diff --git a/DESCRIPTION b/DESCRIPTION index f8497aa0..54a2fb19 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: pomp Type: Package Title: Statistical Inference for Partially Observed Markov Processes -Version: 5.5.0.0 -Date: 2023-12-02 +Version: 5.5.1.0 +Date: 2023-12-18 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/inst/NEWS b/inst/NEWS index 23eee4c6..576f99b5 100644 --- a/inst/NEWS +++ b/inst/NEWS @@ -1,5 +1,12 @@ _N_e_w_s _f_o_r _p_a_c_k_a_g_e '_p_o_m_p' +_C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _5._5._1: + + • C-level functions ‘set_pomp_userdata’ and + ‘unset_pomp_userdata’ are no longer exported. + + • ‘bspline_eval’ is no longer exported. + _C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _5._4._4: • C-level functions ‘set_pomp_userdata’ and diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd index 2dd5e591..94277156 100644 --- a/inst/NEWS.Rd +++ b/inst/NEWS.Rd @@ -1,5 +1,11 @@ \name{NEWS} \title{News for package `pomp'} +\section{Changes in \pkg{pomp} version 5.5.1}{ + \itemize{ + \item C-level functions \code{set_pomp_userdata} and \code{unset_pomp_userdata} are no longer exported. + \item \code{bspline_eval} is no longer exported. + } +} \section{Changes in \pkg{pomp} version 5.4.4}{ \itemize{ \item C-level functions \code{set_pomp_userdata} and \code{unset_pomp_userdata} have been temporarily restored. diff --git a/inst/include/pomp.h b/inst/include/pomp.h index d3347d90..2f72b484 100644 --- a/inst/include/pomp.h +++ b/inst/include/pomp.h @@ -31,12 +31,6 @@ void periodic_bspline_basis_eval_deriv_t (double x, double period, int degree, int nbasis, int deriv, double *y); -// The following is deprecated and will be removed from the API. -typedef -void bspline_eval_t -(double *y, const double *x, int nx, int i, int p, - int d, const double *knots); - typedef const SEXP get_userdata_t (const char *name); typedef const int *get_userdata_int_t (const char *name); typedef const double *get_userdata_double_t (const char *name); diff --git a/revdep/Outputs/check_CollocInfer_stdout.txt b/revdep/Outputs/check_CollocInfer_stdout.txt index 4d720edd..ec7a4fbb 100644 --- a/revdep/Outputs/check_CollocInfer_stdout.txt +++ b/revdep/Outputs/check_CollocInfer_stdout.txt @@ -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 ... [33s/23s] OK +* checking whether package 'CollocInfer' can be installed ... [31s/20s] 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 ... [75s/63s] NOTE +* checking R code for possible problems ... [67s/23s] NOTE Profile.GausNewt: local variable ‘dcdp’ assigned but may not be used Profile.GausNewt: local variable ‘gradnorm0’ assigned but may not be used @@ -80,13 +80,13 @@ Variables with usage in documentation object 'FhNest' but not in code: * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK -* checking examples ... [139s/28s] OK +* checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed -Profile 20.601 72.806 8.283 -FitMatch 3.377 6.552 0.363 -setup 1.120 4.492 4.509 -* checking PDF version of manual ... [11s/239s] OK +Profile 16.405 62.189 1.563 +FitMatch 1.632 4.969 0.164 +smooth 1.260 4.628 0.105 +* 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 diff --git a/revdep/Outputs/check_DTAT_stdout.txt b/revdep/Outputs/check_DTAT_stdout.txt index 6328d7a9..69b6dfce 100644 --- a/revdep/Outputs/check_DTAT_stdout.txt +++ b/revdep/Outputs/check_DTAT_stdout.txt @@ -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 ... [31s/14s] OK +* checking whether package 'DTAT' can be installed ... [33s/14s] OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK @@ -42,7 +42,7 @@ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK -* checking R code for possible problems ... [61s/15s] NOTE +* checking R code for possible problems ... [60s/15s] 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 @@ -62,15 +62,14 @@ initialize,DE: local variable ‘Q1’ assigned but may not be used * checking sizes of PDF files under 'inst/doc' ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK -* checking examples ... [20s/36s] OK +* checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed -Onoue.Friberg 3.027 7.194 9.489 -dtat1000 0.214 0.024 14.430 +Onoue.Friberg 2.597 7.085 2.138 ** 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 ... [55s/225s] OK +* checking re-building