update revdeps

kingaa · Jun 18, 2023 · 27c5d63 · 27c5d63
1 parent 805cfcc
commit 27c5d63
Show file tree

Hide file tree

Showing 23 changed files with 128 additions and 162 deletions.
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
@@ -1,9 +1,9 @@
-* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/CollocInfer.Rcheck'
-* using R version 4.3.0 (2023-04-21)
+* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/CollocInfer.Rcheck'
+* using R version 4.3.1 (2023-06-16)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * R was compiled by
-    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
-    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
+    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
 * using session charset: UTF-8
 * using option '--as-cran'
@@ -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 ... [28s/20s] OK
+* checking whether package 'CollocInfer' can be installed ... [16s/16s] 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 ... [72s/22s] NOTE
+* checking R code for possible problems ... [34s/27s] NOTE
 Profile.GausNewt: local variable ‘dcdp’ assigned but may not be used
 Profile.GausNewt: local variable ‘gradnorm0’ assigned but may not be
   used
@@ -82,11 +82,10 @@ Variables with usage in documentation object 'FhNest' but not in code:
 * checking data for ASCII and uncompressed saves ... OK
 * checking examples ... OK
 Examples with CPU (user + system) or elapsed time > 5s
-            user system elapsed
-Profile   17.417 68.241   1.619
-FitMatch   5.672 12.041   0.402
-ParsMatch  6.026 10.051   0.331
-setup      0.807  4.572   0.132
+           user system elapsed
+Profile   3.412 13.860   1.586
+FitMatch  7.402  5.062   1.270
+ParsMatch 6.758  4.088   1.075
 * 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
@@ -1,9 +1,9 @@
-* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/DTAT.Rcheck'
-* using R version 4.3.0 (2023-04-21)
+* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/DTAT.Rcheck'
+* using R version 4.3.1 (2023-06-16)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * R was compiled by
-    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
-    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
+    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
 * using session charset: UTF-8
 * using option '--as-cran'
@@ -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 ... [29s/13s] OK
+* checking whether package 'DTAT' can be installed ... [15s/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 ... [56s/14s] NOTE
+* checking R code for possible problems ... [25s/16s] 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 3.139  7.253   2.013
 ** 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 ... [41s/28s] OK
+* checking re-building of vignette outputs ... [26s/23s] 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’ [12s/11s]
+  Running ‘mif2.R’ [11s/12s]
   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’ [12s/13s]
   Comparing ‘pmcmc.Rout’ to ‘pmcmc.Rout.save’ ... OK
 
