From ffe4692c5129ba1d5547f091b8aa80fe2160eae5 Mon Sep 17 00:00:00 2001 From: "Aaron A. King" Date: Sat, 2 Dec 2023 09:08:01 -0500 Subject: [PATCH] update revdeps --- revdep/Outputs/check_CollocInfer_stdout.txt | 21 +- revdep/Outputs/check_DTAT_stdout.txt | 19 +- revdep/Outputs/check_circumstance_stderr.txt | 2 +- revdep/Outputs/check_circumstance_stdout.txt | 14 +- revdep/Outputs/check_epimdr2_stdout.txt | 16 +- revdep/Outputs/check_epimdr_stdout.txt | 10 +- revdep/Outputs/check_hte_stderr.txt | 16 +- revdep/Outputs/check_hte_stdout.txt | 71 +++++- revdep/Outputs/check_panelPomp_stderr.txt | 6 +- revdep/Outputs/check_panelPomp_stdout.txt | 39 ++-- revdep/Outputs/check_phylopomp_stderr.txt | 14 +- revdep/Outputs/check_phylopomp_stdout.txt | 22 +- revdep/Outputs/check_pomp_stderr.txt | 14 +- revdep/Outputs/check_pomp_stdout.txt | 24 +- revdep/Outputs/check_spaero_stdout.txt | 14 +- revdep/Outputs/check_spatPomp_stderr.txt | 33 +-- revdep/Outputs/check_spatPomp_stdout.txt | 223 +++++++++++++++++-- revdep/Outputs/check_stops_stdout.txt | 21 +- revdep/timings.tab | 23 +- 19 files changed, 417 insertions(+), 185 deletions(-) diff --git a/revdep/Outputs/check_CollocInfer_stdout.txt b/revdep/Outputs/check_CollocInfer_stdout.txt index 731838e5..4d720edd 100644 --- a/revdep/Outputs/check_CollocInfer_stdout.txt +++ b/revdep/Outputs/check_CollocInfer_stdout.txt @@ -1,10 +1,10 @@ * using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/CollocInfer.Rcheck' -* using R version 4.3.1 (2023-06-16) +* using R version 4.3.2 (2023-10-31) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 - GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 -* running under: Ubuntu 22.04.2 LTS + 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 * 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 ... [34s/20s] OK +* checking whether package 'CollocInfer' can be installed ... [33s/23s] 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 ... [67s/22s] NOTE +* checking R code for possible problems ... [75s/63s] NOTE Profile.GausNewt: local variable ‘dcdp’ assigned but may not be used Profile.GausNewt: local variable ‘gradnorm0’ assigned but may not be used @@ -80,12 +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 ... OK +* checking examples ... [139s/28s] OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed -Profile 13.898 47.310 1.045 -FitMatch 3.457 7.528 0.215 -* checking PDF version of manual ... OK +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 * 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 10a2b81e..6328d7a9 100644 --- a/revdep/Outputs/check_DTAT_stdout.txt +++ b/revdep/Outputs/check_DTAT_stdout.txt @@ -1,10 +1,10 @@ * using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/DTAT.Rcheck' -* using R version 4.3.1 (2023-06-16) +* using R version 4.3.2 (2023-10-31) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 - GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 -* running under: Ubuntu 22.04.2 LTS + 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 * 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 ... [36s/13s] OK +* checking whether package 'DTAT' can be installed ... [31s/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 ... [57s/14s] NOTE +* checking R code for possible problems ... [61s/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 @@ -62,14 +62,15 @@ 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 ... OK +* checking examples ... [20s/36s] OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed -Onoue.Friberg 3.028 7.867 2.106 +Onoue.Friberg 3.027 7.194 9.489 +dtat1000 0.214 0.024 14.430 ** 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 ... [49s/27s] OK +* checking re-building of vignette outputs ... [55s/225s] 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 5060de37..87eb370f 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’ [13s/10s] + Running ‘pmcmc.R’ [16s/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 66c57829..7fd74738 100644 --- a/revdep/Outputs/check_circumstance_stdout.txt +++ b/revdep/Outputs/check_circumstance_stdout.txt @@ -1,10 +1,10 @@ * using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/circumstance.Rcheck' -* using R version 4.3.1 (2023-06-16) +* using R version 4.3.2 (2023-10-31) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 - GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 -* running under: Ubuntu 22.04.2 LTS + 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 * using session charset: UTF-8 * using option '--as-cran' * checking for file 'circumstance/DESCRIPTION' ... OK @@ -55,12 +55,12 @@ * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed -pfilter 5.598 0.288 4.562 +pfilter 6.056 0.405 5.267 ** found \donttest examples: check also with --run-donttest * checking for unstated dependencies in 'tests' ... OK * checking tests ... - [42s/26s] OK -* checking PDF version of manual ... OK + [47s/28s] OK +* checking PDF version of manual ... [7s/388s] 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 8ff2b0c3..049103c0 100644 --- a/revdep/Outputs/check_epimdr2_stdout.txt +++ b/revdep/Outputs/check_epimdr2_stdout.txt @@ -1,10 +1,10 @@ * using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/epimdr2.Rcheck' -* using R version 4.3.1 (2023-06-16) +* using R version 4.3.2 (2023-10-31) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 - GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 -* running under: Ubuntu 22.04.2 LTS + 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 * 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 ... [27s/16s] OK +* checking whether package 'epimdr2' can be installed ... [34s/19s] 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 ... [54s/12s] NOTE +* checking R code for possible problems ... [52s/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/11s] OK +* checking examples ... [20s/53s] OK ** found \donttest examples: check also with --run-donttest -* checking PDF version of manual ... OK +* checking PDF version of manual ... [12s/335s] 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 726d2541..98d4071b 100644 --- a/revdep/Outputs/check_epimdr_stdout.txt +++ b/revdep/Outputs/check_epimdr_stdout.txt @@ -1,10 +1,10 @@ * using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/epimdr.Rcheck' -* using R version 4.3.1 (2023-06-16) +* using R version 4.3.2 (2023-10-31) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 - GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 -* running under: Ubuntu 22.04.2 LTS + 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 * 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 ... [22s/12s] OK +* checking whether package 'epimdr' can be installed ... [27s/14s] 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 47ddcb23..18a882b2 100644 --- a/revdep/Outputs/check_hte_stderr.txt +++ b/revdep/Outputs/check_hte_stderr.txt @@ -1,14 +1,10 @@ - Running ‘fakery.R’ [16s/13s] - Comparing ‘fakery.Rout’ to ‘fakery.Rout.save’ ... OK - Running ‘filter.R’ - Comparing ‘filter.Rout’ to ‘filter.Rout.save’ ... OK - Running ‘indep.R’ - Comparing ‘indep.Rout’ to ‘indep.Rout.save’ ... OK - Running ‘stobfun.R’ + Running ‘fakery.R’ [16s/38s] + 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 ‘stobfun.Rout’ to ‘stobfun.Rout.save’ ... OK - Running ‘transmiss.R’ [27s/22s] - Comparing ‘transmiss.Rout’ to ‘transmiss.Rout.save’ ... OK - + Running ‘transmiss.R’ [26s/28s] + Comparing ‘transmiss.Rout’ to ‘transmiss.Rout.save’ ... See '/userdata/kingaa/projects/Rpkg/pomp/revdep/hte.Rcheck/00check.log' for details. diff --git a/revdep/Outputs/check_hte_stdout.txt b/revdep/Outputs/check_hte_stdout.txt index 114ce57f..ffe691da 100644 --- a/revdep/Outputs/check_hte_stdout.txt +++ b/revdep/Outputs/check_hte_stdout.txt @@ -1,10 +1,10 @@ * using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/hte.Rcheck' -* using R version 4.3.1 (2023-06-16) +* using R version 4.3.2 (2023-10-31) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 - GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 -* running under: Ubuntu 22.04.2 LTS + 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 * using session charset: UTF-8 * using option '--as-cran' * checking for file 'hte/DESCRIPTION' ... OK @@ -20,7 +20,7 @@ * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package 'hte' can be installed ... OK -* used C compiler: 'gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0' +* used C compiler: 'gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0' * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK @@ -64,15 +64,64 @@ 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 ... [237s/34s] OK +* checking examples ... [266s/54s] OK Examples with CPU (user + system) or elapsed time > 5s - user system elapsed -fake_data 29.910 85.907 11.964 -simuldat 27.004 81.279 10.529 + 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 * checking for unstated dependencies in 'tests' ... OK * checking tests ... - [67s/46s] OK -* checking PDF version of manual ... OK +5,9c5,9 +< ✔ dplyr 1.1.4 ✔ readr 2.1.4 +< ✔ forcats 1.0.0 ✔ stringr 1.5.1 +< ✔ ggplot2 3.4.4 ✔ tibble 3.2.1 +< ✔ lubridate 1.9.3 ✔ tidyr 1.3.0 +< ✔ purrr 1.0.2 +--- +> ✔ dplyr 1.1.2 ✔ readr 2.1.4 +> ✔ forcats 1.0.0 ✔ stringr 1.5.0 +> ✔ ggplot2 3.4.2 ✔ tibble 3.2.1 +> ✔ lubridate 1.9.2 ✔ tidyr 1.3.0 +> ✔ purrr 1.0.1 +5,9c5,9 +< ✔ dplyr 1.1.4 ✔ readr 2.1.4 +< ✔ forcats 1.0.0 ✔ stringr 1.5.1 +< ✔ ggplot2 3.4.4 ✔ tibble 3.2.1 +< ✔ lubridate 1.9.3 ✔ tidyr 1.3.0 +< ✔ purrr 1.0.2 +--- +> ✔ dplyr 1.1.2 ✔ readr 2.1.4 +> ✔ forcats 1.0.0 ✔ stringr 1.5.0 +> ✔ ggplot2 3.4.2 ✔ tibble 3.2.1 +> ✔ lubridate 1.9.2 ✔ tidyr 1.3.0 +> ✔ purrr 1.0.1 +5,9c5,9 +< ✔ dplyr 1.1.4 ✔ readr 2.1.4 +< ✔ forcats 1.0.0 ✔ stringr 1.5.1 +< ✔ ggplot2 3.4.4 ✔ tibble 3.2.1 +< ✔ lubridate 1.9.3 ✔ tidyr 1.3.0 +< ✔ purrr 1.0.2 +--- +> ✔ dplyr 1.1.2 ✔ readr 2.1.4 +> ✔ forcats 1.0.0 ✔ stringr 1.5.0 +> ✔ ggplot2 3.4.2 ✔ tibble 3.2.1 +> ✔ lubridate 1.9.2 ✔ tidyr 1.3.0 +> ✔ purrr 1.0.1 +5,9c5,9 +< ✔ dplyr 1.1.4 ✔ readr 2.1.4 +< ✔ forcats 1.0.0 ✔ stringr 1.5.1 +< ✔ ggplot2 3.4.4 ✔ tibble 3.2.1 +< ✔ lubridate 1.9.3 ✔ tidyr 1.3.0 +< ✔ purrr 1.0.2 +--- +> ✔ dplyr 1.1.2 ✔ readr 2.1.4 +> ✔ forcats 1.0.0 ✔ stringr 1.5.0 +> ✔ 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 * 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 80f44387..51876d7d 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’ + Running ‘mif2_methods.R’ [15s/25s] Comparing ‘mif2_methods.Rout’ to ‘mif2_methods.Rout.save’ ... OK Running ‘panelGompertz.R’ - Comparing ‘panelGompertz.Rout’ to ‘panelGompertz.Rout.save’ ... Running ‘panelGompertzLikelihood.R’ + Comparing ‘panelGompertz.Rout’ to ‘panelGompertz.Rout.save’ ... Running ‘panelGompertzLikelihood.R’ [17s/17s] 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’ + Running ‘simulate.R’ [16s/13s] Comparing ‘simulate.Rout’ to ‘simulate.Rout.save’ ... diff --git a/revdep/Outputs/check_panelPomp_stdout.txt b/revdep/Outputs/check_panelPomp_stdout.txt index 112943a7..1f5088b8 100644 --- a/revdep/Outputs/check_panelPomp_stdout.txt +++ b/revdep/Outputs/check_panelPomp_stdout.txt @@ -1,10 +1,10 @@ * using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/panelPomp.Rcheck' -* using R version 4.3.1 (2023-06-16) +* using R version 4.3.2 (2023-10-31) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 - GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 -* running under: Ubuntu 22.04.2 LTS + 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 * using session charset: UTF-8 * using option '--as-cran' * checking for file 'panelPomp/DESCRIPTION' ... OK @@ -51,22 +51,21 @@ * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK -* checking examples ... [111s/13s] OK +* checking examples ... [102s/14s] OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed -unitlogLik 2.432 8.376 0.791 -pfilter 2.327 7.685 0.731 -params 1.924 7.278 0.747 -pparams 1.939 6.973 0.667 -simulate 1.623 7.282 0.809 -unitobjects 1.668 6.802 0.752 -plot 1.859 6.562 0.736 -panelGompertz 1.857 6.510 0.772 -panelGompertzLikelihood 1.444 5.763 0.888 -panelPomp 1.464 5.436 0.765 -panelPomp_methods 1.211 4.968 0.867 -panelRandomWalk 1.385 4.659 0.789 -mif2 1.510 4.407 0.999 +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 ** found \donttest examples: check also with --run-donttest * checking for unstated dependencies in 'tests' ... OK * checking tests ... @@ -106,8 +105,8 @@ mif2 1.510 4.407 0.999 < name [,1] [,2] [,3] [,4] [,5] --- > variable [,1] [,2] [,3] [,4] [,5] - [291s/43s] OK -* checking PDF version of manual ... OK + [313s/143s] OK +* checking PDF version of manual ... [9s/261s] 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 