of vignette outputs ... [53s/32s] OK * checking PDF version of manual ... OK * checking HTML version of manual ... OK * checking for non-standard things in the check directory ... OK diff --git a/revdep/Outputs/check_circumstance_stderr.txt b/revdep/Outputs/check_circumstance_stderr.txt index 87eb370f..1ee859b2 100644 --- a/revdep/Outputs/check_circumstance_stderr.txt +++ b/revdep/Outputs/check_circumstance_stderr.txt @@ -4,7 +4,7 @@ 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’ [16s/11s] + Running ‘pmcmc.R’ [13s/11s] Comparing ‘pmcmc.Rout’ to ‘pmcmc.Rout.save’ ... OK diff --git a/revdep/Outputs/check_circumstance_stdout.txt b/revdep/Outputs/check_circumstance_stdout.txt index 7fd74738..1bbcbec1 100644 --- a/revdep/Outputs/check_circumstance_stdout.txt +++ b/revdep/Outputs/check_circumstance_stdout.txt @@ -55,12 +55,12 @@ * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed -pfilter 6.056 0.405 5.267 +pfilter 5.781 0.372 5.103 ** found \donttest examples: check also with --run-donttest * checking for unstated dependencies in 'tests' ... OK * checking tests ... - [47s/28s] OK -* checking PDF version of manual ... [7s/388s] OK + [46s/27s] OK +* 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 diff --git a/revdep/Outputs/check_epimdr2_stdout.txt b/revdep/Outputs/check_epimdr2_stdout.txt index 049103c0..02f728d2 100644 --- a/revdep/Outputs/check_epimdr2_stdout.txt +++ b/revdep/Outputs/check_epimdr2_stdout.txt @@ -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 ... [34s/19s] OK +* checking whether package 'epimdr2' can be installed ... [31s/18s] 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 ... [52s/12s] NOTE +* checking R code for possible problems ... [51s/12s] 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 @@ -152,9 +152,9 @@ twostrain: local variable ‘res’ assigned but may not be used * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK -* checking examples ... [20s/53s] OK +* checking examples ... [23s/13s] OK ** found \donttest examples: check also with --run-donttest -* checking PDF version of manual ... [12s/335s] OK +* 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 diff --git a/revdep/Outputs/check_epimdr_stdout.txt b/revdep/Outputs/check_epimdr_stdout.txt index 98d4071b..950a8a79 100644 --- a/revdep/Outputs/check_epimdr_stdout.txt +++ b/revdep/Outputs/check_epimdr_stdout.txt @@ -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 ... [27s/14s] OK +* checking whether package 'epimdr' can be installed ... [26s/12s] OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK diff --git a/revdep/Outputs/check_hte_stderr.txt b/revdep/Outputs/check_hte_stderr.txt index 18a882b2..46da4f6c 100644 --- a/revdep/Outputs/check_hte_stderr.txt +++ b/revdep/Outputs/check_hte_stderr.txt @@ -1,9 +1,9 @@ - Running ‘fakery.R’ [16s/38s] + Running ‘fakery.R’ [19s/15s] Comparing ‘fakery.Rout’ to ‘fakery.Rout.save’ ... Running ‘filter.R’ - Comparing ‘filter.Rout’ to ‘filter.Rout.save’ ... Running ‘indep.R’ [9s/10s] - Comparing ‘indep.Rout’ to ‘indep.Rout.save’ ... Running ‘stobfun.R’ [6s/19s] + Comparing ‘filter.Rout’ to ‘filter.Rout.save’ ... Running ‘indep.R’ + Comparing ‘indep.Rout’ to ‘indep.Rout.save’ ... Running ‘stobfun.R’ Comparing ‘stobfun.Rout’ to ‘stobfun.Rout.save’ ... OK - Running ‘transmiss.R’ [26s/28s] + Running ‘transmiss.R’ [26s/23s] Comparing ‘transmiss.Rout’ to ‘transmiss.Rout.save’ ... See '/userdata/kingaa/projects/Rpkg/pomp/revdep/hte.Rcheck/00check.log' diff --git a/revdep/Outputs/check_hte_stdout.txt b/revdep/Outputs/check_hte_stdout.txt index ffe691da..d6bea206 100644 --- a/revdep/Outputs/check_hte_stdout.txt +++ b/revdep/Outputs/check_hte_stdout.txt @@ -64,12 +64,11 @@ 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 ... [266s/54s] OK +* checking examples ... [277s/36s] OK Examples with CPU (user + system) or elapsed time > 5s - user system elapsed -fake_data 33.445 103.801 13.000 -simuldat 27.836 87.526 9.747 -transmission 2.196 0.051 12.139 + user system elapsed +fake_data 34.086 104.419 12.761 +simuldat 30.314 94.112 11.228 * checking for unstated dependencies in 'tests' ... OK * checking tests ... 