update revdep

revdep/Outputs/check_CollocInfer_stderr.txt

@@ -1,6 +1,6 @@
 
 See
-  '/home/kingaa/projects/Rpkg/pomp/revdep/CollocInfer.Rcheck/00check.log'
+  '/userdata/kingaa/projects/Rpkg/pomp/revdep/CollocInfer.Rcheck/00check.log'
 for details.
 
 

revdep/Outputs/check_CollocInfer_stdout.txt

@@ -1,4 +1,4 @@
-* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/CollocInfer.Rcheck'
+* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/CollocInfer.Rcheck'
 * using R version 4.2.2 (2022-10-31)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * using session charset: UTF-8
@@ -14,10 +14,11 @@
 * checking for portable file names ... OK
 * checking for sufficient/correct file permissions ... OK
 * checking serialization versions ... OK
-* checking whether package 'CollocInfer' can be installed ... [16s/15s] OK
+* checking whether package 'CollocInfer' can be installed ... [30s/20s] OK
 * checking installed package size ... OK
 * checking package directory ... OK
-* checking for future file timestamps ... OK
+* checking for future file timestamps ... NOTE
+unable to verify current time
 * checking DESCRIPTION meta-information ... OK
 * checking top-level files ... OK
 * checking for left-over files ... OK
@@ -36,7 +37,7 @@
 * checking S3 generic/method consistency ... OK
 * checking replacement functions ... OK
 * checking foreign function calls ... OK
-* checking R code for possible problems ... [33s/25s] NOTE
+* checking R code for possible problems ... [70s/22s] NOTE
 Profile.GausNewt: local variable ‘dcdp’ assigned but may not be used
 Profile.GausNewt: local variable ‘gradnorm0’ assigned but may not be
   used
@@ -78,11 +79,14 @@ 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 3.967 11.652   1.505
+            user system elapsed
+Profile   17.023 51.743   1.319
+FitMatch   5.882 22.446   0.643
+ParsMatch  3.509 14.718   0.313
+smooth     1.373  4.874   0.113
 * checking PDF version of manual ... 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
 * DONE
-Status: 1 WARNING, 1 NOTE
+Status: 1 WARNING, 2 NOTEs

revdep/Outputs/check_DTAT_stderr.txt

@@ -1,6 +1,6 @@
 
 See
-  '/home/kingaa/projects/Rpkg/pomp/revdep/DTAT.Rcheck/00check.log'
+  '/userdata/kingaa/projects/Rpkg/pomp/revdep/DTAT.Rcheck/00check.log'
 for details.
 
 

revdep/Outputs/check_DTAT_stdout.txt

@@ -1,4 +1,4 @@
-* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/DTAT.Rcheck'
+* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/DTAT.Rcheck'
 * using R version 4.2.2 (2022-10-31)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * using session charset: UTF-8
@@ -16,10 +16,11 @@
 * checking for portable file names ... OK
 * checking for sufficient/correct file permissions ... OK
 * checking serialization versions ... OK
-* checking whether package 'DTAT' can be installed ... [15s/14s] OK
+* checking whether package 'DTAT' can be installed ... [27s/14s] OK
 * checking installed package size ... OK
 * checking package directory ... OK
-* checking for future file timestamps ... OK
+* checking for future file timestamps ... NOTE
+unable to verify current time
 * checking 'build' directory ... OK
 * checking DESCRIPTION meta-information ... OK
 * checking top-level files ... OK
@@ -39,7 +40,7 @@
 * checking S3 generic/method consistency ... OK
 * checking replacement functions ... OK
 * checking foreign function calls ... OK
-* checking R code for possible problems ... [25s/14s] NOTE
+* checking R code for possible problems ... [68s/14s] 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
@@ -59,6 +60,9 @@ 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 3.405  6.673   1.782
 ** found \donttest examples: check also with --run-donttest
 * checking for unstated dependencies in vignettes ... OK
 * checking package vignettes in 'inst/doc' ... OK
@@ -67,4 +71,4 @@ initialize,DE: local variable ‘Q1’ assigned but may not be used
 * checking for non-standard things in the check directory ... OK
 * checking for detritus in the temp directory ... OK
 * DONE
-Status: 1 NOTE
+Status: 2 NOTEs

