diff --git a/DESCRIPTION b/DESCRIPTION index 24b4f7e1..04197d42 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: pomp Type: Package Title: Statistical Inference for Partially Observed Markov Processes -Version: 5.6.1.0 -Date: 2024-03-27 +Version: 5.7.0.1 +Date: 2024-03-30 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")) , person(given="Carles",family="Bretó",role="aut",comment=c(ORCID="0000-0003-4695-4902")), diff --git a/R/spect_match.R b/R/spect_match.R index 41ae3aaa..ebd7765f 100644 --- a/R/spect_match.R +++ b/R/spect_match.R @@ -31,6 +31,11 @@ ##' When called, it will return the (optionally weighted) \eqn{L^2}{L2} distance between the data spectrum and simulated spectra. ##' It is a stateful function: ##' Each time it is called, it will remember the values of the parameters and the discrepancy measure. +##' @references +##' +##' \Reuman2006 +##' +##' \Reuman2008 ##' @inheritSection pomp Note for Windows users ##' @inheritSection objfun Important Note ##' @inheritSection objfun Warning! Objective functions based on C snippets diff --git a/man/spect_match.Rd b/man/spect_match.Rd index 85f7a31b..1e9b07b0 100644 --- a/man/spect_match.Rd +++ b/man/spect_match.Rd @@ -218,6 +218,11 @@ On the other hand, if one retrieves a stored objective function from a file, or } } +\references{ +\Reuman2006 + +\Reuman2008 +} \seealso{ \code{\link{spect}} \code{\link[stats]{optim}} \code{\link[subplex]{subplex}} \code{\link[nloptr]{nloptr}} diff --git a/revdep/Outputs/check_CollocInfer_stdout.txt b/revdep/Outputs/check_CollocInfer_stdout.txt index c3b468e6..ae258887 100644 --- a/revdep/Outputs/check_CollocInfer_stdout.txt +++ b/revdep/Outputs/check_CollocInfer_stdout.txt @@ -1,10 +1,10 @@ * using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/CollocInfer.Rcheck' -* using R version 4.3.2 (2023-10-31) +* using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * 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 -* running under: Ubuntu 22.04.3 LTS +* running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * using option '--as-cran' * checking for file 'CollocInfer/DESCRIPTION' ... OK @@ -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 ... [16s/17s] OK +* checking whether package 'CollocInfer' can be installed ... [18s/19s] OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK @@ -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 2.867 10.974 1.401 -FitMatch 6.497 6.088 1.252 -ParsMatch 6.370 4.570 1.106 +Profile 4.790 20.101 2.358 +FitMatch 6.521 5.813 1.299 +ParsMatch 5.609 3.346 0.865 * 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_stdout.txt b/revdep/Outputs/check_DTAT_stdout.txt index 501be30d..ae4b543d 100644 --- a/revdep/Outputs/check_DTAT_stdout.txt +++ b/revdep/Outputs/check_DTAT_stdout.txt @@ -1,10 +1,10 @@ * using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/DTAT.Rcheck' -* using R version 4.3.2 (2023-10-31) +* using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * 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 -* running under: Ubuntu 22.04.3 LTS +* running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * using option '--as-cran' * checking for file 'DTAT/DESCRIPTION' ... 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 ... [15s/15s] OK +* checking whether package 'DTAT' can be installed ... [16s/16s] 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 ... [24s/18s] NOTE +* checking R code for possible problems ... [25s/19s] 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 @@ -66,7 +66,7 @@ initialize,DE: local variable ‘Q1’ assigned but may not be used ** 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 ... [29s/27s] OK +* checking re-building of vignette outputs ... [28s/26s] 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 index 75592276..0d68465c 100644 --- a/revdep/Outputs/check_circumstance_stderr.txt +++ b/revdep/Outputs/check_circumstance_stderr.txt @@ -1,10 +1,6 @@ - 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/15s] - Comparing ‘pmcmc.Rout’ to ‘pmcmc.Rout.save’ ... OK - + 