5,9c5,9 @@ -120,8 +119,8 @@ transmission 2.196 0.051 12.139 > ✔ ggplot2 3.4.2 ✔ tibble 3.2.1 > ✔ lubridate 1.9.2 ✔ tidyr 1.3.0 > ✔ purrr 1.0.1 - [71s/107s] OK -* checking PDF version of manual ... [11s/236s] OK + [74s/49s] OK +* 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 diff --git a/revdep/Outputs/check_panelPomp_stderr.txt b/revdep/Outputs/check_panelPomp_stderr.txt index 51876d7d..80f44387 100644 --- a/revdep/Outputs/check_panelPomp_stderr.txt +++ b/revdep/Outputs/check_panelPomp_stderr.txt @@ -9,10 +9,10 @@ Comparing ‘mif2.Rout’ to ‘mif2.Rout.save’ ... OK Running ‘mif2_intern.R’ Comparing ‘mif2_intern.Rout’ to ‘mif2_intern.Rout.save’ ... OK - Running ‘mif2_methods.R’ [15s/25s] + Running ‘mif2_methods.R’ Comparing ‘mif2_methods.Rout’ to ‘mif2_methods.Rout.save’ ... OK Running ‘panelGompertz.R’ - Comparing ‘panelGompertz.Rout’ to ‘panelGompertz.Rout.save’ ... Running ‘panelGompertzLikelihood.R’ [17s/17s] + Comparing ‘panelGompertz.Rout’ to ‘panelGompertz.Rout.save’ ... Running ‘panelGompertzLikelihood.R’ Comparing ‘panelGompertzLikelihood.Rout’ to ‘panelGompertzLikelihood.Rout.save’ ... OK Running ‘panelPomp.R’ Comparing ‘panelPomp.Rout’ to ‘panelPomp.Rout.save’ ... OK @@ -32,6 +32,6 @@ 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’ ... OK - Running ‘simulate.R’ [16s/13s] + Running ‘simulate.R’ Comparing ‘simulate.Rout’ to ‘simulate.Rout.save’ ... diff --git a/revdep/Outputs/check_panelPomp_stdout.txt b/revdep/Outputs/check_panelPomp_stdout.txt index 1f5088b8..25de89c3 100644 --- a/revdep/Outputs/check_panelPomp_stdout.txt +++ b/revdep/Outputs/check_panelPomp_stdout.txt @@ -51,21 +51,22 @@ * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK -* checking examples ... [102s/14s] OK +* checking examples ... [115s/14s] OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed -panelPomp 2.409 8.250 0.779 -plot 1.778 7.277 0.796 -pfilter 1.812 6.925 0.865 -unitlogLik 1.464 6.589 0.921 -mif2 1.525 6.305 1.020 -unitobjects 1.323 6.075 0.805 -panelGompertzLikelihood 1.382 5.818 0.874 -panelGompertz 1.342 5.367 0.839 -params 1.238 5.147 0.752 -pparams 0.876 5.470 0.862 -simulate 0.967 4.892 0.887 -panelPomp_methods 1.285 4.458 0.854 +plot 2.309 8.396 0.831 +simulate 2.324 8.378 0.797 +pfilter 2.306 8.360 0.852 +pparams 2.107 7.999 0.741 +panelRandomWalk 1.545 7.080 0.785 +unitlogLik 1.774 6.783 0.725 +panelGompertz 1.904 6.538 0.956 +panelPomp 1.843 6.583 0.902 +panelGompertzLikelihood 1.596 5.808 0.887 +mif2 1.516 5.798 1.129 +unitobjects 1.426 5.828 0.765 +params 1.107 4.944 0.740 +panelPomp_methods 1.044 4.008 1.001 ** found \donttest examples: check also with --run-donttest * checking for unstated dependencies in 'tests' ... OK * checking tests ... @@ -105,8 +106,8 @@ panelPomp_methods 1.285 4.458 0.854 < name [,1] [,2] [,3] [,4] [,5] --- > variable [,1] [,2] [,3] [,4] [,5] - [313s/143s] OK -* checking PDF version of manual ... [9s/261s] OK + [277s/45s] OK +* 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 diff --git a/revdep/Outputs/check_phylopomp_stderr.txt b/revdep/Outputs/check_phylopomp_stderr.txt index 9cb58ad3..1dc708a0 100644 --- a/revdep/Outputs/check_phylopomp_stderr.txt +++ b/revdep/Outputs/check_phylopomp_stderr.txt @@ -1,16 +1,16 @@ - Running ‘curtail.R’ [11s/34s] + Running ‘curtail.R’ Comparing ‘curtail.Rout’ to ‘curtail.Rout.save’ ... OK - Running ‘diagram.R’ [13s/12s] + Running ‘diagram.R’ Comparing ‘diagram.Rout’ to ‘diagram.Rout.save’ ... OK - Running ‘lbdp1.R’ [9s/10s] + Running ‘lbdp1.R’ Comparing ‘lbdp1.Rout’ to ‘lbdp1.Rout.save’ ... OK - Running ‘lbdp2.R’ [24s/41s] + Running ‘lbdp2.R’ [26s/20s] Comparing ‘lbdp2.Rout’ to ‘lbdp2.Rout.save’ ... OK - Running ‘lbdp3.R’ [11s/48s] + Running ‘lbdp3.R’ Comparing ‘lbdp3.Rout’ to ‘lbdp3.Rout.save’ ... OK - Running ‘lineages.R’ [12s/28s] + Running ‘lineages.R’ Comparing ‘lineages.Rout’ to ‘lineages.Rout.save’ ... OK - Running ‘moran1.R’ [42s/52s] + Running ‘moran1.R’ [39s/30s] Comparing ‘moran1.Rout’ to ‘moran1.Rout.save’ ... OK Running ‘parse.R’ Comparing ‘parse.Rout’ to ‘parse.Rout.save’ ... OK @@ -18,7 +18,7 @@ Comparing ‘plot.Rout’ to ‘plot.Rout.save’ ... OK Running ‘seir1.R’ Comparing ‘seir1.Rout’ to ‘seir1.Rout.save’ ... OK - Running ‘seir2.R’ [20s/14s] + Running ‘seir2.R’ [18s/15s] Comparing ‘seir2.Rout’ to ‘seir2.Rout.save’ ... OK Running ‘si2r.R’ Comparing ‘si2r.Rout’ to ‘si2r.Rout.save’ ... OK diff --git a/revdep/Outputs/check_phylopomp_stdout.txt b/revdep/Outputs/check_phylopomp_stdout.txt index 