702880de..9cb58ad3 100644 --- a/revdep/Outputs/check_phylopomp_stderr.txt +++ b/revdep/Outputs/check_phylopomp_stderr.txt @@ -1,16 +1,16 @@ - Running ‘curtail.R’ + Running ‘curtail.R’ [11s/34s] Comparing ‘curtail.Rout’ to ‘curtail.Rout.save’ ... OK - Running ‘diagram.R’ + Running ‘diagram.R’ [13s/12s] Comparing ‘diagram.Rout’ to ‘diagram.Rout.save’ ... OK - Running ‘lbdp1.R’ + Running ‘lbdp1.R’ [9s/10s] Comparing ‘lbdp1.Rout’ to ‘lbdp1.Rout.save’ ... OK - Running ‘lbdp2.R’ [21s/18s] + Running ‘lbdp2.R’ [24s/41s] Comparing ‘lbdp2.Rout’ to ‘lbdp2.Rout.save’ ... OK - Running ‘lbdp3.R’ + Running ‘lbdp3.R’ [11s/48s] Comparing ‘lbdp3.Rout’ to ‘lbdp3.Rout.save’ ... OK - Running ‘lineages.R’ + Running ‘lineages.R’ [12s/28s] Comparing ‘lineages.Rout’ to ‘lineages.Rout.save’ ... OK - Running ‘moran1.R’ [41s/29s] + Running ‘moran1.R’ [42s/52s] Comparing ‘moran1.Rout’ to ‘moran1.Rout.save’ ... OK Running ‘parse.R’ Comparing ‘parse.Rout’ to ‘parse.Rout.save’ ... OK diff --git a/revdep/Outputs/check_phylopomp_stdout.txt b/revdep/Outputs/check_phylopomp_stdout.txt index be85a2ef..9d80876c 100644 --- a/revdep/Outputs/check_phylopomp_stdout.txt +++ b/revdep/Outputs/check_phylopomp_stdout.txt @@ -1,15 +1,15 @@ * using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/phylopomp.Rcheck' -* using R version 4.3.1 (2023-06-16) +* using R version 4.3.2 (2023-10-31) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 - GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 -* running under: Ubuntu 22.04.2 LTS + 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 * using session charset: UTF-8 * using option '--as-cran' * checking for file 'phylopomp/DESCRIPTION' ... OK * checking extension type ... Package -* this is package 'phylopomp' version '0.10.1.1' +* this is package 'phylopomp' version '0.10.1.4' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK @@ -19,9 +19,9 @@ * 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 ... [55s/40s] OK -* used C compiler: 'gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0' -* used C++ compiler: 'g++ (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0' +* checking whether package 'phylopomp' can be installed ... [59s/43s] 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 installed size is 8.5Mb sub-directories of 1Mb or more: @@ -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 ... [57s/10s] OK +* checking R code for possible problems ... [59s/65s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK @@ -62,10 +62,10 @@ * checking compilation flags used ... OK * checking compiled code ... OK * checking installed files from 'inst/doc' ... OK -* checking examples ... [17s/14s] OK +* checking examples ... [18s/30s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... - [192s/109s] OK + [208s/271s] 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 ee2672d5..6a09424c 100644 --- a/revdep/Outputs/check_pomp_stderr.txt +++ b/revdep/Outputs/check_pomp_stderr.txt @@ -1,5 +1,5 @@ - Running ‘R_v_C.R’ [25s/13s] - Running ‘abc.R’ + Running ‘R_v_C.R’ [29s/58s] + Running ‘abc.R’ [30s/12s] Comparing ‘abc.Rout’ to ‘abc.Rout.save’ ... OK Running ‘baddm.R’ Comparing ‘baddm.Rout’ to ‘baddm.Rout.save’ ... OK @@ -13,8 +13,10 @@ Comparing ‘blowflies.Rout’ to ‘blowflies.Rout.save’ ... OK Running ‘bsmc2.R’ Comparing ‘bsmc2.Rout’ to ‘bsmc2.Rout.save’ ... OK - Running ‘bsplines.R’ - Comparing ‘bsplines.Rout’ to ‘bsplines.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’ @@ -27,7 +29,7 @@ Comparing ‘defunct.Rout’ to ‘defunct.Rout.save’ ... OK Running ‘dinit.R’ Comparing ‘dinit.Rout’ to ‘dinit.Rout.save’ ... OK - Running ‘dp.R’ [155s/13s] + Running ‘dp.R’ [144s/14s] Comparing ‘dp.Rout’ to ‘dp.Rout.save’ ... OK Running ‘dprocess.R’ Comparing ‘dprocess.Rout’ to ‘dprocess.Rout.save’ ... OK @@ -39,7 +41,7 @@ Comparing ‘eulermultinom.Rout’ to ‘eulermultinom.Rout.save’ ... OK Running ‘flow.R’ Comparing ‘flow.Rout’ to ‘flow.Rout.save’ ... OK - Running ‘gillespie.R’ [39s/15s] + Running ‘gillespie.R’ [41s/15s] 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 29d0b70d..399515f7 100644 --- a/revdep/Outputs/check_pomp_stdout.txt +++ b/revdep/Outputs/check_pomp_stdout.txt @@ -1,15 +1,15 @@ * using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/pomp.Rcheck' -* using R version 4.3.1 (2023-06-16) +* using R version 4.3.2 (2023-10-31) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 - GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 -* running under: Ubuntu 22.04.2 LTS + 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 * using session charset: UTF-8 * using option '--as-cran' * checking for file 'pomp/DESCRIPTION' ... OK * checking extension type ... Package -* this is package 'pomp' version '5.3.1.3' +* this is package 'pomp' version '5.4.4.