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’ ... diff --git a/revdep/Outputs/check_circumstance_stdout.txt b/revdep/Outputs/check_circumstance_stdout.txt index 058d66a6..da9de7e1 100644 --- a/revdep/Outputs/check_circumstance_stdout.txt +++ b/revdep/Outputs/check_circumstance_stdout.txt @@ -1,10 +1,10 @@ * using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/circumstance.Rcheck' -* using R version 4.3.2 (2023-10-31) +* using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * 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 -* running under: Ubuntu 22.04.3 LTS +* running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * using option '--as-cran' * checking for file 'circumstance/DESCRIPTION' ... 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 ... OK +* checking R code for possible problems ... [14s/11s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK @@ -55,11 +55,67 @@ * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed -pfilter 7.026 0.158 6.821 +pfilter 6.485 0.197 6.454 ** found \donttest examples: check also with --run-donttest * checking for unstated dependencies in 'tests' ... OK * checking tests ... - [34s/36s] OK +9a10,17 +> Welcome to pomp! +> +> As of version 4.6, no user-visible pomp function has a name that +> includes a dot ('.'). Function names have been changed to replace the +> dot with an underscore ('_'). For more information, see the pomp blog: +> https://kingaa.github.io/pomp/blog.html. +> +> +57,58c65 +< Removed 3 rows containing missing values or values outside the scale range +< (`geom_line()`). +--- +> Removed 3 rows containing missing values (`geom_line()`). +88,89c95 +< Removed 3 rows containing missing values or values outside the scale range +< (`geom_line()`). +--- +> Removed 3 rows containing missing values (`geom_line()`). +119,120c125 +< Removed 3 rows containing missing values or values outside the scale range +< (`geom_line()`). +--- +> Removed 3 rows containing missing values (`geom_line()`). +138,139c143 +< Removed 3 rows containing missing values or values outside the scale range +< (`geom_line()`). +--- +> Removed 3 rows containing missing values (`geom_line()`). +9a10,17 +> Welcome to pomp! +> +> As of version 4.6, no user-visible pomp function has a name that +> includes a dot ('.'). Function names have been changed to replace the +> dot with an underscore ('_'). For more information, see the pomp blog: +> https://kingaa.github.io/pomp/blog.html. +> +> +17a18,25 +> Welcome to pomp! +> +> As of version 4.6, no user-visible pomp function has a name that +> includes a dot ('.'). Function names have been changed to replace the +> dot with an underscore ('_'). For more information, see the pomp blog: +> https://kingaa.github.io/pomp/blog.html. +> +> +9a10,17 +> Welcome to pomp! +> +> As of version 4.6, no user-visible pomp function has a name that +> includes a dot ('.'). Function names have been changed to replace the +> dot with an underscore ('_'). For more information, see the pomp blog: +> https://kingaa.github.io/pomp/blog.html. +> +> + [34s/34s] 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_stdout.txt b/revdep/Outputs/check_epimdr2_stdout.txt index 169107a4..290fd5b1 100644 --- a/revdep/Outputs/check_epimdr2_stdout.txt +++ b/revdep/Outputs/check_epimdr2_stdout.txt @@ -1,10 +1,10 @@ * using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/epimdr2.Rcheck' -* using R version 4.3.2 (2023-10-31) +* using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * 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 -* running under: Ubuntu 22.04.3 LTS +* running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * using option '--as-cran' * checking for file 'epimdr2/DESCRIPTION' ... OK @@ -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 ... [15s/15s] OK +* checking whether package 'epimdr2' can be installed ... [17s/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 ... [22s/17s] 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 ... [15s/13s] OK +* checking examples ... [13s/12s] 