9d80876c..892cdf38 100644 --- a/revdep/Outputs/check_phylopomp_stdout.txt +++ b/revdep/Outputs/check_phylopomp_stdout.txt @@ -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 ... [59s/43s] OK +* checking whether package 'phylopomp' can be installed ... [58s/42s] 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 @@ -47,7 +47,7 @@ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK -* checking R code for possible problems ... [59s/65s] OK +* checking R code for possible problems ... [52s/11s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK @@ -62,11 +62,11 @@ * checking compilation flags used ... OK * checking compiled code ... OK * checking installed files from 'inst/doc' ... OK -* checking examples ... [18s/30s] OK +* checking examples ... [19s/14s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... - [208s/271s] OK -* checking PDF version of manual ... OK + [202s/115s] OK +* checking PDF version of manual ... [11s/79s] 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_pomp_stderr.txt b/revdep/Outputs/check_pomp_stderr.txt index 6a09424c..3dc87fb2 100644 --- a/revdep/Outputs/check_pomp_stderr.txt +++ b/revdep/Outputs/check_pomp_stderr.txt @@ -1,5 +1,5 @@ - Running ‘R_v_C.R’ [29s/58s] - Running ‘abc.R’ [30s/12s] + Running ‘R_v_C.R’ [24s/14s] + Running ‘abc.R’ Comparing ‘abc.Rout’ to ‘abc.Rout.save’ ... OK Running ‘baddm.R’ Comparing ‘baddm.Rout’ to ‘baddm.Rout.save’ ... OK @@ -29,7 +29,7 @@ Comparing ‘defunct.Rout’ to ‘defunct.Rout.save’ ... OK Running ‘dinit.R’ Comparing ‘dinit.Rout’ to ‘dinit.Rout.save’ ... OK - Running ‘dp.R’ [144s/14s] + Running ‘dp.R’ [157s/14s] Comparing ‘dp.Rout’ to ‘dp.Rout.save’ ... OK Running ‘dprocess.R’ Comparing ‘dprocess.Rout’ to ‘dprocess.Rout.save’ ... OK @@ -41,7 +41,7 @@ Comparing ‘eulermultinom.Rout’ to ‘eulermultinom.Rout.save’ ... OK Running ‘flow.R’ Comparing ‘flow.Rout’ to ‘flow.Rout.save’ ... OK - Running ‘gillespie.R’ [41s/15s] + Running ‘gillespie.R’ [42s/14s] Comparing ‘gillespie.Rout’ to ‘gillespie.Rout.save’ ... OK Running ‘gompertz.R’ Comparing ‘gompertz.Rout’ to ‘gompertz.Rout.save’ ... OK diff --git a/revdep/Outputs/check_pomp_stdout.txt b/revdep/Outputs/check_pomp_stdout.txt index 399515f7..4abd6ccc 100644 --- a/revdep/Outputs/check_pomp_stdout.txt +++ b/revdep/Outputs/check_pomp_stdout.txt @@ -9,7 +9,7 @@ * using option '--as-cran' * checking for file 'pomp/DESCRIPTION' ... OK * checking extension type ... Package -* this is package 'pomp' version '5.4.4.0' +* this is package 'pomp' version '5.5.1.0' * 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 'pomp' can be installed ... [44s/34s] OK +* checking whether package 'pomp' can be installed ... [38s/31s] OK * used C compiler: 'gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0' * checking installed package size ... OK * checking package directory ... 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 ... [71s/37s] OK +* checking R code for possible problems ... [55s/20s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK @@ -68,14 +68,14 @@ * checking compilation flags used ... OK * checking compiled code ... OK * checking installed files from 'inst/doc' ... OK -* checking examples ... [21s/40s] OK +* checking examples ... [22s/10s] OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed -ricker 2.026 7.006 14.904 +ricker 2.045 7.776 0.822 ** found \donttest examples: check also with --run-donttest * checking for unstated dependencies in 'tests' ... OK * checking tests ... - [1764s/322s] OK + [1781s/274s] OK * checking PDF version of manual ... [15s/11s] OK * checking HTML version of manual ... OK * checking for non-standard things in the check directory ... OK diff --git a/revdep/Outputs/check_spaero_stdout.txt b/revdep/Outputs/check_spaero_stdout.txt index 8ddc8d90..8849420b 100644 --- a/revdep/Outputs/check_spaero_stdout.txt +++ b/revdep/Outputs/check_spaero_stdout.txt @@ -62,13 +62,13 @@ Namespace in Imports field not imported from: ‘utils’ * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed -create_simulator 1.766 5.521 1.32 +create_simulator 2.471 7.934 1.39 * checking for unstated dependencies in 'tests' ... OK * checking tests ... - [31s/10s] OK + OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK -* checking re-building of vignette outputs ... [38s/21s] OK +* checking re-building of