.Rout.save b/tests/gillespie.Rout.save
@@ -1,7 +1,7 @@
 
-R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+R version 4.4.0 (2024-04-24) -- "Puppy Cup"
 Copyright (C) 2024 The R Foundation for Statistical Computing
-Platform: x86_64-pc-linux-gnu (64-bit)
+Platform: x86_64-pc-linux-gnu
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.

diff --git a/tests/gompertz.Rout.save b/tests/gompertz.Rout.save
@@ -1,7 +1,7 @@
 
-R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
+R version 4.4.0 (2024-04-24) -- "Puppy Cup"
 Copyright (C) 2024 The R Foundation for Statistical Computing
-Platform: x86_64-pc-linux-gnu (64-bit)
+Platform: x86_64-pc-linux-gnu
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.