CRAN version

.Rbuildignore

@@ -13,10 +13,7 @@
 ^yaml
 ^Makefile
 ^rules.mk
-^tests/Makefile
-^tests/(.+?)\.png$
-^tests/(.+?)\.pdf$
-^tests/(.+?)\.Rout$
+^tests
 ^inst/doc/Makefile
 ^inst/doc/(.+?).md
 ^inst/doc/(.+?).Rmd

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: pomp
 Type: Package
 Title: Statistical Inference for Partially Observed Markov Processes
-Version: 5.10.0.0
+Version: 5.10
 Date: 2024-07-01
 Authors@R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),email="kingaa@umich.edu",comment=c(ORCID="0000-0001-6159-3207")),
 	  person(given=c("Edward","L."),family="Ionides",role="aut",comment=c(ORCID="0000-0002-4190-0174"))	,

revdep/Outputs/check_CollocInfer_stderr.txt

@@ -1,6 +1,5 @@
 
 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

@@ -1,6 +1,6 @@
-* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/CollocInfer.Rcheck'
-* using R version 4.3.3 (2024-02-29)
-* using platform: x86_64-pc-linux-gnu (64-bit)
+* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/CollocInfer.Rcheck'
+* using R version 4.4.1 (2024-06-14)
+* using platform: x86_64-pc-linux-gnu
 * R was compiled by
     gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
     GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
@@ -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 ... [18s/19s] OK
+* checking whether package 'CollocInfer' can be installed ... [25s/21s] OK
 * checking installed package size ... OK
 * checking package directory ... OK
 * checking for future file timestamps ... OK
@@ -27,7 +27,7 @@
 * checking for left-over files ... OK
 * checking index information ... OK
 * checking package subdirectories ... OK
-* checking R files for non-ASCII characters ... OK
+* checking code files for non-ASCII characters ... OK
 * checking R files for syntax errors ... OK
 * checking whether the package can be loaded ... OK
 * checking whether the package can be loaded with stated dependencies ... 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 ... [36s/31s] NOTE
+* checking R code for possible problems ... [68s/24s] NOTE
 Profile.GausNewt: local variable ‘dcdp’ assigned but may not be used
 Profile.GausNewt: local variable ‘gradnorm0’ assigned but may not be
   used
@@ -64,13 +64,142 @@ make.genlin : <anonymous>: local variable ‘r’ assigned but may not be
 make.logtrans: local variable ‘more’ assigned but may not be used
 outeropt: local variable ‘g’ assigned but may not be used
 outeropt: local variable ‘resid’ assigned but may not be used
-* checking Rd files ... OK
+* checking Rd files ... NOTE
+checkRd: (-1) ChemoData.rd:14: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) ChemoData.rd:15: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) ChemoData.rd:16: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) ChemoData.rd:17: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) ChemoData.rd:18: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) ChemoRMData.rd:14: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) ChemoRMData.rd:15: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) ChemoRMData.rd:16: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) ChemoRMData.rd:17: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) ChemoRMData.rd:18: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) FhNdata.rd:14: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) FhNdata.rd:15: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) FhNdata.rd:16: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) FhNdata.rd:17: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) FhNdata.rd:18: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) FhNest.rd:11: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) FhNest.rd:12: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) FitMatch.rd:33: Lost braces in \itemize; \value handles \item{}{} directly
+checkRd: (-1) FitMatch.rd:34: Lost braces in \itemize; \value handles \item{}{} directly
+checkRd: (-1) IntegrateForward.rd:20: Lost braces in \itemize; \value handles \item{}{} directly
+checkRd: (-1) IntegrateForward.rd:21: Lost braces in \itemize; \value handles \item{}{} directly
+checkRd: (-1) NSdata.rd:12: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) NSdata.rd:13: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) NSdata.rd:14: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) ParsMatch.rd:30: Lost braces in \itemize; \value handles \item{}{} directly
+checkRd: (-1) ParsMatch.rd:31: Lost braces in \itemize; \value handles \item{}{} directly
+checkRd: (-1) Profile.rd:24: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) Profile.rd:25: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) Profile.rd:26: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) Profile.rd:27-28: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) Profile.rd:34: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) Profile.rd:35: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) Profile.rd:36: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) Profile.rd:37: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) Profile.rd:38: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) Profile.rd:50: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) Profile.rd:51: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) Profile.rd:52: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) Profile.rd:61: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) Profile.rd:62: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) Profile.rd:68-69: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) Profile.rd:70-71: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) ProfileObjective.rd:47: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) ProfileObjective.rd:48: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) ProfileObjective.rd:49: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) ProfileObjective.rd:50-51: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) ProfileObjective.rd:81: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) ProfileObjective.rd:82: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) ProfileObjective.rd:83: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) ProfileObjective.rd:58: Lost braces in \itemize; \value handles \item{}{} directly
+checkRd: (-1) ProfileObjective.rd:59: Lost braces in \itemize; \value handles \item{}{} directly
+checkRd: (-1) ProfileObjective.rd:60: Lost braces in \itemize; \value handles \item{}{} directly
+checkRd: (-1) ProfileObjective.rd:65: Lost braces in \itemize; \value handles \item{}{} directly
+checkRd: (-1) ProfileObjective.rd:66: Lost braces in \itemize; \value handles \item{}{} directly
+checkRd: (-1) ProfileObjective.rd:67: Lost braces in \itemize; \value handles \item{}{} directly
+checkRd: (-1) ProfileObjective.rd:68: Lost braces in \itemize; \value handles \item{}{} directly
+checkRd: (-1) SEIRdata.rd:14: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) SEIRdata.rd:15: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) SEIRdata.rd:16: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) SEIRdata.rd:17: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) SEIRdata.rd:18: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) SplineCoefs.Rd:37: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) SplineCoefs.Rd:38: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) SplineCoefs.Rd:39: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) SplineCoefs.Rd:40-41: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) SplineCoefs.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
+checkRd: (-1) SplineCoefs.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
+checkRd: (-1) SplineCoefs.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
+checkRd: (-1) SplineCoefs.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
+checkRd: (-1) SplineCoefs.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
+checkRd: (-1) SplineCoefs.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
+checkRd: (-1) SplineCoefs.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
+checkRd: (-1) make.lik.rd:21: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) make.lik.rd:22: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) make.lik.rd:23: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) make.lik.rd:24: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) make.lik.rd:25: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) make.lik.rd:30: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) make.lik.rd:31: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) make.lik.rd:32: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) make.lik.rd:33: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) make.lik.rd:34: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) make.proc.rd:24: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) make.proc.rd:25: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) make.proc.rd:26: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) make.proc.rd:27: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) make.proc.rd:28: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) make.transform.rd:58-59: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) make.transform.rd:60-63: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) make.transform.rd:64: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) make.transform.rd:65-66: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) make.transform.rd:67-68: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) make.transform.rd:74: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) make.transform.rd:75: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) make.transform.rd:76-77: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) make.transform.rd:78: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) make.transform.rd:85-87: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) make.transform.rd:88-90: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) make.transform.rd:91: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) setup.rd:23: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) setup.rd:24: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) setup.rd:25: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) setup.rd:26: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) setup.rd:32: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) setup.rd:33: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) setup.rd:34: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) setup.rd:35: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) setup.rd:36-37: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) setup.rd:48: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) setup.rd:49: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) setup.rd:50: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) setup.rd:68: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) setup.rd:69: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) setup.rd:99: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) setup.rd:100: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) smooth.rd:21: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) smooth.rd:22: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) smooth.rd:23: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) smooth.rd:24: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) smooth.rd:31: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) smooth.rd:32: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) smooth.rd:33: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) smooth.rd:34: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) smooth.rd:35-36: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) smooth.rd:47: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) smooth.rd:48: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) smooth.rd:49: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) smooth.rd:58: Lost braces in \itemize; meant \describe ?
+checkRd: (-1) smooth.rd:59: Lost braces in \itemize; meant \describe ?
 * checking Rd metadata ... OK
 * checking Rd line widths ... OK
 * checking Rd cross-references ... OK
 * checking for missing documentation entries ... OK
 * checking for code/documentation mismatches ... WARNING
-Variables with usage in documentation object 'FhNest' but not in code:
+Variables with usage in Rd file 'FhNest.rd' but not in code:
   ‘FhNest’
 