vignette outputs ... [44s/21s] 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 294aa248..9eef9301 100644 --- a/revdep/Outputs/check_spatPomp_stderr.txt +++ b/revdep/Outputs/check_spatPomp_stderr.txt @@ -1,29 +1,35 @@ Running ‘abf.R’ Running ‘abfir.R’ Running ‘arma_benchmark.R’ - Running ‘bm.R’ [62s/28s] - Comparing ‘bm.Rout’ to ‘bm.Rout.save’ ... Running ‘bm2.R’ - Comparing ‘bm2.Rout’ to ‘bm2.Rout.save’ ... Running ‘bpfilter.R’ - Running ‘concat.R’ [81s/18s] + Running ‘bm.R’ + Comparing ‘bm.Rout’ to ‘bm.Rout.save’ ... OK + Running ‘bm2.R’ + Comparing ‘bm2.Rout’ to ‘bm2.Rout.save’ ... OK + Running ‘bpfilter.R’ + Running ‘concat.R’ Running ‘enkf.R’ - Running ‘gbm.R’ [32s/16s] - Comparing ‘gbm.Rout’ to ‘gbm.Rout.save’ ... Running ‘girf.R’ - Running ‘he10.R’ [34s/21s] - Comparing ‘he10.Rout’ to ‘he10.Rout.save’ ... Running ‘ibpf.R’ + Running ‘gbm.R’ + Comparing ‘gbm.Rout’ to ‘gbm.Rout.save’ ... OK + Running ‘girf.R’ + Running ‘he10.R’ + Comparing ‘he10.Rout’ to ‘he10.Rout.save’ ... OK + Running ‘ibpf.R’ Running ‘ienkf.R’ Running ‘igirf.R’ Running ‘iter_filter.R’ Comparing ‘iter_filter.Rout’ to ‘iter_filter.Rout.save’ ... OK Running ‘iubf.R’ Running ‘lorenz.R’ - Comparing ‘lorenz.Rout’ to ‘lorenz.Rout.save’ ... Running ‘measles.R’ [60s/28s] - Comparing ‘measles.Rout’ to ‘measles.Rout.save’ ... Running ‘measles2.R’ [108s/39s] - Comparing ‘measles2.Rout’ to ‘measles2.Rout.save’ ... Running ‘param_formats.R’ + Comparing ‘lorenz.Rout’ to ‘lorenz.Rout.save’ ... OK + Running ‘measles.R’ + Comparing ‘measles.Rout’ to ‘measles.Rout.save’ ... OK + Running ‘measles2.R’ + Comparing ‘measles2.Rout’ to ‘measles2.Rout.save’ ... OK + Running ‘param_formats.R’ Comparing ‘param_formats.Rout’ to ‘param_formats.Rout.save’ ... OK Running ‘pfilter.R’ Running ‘plot.R’ - Running ‘simulate.R’ [6s/32s] + Running ‘simulate.R’ Running ‘spatPomp.R’ - Running ‘xtests.R’ [7s/12s] diff --git a/revdep/Outputs/check_spatPomp_stdout.txt b/revdep/Outputs/check_spatPomp_stdout.txt index 21011a98..6aa28e24 100644 --- a/revdep/Outputs/check_spatPomp_stdout.txt +++ b/revdep/Outputs/check_spatPomp_stdout.txt @@ -9,7 +9,7 @@ * using option '--as-cran' * checking for file 'spatPomp/DESCRIPTION' ... OK * checking extension type ... Package -* this is package 'spatPomp' version '0.33.0' +* this is package 'spatPomp' version '0.34.0' * 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 'spatPomp' can be installed ... [43s/21s] OK +* checking whether package 'spatPomp' can be installed ... [40s/20s] 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 ... [57s/18s] OK +* checking R code for possible problems ... [62s/18s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK @@ -60,205 +60,11 @@ * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK -* checking examples ... [6s/22s] OK +* checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... -84,93c84,85 -< Warning messages: -< 1: executing %dopar% sequentially: no parallel backend registered -< 2: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 3: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 4: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 5: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 6: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 7: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 8: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 9: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. ---- -> Warning message: -> executing %dopar% sequentially: no parallel backend registered -99,107d90 -< Warning messages: -< 1: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 2: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 3: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 4: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 5: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 6: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 7: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 8: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -117d99 -< There were 44 warnings (use warnings() to see them) -127,131d108 -< Warning messages: -< 1: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 2: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 3: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 4: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -136,140d112 -< Warning messages: -< 1: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 2: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 3: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 4: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -150,154d121 -< Warning messages: -< 1: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 2: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 3: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 4: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -165d131 -< There were 18 warnings (use warnings() to see them) -173,181d138 -< Warning messages: -< 1: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 2: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 3: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 4: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 5: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 6: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 7: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 8: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -187,195d143 -< Warning messages: -< 1: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 2: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 3: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 4: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 5: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 6: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 7: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 8: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -228d175 -< There were 36 warnings (use warnings() to see them) -234d180 -< There were 16 warnings (use warnings() to see them) -258d203 -< There were 36 warnings (use warnings() to see them) -284,292d228 -< Warning messages: -< 1: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 2: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 3: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 4: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 5: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 6: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 7: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 8: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -306,314d241 -< Warning messages: -< 1: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 2: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 3: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 4: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 5: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 6: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 7: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 8: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -333d259 -< There were 40 warnings (use warnings() to see them) -359d284 -< There were 40 warnings (use warnings() to see them) -427,428d351 -< Warning message: -< 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -437,438d359 -< Warning message: -< 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -458,459d378 -< Warning message: -< 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -466,467d384 -< Warning message: -< 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -476,477d392 -< Warning message: -< 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -486,488d400 -< Warning messages: -< 1: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 2: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -517,518d428 -< Warning message: -< 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -526,527d435 -< Warning message: -< 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -539,540d446 -< Warning message: -< 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -545,546d450 -< Warning message: -< 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -554,555d457 -< Warning message: -< 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -621,623d522 -< Warning messages: -< 1: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 2: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -628d526 -< There were 18 warnings (use warnings() to see them) -636,644d533 -< Warning messages: -< 1: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 2: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 3: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 