 
diff --git a/revdep/Outputs/check_circumstance_stdout.txt b/revdep/Outputs/check_circumstance_stdout.txt
@@ -1,9 +1,9 @@
-* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/circumstance.Rcheck'
-* using R version 4.3.0 (2023-04-21)
+* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/circumstance.Rcheck'
+* using R version 4.3.1 (2023-06-16)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * R was compiled by
-    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
-    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
+    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
 * using session charset: UTF-8
 * using option '--as-cran'
@@ -55,11 +55,11 @@
 * checking examples ... OK
 Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
-pfilter 6.118  0.304     5.1
+pfilter 7.133  0.197   6.915
 ** found \donttest examples: check also with --run-donttest
 * checking for unstated dependencies in 'tests' ... OK
 * checking tests ...
- [40s/28s] OK
+ [32s/32s] 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
@@ -1,9 +1,9 @@
-* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/epimdr2.Rcheck'
-* using R version 4.3.0 (2023-04-21)
+* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/epimdr2.Rcheck'
+* using R version 4.3.1 (2023-06-16)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * R was compiled by
-    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
-    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
+    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
 * using session charset: UTF-8
 * using option '--as-cran'
@@ -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 ... [32s/17s] OK
+* checking whether package 'epimdr2' can be installed ... [15s/14s] 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 ... [57s/11s] NOTE
+* checking R code for possible problems ... [22s/15s] 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 ... [20s/11s] OK
+* checking examples ... [14s/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
@@ -1,9 +1,9 @@
-* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/epimdr.Rcheck'
-* using R version 4.3.0 (2023-04-21)
+* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/epimdr.Rcheck'
+* using R version 4.3.1 (2023-06-16)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * R was compiled by
-    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
-    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
+    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
 * using session charset: UTF-8
 * using option '--as-cran'
@@ -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 ... [29s/11s] 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 ... [18s/12s] 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
@@ -1,17 +1,16 @@
-  Running ‘fakery.R’ [15s/14s]
+  Running ‘fakery.R’ [16s/17s]
   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 ‘test_time.R’ [23s/19s]
-  Comparing ‘test_time.Rout’ to ‘test_time.Rout.save’ ...  Running ‘transmiss.R’ [20s/16s]
+  Running ‘transmiss.R’ [21s/21s]
   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
@@ -1,15 +1,15 @@
-* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/hte.Rcheck'
-* using R version 4.3.0 (2023-04-21)
+* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/hte.Rcheck'
+* using R version 4.3.1 (2023-06-16)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * R was compiled by
-    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
-    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
+    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
 * using session charset: UTF-8
 * using option '--as-cran'
 * checking for file 'hte/DESCRIPTION' ... OK
 * checking extension type ... Package
-* this is package 'hte' version '0.0.12.0'
+* this is package 'hte' version '0.0.14.0'
 * 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 ... [17s/10s] 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
@@ -64,22 +64,18 @@ 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 ... [262s/36s] OK
+* checking examples ... [92s/45s] OK
 Examples with CPU (user + system) or elapsed time > 5s
-            user system elapsed
-fake_data 32.968 94.052  12.694
-simuldat  29.368 90.180  10.999
+                   user system elapsed
+fake_data        19.212 25.072  16.718
+simuldat         15.606 18.422  13.495
+bernoulli_filter  4.568  0.086   5.579
 * checking for unstated dependencies in 'tests' ... OK
 * checking tests ...
-175c175
-< [1] 0.0514613
----
-> [1] 0.05579485
- [89s/60s] OK
+ [50s/46s] OK
 * checking PDF version of manual ... OK
-* checking HTML version of manual ... NOTE
-Skipping checking math rendering: package 'V8' unavailable
+* checking HTML version of manual ... OK
 * checking for non-standard things in the check directory ... OK
 * checking for detritus in the temp directory ... OK
 * DONE
-Status: 2 NOTEs
+Status: 1 NOTE
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’ [13s/12s]
   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
@@ -1,9 +1,9 @@
-* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/panelPomp.Rcheck'
-* using R version 4.3.0 (2023-04-21)
+* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/panelPomp.Rcheck'
+* using R version 4.3.1 (2023-06-16)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * R was compiled by
-    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
-    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
+    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
 * using session charset: UTF-8
 * using option '--as-cran'
@@ -51,22 +51,7 @@
 * checking Rd \usage sections ... OK
 * checking Rd contents ... OK
 * checking for unstated dependencies in examples ... OK
-* checking examples ... [111s/13s] OK
-Examples with CPU (user + system) or elapsed time > 5s
-                         user system elapsed
-simulate                2.287  8.430   0.725
-unitobjects             2.463  8.220   0.712
-unitlogLik              1.947  7.041   0.834
-plot                    1.715  6.837   0.815
-mif2                    1.928  6.195   0.986
-pparams                 1.663  6.333   0.730
-panelGompertzLikelihood 1.487  5.985   0.995
-panelRandomWalk         1.497  5.869   0.743
-params                  1.297  5.794   0.825
-pfilter                 1.381  5.686   0.729
-panelPomp_methods       1.394  5.223   0.788
-panelGompertz           1.423  4.937   0.926
-panelPomp               1.379  4.974   0.785
+* checking examples ... [32s/15s] OK
 ** found \donttest examples: check also with --run-donttest
 * checking for unstated dependencies in 'tests' ... OK
 * checking tests ...
@@ -106,7 +91,7 @@ panelPomp               1.379  4.974   0.785
 < name     [,1]     [,2]     [,3]     [,4]      [,5]
 ---
 > variable     [,1]     [,2]     [,3]     [,4]      [,5]
- [268s/44s] OK
+ [96s/49s] OK
 * checking PDF version of manual ... OK
 * checking HTML version of manual ... OK
 * checking for non-standard things in the check directory ... OK