update revdeps

kingaa · Jan 11, 2024 · 37318fd · 37318fd
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commit 37318fd
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diff --git a/revdep/Outputs/check_CollocInfer_stderr.txt b/revdep/Outputs/check_CollocInfer_stderr.txt
@@ -1,6 +1,6 @@
 
 See
-  '/userdata/kingaa/projects/Rpkg/pomp/revdep/CollocInfer.Rcheck/00check.log'
+  '/home/kingaa/projects/Rpkg/pomp/revdep/CollocInfer.Rcheck/00check.log'
 for details.
 
 
diff --git a/revdep/Outputs/check_CollocInfer_stdout.txt b/revdep/Outputs/check_CollocInfer_stdout.txt
@@ -1,4 +1,4 @@
-* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/CollocInfer.Rcheck'
+* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/CollocInfer.Rcheck'
 * using R version 4.3.2 (2023-10-31)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * R was compiled by
@@ -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 ... [31s/20s] OK
+* checking whether package 'CollocInfer' can be installed ... [16s/17s] 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/23s] NOTE
+* checking R code for possible problems ... [36s/31s] NOTE
 Profile.GausNewt: local variable ‘dcdp’ assigned but may not be used
 Profile.GausNewt: local variable ‘gradnorm0’ assigned but may not be
   used
@@ -83,9 +83,9 @@ Variables with usage in documentation object 'FhNest' but not in code:
 * checking examples ... OK
 Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
-Profile  16.405 62.189   1.563
-FitMatch  1.632  4.969   0.164
-smooth    1.260  4.628   0.105
+Profile   2.867 10.974   1.401
+FitMatch  6.497  6.088   1.252
+ParsMatch 6.370  4.570   1.106
 * 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_DTAT_stderr.txt b/revdep/Outputs/check_DTAT_stderr.txt
@@ -1,6 +1,6 @@
 
 See
-  '/userdata/kingaa/projects/Rpkg/pomp/revdep/DTAT.Rcheck/00check.log'
+  '/home/kingaa/projects/Rpkg/pomp/revdep/DTAT.Rcheck/00check.log'
 for details.
 
 
diff --git a/revdep/Outputs/check_DTAT_stdout.txt b/revdep/Outputs/check_DTAT_stdout.txt
@@ -1,4 +1,4 @@
-* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/DTAT.Rcheck'
+* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/DTAT.Rcheck'
 * using R version 4.3.2 (2023-10-31)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * R was compiled by
@@ -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 ... [33s/14s] OK
+* checking whether package 'DTAT' can be installed ... [15s/15s] 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 ... [60s/15s] NOTE
+* checking R code for possible problems ... [24s/18s] 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
@@ -63,13 +63,10 @@ initialize,DE: local variable ‘Q1’ assigned but may not be used
 * checking installed files from 'inst/doc' ... OK
 * checking files in 'vignettes' ... OK
 * checking examples ... OK
-Examples with CPU (user + system) or elapsed time > 5s
-               user system elapsed
-Onoue.Friberg 2.597  7.085   2.138
 ** 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 ... [53s/32s] OK
+* checking re-building of vignette outputs ... [29s/27s] 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
@@ -1,10 +1,10 @@
-  Running ‘mif2.R’
+  Running ‘mif2.R’ [11s/13s]
   Comparing ‘mif2.Rout’ to ‘mif2.Rout.save’ ... OK
   Running ‘pfilter.R’
   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/11s]
+  Running ‘pmcmc.R’ [13s/15s]
   Comparing ‘pmcmc.Rout’ to ‘pmcmc.Rout.save’ ... OK
 
 
diff --git a/revdep/Outputs/check_circumstance_stdout.txt b/revdep/Outputs/check_circumstance_stdout.txt
@@ -1,4 +1,4 @@
-* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/circumstance.Rcheck'
+* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/circumstance.Rcheck'
 * using R version 4.3.2 (2023-10-31)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * R was compiled by
@@ -55,11 +55,11 @@
 * checking examples ... OK
 Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
-pfilter 5.781  0.372   5.103
+pfilter 7.026  0.158   6.821
 ** found \donttest examples: check also with --run-donttest
 * checking for unstated dependencies in 'tests' ... OK
 * checking tests ...
- [46s/27s] OK
+ [34s/36s] 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_epimdr2_stderr.txt b/revdep/Outputs/check_epimdr2_stderr.txt
@@ -1,6 +1,6 @@
 