4: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 5: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 6: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 7: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 8: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -650,654d538 -< Warning messages: -< 1: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 2: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 3: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 4: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -18,26d17 -< Warning messages: -< 1: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 2: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 3: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 4: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 5: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 6: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 7: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 8: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -51d41 -< There were 16 warnings (use warnings() to see them) -69d58 -< There were 16 warnings (use warnings() to see them) -77d65 -< There were 16 warnings (use warnings() to see them) -87d74 -< There were 16 warnings (use warnings() to see them) -35d34 -< There were 44 warnings (use warnings() to see them) -68d67 -< There were 50 or more warnings (use warnings() to see the first 50) -107d105 -< There were 50 or more warnings (use warnings() to see the first 50) -111d108 -< There were 50 or more warnings (use warnings() to see the first 50) -143d139 -< There were 50 or more warnings (use warnings() to see the first 50) -35d34 -< There were 50 or more warnings (use warnings() to see the first 50) -78c78,80 -< There were 50 or more warnings (use warnings() to see the first 50) ---- -> Warning messages: -> 1: in 'table_lookup': extrapolating at 1.965000e+03. -> 2: in 'table_lookup': extrapolating at 1.965002e+03. -120,124d119 -< Warning messages: -< 1: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 2: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 3: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. -< 4: 'unset_pomp_userdata' is now deprecated and will be removed in a future release. - [553s/255s] OK -* checking PDF version of manual ... [12s/49s] OK + [451s/57s] OK +* 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 diff --git a/revdep/Outputs/check_stops_stdout.txt b/revdep/Outputs/check_stops_stdout.txt index 98b5f251..105a04f0 100644 --- a/revdep/Outputs/check_stops_stdout.txt +++ b/revdep/Outputs/check_stops_stdout.txt @@ -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 ... [41s/22s] WARNING +* checking whether package 'stops' can be installed ... [35s/20s] WARNING Found the following significant warnings: Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'. See '/userdata/kingaa/projects/Rpkg/pomp/revdep/stops.Rcheck/00install.out' for details. @@ -44,7 +44,7 @@ See '/userdata/kingaa/projects/Rpkg/pomp/revdep/stops.Rcheck/00install.out' for * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK -* checking R code for possible problems ... [89s/261s] NOTE +* checking R code for possible problems ... [71s/23s] 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 @@ -77,7 +77,7 @@ stoploss: local variable ‘cstriatedness’ assigned but may not be used stoploss: local variable ‘cstringiness’ assigned but may not be used tgpoptim: local variable ‘fold’ assigned but may not be used tgpoptim: local variable ‘valsorig’ assigned but may not be used -* checking Rd files ... [5s/20s] OK +* checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK @@ -92,7 +92,7 @@ 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 ... [34s/13s] OK +* checking examples ... [36s/13s] 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 8c52d98d..8353bd3f 100644 --- a/revdep/timings.tab +++ b/revdep/timings.tab @@ -1,13 +1,13 @@ "user" "system" "elapsed" -"pomp" 587.134 1521.785 684.952 -"CollocInfer" 144.16 304.68 461.608 -"DTAT" 145.611 244.966 477.217 -"epimdr" 71.811 171.978 65.374 -"epimdr2" 97.886 187.975 461.546 -"spaero" 77.642 227.99 63.069 -"spatPomp" 233.864 612.866 464.548 -"stops" 165.015 247.554 500.706 -"circumstance" 92.775 187.164 458.546 -"hte" 185.779 401.547 460.988 -"panelPomp" 159.403 468.413 460.905 -"phylopomp" 