revdep/Outputs/check_circumstance_stderr.txt

@@ -1,6 +1,10 @@
+  Running ‘mif2.R’
+  Comparing ‘mif2.Rout’ to ‘mif2.Rout.save’ ... OK
   Running ‘pfilter.R’
-  Comparing ‘pfilter.Rout’ to ‘pfilter.Rout.save’ ...
+  Comparing ‘pfilter.Rout’ to ‘pfilter.Rout.save’ ... OK
+
 See
-  '/home/kingaa/projects/Rpkg/pomp/revdep/circumstance.Rcheck/00check.log'
+  '/userdata/kingaa/projects/Rpkg/pomp/revdep/circumstance.Rcheck/00check.log'
 for details.
 
+

revdep/Outputs/check_circumstance_stdout.txt

@@ -1,15 +1,14 @@
-* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/circumstance.Rcheck'
+* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/circumstance.Rcheck'
 * using R version 4.2.2 (2022-10-31)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * using session charset: UTF-8
 * using option '--as-cran'
 * checking for file 'circumstance/DESCRIPTION' ... OK
 * checking extension type ... Package
-* this is package 'circumstance' version '0.0.2.0'
+* this is package 'circumstance' version '0.0.5.2'
 * package encoding: UTF-8
 * checking package namespace information ... OK
-* checking package dependencies ... NOTE
-Suggests orphaned package: 'doRNG'
+* checking package dependencies ... OK
 * checking if this is a source package ... OK
 * checking if there is a namespace ... OK
 * checking for executable files ... OK
@@ -19,7 +18,8 @@ Suggests orphaned package: 'doRNG'
 * checking whether package 'circumstance' can be installed ... OK
 * checking installed package size ... OK
 * checking package directory ... OK
-* checking for future file timestamps ... OK
+* checking for future file timestamps ... NOTE
+unable to verify current time
 * checking DESCRIPTION meta-information ... OK
 * checking top-level files ... OK
 * checking for left-over files ... OK
@@ -34,10 +34,7 @@ Suggests orphaned package: 'doRNG'
 * checking whether the namespace can be unloaded cleanly ... OK
 * checking loading without being on the library search path ... OK
 * checking use of S3 registration ... OK
-* checking dependencies in R code ... NOTE
-Package in Depends field not imported from: ‘parallel’
-  These packages need to be imported from (in the NAMESPACE file)
-  for when this namespace is loaded but not attached.
+* checking dependencies in R code ... OK
 * checking S3 generic/method consistency ... OK
 * checking replacement functions ... OK
 * checking foreign function calls ... OK
@@ -51,48 +48,16 @@ Package in Depends field not imported from: ‘parallel’
 * checking Rd \usage sections ... OK
 * checking Rd contents ... OK
 * checking for unstated dependencies in examples ... OK
-* checking examples ... ERROR
-Running examples in 'circumstance-Ex.R' failed
-The error most likely occurred in:
-
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
-> ### Name: pfilter
-> ### Title: Parallel particle filter computations
-> ### Aliases: pfilter pfilter,ANY,numeric-method pfilter-ANY,numeric
-> ###   pfilter,ANY,missing-method pfilter-ANY,missing
-> ###   pfilter,pompList,numeric-method pfilter-pompList,numeric
-> ###   pfilter,pompList,missing-method pfilter-pompList,missing
-> 
-> ### ** Examples
-> 
-> library(circumstance)
-> 
-> ou2() -> ou2
-> ou2 %>% pfilter(Np=1000,Nrep=6) -> pfs
-Error in ou2 %>% pfilter(Np = 1000, Nrep = 6) : 
-  could not find function "%>%"
-Execution halted
+* checking installed files from 'inst/doc' ... OK
+* checking examples ... OK
+Examples with CPU (user + system) or elapsed time > 5s
+         user system elapsed
+pfilter 5.239  0.297   4.529
 * checking for unstated dependencies in 'tests' ... OK
 * checking tests ...
-47,53c47,53
-<   .id time    y1    y2     x1    x2   ess cond.logLik
-< 1   1    1 -4.05 4.781 -3.718  4.25 160.6       -4.31
-< 2   1    2  1.83 6.273  0.940  6.84 148.1       -4.42
-< 3   1    3 -1.32 7.556 -0.373  7.59  71.4       -5.20
-< 4   1    4  6.64 5.730  5.809  6.49  76.1       -5.01
-< 5   1    5  6.58 1.561  5.605  1.84 217.1       -3.99
-< 6   1    6  7.54 0.176  7.355 -1.57 135.8       -4.51
----
->   time    y1    y2     x1    x2   ess cond.logLik .id
-> 1    1 -4.05 4.781 -3.718  4.25 160.6       -4.31   1
-> 2    2  1.83 6.273  0.940  6.84 148.1       -4.42   1
-> 3    3 -1.32 7.556 -0.373  7.59  71.4       -5.20   1
-> 4    4  6.64 5.730  5.809  6.49  76.1       -5.01   1
-> 5    5  6.58 1.561  5.605  1.84 217.1       -3.99   1
-> 6    6  7.54 0.176  7.355 -1.57 135.8       -4.51   1
- OK
+ [20s/13s] OK
 * checking PDF version of manual ... OK
 * checking for non-standard things in the check directory ... OK
 * checking for detritus in the temp directory ... OK
 * DONE
-Status: 1 ERROR, 2 NOTEs
+Status: 1 NOTE

