From 1245b243433fbe4abed96b0821c933a05e762107 Mon Sep 17 00:00:00 2001 From: "Aaron A. King" Date: Thu, 2 Mar 2023 12:10:06 -0500 Subject: [PATCH] update revdep --- revdep/Outputs/check_CollocInfer_stderr.txt | 2 +- revdep/Outputs/check_CollocInfer_stdout.txt | 18 +- revdep/Outputs/check_DTAT_stderr.txt | 2 +- revdep/Outputs/check_DTAT_stdout.txt | 14 +- revdep/Outputs/check_circumstance_stderr.txt | 8 +- revdep/Outputs/check_circumstance_stdout.txt | 61 +--- revdep/Outputs/check_epimdr2_stderr.txt | 2 +- revdep/Outputs/check_epimdr2_stdout.txt | 13 +- revdep/Outputs/check_epimdr_stderr.txt | 2 +- revdep/Outputs/check_epimdr_stdout.txt | 4 +- revdep/Outputs/check_panelPomp_stderr.txt | 41 +-- revdep/Outputs/check_panelPomp_stdout.txt | 320 ++++++++++++------- revdep/Outputs/check_phylopomp_stderr.txt | 6 +- revdep/Outputs/check_phylopomp_stdout.txt | 22 +- revdep/Outputs/check_pomp_stderr.txt | 12 +- revdep/Outputs/check_pomp_stdout.txt | 37 +-- revdep/Outputs/check_spaero_stderr.txt | 2 +- revdep/Outputs/check_spaero_stdout.txt | 12 +- revdep/Outputs/check_spatPomp_stderr.txt | 26 +- revdep/Outputs/check_spatPomp_stdout.txt | 53 +-- revdep/Outputs/check_stops_stderr.txt | 6 + revdep/Outputs/check_stops_stdout.txt | 101 ++++++ revdep/Outputs/install_pomp.out | 77 ++--- revdep/timings.tab | 21 +- 24 files changed, 496 insertions(+), 366 deletions(-) create mode 100644 revdep/Outputs/check_stops_stderr.txt create mode 100644 revdep/Outputs/check_stops_stdout.txt diff --git a/revdep/Outputs/check_CollocInfer_stderr.txt b/revdep/Outputs/check_CollocInfer_stderr.txt index 906b2800a..e5c90c789 100644 --- a/revdep/Outputs/check_CollocInfer_stderr.txt +++ b/revdep/Outputs/check_CollocInfer_stderr.txt @@ -1,6 +1,6 @@ See - '/home/kingaa/projects/Rpkg/pomp/revdep/CollocInfer.Rcheck/00check.log' + '/userdata/kingaa/projects/Rpkg/pomp/revdep/CollocInfer.Rcheck/00check.log' for details. diff --git a/revdep/Outputs/check_CollocInfer_stdout.txt b/revdep/Outputs/check_CollocInfer_stdout.txt index f424c3c7a..ce604543f 100644 --- a/revdep/Outputs/check_CollocInfer_stdout.txt +++ b/revdep/Outputs/check_CollocInfer_stdout.txt @@ -1,4 +1,4 @@ -* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/CollocInfer.Rcheck' +* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/CollocInfer.Rcheck' * using R version 4.2.2 (2022-10-31) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 @@ -14,10 +14,11 @@ * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking serialization versions ... OK -* checking whether package 'CollocInfer' can be installed ... [16s/15s] OK +* checking whether package 'CollocInfer' can be installed ... [30s/20s] OK * checking installed package size ... OK * checking package directory ... OK -* checking for future file timestamps ... OK +* checking for future file timestamps ... NOTE +unable to verify current time * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK @@ -36,7 +37,7 @@ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK -* checking R code for possible problems ... [33s/25s] NOTE +* checking R code for possible problems ... [70s/22s] NOTE Profile.GausNewt: local variable ‘dcdp’ assigned but may not be used Profile.GausNewt: local variable ‘gradnorm0’ assigned but may not be used @@ -78,11 +79,14 @@ Variables with usage in documentation object 'FhNest' but not in code: * checking data for ASCII and uncompressed saves ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s - user system elapsed -Profile 3.967 11.652 1.505 + user system elapsed +Profile 17.023 51.743 1.319 +FitMatch 5.882 22.446 0.643 +ParsMatch 3.509 14.718 0.313 +smooth 1.373 4.874 0.113 * 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 * DONE -Status: 1 