remove deprecated elements of the C API

kingaa · Dec 18, 2023 · c9a9cae · c9a9cae
1 parent 99a32b3
commit c9a9cae
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Showing 28 changed files with 135 additions and 334 deletions.
diff --git 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="[email protected]",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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -1,24 +1,24 @@
-  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
   Running ‘plot.R’
   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
@@ -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
@@ -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