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK @@ -19,8 +19,8 @@ * 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 ... [38s/29s] OK -* used C compiler: 'gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0' +* checking whether package 'pomp' can be installed ... [44s/34s] OK +* used C compiler: 'gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0' * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... 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 ... [65s/18s] OK +* checking R code for possible problems ... [71s/37s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK @@ -68,15 +68,15 @@ * checking compilation flags used ... OK * checking compiled code ... OK * checking installed files from 'inst/doc' ... OK -* checking examples ... [22s/11s] OK +* checking examples ... [21s/40s] OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed -ricker 1.938 6.471 1.307 +ricker 2.026 7.006 14.904 ** found \donttest examples: check also with --run-donttest * checking for unstated dependencies in 'tests' ... OK * checking tests ... - [1707s/230s] OK -* checking PDF version of manual ... [15s/10s] OK + [1764s/322s] 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 * checking for detritus in the temp directory ... OK diff --git a/revdep/Outputs/check_spaero_stdout.txt b/revdep/Outputs/check_spaero_stdout.txt index 805e211a..8ddc8d90 100644 --- a/revdep/Outputs/check_spaero_stdout.txt +++ b/revdep/Outputs/check_spaero_stdout.txt @@ -1,10 +1,10 @@ * using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/spaero.Rcheck' -* using R version 4.3.1 (2023-06-16) +* using R version 4.3.2 (2023-10-31) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 - GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 -* running under: Ubuntu 22.04.2 LTS + 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 * using session charset: UTF-8 * using option '--as-cran' * checking for file 'spaero/DESCRIPTION' ... OK @@ -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 1.492 4.797 1.263 +create_simulator 1.766 5.521 1.32 * checking for unstated dependencies in 'tests' ... OK * checking tests ... - OK + [31s/10s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK -* checking re-building of vignette outputs ... [41s/20s] OK +* checking re-building of vignette outputs ... [38s/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 483137ce..294aa248 100644 --- a/revdep/Outputs/check_spatPomp_stderr.txt +++ b/revdep/Outputs/check_spatPomp_stderr.txt @@ -1,38 +1,29 @@ Running ‘abf.R’ Running ‘abfir.R’ Running ‘arma_benchmark.R’ - 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 ‘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 ‘enkf.R’ - Running ‘gbm.R’ + Running ‘gbm.R’ [32s/16s] Comparing ‘gbm.Rout’ to ‘gbm.Rout.save’ ... Running ‘girf.R’ - Running ‘he10.R’ - Comparing ‘he10.Rout’ to ‘he10.Rout.save’ ... OK - Running ‘ibpf.R’ + Running ‘he10.R’ [34s/21s] + Comparing ‘he10.Rout’ to ‘he10.Rout.save’ ... 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’ ... 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 ‘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 ‘param_formats.Rout’ to ‘param_formats.Rout.save’ ... OK Running ‘pfilter.R’ Running ‘plot.R’ - Running ‘simulate.R’ + Running ‘simulate.R’ [6s/32s] Running ‘spatPomp.R’ - Running ‘xtests.R’ - -See - '/userdata/kingaa/projects/Rpkg/pomp/revdep/spatPomp.Rcheck/00check.log' -for details. + Running ‘xtests.R’ [7s/12s] diff --git a/revdep/Outputs/check_spatPomp_stdout.txt b/revdep/Outputs/check_spatPomp_stdout.txt index e041660a..21011a98 100644 --- a/revdep/Outputs/check_spatPomp_stdout.txt +++ b/revdep/Outputs/check_spatPomp_stdout.txt @@ -1,15 +1,15 @@ * using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/spatPomp.Rcheck' -* using R version 4.3.0 (2023-04-21) +* using R version 4.3.2 (2023-10-31) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 - GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 -* running under: Ubuntu 22.04.2 LTS + 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 * using session charset: UTF-8 * using option '--as-cran' * checking for file 'spatPomp/DESCRIPTION' ... OK * checking extension type ... Package -* this is package 'spatPomp' version '0.32.0' +* this is package 'spatPomp' version '0.33.