update revdeps

kingaa · Dec 2, 2023 · ffe4692 · ffe4692
1 parent 814d25d
commit ffe4692
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Showing 19 changed files with 417 additions and 185 deletions.
diff --git a/revdep/Outputs/check_CollocInfer_stdout.txt b/revdep/Outputs/check_CollocInfer_stdout.txt
@@ -1,10 +1,10 @@
 * using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/CollocInfer.Rcheck'
-* using R version 4.3.1 (2023-06-16)
+* using R version 4.3.2 (2023-10-31)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * R was compiled by
-    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
-    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
-* running under: Ubuntu 22.04.2 LTS
+    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.3 LTS
 * using session charset: UTF-8
 * using option '--as-cran'
 * checking for file 'CollocInfer/DESCRIPTION' ... OK
@@ -18,7 +18,7 @@
 * checking for portable file names ... OK
 * checking for sufficient/correct file permissions ... OK
 * checking serialization versions ... OK
-* checking whether package 'CollocInfer' can be installed ... [34s/20s] OK
+* checking whether package 'CollocInfer' can be installed ... [33s/23s] OK
 * checking installed package size ... OK
 * checking package directory ... OK
 * checking for future file timestamps ... OK
@@ -40,7 +40,7 @@
 * checking S3 generic/method consistency ... OK
 * checking replacement functions ... OK
 * checking foreign function calls ... OK
-* checking R code for possible problems ... [67s/22s] NOTE
+* checking R code for possible problems ... [75s/63s] NOTE
 Profile.GausNewt: local variable ‘dcdp’ assigned but may not be used
 Profile.GausNewt: local variable ‘gradnorm0’ assigned but may not be
   used
@@ -80,12 +80,13 @@ Variables with usage in documentation object 'FhNest' but not in code:
 * checking data for non-ASCII characters ... OK
 * checking LazyData ... OK
 * checking data for ASCII and uncompressed saves ... OK
-* checking examples ... OK
+* checking examples ... [139s/28s] OK
 Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
-Profile  13.898 47.310   1.045
-FitMatch  3.457  7.528   0.215
-* checking PDF version of manual ... OK
+Profile  20.601 72.806   8.283
+FitMatch  3.377  6.552   0.363
+setup     1.120  4.492   4.509
+* checking PDF version of manual ... [11s/239s] 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

diff --git a/revdep/Outputs/check_DTAT_stdout.txt b/revdep/Outputs/check_DTAT_stdout.txt
@@ -1,10 +1,10 @@
 * using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/DTAT.Rcheck'
-* using R version 4.3.1 (2023-06-16)
+* using R version 4.3.2 (2023-10-31)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * R was compiled by
-    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
-    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
-* running under: Ubuntu 22.04.2 LTS
+    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.3 LTS
 * using session charset: UTF-8
 * using option '--as-cran'
 * checking for file 'DTAT/DESCRIPTION' ... OK
@@ -19,7 +19,7 @@
 * checking for hidden files and directories ... OK
 * checking for portable file names ... OK
 * checking for sufficient/correct file permissions ... OK
-* checking whether package 'DTAT' can be installed ... [36s/13s] OK
+* checking whether package 'DTAT' can be installed ... [31s/14s] OK
 * checking installed package size ... OK
 * checking package directory ... OK
 * checking for future file timestamps ... OK
@@ -42,7 +42,7 @@
 * checking S3 generic/method consistency ... OK
 * checking replacement functions ... OK
 * checking foreign function calls ... OK
-* checking R code for possible problems ... [57s/14s] NOTE
+* checking R code for possible problems ... [61s/15s] NOTE
 dose.survfit: local variable ‘S’ assigned but may not be used
 as_d3_data,DE : rel_dose: local variable ‘where_na’ assigned but may
   not be used
@@ -62,14 +62,15 @@ initialize,DE: local variable ‘Q1’ assigned but may not be used
 * checking sizes of PDF files under 'inst/doc' ... OK
 * checking installed files from 'inst/doc' ... OK
 * checking files in 'vignettes' ... OK
-* checking examples ... OK
+* checking examples ... [20s/36s] OK
 Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
-Onoue.Friberg 3.028  7.867   2.106
+Onoue.Friberg 3.027  7.194   9.489
+dtat1000      0.214  0.024  14.430
 ** found \donttest examples: check also with --run-donttest
 * checking for unstated dependencies in vignettes ... OK
 * checking package vignettes in 'inst/doc' ... OK
-* checking re-building of vignette outputs ... [49s/27s] OK
+* checking re-building of vignette outputs ... [55s/225s] OK
 * checking PDF version of manual ... OK
 * checking HTML version of manual ... OK
 * checking for non-standard things in the check directory ... OK