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_stdout.txt b/revdep/Outputs/check_epimdr_stdout.txt index 4d631c88..01b8d20f 100644 --- a/revdep/Outputs/check_epimdr_stdout.txt +++ b/revdep/Outputs/check_epimdr_stdout.txt @@ -1,10 +1,10 @@ * using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/epimdr.Rcheck' -* using R version 4.3.2 (2023-10-31) +* using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * 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 -* running under: Ubuntu 22.04.3 LTS +* running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * using option '--as-cran' * checking for file 'epimdr/DESCRIPTION' ... OK @@ -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 ... OK +* checking whether package 'epimdr' can be installed ... [12s/10s] 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 ... [19s/13s] NOTE +* checking R code for possible problems ... [18s/14s] 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 index aab110d8..422a735f 100644 --- a/revdep/Outputs/check_hte_stderr.txt +++ b/revdep/Outputs/check_hte_stderr.txt @@ -1,4 +1,4 @@ - Running ‘fakery.R’ [17s/19s] + Running ‘fakery.R’ [14s/15s] Comparing ‘fakery.Rout’ to ‘fakery.Rout.save’ ... OK Running ‘filter.R’ Comparing ‘filter.Rout’ to ‘filter.Rout.save’ ... OK @@ -6,7 +6,7 @@ Comparing ‘indep.Rout’ to ‘indep.Rout.save’ ... OK Running ‘stobfun.R’ Comparing ‘stobfun.Rout’ to ‘stobfun.Rout.save’ ... OK - Running ‘transmiss.R’ [25s/24s] + Running ‘transmiss.R’ [21s/21s] Comparing ‘transmiss.Rout’ to ‘transmiss.Rout.save’ ... OK See diff --git a/revdep/Outputs/check_hte_stdout.txt b/revdep/Outputs/check_hte_stdout.txt index 8be83665..908cf189 100644 --- a/revdep/Outputs/check_hte_stdout.txt +++ b/revdep/Outputs/check_hte_stdout.txt @@ -1,15 +1,15 @@ * using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/hte.Rcheck' -* using R version 4.3.2 (2023-10-31) +* using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * 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 -* running under: Ubuntu 22.04.3 LTS +* running under: Ubuntu 22.04.4 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 '0.0.15.0' +* this is package 'hte' version '0.0.16.0' * 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 ... [18s/11s] NOTE +* checking R code for possible problems ... [18s/12s] 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 @@ -64,15 +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 ... [94s/49s] OK +* checking examples ... [96s/49s] OK Examples with CPU (user + system) or elapsed time > 5s 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 +fake_data 18.967 24.513 17.851 +simuldat 16.912 21.792 15.537 +bernoulli_filter 4.716 0.104 5.665 * checking for unstated dependencies in 'tests' ... OK * checking tests ... - [57s/53s] OK + [50s/48s] 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 index 578bb77a..06bdbed9 100644 --- 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’ [14s/13s] + Running ‘contacts.R’ [12s/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 index 00bbf0ca..aba500ed 100644 --- a/revdep/Outputs/check_panelPomp_stdout.txt +++ b/revdep/Outputs/check_panelPomp_stdout.txt @@ -1,10 +1,10 @@ * using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/panelPomp.Rcheck' -* using R version 4.3.2 (2023-10-31) +* using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * 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 -* running under: Ubuntu 22.04.3 LTS +* running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * using option '--as-cran' * checking for file 'panelPomp/DESCRIPTION' ... 