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK @@ -19,8 +19,8 @@ * 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 ... [33s/18s] OK -* used C compiler: 'gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0' +* checking whether package 'spatPomp' can be installed ... [43s/21s] OK +* used C compiler: 'gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0' * 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 ... [59s/17s] OK +* checking R code for possible problems ... [57s/18s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK @@ -60,18 +60,207 @@ * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK -* checking examples ... OK +* checking examples ... [6s/22s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... -46c46 -< [1] "ARMA benchmark: 197.4929061052" +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. --- -> [1] "ARMA benchmark: 196.3173327754" - [367s/46s] OK -* checking PDF version of manual ... OK -* checking HTML version of manual ... NOTE -Skipping checking math rendering: package 'V8' unavailable +> 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 +* checking HTML version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE -Status: 1 NOTE +Status: OK diff --git a/revdep/Outputs/check_stops_stdout.txt b/revdep/Outputs/check_stops_stdout.txt index f1fbcf77..98b5f251 100644 --- a/revdep/Outputs/check_stops_stdout.txt +++ b/revdep/Outputs/check_stops_stdout.txt @@ -1,10 +1,10 @@ * using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/stops.Rcheck' -* using R version 4.3.1 (2023-06-16) +* using R version 4.3.2 (2023-10-31) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 - GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 -* running under: Ubuntu 22.04.2 LTS + 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 * using session charset: UTF-8 * using option '--as-cran' * checking for file 'stops/DESCRIPTION' ... OK @@ -18,7 +18,10 @@ * 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 ... [34s/20s] OK +* checking whether package 'stops' can be installed ... [41s/22s] 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. * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK @@ -41,7 +44,7 @@ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK -* checking R code for possible problems ... [75s/23s] NOTE +* checking R code for possible problems ... [89s/261s] 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 @@ -74,7 +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 ... OK +* checking Rd files ... [5s/20s] OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK @@ -89,7 +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 ... [36s/12s] OK +* checking examples ... [34s/13s] OK ** found \donttest examples: check also with --run-donttest * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK @@ -99,4 +102,4 @@ tgpoptim: local variable ‘valsorig’ assigned but may not be used * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE -Status: 1 NOTE +Status: 1 WARNING, 1 NOTE diff --git a/revdep/timings.tab b/revdep/timings.tab index 9f62ca7b..8c52d98d 100644 --- a/revdep/timings.tab +++ b/revdep/timings.tab @@ -1,12 +1,13 @@ "user" "system" "elapsed" -"pomp" 577.744 1445.133 343.829 -"CollocInfer" 133.22 268.508 110.046 -"DTAT" 141.193 221.796 130.84 -"epimdr" 70.067 163.62 60.59 -"epimdr2" 93.517 174.593 85.629 -"spaero" 79.553 231.836 59.315 -"stops" 159.017 219.647 148.303 -"circumstance" 90.999 179.12 72.743 -"hte" 181.567 372.072 130.787 -"panelPomp" 164.886 471.218 102.516 -"phylopomp" 241.03 268.078 217.609 +"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