diff --git a/revdep/Outputs/check_circumstance_stderr.txt b/revdep/Outputs/check_circumstance_stderr.txt
@@ -4,7 +4,7 @@
   Comparing ‘pfilter.Rout’ to ‘pfilter.Rout.save’ ... OK
   Running ‘plot_matrix.R’
   Comparing ‘plot_matrix.Rout’ to ‘plot_matrix.Rout.save’ ... OK
-  Running ‘pmcmc.R’ [13s/10s]
+  Running ‘pmcmc.R’ [16s/11s]
   Comparing ‘pmcmc.Rout’ to ‘pmcmc.Rout.save’ ... OK
 
 
diff --git a/revdep/Outputs/check_circumstance_stdout.txt b/revdep/Outputs/check_circumstance_stdout.txt
@@ -1,10 +1,10 @@
 * using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/circumstance.Rcheck'
-* using R version 4.3.1 (2023-06-16)
+* using R version 4.3.2 (2023-10-31)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * R was compiled by
-    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
-    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
-* running under: Ubuntu 22.04.2 LTS
+    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.3 LTS
 * using session charset: UTF-8
 * using option '--as-cran'
 * checking for file 'circumstance/DESCRIPTION' ... OK
@@ -55,12 +55,12 @@
 * checking examples ... OK
 Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
-pfilter 5.598  0.288   4.562
+pfilter 6.056  0.405   5.267
 ** found \donttest examples: check also with --run-donttest
 * checking for unstated dependencies in 'tests' ... OK
 * checking tests ...
- [42s/26s] OK
-* checking PDF version of manual ... OK
+ [47s/28s] OK
+* checking PDF version of manual ... [7s/388s] 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

diff --git a/revdep/Outputs/check_epimdr2_stdout.txt b/revdep/Outputs/check_epimdr2_stdout.txt
@@ -1,10 +1,10 @@
 * using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/epimdr2.Rcheck'
-* using R version 4.3.1 (2023-06-16)
+* using R version 4.3.2 (2023-10-31)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * R was compiled by
-    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
-    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
-* running under: Ubuntu 22.04.2 LTS
+    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.3 LTS
 * using session charset: UTF-8
 * using option '--as-cran'
 * checking for file 'epimdr2/DESCRIPTION' ... OK
@@ -18,7 +18,7 @@
 * checking for hidden files and directories ... OK
 * checking for portable file names ... OK
 * checking for sufficient/correct file permissions ... OK
-* checking whether package 'epimdr2' can be installed ... [27s/16s] OK
+* checking whether package 'epimdr2' can be installed ... [34s/19s] OK
 * checking installed package size ... OK
 * checking package directory ... OK
 * checking for future file timestamps ... OK
@@ -40,7 +40,7 @@
 * checking S3 generic/method consistency ... OK
 * checking replacement functions ... OK
 * checking foreign function calls ... OK
-* checking R code for possible problems ... [54s/12s] NOTE
+* checking R code for possible problems ... [52s/12s] NOTE
 coyne: local variable ‘H1’ assigned but may not be used
 coyne: local variable ‘H2’ assigned but may not be used
 coyne: local variable ‘I’ assigned but may not be used
@@ -152,9 +152,9 @@ twostrain: local variable ‘res’ assigned but may not be used
 * checking data for non-ASCII characters ... OK
 * checking LazyData ... OK
 * checking data for ASCII and uncompressed saves ... OK
-* checking examples ... [20s/11s] OK
+* checking examples ... [20s/53s] OK
 ** found \donttest examples: check also with --run-donttest
-* checking PDF version of manual ... OK
+* checking PDF version of manual ... [12s/335s] 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

