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‎.Rbuildignore

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@@ -6,14 +6,11 @@ tools
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wiki
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www
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yaml
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tests/Makefile
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tests/(.+?)\.png$
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tests/(.+?)\.pdf$
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tests/(.+?)\.Rout$
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inst/doc/Makefile
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inst/doc/(.+?).md
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inst/doc/(.+?).Rmd
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man/roxygen
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tests
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Doxyfile
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LICENSE\.md$
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README\.md$

‎DESCRIPTION

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Package: pomp
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Type: Package
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Title: Statistical Inference for Partially Observed Markov Processes
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Version: 5.6.1.0
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Date: 2024-03-27
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Version: 5.7
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Date: 2024-03-30
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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")),
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person(given=c("Edward","L."),family="Ionides",role="aut",comment=c(ORCID="0000-0002-4190-0174")) ,
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person(given="Carles",family="Bretó",role="aut",comment=c(ORCID="0000-0003-4695-4902")),

‎inst/NEWS

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‎inst/NEWS.Rd

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‎revdep/Outputs/check_CollocInfer_stdout.txt

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* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/CollocInfer.Rcheck'
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* using R version 4.3.2 (2023-10-31)
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* using R version 4.3.3 (2024-02-29)
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* using platform: x86_64-pc-linux-gnu (64-bit)
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* R was compiled by
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gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
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GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
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* running under: Ubuntu 22.04.3 LTS
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* running under: Ubuntu 22.04.4 LTS
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* using session charset: UTF-8
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* using option '--as-cran'
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* checking for file 'CollocInfer/DESCRIPTION' ... OK
@@ -18,7 +18,7 @@
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* checking for portable file names ... OK
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* checking for sufficient/correct file permissions ... OK
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* checking serialization versions ... OK
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* checking whether package 'CollocInfer' can be installed ... [16s/17s] OK
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* checking whether package 'CollocInfer' can be installed ... [18s/19s] OK
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* checking installed package size ... OK
2323
* checking package directory ... OK
2424
* checking for future file timestamps ... OK
@@ -83,9 +83,9 @@ Variables with usage in documentation object 'FhNest' but not in code:
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* checking examples ... OK
8484
Examples with CPU (user + system) or elapsed time > 5s
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user system elapsed
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Profile 2.867 10.974 1.401
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FitMatch 6.497 6.088 1.252
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ParsMatch 6.370 4.570 1.106
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Profile 4.790 20.101 2.358
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FitMatch 6.521 5.813 1.299
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ParsMatch 5.609 3.346 0.865
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* checking PDF version of manual ... OK
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* checking HTML version of manual ... OK
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* checking for non-standard things in the check directory ... OK

‎revdep/Outputs/check_DTAT_stdout.txt

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* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/DTAT.Rcheck'
2-
* using R version 4.3.2 (2023-10-31)
2+
* using R version 4.3.3 (2024-02-29)
33
* using platform: x86_64-pc-linux-gnu (64-bit)
44
* R was compiled by
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gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
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GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
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* running under: Ubuntu 22.04.3 LTS
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* running under: Ubuntu 22.04.4 LTS
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* using session charset: UTF-8
99
* using option '--as-cran'
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* checking for file 'DTAT/DESCRIPTION' ... OK
@@ -19,7 +19,7 @@
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* checking for hidden files and directories ... OK
2020
* checking for portable file names ... OK
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* checking for sufficient/correct file permissions ... OK
22-
* checking whether package 'DTAT' can be installed ... [15s/15s] OK
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* checking whether package 'DTAT' can be installed ... [16s/16s] OK
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* checking installed package size ... OK
2424
* checking package directory ... OK
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* checking for future file timestamps ... OK
@@ -42,7 +42,7 @@
4242
* checking S3 generic/method consistency ... OK
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* checking replacement functions ... OK
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* checking foreign function calls ... OK
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* checking R code for possible problems ... [24s/18s] NOTE
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* checking R code for possible problems ... [25s/19s] NOTE
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dose.survfit: local variable ‘S’ assigned but may not be used
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as_d3_data,DE : rel_dose: local variable ‘where_na’ assigned but may
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not be used
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** found \donttest examples: check also with --run-donttest
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* checking for unstated dependencies in vignettes ... OK
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* checking package vignettes in 'inst/doc' ... OK
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* checking re-building of vignette outputs ... [29s/27s] OK
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* checking re-building of vignette outputs ... [28s/26s] OK
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* checking PDF version of manual ... OK
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* checking HTML version of manual ... OK
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* checking for non-standard things in the check directory ... OK