 * checking Rd \usage sections ... OK
@@ -83,12 +212,11 @@ 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   4.790 20.101   2.358
-FitMatch  6.521  5.813   1.299
-ParsMatch 5.609  3.346   0.865
+Profile  12.755 48.699   1.091
+FitMatch  4.335  9.159   0.316
 * 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 +1,5 @@
 
 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

@@ -1,6 +1,6 @@
-* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/DTAT.Rcheck'
-* using R version 4.3.3 (2024-02-29)
-* using platform: x86_64-pc-linux-gnu (64-bit)
+* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/DTAT.Rcheck'
+* using R version 4.4.1 (2024-06-14)
+* using platform: x86_64-pc-linux-gnu
 * R was compiled by
     gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
     GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
@@ -9,7 +9,7 @@
 * using option '--as-cran'
 * checking for file 'DTAT/DESCRIPTION' ... OK
 * checking extension type ... Package
-* this is package 'DTAT' version '0.3-6'
+* this is package 'DTAT' version '0.3-7'
 * package encoding: UTF-8
 * checking package namespace information ... OK
 * checking package dependencies ... 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 ... [16s/16s] OK
+* checking whether package 'DTAT' can be installed ... [28s/13s] OK
 * checking installed package size ... OK
 * checking package directory ... OK
 * checking for future file timestamps ... OK
@@ -29,7 +29,7 @@
 * checking for left-over files ... OK
 * checking index information ... OK
 * checking package subdirectories ... OK
-* checking R files for non-ASCII characters ... OK
+* checking code files for non-ASCII characters ... OK
 * checking R files for syntax errors ... OK
 * checking whether the package can be loaded ... OK
 * checking whether the package can be loaded with stated dependencies ... 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 ... [25s/19s] NOTE
+* checking R code for possible problems ... [58s/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
@@ -63,10 +63,13 @@ 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 2.733  6.198   1.996
 ** 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 ... [28s/26s] OK
+* checking package vignettes ... OK
+* checking re-building of vignette outputs ... [53s/30s] OK
 * checking PDF version of manual ... OK
 * checking HTML version of manual ... OK
 * checking for non-standard things in the check directory ... OK

revdep/Outputs/check_circumstance_stderr.txt

@@ -1,6 +1,10 @@
-  Running ‘mif2.R’ [11s/12s]
-  Comparing ‘mif2.Rout’ to ‘mif2.Rout.save’ ...  Running ‘pfilter.R’
-  Comparing ‘pfilter.Rout’ to ‘pfilter.Rout.save’ ...  Running ‘plot_matrix.R’
-  Comparing ‘plot_matrix.Rout’ to ‘plot_matrix.Rout.save’ ...  Running ‘pmcmc.R’ [14s/14s]
-  Comparing ‘pmcmc.Rout’ to ‘pmcmc.Rout.save’ ...
+  Running ‘mif2.R’
+  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’ [12s/10s]
+  Comparing ‘pmcmc.Rout’ to ‘pmcmc.Rout.save’ ... OK
+