diff --git a/revdep/Outputs/check_epimdr_stdout.txt b/revdep/Outputs/check_epimdr_stdout.txt
@@ -1,10 +1,10 @@
 * using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/epimdr.Rcheck'
-* using R version 4.3.1 (2023-06-16)
+* using R version 4.3.2 (2023-10-31)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * R was compiled by
-    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
-    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
-* running under: Ubuntu 22.04.2 LTS
+    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.3 LTS
 * using session charset: UTF-8
 * using option '--as-cran'
 * checking for file 'epimdr/DESCRIPTION' ... OK
@@ -19,7 +19,7 @@
 * checking for portable file names ... OK
 * checking for sufficient/correct file permissions ... OK
 * checking serialization versions ... OK
-* checking whether package 'epimdr' can be installed ... [22s/12s] OK
+* checking whether package 'epimdr' can be installed ... [27s/14s] OK
 * checking installed package size ... OK
 * checking package directory ... OK
 * checking for future file timestamps ... OK

diff --git a/revdep/Outputs/check_hte_stderr.txt b/revdep/Outputs/check_hte_stderr.txt
@@ -1,14 +1,10 @@
-  Running ‘fakery.R’ [16s/13s]
-  Comparing ‘fakery.Rout’ to ‘fakery.Rout.save’ ... OK
-  Running ‘filter.R’
-  Comparing ‘filter.Rout’ to ‘filter.Rout.save’ ... OK
-  Running ‘indep.R’
-  Comparing ‘indep.Rout’ to ‘indep.Rout.save’ ... OK
-  Running ‘stobfun.R’
+  Running ‘fakery.R’ [16s/38s]
+  Comparing ‘fakery.Rout’ to ‘fakery.Rout.save’ ...  Running ‘filter.R’
+  Comparing ‘filter.Rout’ to ‘filter.Rout.save’ ...  Running ‘indep.R’ [9s/10s]
+  Comparing ‘indep.Rout’ to ‘indep.Rout.save’ ...  Running ‘stobfun.R’ [6s/19s]
   Comparing ‘stobfun.Rout’ to ‘stobfun.Rout.save’ ... OK
-  Running ‘transmiss.R’ [27s/22s]
-  Comparing ‘transmiss.Rout’ to ‘transmiss.Rout.save’ ... OK
-
+  Running ‘transmiss.R’ [26s/28s]
+  Comparing ‘transmiss.Rout’ to ‘transmiss.Rout.save’ ...
 See
   '/userdata/kingaa/projects/Rpkg/pomp/revdep/hte.Rcheck/00check.log'
 for details.