WARNING, 1 NOTE +Status: 1 WARNING, 2 NOTEs diff --git a/revdep/Outputs/check_DTAT_stderr.txt b/revdep/Outputs/check_DTAT_stderr.txt index e91f8e13b..06d643237 100644 --- a/revdep/Outputs/check_DTAT_stderr.txt +++ b/revdep/Outputs/check_DTAT_stderr.txt @@ -1,6 +1,6 @@ See - '/home/kingaa/projects/Rpkg/pomp/revdep/DTAT.Rcheck/00check.log' + '/userdata/kingaa/projects/Rpkg/pomp/revdep/DTAT.Rcheck/00check.log' for details. diff --git a/revdep/Outputs/check_DTAT_stdout.txt b/revdep/Outputs/check_DTAT_stdout.txt index 99b509b2b..1fe5f5d1f 100644 --- a/revdep/Outputs/check_DTAT_stdout.txt +++ b/revdep/Outputs/check_DTAT_stdout.txt @@ -1,4 +1,4 @@ -* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/DTAT.Rcheck' +* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/DTAT.Rcheck' * using R version 4.2.2 (2022-10-31) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 @@ -16,10 +16,11 @@ * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking serialization versions ... OK -* checking whether package 'DTAT' can be installed ... [15s/14s] OK +* checking whether package 'DTAT' can be installed ... [27s/14s] OK * checking installed package size ... OK * checking package directory ... OK -* checking for future file timestamps ... OK +* checking for future file timestamps ... NOTE +unable to verify current time * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK @@ -39,7 +40,7 @@ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK -* checking R code for possible problems ... [25s/14s] NOTE +* checking R code for possible problems ... [68s/14s] 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 @@ -59,6 +60,9 @@ initialize,DE: local variable ‘Q1’ assigned but may not be used * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK +Examples with CPU (user + system) or elapsed time > 5s + user system elapsed +Onoue.Friberg 3.405 6.673 1.782 ** found \donttest examples: check also with --run-donttest * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK @@ -67,4 +71,4 @@ initialize,DE: local variable ‘Q1’ 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: 2 NOTEs diff --git a/revdep/Outputs/check_circumstance_stderr.txt b/revdep/Outputs/check_circumstance_stderr.txt index ea37d6140..25cd82443 100644 --- a/revdep/Outputs/check_circumstance_stderr.txt +++ b/revdep/Outputs/check_circumstance_stderr.txt @@ -1,6 +1,10 @@ + Running ‘mif2.R’ + Comparing ‘mif2.Rout’ to ‘mif2.Rout.save’ ... OK Running ‘pfilter.R’ - Comparing ‘pfilter.Rout’ to ‘pfilter.Rout.save’ ... + Comparing ‘pfilter.Rout’ to ‘pfilter.Rout.save’ ... OK + See - '/home/kingaa/projects/Rpkg/pomp/revdep/circumstance.Rcheck/00check.log' + '/userdata/kingaa/projects/Rpkg/pomp/revdep/circumstance.Rcheck/00check.log' for details. + diff --git a/revdep/Outputs/check_circumstance_stdout.txt b/revdep/Outputs/check_circumstance_stdout.txt index 3b7fba48d..e7cc209fb 100644 --- a/revdep/Outputs/check_circumstance_stdout.txt +++ b/revdep/Outputs/check_circumstance_stdout.txt @@ -1,15 +1,14 @@ -* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/circumstance.Rcheck' +* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/circumstance.Rcheck' * using R version 4.2.2 (2022-10-31) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option '--as-cran' * checking for file 'circumstance/DESCRIPTION' ... OK * checking extension type ... Package -* this is package 'circumstance' version '0.0.2.0' +* this is package 'circumstance' version '0.0.5.2' * package encoding: UTF-8 * checking package namespace information ... OK -* checking package dependencies ... NOTE -Suggests orphaned package: 'doRNG' +* checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK @@ -19,7 +18,8 @@ Suggests orphaned package: 