revdep/Outputs/check_epimdr2_stderr.txt

@@ -1,6 +1,6 @@
 
 See
-  '/home/kingaa/projects/Rpkg/pomp/revdep/epimdr2.Rcheck/00check.log'
+  '/userdata/kingaa/projects/Rpkg/pomp/revdep/epimdr2.Rcheck/00check.log'
 for details.
 
 

revdep/Outputs/check_epimdr2_stdout.txt

@@ -1,4 +1,4 @@
-* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/epimdr2.Rcheck'
+* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/epimdr2.Rcheck'
 * using R version 4.2.2 (2022-10-31)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * using session charset: UTF-8
@@ -14,10 +14,11 @@
 * 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 ... [16s/14s] OK
+* checking whether package 'epimdr2' can be installed ... [31s/17s] OK
 * checking installed package size ... OK
 * checking package directory ... OK
-* checking for future file timestamps ... OK
+* checking for future file timestamps ... NOTE
+unable to verify current time
 * checking DESCRIPTION meta-information ... OK
 * checking top-level files ... OK
 * checking for left-over files ... OK
@@ -36,7 +37,7 @@
 * checking S3 generic/method consistency ... OK
 * checking replacement functions ... OK
 * checking foreign function calls ... OK
-* checking R code for possible problems ... [22s/14s] NOTE
+* checking R code for possible problems ... [53s/11s] 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
@@ -148,10 +149,10 @@ 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 ... [14s/12s] OK
+* checking examples ... [20s/11s] OK
 ** found \donttest examples: check also with --run-donttest
 * checking PDF version of manual ... OK
 * checking for non-standard things in the check directory ... OK
 * checking for detritus in the temp directory ... OK
 * DONE
-Status: 1 NOTE
+Status: 2 NOTEs

revdep/Outputs/check_epimdr_stderr.txt

@@ -1,6 +1,6 @@
 
 See
-  '/home/kingaa/projects/Rpkg/pomp/revdep/epimdr.Rcheck/00check.log'
+  '/userdata/kingaa/projects/Rpkg/pomp/revdep/epimdr.Rcheck/00check.log'
 for details.
 
 

revdep/Outputs/check_epimdr_stdout.txt

@@ -1,4 +1,4 @@
-* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/epimdr.Rcheck'
+* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/epimdr.Rcheck'
 * using R version 4.2.2 (2022-10-31)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * using session charset: UTF-8
@@ -15,7 +15,7 @@
 * checking for portable file names ... OK
 * checking for sufficient/correct file permissions ... OK
 * checking serialization versions ... OK
-* checking whether package 'epimdr' can be installed ... OK
+* checking whether package 'epimdr' can be installed ... [28s/12s] OK
 * checking installed package size ... OK
 * checking package directory ... OK
 * checking for future file timestamps ... OK