diff --git a/revdep/Outputs/check_hte_stdout.txt b/revdep/Outputs/check_hte_stdout.txt
@@ -1,10 +1,10 @@
 * using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/hte.Rcheck'
-* using R version 4.3.1 (2023-06-16)
+* using R version 4.3.2 (2023-10-31)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * R was compiled by
-    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
-    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
-* running under: Ubuntu 22.04.2 LTS
+    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.3 LTS
 * using session charset: UTF-8
 * using option '--as-cran'
 * checking for file 'hte/DESCRIPTION' ... OK
@@ -20,7 +20,7 @@
 * checking for portable file names ... OK
 * checking for sufficient/correct file permissions ... OK
 * checking whether package 'hte' can be installed ... OK
-* used C compiler: 'gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0'
+* used C compiler: 'gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0'
 * checking installed package size ... OK
 * checking package directory ... OK
 * checking for future file timestamps ... OK
@@ -64,15 +64,64 @@ stobfun : ofun: local variable ‘theta’ assigned but may not be used
 * checking compilation flags used ... OK
 * checking compiled code ... OK
 * checking installed files from 'inst/doc' ... OK
-* checking examples ... [237s/34s] OK
+* checking examples ... [266s/54s] OK
 Examples with CPU (user + system) or elapsed time > 5s
-            user system elapsed
-fake_data 29.910 85.907  11.964
-simuldat  27.004 81.279  10.529
+               user  system elapsed
+fake_data    33.445 103.801  13.000
+simuldat     27.836  87.526   9.747
+transmission  2.196   0.051  12.139
 * checking for unstated dependencies in 'tests' ... OK
 * checking tests ...
- [67s/46s] OK
-* checking PDF version of manual ... OK
+5,9c5,9
+< ✔ dplyr     1.1.4     ✔ readr     2.1.4
+< ✔ forcats   1.0.0     ✔ stringr   1.5.1
+< ✔ ggplot2   3.4.4     ✔ tibble    3.2.1
+< ✔ lubridate 1.9.3     ✔ tidyr     1.3.0
+< ✔ purrr     1.0.2     
+---
+> ✔ dplyr     1.1.2     ✔ readr     2.1.4
+> ✔ forcats   1.0.0     ✔ stringr   1.5.0
+> ✔ ggplot2   3.4.2     ✔ tibble    3.2.1
+> ✔ lubridate 1.9.2     ✔ tidyr     1.3.0
+> ✔ purrr     1.0.1     
+5,9c5,9
+< ✔ dplyr     1.1.4     ✔ readr     2.1.4
+< ✔ forcats   1.0.0     ✔ stringr   1.5.1
+< ✔ ggplot2   3.4.4     ✔ tibble    3.2.1
+< ✔ lubridate 1.9.3     ✔ tidyr     1.3.0
+< ✔ purrr     1.0.2     
+---
+> ✔ dplyr     1.1.2     ✔ readr     2.1.4
+> ✔ forcats   1.0.0     ✔ stringr   1.5.0
+> ✔ ggplot2   3.4.2     ✔ tibble    3.2.1
+> ✔ lubridate 1.9.2     ✔ tidyr     1.3.0
+> ✔ purrr     1.0.1     
+5,9c5,9
+< ✔ dplyr     1.1.4     ✔ readr     2.1.4
+< ✔ forcats   1.0.0     ✔ stringr   1.5.1
+< ✔ ggplot2   3.4.4     ✔ tibble    3.2.1
+< ✔ lubridate 1.9.3     ✔ tidyr     1.3.0
+< ✔ purrr     1.0.2     
+---
+> ✔ dplyr     1.1.2     ✔ readr     2.1.4
+> ✔ forcats   1.0.0     ✔ stringr   1.5.0
+> ✔ ggplot2   3.4.2     ✔ tibble    3.2.1
+> ✔ lubridate 1.9.2     ✔ tidyr     1.3.0
+> ✔ purrr     1.0.1     
+5,9c5,9
+< ✔ dplyr     1.1.4     ✔ readr     2.1.4
+< ✔ forcats   1.0.0     ✔ stringr   1.5.1
+< ✔ ggplot2   3.4.4     ✔ tibble    3.2.1
+< ✔ lubridate 1.9.3     ✔ tidyr     1.3.0
+< ✔ purrr     1.0.2     
+---
+> ✔ dplyr     1.1.2     ✔ readr     2.1.4
+> ✔ forcats   1.0.0     ✔ stringr   1.5.0
+> ✔ ggplot2   3.4.2     ✔ tibble    3.2.1
+> ✔ lubridate 1.9.2     ✔ tidyr     1.3.0
+> ✔ purrr     1.0.1     
+ [71s/107s] OK
+* checking PDF version of manual ... [11s/236s] 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

diff --git a/revdep/Outputs/check_panelPomp_stderr.txt b/revdep/Outputs/check_panelPomp_stderr.txt
@@ -9,10 +9,10 @@
   Comparing ‘mif2.Rout’ to ‘mif2.Rout.save’ ... OK
   Running ‘mif2_intern.R’
   Comparing ‘mif2_intern.Rout’ to ‘mif2_intern.Rout.save’ ... OK
-  Running ‘mif2_methods.R’
+  Running ‘mif2_methods.R’ [15s/25s]
   Comparing ‘mif2_methods.Rout’ to ‘mif2_methods.Rout.save’ ... OK
   Running ‘panelGompertz.R’
-  Comparing ‘panelGompertz.Rout’ to ‘panelGompertz.Rout.save’ ...  Running ‘panelGompertzLikelihood.R’
+  Comparing ‘panelGompertz.Rout’ to ‘panelGompertz.Rout.save’ ...  Running ‘panelGompertzLikelihood.R’ [17s/17s]
   Comparing ‘panelGompertzLikelihood.Rout’ to ‘panelGompertzLikelihood.Rout.save’ ... OK
   Running ‘panelPomp.R’
   Comparing ‘panelPomp.Rout’ to ‘panelPomp.Rout.save’ ... OK
@@ -32,6 +32,6 @@
   Running ‘print-results.R’
   Comparing ‘print-results.Rout’ to ‘print-results.Rout.save’ ...  Running ‘seeded-results.R’
   Comparing ‘seeded-results.Rout’ to ‘seeded-results.Rout.save’ ... OK
-  Running ‘simulate.R’
+  Running ‘simulate.R’ [16s/13s]
   Comparing ‘simulate.Rout’ to ‘simulate.Rout.save’ ...