251.592 289.482 528.498 +"pomp" 590.852 1491.714 394.952 +"CollocInfer" 139.403 284.371 116.818 +"DTAT" 148.63 236.006 141.201 +"epimdr" 70.345 163.153 64.66 +"epimdr2" 98.431 182.536 93.186 +"spaero" 81.809 240.485 63.034 +"spatPomp" 211.988 532.907 151.091 +"stops" 158.436 211.838 151.275 +"circumstance" 92.849 186.086 77.426 +"hte" 194.711 405.518 140.231 +"panelPomp" 158.561 454.556 108.143 +"phylopomp" 251.465 268.861 306.509 diff --git a/src/bspline.c b/src/bspline.c index 17a31e0f..33c7ab76 100644 --- a/src/bspline.c +++ b/src/bspline.c @@ -6,8 +6,9 @@ // B-spline of given degree with given knots at each of the nx points in x. // knots must point to an array of length nbasis+degree+1 // The results are stored in y. -void bspline_eval (double *y, const double *x, int nx, int i, - int degree, int deriv, const double *knots) +static void bspline_eval +(double *y, const double *x, int nx, int i, + int degree, int deriv, const double *knots) { int j; if (deriv > degree) { diff --git a/src/decls.h b/src/decls.h index 1b2a3f9c..af41c0fa 100644 --- a/src/decls.h +++ b/src/decls.h @@ -1,5 +1,4 @@ /* src/bspline.c */ -extern void bspline_eval(double *y, const double *x, int nx, int i, int degree, int deriv, const double *knots); extern SEXP bspline_basis(SEXP range, SEXP x, SEXP nbasis, SEXP degree, SEXP deriv); extern SEXP periodic_bspline_basis(SEXP x, SEXP nbasis, SEXP degree, SEXP period, SEXP deriv); extern void bspline_basis_eval_deriv(double x, double *knots, int degree, int nbasis, int deriv, double *y); @@ -112,7 +111,6 @@ extern SEXP set_pomp_userdata(SEXP userdata); extern const SEXP get_userdata(const char *name); extern const int *get_userdata_int(const char *name); extern const double *get_userdata_double(const char *name); -extern void unset_pomp_userdata(void); /* src/vmeasure.c */ extern SEXP do_vmeasure(SEXP object, SEXP x, SEXP times, SEXP params, SEXP gnsi); /* src/wpfilter.c */ diff --git a/src/init.c b/src/init.c index 0bc6e435..f25c89c1 100644 --- a/src/init.c +++ b/src/init.c @@ -54,7 +54,6 @@ void R_init_pomp (DllInfo *info) { // C functions provided for users R_RegisterCCallable("pomp","bspline_basis_eval_deriv",(DL_FUNC) &bspline_basis_eval_deriv); R_RegisterCCallable("pomp","periodic_bspline_basis_eval_deriv",(DL_FUNC) &periodic_bspline_basis_eval_deriv); - R_RegisterCCallable("pomp","bspline_eval",(DL_FUNC) &bspline_eval); /* DEPRECATED */ R_RegisterCCallable("pomp","get_userdata",(DL_FUNC) &get_userdata); R_RegisterCCallable("pomp","get_userdata_int",(DL_FUNC) &get_userdata_int); R_RegisterCCallable("pomp","get_userdata_double",(DL_FUNC) &get_userdata_double); @@ -69,9 +68,6 @@ void R_init_pomp (DllInfo *info) { R_RegisterCCallable("pomp","apply_probe_sim",(DL_FUNC) &apply_probe_sim); R_RegisterCCallable("pomp","systematic_resampling",(DL_FUNC) &systematic_resampling); R_RegisterCCallable("pomp","randwalk_perturbation", (DL_FUNC) &randwalk_perturbation); - // THE FOLLOWING TWO FUNCTIONS WILL GO AWAY SOON - R_RegisterCCallable("pomp","set_pomp_userdata",(DL_FUNC) &set_pomp_userdata); - R_RegisterCCallable("pomp","unset_pomp_userdata",(DL_FUNC) &unset_pomp_userdata); // Register routines R_registerRoutines(info,NULL,callMethods,NULL,NULL); diff --git a/src/pomp.h b/src/pomp.h index d3347d90..2f72b484 100644 --- a/src/pomp.h +++ b/src/pomp.h @@ -31,12 +31,6 @@ void periodic_bspline_basis_eval_deriv_t (double x, double period, int degree, int nbasis, int deriv, double *y); -// The following is deprecated and will be removed from the API. -typedef -void bspline_eval_t -(double *y, const double *x, int nx, int i, int p, - int d, const double *knots); - typedef const SEXP get_userdata_t (const char *name); typedef const int *get_userdata_int_t (const char *name); typedef const double *get_userdata_double_t (const char *name); diff --git a/src/userdata.c b/src/userdata.c index 83f8aaef..a70ed5ff 100644 --- a/src/userdata.c +++ b/src/userdata.c @@ -29,9 +29,3 @@ const double *get_userdata_double (const char *name) { if (!isReal(elt)) err("user-data element '%s' is not a numeric vector.",name); return REAL(elt); } - -// WILL GO AWAY SOON -void unset_pomp_userdata (void) { // #nocov - warn("'unset_pomp_userdata' is now deprecated and will be removed in a future release."); // #nocov - USERDATA = R_NilValue; // #nocov -}