‎revdep/Outputs/check_circumstance_stderr.txt

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Running ‘mif2.R’ [11s/13s]
2-
Comparing ‘mif2.Rout’ to ‘mif2.Rout.save’ ... OK
3-
Running ‘pfilter.R’
4-
Comparing ‘pfilter.Rout’ to ‘pfilter.Rout.save’ ... OK
5-
Running ‘plot_matrix.R’
6-
Comparing ‘plot_matrix.Rout’ to ‘plot_matrix.Rout.save’ ... OK
7-
Running ‘pmcmc.R’ [13s/15s]
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Comparing ‘pmcmc.Rout’ to ‘pmcmc.Rout.save’ ... OK
9-
1+
Running ‘mif2.R’ [11s/12s]
2+
Comparing ‘mif2.Rout’ to ‘mif2.Rout.save’ ... Running ‘pfilter.R’
3+
Comparing ‘pfilter.Rout’ to ‘pfilter.Rout.save’ ... Running ‘plot_matrix.R’
4+
Comparing ‘plot_matrix.Rout’ to ‘plot_matrix.Rout.save’ ... Running ‘pmcmc.R’ [14s/14s]
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Comparing ‘pmcmc.Rout’ to ‘pmcmc.Rout.save’ ...
106

‎revdep/Outputs/check_circumstance_stdout.txt

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* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/circumstance.Rcheck'
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* using R version 4.3.2 (2023-10-31)
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* using R version 4.3.3 (2024-02-29)
33
* using platform: x86_64-pc-linux-gnu (64-bit)
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* R was compiled by
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gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
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GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
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* running under: Ubuntu 22.04.3 LTS
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* running under: Ubuntu 22.04.4 LTS
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* using session charset: UTF-8
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* using option '--as-cran'
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* checking for file 'circumstance/DESCRIPTION' ... OK
@@ -41,7 +41,7 @@
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* checking S3 generic/method consistency ... OK
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* checking replacement functions ... OK
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* checking foreign function calls ... OK
44-
* checking R code for possible problems ... OK
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* checking R code for possible problems ... [14s/11s] OK
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* checking Rd files ... OK
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* checking Rd metadata ... OK
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* checking Rd line widths ... OK
@@ -55,11 +55,67 @@
5555
* checking examples ... OK
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Examples with CPU (user + system) or elapsed time > 5s
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user system elapsed
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pfilter 7.026 0.158 6.821
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pfilter 6.485 0.197 6.454
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** found \donttest examples: check also with --run-donttest
6060
* checking for unstated dependencies in 'tests' ... OK
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* checking tests ...
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[34s/36s] OK
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9a10,17
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> Welcome to pomp!
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>
65+
> As of version 4.6, no user-visible pomp function has a name that
66+
> includes a dot ('.'). Function names have been changed to replace the
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> dot with an underscore ('_'). For more information, see the pomp blog:
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> https://kingaa.github.io/pomp/blog.html.
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>
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>
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57,58c65
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< Removed 3 rows containing missing values or values outside the scale range
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< (`geom_line()`).
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---
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> Removed 3 rows containing missing values (`geom_line()`).
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88,89c95
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< Removed 3 rows containing missing values or values outside the scale range
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< (`geom_line()`).
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---
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> Removed 3 rows containing missing values (`geom_line()`).
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119,120c125
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< Removed 3 rows containing missing values or values outside the scale range
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< (`geom_line()`).
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---
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> Removed 3 rows containing missing values (`geom_line()`).
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138,139c143
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< Removed 3 rows containing missing values or values outside the scale range
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< (`geom_line()`).
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---
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> Removed 3 rows containing missing values (`geom_line()`).
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9a10,17
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> Welcome to pomp!
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>
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> As of version 4.6, no user-visible pomp function has a name that
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> includes a dot ('.'). Function names have been changed to replace the
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> dot with an underscore ('_'). For more information, see the pomp blog:
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> https://kingaa.github.io/pomp/blog.html.
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>
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>
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17a18,25
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> Welcome to pomp!
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>
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> As of version 4.6, no user-visible pomp function has a name that
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> includes a dot ('.'). Function names have been changed to replace the
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> dot with an underscore ('_'). For more information, see the pomp blog:
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> https://kingaa.github.io/pomp/blog.html.
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>
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>
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9a10,17
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> Welcome to pomp!
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>
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> As of version 4.6, no user-visible pomp function has a name that
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> includes a dot ('.'). Function names have been changed to replace the
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> dot with an underscore ('_'). For more information, see the pomp blog:
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> https://kingaa.github.io/pomp/blog.html.
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>
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>
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[34s/34s] OK
63119
* checking PDF version of manual ... OK
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* checking HTML version of manual ... OK
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* checking for non-standard things in the check directory ... OK