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 ... [18s/11s] OK +* checking R code for possible problems ... [18s/12s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK @@ -51,7 +51,7 @@ * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK -* checking examples ... [33s/16s] OK +* checking examples ... [32s/16s] OK ** found \donttest examples: check also with --run-donttest * checking for unstated dependencies in 'tests' ... OK * checking tests ... @@ -91,7 +91,7 @@ < name [,1] [,2] [,3] [,4] [,5] --- > variable [,1] [,2] [,3] [,4] [,5] - [96s/54s] OK + [96s/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_phylopomp_stderr.txt b/revdep/Outputs/check_phylopomp_stderr.txt index 968559a3..3ffe5d8a 100644 --- a/revdep/Outputs/check_phylopomp_stderr.txt +++ b/revdep/Outputs/check_phylopomp_stderr.txt @@ -1,32 +1,29 @@ Running ‘curtail.R’ Comparing ‘curtail.Rout’ to ‘curtail.Rout.save’ ... OK Running ‘diagram.R’ - Comparing ‘diagram.Rout’ to ‘diagram.Rout.save’ ... OK - Running ‘lbdp1.R’ + Comparing ‘diagram.Rout’ to ‘diagram.Rout.save’ ... Running ‘lbdp1.R’ Comparing ‘lbdp1.Rout’ to ‘lbdp1.Rout.save’ ... OK - Running ‘lbdp2.R’ [19s/19s] + Running ‘lbdp2.R’ [17s/16s] Comparing ‘lbdp2.Rout’ to ‘lbdp2.Rout.save’ ... OK Running ‘lbdp3.R’ Comparing ‘lbdp3.Rout’ to ‘lbdp3.Rout.save’ ... OK Running ‘lineages.R’ Comparing ‘lineages.Rout’ to ‘lineages.Rout.save’ ... OK - Running ‘moran1.R’ [41s/37s] + Running ‘moran1.R’ [30s/26s] Comparing ‘moran1.Rout’ to ‘moran1.Rout.save’ ... OK Running ‘parse.R’ Comparing ‘parse.Rout’ to ‘parse.Rout.save’ ... OK Running ‘plot.R’ - Comparing ‘plot.Rout’ to ‘plot.Rout.save’ ... OK - Running ‘seir1.R’ + Comparing ‘plot.Rout’ to ‘plot.Rout.save’ ... Running ‘seir1.R’ Comparing ‘seir1.Rout’ to ‘seir1.Rout.save’ ... OK - Running ‘seir2.R’ [16s/14s] + Running ‘seir2.R’ [13s/11s] Comparing ‘seir2.Rout’ to ‘seir2.Rout.save’ ... OK Running ‘si2r.R’ Comparing ‘si2r.Rout’ to ‘si2r.Rout.save’ ... OK Running ‘siir1.R’ Comparing ‘siir1.Rout’ to ‘siir1.Rout.save’ ... OK Running ‘simulate.R’ - Comparing ‘simulate.Rout’ to ‘simulate.Rout.save’ ... OK - Running ‘sir1.R’ + Comparing ‘simulate.Rout’ to ‘simulate.Rout.save’ ... Running ‘sir1.R’ Comparing ‘sir1.Rout’ to ‘sir1.Rout.save’ ... OK See diff --git a/revdep/Outputs/check_phylopomp_stdout.txt b/revdep/Outputs/check_phylopomp_stdout.txt index 19cb7ae3..2ccd7fa8 100644 --- a/revdep/Outputs/check_phylopomp_stdout.txt +++ b/revdep/Outputs/check_phylopomp_stdout.txt @@ -1,15 +1,15 @@ * using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/phylopomp.Rcheck' -* using R version 4.3.2 (2023-10-31) +* using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * 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 -* running under: Ubuntu 22.04.3 LTS +* running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * using option '--as-cran' * checking for file 'phylopomp/DESCRIPTION' ... OK * checking extension type ... Package -* this is package 'phylopomp' version '0.10.1.4' +* this is package 'phylopomp' version '0.10.3.0' * 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 'phylopomp' can be installed ... [48s/57s] OK +* checking whether package 'phylopomp' can be installed ... [52s/63s] OK * used C compiler: 'gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0' * used C++ compiler: 'g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0' * checking installed package size ... NOTE @@ -62,10 +62,103 @@ * checking compilation flags used ... OK * checking compiled code ... OK * checking installed files from 'inst/doc' ... OK -* checking examples ... [15s/16s] OK +* checking examples ... [16s/16s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... - [142s/118s] OK +3a4,33 +> Registered S3 methods overwritten by 'treeio': +> method from +> MRCA.phylo tidytree +> MRCA.treedata tidytree +> Nnode.treedata tidytree +> Ntip.treedata tidytree +> ancestor.phylo tidytree +> ancestor.treedata tidytree +> child.phylo tidytree +> child.treedata tidytree +> full_join.phylo tidytree +> full_join.treedata tidytree +> groupClade.phylo tidytree +> groupClade.treedata tidytree +> groupOTU.phylo tidytree +> groupOTU.treedata tidytree +> inner_join.phylo tidytree +> inner_join.treedata tidytree +> is.rooted.treedata tidytree +> nodeid.phylo tidytree +> nodeid.treedata tidytree +> nodelab.phylo tidytree +> nodelab.treedata tidytree +> offspring.phylo tidytree +> offspring.treedata tidytree +> parent.phylo tidytree +> parent.treedata tidytree +> root.treedata tidytree +> rootnode.phylo tidytree +> sibling.phylo tidytree +5a6,35 +> Registered S3 methods overwritten by 'treeio': +> method from +> MRCA.phylo tidytree +> MRCA.treedata tidytree +> Nnode.treedata tidytree +> Ntip.treedata tidytree +> ancestor.phylo tidytree +> ancestor.treedata tidytree +> child.phylo tidytree +> child.treedata tidytree +> full_join.phylo tidytree +> full_join.treedata tidytree +> groupClade.phylo tidytree +> groupClade.treedata tidytree +> groupOTU.phylo tidytree +> groupOTU.treedata tidytree +> inner_join.phylo tidytree +> inner_join.treedata tidytree +> is.rooted.treedata tidytree +> nodeid.phylo tidytree +> nodeid.treedata tidytree +> nodelab.phylo tidytree +> nodelab.treedata tidytree +> offspring.phylo tidytree +> offspring.treedata tidytree +> parent.phylo tidytree +> parent.treedata tidytree +> root.treedata tidytree +> rootnode.phylo tidytree +> sibling.phylo tidytree +3a4,33 +> Registered S3 methods overwritten by 'treeio': +> method from +> MRCA.phylo tidytree +> MRCA.treedata tidytree +> Nnode.treedata tidytree +> Ntip.treedata tidytree +> ancestor.phylo tidytree +> ancestor.treedata tidytree +> child.phylo tidytree +> child.treedata tidytree +> full_join.phylo tidytree +> full_join.treedata tidytree +> groupClade.phylo tidytree +> groupClade.treedata tidytree +> groupOTU.phylo tidytree +> groupOTU.treedata tidytree +> inner_join.phylo tidytree +> inner_join.treedata tidytree +> is.rooted.treedata tidytree +> nodeid.phylo tidytree +> nodeid.treedata tidytree +> nodelab.phylo tidytree +> nodelab.treedata tidytree +> offspring.phylo tidytree +> offspring.treedata tidytree +> parent.phylo tidytree +> parent.treedata tidytree +> root.treedata tidytree +> rootnode.phylo tidytree +> sibling.phylo tidytree + [117s/90s] 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_pomp_stderr.txt b/revdep/Outputs/check_pomp_stderr.txt index 158ed0c4..139597f9 100644 --- a/revdep/Outputs/check_pomp_stderr.txt +++ b/revdep/Outputs/check_pomp_stderr.txt @@ -1,170 +1,2 @@ - Running ‘R_v_C.R’ [19s/19s] - Running ‘abc.R’ - Comparing ‘abc.Rout’ to ‘abc.Rout.save’ ... OK - Running ‘baddm.R’ - Comparing ‘baddm.Rout’ to ‘baddm.Rout.save’ ... OK - Running ‘bake.R’ - Comparing ‘bake.Rout’ to ‘bake.Rout.save’ ... OK - Running ‘basic_probes.R’ - Comparing ‘basic_probes.Rout’ to ‘basic_probes.Rout.save’ ... OK - Running ‘betabinom.R’ - Comparing ‘betabinom.Rout’ to ‘betabinom.Rout.save’ ... OK - Running ‘blowflies.R’ - Comparing ‘blowflies.Rout’ to ‘blowflies.Rout.save’ ... OK - Running ‘bsmc2.R’ - Comparing ‘bsmc2.Rout’ to ‘bsmc2.Rout.save’ ... OK - Running ‘bsplines1.R’ - Comparing ‘bsplines1.Rout’ to ‘bsplines1.Rout.save’ ... OK - Running ‘bsplines2.R’ - Comparing ‘bsplines2.Rout’ to ‘bsplines2.Rout.save’ ... OK - Running ‘concat.R’ - Comparing ‘concat.Rout’ to ‘concat.Rout.save’ ... OK - Running ‘covmat.R’ - Comparing ‘covmat.Rout’ to ‘covmat.Rout.save’ ... OK - Running ‘csnippet.R’ - Comparing ‘csnippet.Rout’ to ‘csnippet.Rout.save’ ... OK - Running ‘dacca.R’ - Comparing ‘dacca.Rout’ to ‘dacca.Rout.save’ ... OK - Running ‘defunct.R’ - Comparing ‘defunct.Rout’ to ‘defunct.Rout.save’ ... OK - Running ‘dinit.R’ - Comparing ‘dinit.Rout’ to ‘dinit.Rout.save’ ... OK - Running ‘dp.R’ - Comparing ‘dp.Rout’ to ‘dp.Rout.save’ ... OK - Running ‘dprocess.R’ - Comparing ‘dprocess.Rout’ to ‘dprocess.Rout.save’ ... OK - Running ‘ebola.R’ - Comparing ‘ebola.Rout’ to ‘ebola.Rout.save’ ... OK - Running ‘emeasure.R’ - Comparing ‘emeasure.Rout’ to ‘emeasure.Rout.save’ ... OK - Running ‘eulermultinom.R’ - Comparing ‘eulermultinom.Rout’ to ‘eulermultinom.Rout.save’ ... OK - Running ‘flow.R’ - Comparing ‘flow.Rout’ to ‘flow.Rout.save’ ... OK - Running ‘gillespie.R’ [21s/13s] - Comparing ‘gillespie.Rout’ to ‘gillespie.Rout.save’ ... OK - Running ‘gompertz.R’ - Comparing ‘gompertz.Rout’ to ‘gompertz.Rout.save’ ... OK - Running ‘helpers.R’ - Comparing ‘helpers.Rout’ to ‘helpers.Rout.save’ ... OK - Running ‘hitch.R’ - Comparing ‘hitch.Rout’ to ‘hitch.Rout.save’ ... OK - Running ‘issue109.R’ - Comparing ‘issue109.Rout’ to ‘issue109.Rout.save’ ... OK - Running ‘issue56.R’ - Comparing ‘issue56.Rout’ to ‘issue56.Rout.save’ ... OK - Running ‘kalman.R’ - Comparing ‘kalman.Rout’ to ‘kalman.Rout.save’ ... OK - Running ‘kalman2.R’ - Comparing ‘kalman2.Rout’ to ‘kalman2.Rout.save’ ... OK - Running ‘link.R’ - Comparing ‘link.Rout’ to ‘link.Rout.save’ ... OK - Running ‘load.R’ - Comparing ‘load.Rout’ to ‘load.Rout.save’ ... OK - Running ‘logmeanexp.R’ - Comparing ‘logmeanexp.Rout’ to ‘logmeanexp.Rout.save’ ... OK - Running ‘lookup.R’ - Comparing ‘lookup.Rout’ to ‘lookup.Rout.save’ ... OK - Running ‘map.R’ - Comparing ‘map.Rout’ to ‘map.Rout.save’ ... OK - Running ‘mcap.R’ - Comparing ‘mcap.Rout’ to ‘mcap.Rout.save’ ... OK - Running ‘measure.R’ - Comparing ‘measure.Rout’ to ‘measure.Rout.save’ ... OK - Running ‘mif2.R’ - Comparing ‘mif2.Rout’ to ‘mif2.Rout.save’ ... OK - Running ‘mif2_index.R’ - Comparing ‘mif2_index.Rout’ to ‘mif2_index.Rout.save’ ... OK - Running ‘mif2_kf.R’ - Comparing ‘mif2_kf.Rout’ to ‘mif2_kf.Rout.save’ ... OK - Running ‘nlf.R’ - Comparing ‘nlf.Rout’ to ‘nlf.Rout.save’ ... OK - Running ‘nullcases.R’ - Comparing ‘nullcases.Rout’ to ‘nullcases.Rout.save’ ... OK - Running ‘ou2.R’ - Comparing ‘ou2.Rout’ to ‘ou2.Rout.save’ ... OK - Running ‘parmat.R’ - Comparing ‘parmat.Rout’ to ‘parmat.Rout.save’ ... OK - Running ‘partrans.R’ - Comparing ‘partrans.Rout’ to ‘partrans.Rout.save’ ... OK - Running ‘pfilter.R’ - Comparing ‘pfilter.Rout’ to ‘pfilter.Rout.save’ ... OK - Running ‘pfilter2.R’ - Comparing ‘pfilter2.Rout’ to ‘pfilter2.Rout.save’ ... OK - Running ‘pmcmc.R’ - Comparing ‘pmcmc.Rout’ to ‘pmcmc.Rout.save’ ... OK - Running ‘pomp.R’ - Comparing ‘pomp.Rout’ to ‘pomp.Rout.save’ ... OK - Running ‘pomp_fun.R’ - Comparing ‘pomp_fun.Rout’ to ‘pomp_fun.Rout.save’ ... OK - Running ‘pomp_methods.R’ - Comparing ‘pomp_methods.Rout’ to ‘pomp_methods.Rout.save’ ... OK - Running ‘prior.R’ - Comparing ‘prior.Rout’ to ‘prior.Rout.save’ ... OK - Running ‘probe.R’ - Comparing ‘probe.Rout’ to ‘probe.Rout.save’ ... OK - Running ‘probe_match.R’ - Comparing ‘probe_match.Rout’ to ‘probe_match.Rout.save’ ... OK - Running ‘process.R’ - Comparing ‘process.Rout’ to ‘process.Rout.save’ ... OK - Running ‘profile_design.R’ - Comparing ‘profile_design.Rout’ to ‘profile_design.Rout.save’ ... OK - Running ‘proposals.R’ - Comparing ‘proposals.Rout’ to ‘proposals.Rout.save’ ... OK - Running ‘resample.R’ - Comparing ‘resample.Rout’ to ‘resample.Rout.save’ ... OK - Running ‘rgammawn.R’ - Comparing ‘rgammawn.Rout’ to ‘rgammawn.Rout.save’ ... OK - Running ‘ricker.R’ - Comparing ‘ricker.Rout’ to ‘ricker.Rout.save’ ... OK - Running ‘rinit.R’ - Comparing ‘rinit.Rout’ to ‘rinit.Rout.save’ ... OK - Running ‘runif_design.R’ - Comparing ‘runif_design.Rout’ to ‘runif_design.Rout.save’ ... OK - Running ‘rw2.R’ - Comparing ‘rw2.Rout’ to ‘rw2.Rout.save’ ... OK - Running ‘sannbox.R’ - Comparing ‘sannbox.Rout’ to ‘sannbox.Rout.save’ ... OK - Running ‘simulate.R’ - Comparing ‘simulate.Rout’ to ‘simulate.Rout.save’ ... OK - Running ‘simulate_data_frame.R’ - Comparing ‘simulate_data_frame.Rout’ to ‘simulate_data_frame.Rout.save’ ... OK - Running ‘sir.R’ - Comparing ‘sir.Rout’ to ‘sir.Rout.save’ ... OK - Running ‘sir2.R’ - Comparing ‘sir2.Rout’ to ‘sir2.Rout.save’ ... OK - Running ‘skeleton.R’ - Comparing ‘skeleton.Rout’ to ‘skeleton.Rout.save’ ... OK - Running ‘slice_design.R’ - Comparing ‘slice_design.Rout’ to ‘slice_design.Rout.save’ ... OK - Running ‘sobol.R’ - Comparing ‘sobol.Rout’ to ‘sobol.Rout.save’ ... OK - Running ‘spect.R’ - Comparing ‘spect.Rout’ to ‘spect.Rout.save’ ... OK - Running ‘spect_match.R’ - Comparing ‘spect_match.Rout’ to ‘spect_match.Rout.save’ ... OK - Running ‘spy.R’ - Running ‘steps.R’ - Comparing ‘steps.Rout’ to ‘steps.Rout.save’ ... OK - Running ‘synlik.R’ - Comparing ‘synlik.Rout’ to ‘synlik.Rout.save’ ... OK - Running ‘traj_match.R’ - Comparing ‘traj_match.Rout’ to ‘traj_match.Rout.save’ ... OK - Running ‘trajectory.R’ - Comparing ‘trajectory.Rout’ to ‘trajectory.Rout.save’ ... OK - Running ‘transformations.R’ - Comparing ‘transformations.Rout’ to ‘transformations.Rout.save’ ... OK - Running ‘undefined.R’ - Comparing ‘undefined.Rout’ to ‘undefined.Rout.save’ ... OK - Running ‘userdata.R’ - Comparing ‘userdata.Rout’ to ‘userdata.Rout.save’ ... OK - Running ‘verhulst.R’ - Comparing ‘verhulst.Rout’ to ‘verhulst.Rout.save’ ... OK - Running ‘vmeasure.R’ - Comparing ‘vmeasure.Rout’ to ‘vmeasure.Rout.save’ ... OK - Running ‘wpfilter.R’ - Comparing ‘wpfilter.Rout’ to ‘wpfilter.Rout.save’ ... OK - Running ‘wquant.R’ - Comparing ‘wquant.Rout’ to ‘wquant.Rout.save’ ... OK diff --git a/revdep/Outputs/check_pomp_stdout.txt b/revdep/Outputs/check_pomp_stdout.txt index 39cbef55..53d4c038 100644 --- a/revdep/Outputs/check_pomp_stdout.txt +++ b/revdep/Outputs/check_pomp_stdout.txt @@ -1,15 +1,15 @@ * using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/pomp.Rcheck' -* using R version 4.3.2 (2023-10-31) +* using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * 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 -* running under: Ubuntu 22.04.3 LTS +* running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * using option '--as-cran' * checking for file 'pomp/DESCRIPTION' ... OK * checking extension type ... Package -* this is package 'pomp' version '5.5.1.0' +* this is package 'pomp' version '5.7' * 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 'pomp' can be installed ... [28s/34s] OK +* checking whether package 'pomp' can be installed ... [32s/39s] OK * used C compiler: 'gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0' * checking installed package size ... OK * checking package directory ... OK @@ -37,13 +37,12 @@ * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK -* checking startup messages can be suppressed ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK -* checking R code for possible problems ... [32s/25s] OK +* checking R code for possible problems ... [33s/26s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK @@ -70,10 +69,7 @@ * checking installed files from 'inst/doc' ... OK * checking examples ... [13s/11s] OK ** found \donttest examples: check also with --run-donttest -* checking for unstated dependencies in 'tests' ... OK -* checking tests ... - [677s/208s] OK -* checking PDF version of manual ... OK +* checking PDF version of manual ... [13s/14s] 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 diff --git a/revdep/Outputs/check_spaero_stderr.txt b/revdep/Outputs/check_spaero_stderr.txt index ce247227..6bf1027f 100644 --- a/revdep/Outputs/check_spaero_stderr.txt +++ b/revdep/Outputs/check_spaero_stderr.txt @@ -1,4 +1,4 @@ - Running ‘testthat.R’ [15s/13s] + Running ‘testthat.R’ [14s/14s] See '/home/kingaa/projects/Rpkg/pomp/revdep/spaero.Rcheck/00check.log' diff --git a/revdep/Outputs/check_spaero_stdout.txt b/revdep/Outputs/check_spaero_stdout.txt index 08827a5f..68091e71 100644 --- a/revdep/Outputs/check_spaero_stdout.txt +++ b/revdep/Outputs/check_spaero_stdout.txt @@ -1,10 +1,10 @@ * using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/spaero.Rcheck' -* using R version 4.3.2 (2023-10-31) +* using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * 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 -* running under: Ubuntu 22.04.3 LTS +* running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * using option '--as-cran' * checking for file 'spaero/DESCRIPTION' ... OK @@ -62,10 +62,10 @@ Namespace in Imports field not imported from: ‘utils’ * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... - [15s/13s] OK + [15s/14s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK -* checking re-building of vignette outputs ... [23s/23s] OK +* checking re-building of vignette outputs ... [23s/24s] 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_spatPomp_stderr.txt b/revdep/Outputs/check_spatPomp_stderr.txt index 9eef9301..66ed3f44 100644 --- a/revdep/Outputs/check_spatPomp_stderr.txt +++ b/revdep/Outputs/check_spatPomp_stderr.txt @@ -1,7 +1,7 @@ Running ‘abf.R’ Running ‘abfir.R’ Running ‘arma_benchmark.R’ - Running ‘bm.R’ + Running ‘bm.R’ [19s/10s] Comparing ‘bm.Rout’ to ‘bm.Rout.save’ ... OK Running ‘bm2.R’ Comparing ‘bm2.Rout’ to ‘bm2.Rout.save’ ... OK diff --git a/revdep/Outputs/check_spatPomp_stdout.txt b/revdep/Outputs/check_spatPomp_stdout.txt index fa78e39f..8755c9ec 100644 --- a/revdep/Outputs/check_spatPomp_stdout.txt +++ b/revdep/Outputs/check_spatPomp_stdout.txt @@ -1,15 +1,15 @@ * using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/spatPomp.Rcheck' -* using R version 4.3.2 (2023-10-31) +* using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * 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 -* running under: Ubuntu 22.04.3 LTS +* running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * using option '--as-cran' * checking for file 'spatPomp/DESCRIPTION' ... OK * checking extension type ... Package -* this is package 'spatPomp' version '0.34.0' +* this is package 'spatPomp' version '0.34.2' * 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 'spatPomp' can be installed ... [19s/20s] OK +* checking whether package 'spatPomp' can be installed ... [22s/24s] OK * used C compiler: 'gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0' * checking installed package size ... OK * checking package directory ... 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 ... [31s/25s] OK +* checking R code for possible problems ... [30s/25s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK @@ -63,7 +63,7 @@ * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... - [140s/56s] OK + [142s/54s] 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_stops_stdout.txt b/revdep/Outputs/check_stops_stdout.txt index b633f8ab..5c9797c2 100644 --- a/revdep/Outputs/check_stops_stdout.txt +++ b/revdep/Outputs/check_stops_stdout.txt @@ -1,10 +1,10 @@ * using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/stops.Rcheck' -* using R version 4.3.2 (2023-10-31) +* using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * 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 -* running under: Ubuntu 22.04.3 LTS +* running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * using option '--as-cran' * checking for file 'stops/DESCRIPTION' ... OK @@ -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 'stops' can be installed ... [21s/24s] OK +* checking whether package 'stops' can be installed ... [23s/27s] 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 ... [36s/29s] NOTE +* checking R code for possible problems ... [34s/28s] NOTE bcStressMin: local variable ‘lambdaorig’ assigned but may not be used bcStressMin: local variable ‘t’ assigned but may not be used c_inequality: local variable ‘out’ assigned but may not be used @@ -89,7 +89,7 @@ tgpoptim: local variable ‘valsorig’ assigned but may not be used * checking data for ASCII and uncompressed saves ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK -* checking examples ... [32s/12s] OK +* checking examples ... [32s/11s] OK ** found \donttest examples: check also with --run-donttest * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK diff --git a/revdep/timings.tab b/revdep/timings.tab index 1880aeab..3afde10b 100644 --- a/revdep/timings.tab +++ b/revdep/timings.tab @@ -1,13 +1,13 @@ "user" "system" "elapsed" -"pomp" 376.707 450.858 333.385 -"CollocInfer" 118.665 68.3 128.208 -"DTAT" 123.457 51.499 148.539 -"epimdr" 54.887 37.947 69.255 -"epimdr2" 79.74 38.966 100.032 -"spaero" 52.106 49.757 68.967 -"spatPomp" 143.073 125.296 161.17 -"stops" 144.626 68.837 167.464 -"circumstance" 77.226 39.054 93.443 -"hte" 146.645 89.635 162.029 -"panelPomp" 102.478 104.389 125.204 -"phylopomp" 232.404 70.339 252.819 +"pomp" 111.108 48.259 137.278 +"CollocInfer" 123.751 76.234 135.114 +"DTAT" 126.728 52.866 153.794 +"epimdr" 57.984 35.738 74.689 +"epimdr2" 83.161 38.813 105.265 +"spaero" 55.888 48.234 75.088 +"spatPomp" 143.034 127.359 160.487 +"stops" 142.311 67.553 166.941 +"circumstance" 78.879 38.082 95.137 +"hte" 142.903 91.302 159.014 +"panelPomp" 105.483 104.443 130.351 +"phylopomp" 207.219 70.173 229.625