 See
-  '/userdata/kingaa/projects/Rpkg/pomp/revdep/epimdr2.Rcheck/00check.log'
+  '/home/kingaa/projects/Rpkg/pomp/revdep/epimdr2.Rcheck/00check.log'
 for details.
 
 
diff --git a/revdep/Outputs/check_epimdr2_stdout.txt b/revdep/Outputs/check_epimdr2_stdout.txt
@@ -1,4 +1,4 @@
-* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/epimdr2.Rcheck'
+* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/epimdr2.Rcheck'
 * using R version 4.3.2 (2023-10-31)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * R was compiled by
@@ -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 ... [31s/18s] OK
+* checking whether package 'epimdr2' can be installed ... [15s/15s] 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 ... [51s/12s] NOTE
+* checking R code for possible problems ... [22s/17s] 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
@@ -152,7 +152,7 @@ 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 ... [23s/13s] OK
+* checking examples ... [15s/13s] OK
 ** found \donttest examples: check also with --run-donttest
 * checking PDF version of manual ... OK
 * checking HTML version of manual ... OK

diff --git a/revdep/Outputs/check_epimdr_stderr.txt b/revdep/Outputs/check_epimdr_stderr.txt
@@ -1,6 +1,6 @@
 
 See
-  '/userdata/kingaa/projects/Rpkg/pomp/revdep/epimdr.Rcheck/00check.log'
+  '/home/kingaa/projects/Rpkg/pomp/revdep/epimdr.Rcheck/00check.log'
 for details.
 
 
diff --git a/revdep/Outputs/check_epimdr_stdout.txt b/revdep/Outputs/check_epimdr_stdout.txt
@@ -1,4 +1,4 @@
-* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/epimdr.Rcheck'
+* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/epimdr.Rcheck'
 * using R version 4.3.2 (2023-10-31)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * R was compiled by
@@ -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 ... [26s/12s] OK
+* checking whether package 'epimdr' can be installed ... OK
 * checking installed package size ... OK
 * checking package directory ... OK
 * checking for future file timestamps ... OK
@@ -41,7 +41,7 @@
 * checking S3 generic/method consistency ... OK
 * checking replacement functions ... OK
 * checking foreign function calls ... OK
-* checking R code for possible problems ... NOTE
+* checking R code for possible problems ... [19s/13s] NOTE
 chainSIR: local variable ‘I’ assigned but may not be used
 chainSIR: local variable ‘R’ assigned but may not be used
 chainSIR: local variable ‘S’ assigned but may not be used