‎revdep/Outputs/check_epimdr2_stdout.txt

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* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/epimdr2.Rcheck'
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* using R version 4.3.2 (2023-10-31)
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* using R version 4.3.3 (2024-02-29)
33
* using platform: x86_64-pc-linux-gnu (64-bit)
44
* R was compiled by
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gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
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GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
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* running under: Ubuntu 22.04.3 LTS
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* running under: Ubuntu 22.04.4 LTS
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* using session charset: UTF-8
99
* using option '--as-cran'
1010
* checking for file 'epimdr2/DESCRIPTION' ... OK
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1818
* checking for hidden files and directories ... OK
1919
* checking for portable file names ... OK
2020
* checking for sufficient/correct file permissions ... OK
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* checking whether package 'epimdr2' can be installed ... [15s/15s] OK
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* checking whether package 'epimdr2' can be installed ... [17s/17s] OK
2222
* checking installed package size ... OK
2323
* checking package directory ... OK
2424
* checking for future file timestamps ... OK
@@ -40,7 +40,7 @@
4040
* checking S3 generic/method consistency ... OK
4141
* checking replacement functions ... OK
4242
* checking foreign function calls ... OK
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* checking R code for possible problems ... [22s/17s] NOTE
43+
* checking R code for possible problems ... [22s/15s] NOTE
4444
coyne: local variable ‘H1’ assigned but may not be used
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coyne: local variable ‘H2’ assigned but may not be used
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coyne: local variable ‘I’ assigned but may not be used
@@ -152,7 +152,7 @@ twostrain: local variable ‘res’ assigned but may not be used
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* checking data for non-ASCII characters ... OK
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* checking LazyData ... OK
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* checking data for ASCII and uncompressed saves ... OK
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* checking examples ... [15s/13s] OK
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* checking examples ... [13s/12s] OK
156156
** found \donttest examples: check also with --run-donttest
157157
* checking PDF version of manual ... OK
158158
* checking HTML version of manual ... OK

‎revdep/Outputs/check_epimdr_stdout.txt

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* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/epimdr.Rcheck'
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* using R version 4.3.2 (2023-10-31)
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* using R version 4.3.3 (2024-02-29)
33
* using platform: x86_64-pc-linux-gnu (64-bit)
44
* R was compiled by
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gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
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GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
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* running under: Ubuntu 22.04.3 LTS
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* running under: Ubuntu 22.04.4 LTS
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* using session charset: UTF-8
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* using option '--as-cran'
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* checking for file 'epimdr/DESCRIPTION' ... OK
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* checking for portable file names ... OK
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* checking for sufficient/correct file permissions ... OK
2121
* checking serialization versions ... OK
22-
* checking whether package 'epimdr' can be installed ... OK
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* checking whether package 'epimdr' can be installed ... [12s/10s] OK
2323
* checking installed package size ... OK
2424
* checking package directory ... OK
2525
* checking for future file timestamps ... OK
@@ -41,7 +41,7 @@
4141
* checking S3 generic/method consistency ... OK
4242
* checking replacement functions ... OK
4343
* checking foreign function calls ... OK
44-
* checking R code for possible problems ... [19s/13s] NOTE
44+
* checking R code for possible problems ... [18s/14s] NOTE
4545
chainSIR: local variable ‘I’ assigned but may not be used
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chainSIR: local variable ‘R’ assigned but may not be used
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chainSIR: local variable ‘S’ assigned but may not be used

‎revdep/Outputs/check_hte_stderr.txt

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Running ‘fakery.R’ [17s/19s]
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Running ‘fakery.R’ [14s/15s]
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Comparing ‘fakery.Rout’ to ‘fakery.Rout.save’ ... OK
33
Running ‘filter.R’
44
Comparing ‘filter.Rout’ to ‘filter.Rout.save’ ... OK
55
Running ‘indep.R’
66
Comparing ‘indep.Rout’ to ‘indep.Rout.save’ ... OK
77
Running ‘stobfun.R’
88
Comparing ‘stobfun.Rout’ to ‘stobfun.Rout.save’ ... OK
9-
Running ‘transmiss.R’ [25s/24s]
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Running ‘transmiss.R’ [21s/21s]
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Comparing ‘transmiss.Rout’ to ‘transmiss.Rout.save’ ... OK
1111