revdep/Outputs/check_panelPomp_stderr.txt

@@ -2,35 +2,26 @@
   Running ‘aaa.R’
   Comparing ‘aaa.Rout’ to ‘aaa.Rout.save’ ... OK
   Running ‘contacts.R’
-  Comparing ‘contacts.Rout’ to ‘contacts.Rout.save’ ... OK
-  Running ‘get_col_row.R’
-  Comparing ‘get_col_row.Rout’ to ‘get_col_row.Rout.save’ ... OK
-  Running ‘mif2.R’
+  Comparing ‘contacts.Rout’ to ‘contacts.Rout.save’ ...  Running ‘get_col_row.R’
+  Comparing ‘get_col_row.Rout’ to ‘get_col_row.Rout.save’ ...  Running ‘mif2.R’
   Comparing ‘mif2.Rout’ to ‘mif2.Rout.save’ ...  Running ‘mif2_intern.R’
   Comparing ‘mif2_intern.Rout’ to ‘mif2_intern.Rout.save’ ...  Running ‘mif2_methods.R’
   Comparing ‘mif2_methods.Rout’ to ‘mif2_methods.Rout.save’ ...  Running ‘panelGompertz.R’
-  Comparing ‘panelGompertz.Rout’ to ‘panelGompertz.Rout.save’ ... OK
-  Running ‘panelGompertzLikelihood.R’
+  Comparing ‘panelGompertz.Rout’ to ‘panelGompertz.Rout.save’ ...  Running ‘panelGompertzLikelihood.R’
   Comparing ‘panelGompertzLikelihood.Rout’ to ‘panelGompertzLikelihood.Rout.save’ ...  Running ‘panelPomp.R’
-  Comparing ‘panelPomp.Rout’ to ‘panelPomp.Rout.save’ ... OK
-  Running ‘panelPomp_methods.R’
-  Comparing ‘panelPomp_methods.Rout’ to ‘panelPomp_methods.Rout.save’ ... OK
-  Running ‘panelRandomWalk.R’
-  Comparing ‘panelRandomWalk.Rout’ to ‘panelRandomWalk.Rout.save’ ... OK
-  Running ‘panel_loglik.R’
-  Comparing ‘panel_loglik.Rout’ to ‘panel_loglik.Rout.save’ ... OK
-  Running ‘params.R’
-  Comparing ‘params.Rout’ to ‘params.Rout.save’ ... OK
-  Running ‘pfilter.R’
-  Comparing ‘pfilter.Rout’ to ‘pfilter.Rout.save’ ... OK
-  Running ‘pfilter_methods.R’
-  Comparing ‘pfilter_methods.Rout’ to ‘pfilter_methods.Rout.save’ ... OK
-  Running ‘plot.R’
-  Comparing ‘plot.Rout’ to ‘plot.Rout.save’ ... OK
-  Running ‘print-results.R’
-  Comparing ‘print-results.Rout’ to ‘print-results.Rout.save’ ... OK
-  Running ‘seeded-results.R’
+  Comparing ‘panelPomp.Rout’ to ‘panelPomp.Rout.save’ ...  Running ‘panelPomp_methods.R’
+  Comparing ‘panelPomp_methods.Rout’ to ‘panelPomp_methods.Rout.save’ ...  Running ‘panelRandomWalk.R’
+  Comparing ‘panelRandomWalk.Rout’ to ‘panelRandomWalk.Rout.save’ ...  Running ‘panel_loglik.R’
+  Comparing ‘panel_loglik.Rout’ to ‘panel_loglik.Rout.save’ ...  Running ‘params.R’
+  Comparing ‘params.Rout’ to ‘params.Rout.save’ ...  Running ‘pfilter.R’
+  Comparing ‘pfilter.Rout’ to ‘pfilter.Rout.save’ ...  Running ‘pfilter_methods.R’
+  Comparing ‘pfilter_methods.Rout’ to ‘pfilter_methods.Rout.save’ ...  Running ‘plot.R’
+  Comparing ‘plot.Rout’ to ‘plot.Rout.save’ ...  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’ ...  Running ‘simulate.R’
-  Comparing ‘simulate.Rout’ to ‘simulate.Rout.save’ ... OK
+  Comparing ‘simulate.Rout’ to ‘simulate.Rout.save’ ...
+See
+  '/userdata/kingaa/projects/Rpkg/pomp/revdep/panelPomp.Rcheck/00check.log'
+for details.