diff --git a/revdep/Outputs/check_hte_stderr.txt b/revdep/Outputs/check_hte_stderr.txt
@@ -1,12 +1,16 @@
-  Running ‘fakery.R’ [19s/15s]
-  Comparing ‘fakery.Rout’ to ‘fakery.Rout.save’ ...  Running ‘filter.R’
-  Comparing ‘filter.Rout’ to ‘filter.Rout.save’ ...  Running ‘indep.R’
-  Comparing ‘indep.Rout’ to ‘indep.Rout.save’ ...  Running ‘stobfun.R’
+  Running ‘fakery.R’ [17s/19s]
+  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’
   Comparing ‘stobfun.Rout’ to ‘stobfun.Rout.save’ ... OK
-  Running ‘transmiss.R’ [26s/23s]
-  Comparing ‘transmiss.Rout’ to ‘transmiss.Rout.save’ ...
+  Running ‘transmiss.R’ [25s/24s]
+  Comparing ‘transmiss.Rout’ to ‘transmiss.Rout.save’ ... OK
+
 See
-  '/userdata/kingaa/projects/Rpkg/pomp/revdep/hte.Rcheck/00check.log'
+  '/home/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
@@ -1,4 +1,4 @@
-* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/hte.Rcheck'
+* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/hte.Rcheck'
 * using R version 4.3.2 (2023-10-31)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * R was compiled by
@@ -9,7 +9,7 @@
 * using option '--as-cran'
 * checking for file 'hte/DESCRIPTION' ... OK
 * checking extension type ... Package
-* this is package 'hte' version '0.0.14.0'
+* this is package 'hte' version '0.0.15.0'
 * package encoding: UTF-8
 * checking package namespace information ... OK
 * checking package dependencies ... OK
@@ -43,7 +43,7 @@
 * checking S3 generic/method consistency ... OK
 * checking replacement functions ... OK
 * checking foreign function calls ... OK
-* checking R code for possible problems ... NOTE
+* checking R code for possible problems ... [18s/11s] NOTE
 filterfun : fun: local variable ‘theta’ assigned but may not be used
 stobfun : ofun: local variable ‘theta’ assigned but may not be used
 * checking Rd files ... OK
@@ -64,62 +64,15 @@ 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 ... [277s/36s] OK
+* checking examples ... [94s/49s] OK
 Examples with CPU (user + system) or elapsed time > 5s
-            user  system elapsed
-fake_data 34.086 104.419  12.761
-simuldat  30.314  94.112  11.228
+                   user system elapsed
+fake_data        20.187 23.818  17.923
+simuldat         16.936 18.546  15.764
+bernoulli_filter  4.686  0.117   5.816
 * checking for unstated dependencies in 'tests' ... OK
 * checking tests ...
-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     
- [74s/49s] OK
+ [57s/53s] 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_panelPomp_stderr.txt b/revdep/Outputs/check_panelPomp_stderr.txt
@@ -2,7 +2,7 @@
   Comparing ‘_options.Rout’ to ‘_options.Rout.save’ ... OK
   Running ‘aaa.R’
   Comparing ‘aaa.Rout’ to ‘aaa.Rout.save’ ... OK
-  Running ‘contacts.R’
+  Running ‘contacts.R’ [14s/13s]
   Comparing ‘contacts.Rout’ to ‘contacts.Rout.save’ ...  Running ‘get_col_row.R’
   Comparing ‘get_col_row.Rout’ to ‘get_col_row.Rout.save’ ... OK
   Running ‘mif2.R’

diff --git a/revdep/Outputs/check_panelPomp_stdout.txt b/revdep/Outputs/check_panelPomp_stdout.txt
@@ -1,4 +1,4 @@
-* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/panelPomp.Rcheck'
+* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/panelPomp.Rcheck'
 * using R version 4.3.2 (2023-10-31)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * R was compiled by
@@ -41,7 +41,7 @@
 * checking S3 generic/method consistency ... OK
 * checking replacement functions ... OK
 * checking foreign function calls ... OK
-* checking R code for possible problems ... OK
+* checking R code for possible problems ... [18s/11s] OK
 * checking Rd files ... OK
 * checking Rd metadata ... OK
 * checking Rd line widths ... OK
@@ -51,22 +51,7 @@
 * checking Rd \usage sections ... OK
 * checking Rd contents ... OK
 * checking for unstated dependencies in examples ... OK
-* checking examples ... [115s/14s] OK
-Examples with CPU (user + system) or elapsed time > 5s
-                         user system elapsed
-plot                    2.309  8.396   0.831
-simulate                2.324  8.378   0.797
-pfilter                 2.306  8.360   0.852
-pparams                 2.107  7.999   0.741
-panelRandomWalk         1.545  7.080   0.785
-unitlogLik              1.774  6.783   0.725
-panelGompertz           1.904  6.538   0.956
-panelPomp               1.843  6.583   0.902
-panelGompertzLikelihood 1.596  5.808   0.887
-mif2                    1.516  5.798   1.129
-unitobjects             1.426  5.828   0.765
-params                  1.107  4.944   0.740
-panelPomp_methods       1.044  4.008   1.001
+* checking examples ... [33s/16s] OK
 ** found \donttest examples: check also with --run-donttest
 * checking for unstated dependencies in 'tests' ... OK
 * checking tests ...
@@ -106,7 +91,7 @@ panelPomp_methods       1.044  4.008   1.001
 < name     [,1]     [,2]     [,3]     [,4]      [,5]
 ---
 > variable     [,1]     [,2]     [,3]     [,4]      [,5]
- [277s/45s] OK
+ [96s/54s] OK
 * checking PDF version of manual ... OK
 * checking HTML version of manual ... OK
 * checking for non-standard things in the check directory ... OK