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See

‎revdep/Outputs/check_hte_stdout.txt

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* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/hte.Rcheck'
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* using R version 4.3.2 (2023-10-31)
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* using R version 4.3.3 (2024-02-29)
33
* using platform: x86_64-pc-linux-gnu (64-bit)
44
* R was compiled by
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gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
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GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
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* running under: Ubuntu 22.04.3 LTS
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* running under: Ubuntu 22.04.4 LTS
88
* using session charset: UTF-8
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* using option '--as-cran'
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* checking for file 'hte/DESCRIPTION' ... OK
1111
* checking extension type ... Package
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* this is package 'hte' version '0.0.15.0'
12+
* this is package 'hte' version '0.0.16.0'
1313
* package encoding: UTF-8
1414
* checking package namespace information ... OK
1515
* checking package dependencies ... OK
@@ -43,7 +43,7 @@
4343
* checking S3 generic/method consistency ... OK
4444
* checking replacement functions ... OK
4545
* checking foreign function calls ... OK
46-
* checking R code for possible problems ... [18s/11s] NOTE
46+
* checking R code for possible problems ... [18s/12s] NOTE
4747
filterfun : fun: local variable ‘theta’ assigned but may not be used
4848
stobfun : ofun: local variable ‘theta’ assigned but may not be used
4949
* checking Rd files ... OK
@@ -64,15 +64,15 @@ stobfun : ofun: local variable ‘theta’ assigned but may not be used
6464
* checking compilation flags used ... OK
6565
* checking compiled code ... OK
6666
* checking installed files from 'inst/doc' ... OK
67-
* checking examples ... [94s/49s] OK
67+
* checking examples ... [96s/49s] OK
6868
Examples with CPU (user + system) or elapsed time > 5s
6969
user system elapsed
70-
fake_data 20.187 23.818 17.923
71-
simuldat 16.936 18.546 15.764
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bernoulli_filter 4.686 0.117 5.816
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fake_data 18.967 24.513 17.851
71+
simuldat 16.912 21.792 15.537
72+
bernoulli_filter 4.716 0.104 5.665
7373
* checking for unstated dependencies in 'tests' ... OK
7474
* checking tests ...
75-
[57s/53s] OK
75+
[50s/48s] OK
7676
* checking PDF version of manual ... OK
7777
* checking HTML version of manual ... OK
7878
* checking for non-standard things in the check directory ... OK

‎revdep/Outputs/check_panelPomp_stderr.txt

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Comparing ‘_options.Rout’ to ‘_options.Rout.save’ ... OK
33
Running ‘aaa.R’
44
Comparing ‘aaa.Rout’ to ‘aaa.Rout.save’ ... OK
5-
Running ‘contacts.R’ [14s/13s]
5+
Running ‘contacts.R’ [12s/13s]
66
Comparing ‘contacts.Rout’ to ‘contacts.Rout.save’ ... Running ‘get_col_row.R’
77
Comparing ‘get_col_row.Rout’ to ‘get_col_row.Rout.save’ ... OK
88
Running ‘mif2.R’

‎revdep/Outputs/check_panelPomp_stdout.txt

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* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/panelPomp.Rcheck'
2-
* using R version 4.3.2 (2023-10-31)
2+
* using R version 4.3.3 (2024-02-29)
33
* using platform: x86_64-pc-linux-gnu (64-bit)
44
* R was compiled by
55
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
66
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
7-
* running under: Ubuntu 22.04.3 LTS
7+
* running under: Ubuntu 22.04.4 LTS
88
* using session charset: UTF-8
99
* using option '--as-cran'
1010
* checking for file 'panelPomp/DESCRIPTION' ... OK
@@ -41,7 +41,7 @@
4141
* checking S3 generic/method consistency ... OK
4242
* checking replacement functions ... OK
4343
* checking foreign function calls ... OK
44-
* checking R code for possible problems ... [18s/11s] OK
44+
* checking R code for possible problems ... [18s/12s] OK
4545
* checking Rd files ... OK
4646
* checking Rd metadata ... OK
4747
* checking Rd line widths ... OK
@@ -51,7 +51,7 @@
5151
* checking Rd \usage sections ... OK
5252
* checking Rd contents ... OK
5353
* checking for unstated dependencies in examples ... OK
54-
* checking examples ... [33s/16s] OK
54+
* checking examples ... [32s/16s] OK
5555
** found \donttest examples: check also with --run-donttest
5656
* checking for unstated dependencies in 'tests' ... OK
5757
* checking tests ...
@@ -91,7 +91,7 @@
9191
< name [,1] [,2] [,3] [,4] [,5]
9292
---
9393
> variable [,1] [,2] [,3] [,4] [,5]
94-
[96s/54s] OK
94+
[96s/53s] OK
9595
* checking PDF version of manual ... OK
9696
* checking HTML version of manual ... OK
9797
* checking for non-standard things in the check directory ... OK

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