'doRNG' * checking whether package 'circumstance' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK -* checking for future file timestamps ... OK +* checking for future file timestamps ... NOTE +unable to verify current time * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK @@ -34,10 +34,7 @@ Suggests orphaned package: 'doRNG' * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking use of S3 registration ... OK -* checking dependencies in R code ... NOTE -Package in Depends field not imported from: ‘parallel’ - These packages need to be imported from (in the NAMESPACE file) - for when this namespace is loaded but not attached. +* checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK @@ -51,48 +48,16 @@ Package in Depends field not imported from: ‘parallel’ * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK -* checking examples ... ERROR -Running examples in 'circumstance-Ex.R' failed -The error most likely occurred in: - -> base::assign(".ptime", proc.time(), pos = "CheckExEnv") -> ### Name: pfilter -> ### Title: Parallel particle filter computations -> ### Aliases: pfilter pfilter,ANY,numeric-method pfilter-ANY,numeric -> ### pfilter,ANY,missing-method pfilter-ANY,missing -> ### pfilter,pompList,numeric-method pfilter-pompList,numeric -> ### pfilter,pompList,missing-method pfilter-pompList,missing -> -> ### ** Examples -> -> library(circumstance) -> -> ou2() -> ou2 -> ou2 %>% pfilter(Np=1000,Nrep=6) -> pfs -Error in ou2 %>% pfilter(Np = 1000, Nrep = 6) : - could not find function "%>%" -Execution halted +* checking installed files from 'inst/doc' ... OK +* checking examples ... OK +Examples with CPU (user + system) or elapsed time > 5s + user system elapsed +pfilter 5.239 0.297 4.529 * checking for unstated dependencies in 'tests' ... OK * checking tests ... -47,53c47,53 -< .id time y1 y2 x1 x2 ess cond.logLik -< 1 1 1 -4.05 4.781 -3.718 4.25 160.6 -4.31 -< 2 1 2 1.83 6.273 0.940 6.84 148.1 -4.42 -< 3 1 3 -1.32 7.556 -0.373 7.59 71.4 -5.20 -< 4 1 4 6.64 5.730 5.809 6.49 76.1 -5.01 -< 5 1 5 6.58 1.561 5.605 1.84 217.1 -3.99 -< 6 1 6 7.54 0.176 7.355 -1.57 135.8 -4.51 ---- -> time y1 y2 x1 x2 ess cond.logLik .id -> 1 1 -4.05 4.781 -3.718 4.25 160.6 -4.31 1 -> 2 2 1.83 6.273 0.940 6.84 148.1 -4.42 1 -> 3 3 -1.32 7.556 -0.373 7.59 71.4 -5.20 1 -> 4 4 6.64 5.730 5.809 6.49 76.1 -5.01 1 -> 5 5 6.58 1.561 5.605 1.84 217.1 -3.99 1 -> 6 6 7.54 0.176 7.355 -1.57 135.8 -4.51 1 - OK + [20s/13s] OK * checking PDF 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 ERROR, 2 NOTEs +Status: 1 NOTE diff --git a/revdep/Outputs/check_epimdr2_stderr.txt b/revdep/Outputs/check_epimdr2_stderr.txt index d40e12fc1..34c457c15 100644 --- a/revdep/Outputs/check_epimdr2_stderr.txt +++ b/revdep/Outputs/check_epimdr2_stderr.txt @@ -1,6 +1,6 @@ See - '/home/kingaa/projects/Rpkg/pomp/revdep/epimdr2.Rcheck/00check.log' + '/userdata/kingaa/projects/Rpkg/pomp/revdep/epimdr2.Rcheck/00check.log' for details. diff --git a/revdep/Outputs/check_epimdr2_stdout.txt b/revdep/Outputs/check_epimdr2_stdout.txt index a325462bd..2019cfeb7 100644 --- a/revdep/Outputs/check_epimdr2_stdout.txt +++ b/revdep/Outputs/check_epimdr2_stdout.txt @@ -1,4 +1,4 @@ -* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/epimdr2.Rcheck' +* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/epimdr2.Rcheck' * using R version 4.2.2 (2022-10-31) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 @@ -14,10 +14,11 @@ * 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 ... [16s/14s] OK +* checking whether package 'epimdr2' can be installed ... [31s/17s] OK * checking installed package size ... OK * checking package directory ... OK -* checking for future file timestamps ... OK +* checking for future file timestamps ... NOTE +unable to verify current time * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK @@ -36,7 +37,7 @@ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK -* checking R code for possible problems ... [22s/14s] NOTE +* checking R code for possible problems ... [53s/11s] 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 @@ -148,10 +149,10 @@ 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 ... [14s/12s] OK +* checking examples ... [20s/11s] OK ** found \donttest examples: check also with --run-donttest * checking PDF 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: 2 NOTEs diff --git a/revdep/Outputs/check_epimdr_stderr.txt b/revdep/Outputs/check_epimdr_stderr.txt index 5b2bdb870..c3f294215 100644 --- a/revdep/Outputs/check_epimdr_stderr.txt +++ b/revdep/Outputs/check_epimdr_stderr.txt @@ -1,6 +1,6 @@ See - '/home/kingaa/projects/Rpkg/pomp/revdep/epimdr.Rcheck/00check.log' + '/userdata/kingaa/projects/Rpkg/pomp/revdep/epimdr.Rcheck/00check.log' for details. diff --git a/revdep/Outputs/check_epimdr_stdout.txt b/revdep/Outputs/check_epimdr_stdout.txt index 2e00d6d99..2cea9eaf6 100644 --- a/revdep/Outputs/check_epimdr_stdout.txt +++ b/revdep/Outputs/check_epimdr_stdout.txt @@ -1,4 +1,4 @@ -* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/epimdr.Rcheck' +* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/epimdr.Rcheck' * using R version 4.2.2 (2022-10-31) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 @@ -15,7 +15,7 @@ * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking serialization versions ... OK -* checking whether package 'epimdr' can be installed ... OK +* checking whether package 'epimdr' can be installed ... [28s/12s] OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK diff --git a/revdep/Outputs/check_panelPomp_stderr.txt b/revdep/Outputs/check_panelPomp_stderr.txt index c10463872..56031e2b9 100644 --- a/revdep/Outputs/check_panelPomp_stderr.txt +++ b/revdep/Outputs/check_panelPomp_stderr.txt @@ -2,35 +2,26 @@ Running ‘aaa.R’ Comparing ‘aaa.Rout’ to ‘aaa.Rout.save’ ... OK Running ‘contacts.R’ - Comparing ‘contacts.Rout’ to ‘contacts.Rout.save’ ... OK - Running ‘get_col_row.R’ - Comparing ‘get_col_row.Rout’ to ‘get_col_row.Rout.save’ ... OK - Running ‘mif2.R’ + Comparing ‘contacts.Rout’ to ‘contacts.Rout.save’ ... Running ‘get_col_row.R’ + Comparing ‘get_col_row.Rout’ to ‘get_col_row.Rout.save’ ... Running ‘mif2.R’ Comparing ‘mif2.Rout’ to ‘mif2.Rout.save’ ... Running ‘mif2_intern.R’ Comparing ‘mif2_intern.Rout’ to ‘mif2_intern.Rout.save’ ... Running ‘mif2_methods.R’ Comparing ‘mif2_methods.Rout’ to ‘mif2_methods.Rout.save’ ... Running ‘panelGompertz.R’ - Comparing ‘panelGompertz.Rout’ to ‘panelGompertz.Rout.save’ ... OK - Running ‘panelGompertzLikelihood.R’ + Comparing ‘panelGompertz.Rout’ to ‘panelGompertz.Rout.save’ ... Running ‘panelGompertzLikelihood.R’ Comparing ‘panelGompertzLikelihood.Rout’ to ‘panelGompertzLikelihood.Rout.save’ ... Running ‘panelPomp.R’ - Comparing ‘panelPomp.Rout’ to ‘panelPomp.Rout.save’ ... OK - Running ‘panelPomp_methods.R’ - Comparing ‘panelPomp_methods.Rout’ to ‘panelPomp_methods.Rout.save’ ... OK - Running ‘panelRandomWalk.R’ - Comparing ‘panelRandomWalk.Rout’ to ‘panelRandomWalk.Rout.save’ ... OK - Running ‘panel_loglik.R’ - Comparing ‘panel_loglik.Rout’ to ‘panel_loglik.Rout.save’ ... OK - Running ‘params.R’ - Comparing ‘params.Rout’ to ‘params.Rout.save’ ... OK - Running ‘pfilter.R’ - Comparing ‘pfilter.Rout’ to ‘pfilter.Rout.save’ ... OK - Running ‘pfilter_methods.R’ - Comparing ‘pfilter_methods.Rout’ to ‘pfilter_methods.Rout.save’ ... OK - Running ‘plot.R’ - Comparing ‘plot.Rout’ to ‘plot.Rout.save’ ... OK - Running ‘print-results.R’ - Comparing ‘print-results.Rout’ to ‘print-results.Rout.save’ ... OK - Running ‘seeded-results.R’ + Comparing ‘panelPomp.Rout’ to ‘panelPomp.Rout.save’ ... Running ‘panelPomp_methods.R’ + Comparing ‘panelPomp_methods.Rout’ to ‘panelPomp_methods.Rout.save’ ... Running ‘panelRandomWalk.R’ + Comparing ‘panelRandomWalk.Rout’ to ‘panelRandomWalk.Rout.save’ ... Running ‘panel_loglik.R’ + Comparing ‘panel_loglik.Rout’ to ‘panel_loglik.Rout.save’ ... Running ‘params.R’ + Comparing ‘params.Rout’ to ‘params.Rout.save’ ... Running ‘pfilter.R’ + Comparing ‘pfilter.Rout’ to ‘pfilter.Rout.save’ ... Running ‘pfilter_methods.R’ + Comparing ‘pfilter_methods.Rout’ to ‘pfilter_methods.Rout.save’ ... Running ‘plot.R’ + Comparing ‘plot.Rout’ to ‘plot.Rout.save’ ... 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’ ... Running ‘simulate.R’ - Comparing ‘simulate.Rout’ to ‘simulate.Rout.save’ ... OK + Comparing ‘simulate.Rout’ to ‘simulate.Rout.save’ ... +See + '/userdata/kingaa/projects/Rpkg/pomp/revdep/panelPomp.Rcheck/00check.log' +for details. diff --git a/revdep/Outputs/check_panelPomp_stdout.txt b/revdep/Outputs/check_panelPomp_stdout.txt index 695f15364..f9466422d 100644 --- a/revdep/Outputs/check_panelPomp_stdout.txt +++ b/revdep/Outputs/check_panelPomp_stdout.txt @@ -1,11 +1,11 @@ -* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/panelPomp.Rcheck' +* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/panelPomp.Rcheck' * using R version 4.2.2 (2022-10-31) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option '--as-cran' * checking for file 'panelPomp/DESCRIPTION' ... OK * checking extension type ... Package -* this is package 'panelPomp' version '0.15.0' +* this is package 'panelPomp' version '0.16.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK @@ -18,7 +18,8 @@ * checking whether package 'panelPomp' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK -* checking for future file timestamps ... OK +* checking for future file timestamps ... NOTE +unable to verify current time * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK @@ -37,7 +38,7 @@ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK -* checking R code for possible problems ... [19s/12s] OK +* checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK @@ -50,118 +51,207 @@ * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... -34,37d33 -< Warning message: -< 'rw.sd' is deprecated. -< Use 'rw_sd' instead. -< See help("Deprecated") -43,46d38 -< Warning message: -< 'rw.sd' is deprecated. -< Use 'rw_sd' instead. -< See help("Deprecated") -53,56d44 -< Warning message: -< 'rw.sd' is deprecated. -< Use 'rw_sd' instead. -< See help("Deprecated") -63,66d50 -< Warning message: -< 'rw.sd' is deprecated. -< Use 'rw_sd' instead. -< See help("Deprecated") -73,76d56 -< Warning message: -< 'rw.sd' is deprecated. -< Use 'rw_sd' instead. -< See help("Deprecated") -83,86d62 -< Warning message: -< 'rw.sd' is deprecated. -< Use 'rw_sd' instead. -< See help("Deprecated") -93,96d68 -< Warning message: -< 'rw.sd' is deprecated. -< Use 'rw_sd' instead. -< See help("Deprecated") -107,110d78 -< Warning message: -< 'rw.sd' is deprecated. -< Use 'rw_sd' instead. -< See help("Deprecated") -141,144d108 -< Warning message: -< 'rw.sd' is deprecated. -< Use 'rw_sd' instead. -< See help("Deprecated") -154,157d117 -< Warning message: -< 'rw.sd' is deprecated. -< Use 'rw_sd' instead. -< See help("Deprecated") -165,168d124 -< Warning message: -< 'rw.sd' is deprecated. -< Use 'rw_sd' instead. -< See help("Deprecated") -172,175d127 -< Warning message: -< 'rw.sd' is deprecated. -< Use 'rw_sd' instead. -< See help("Deprecated") -20,23d19 -< Warning message: -< 'rw.sd' is deprecated. -< Use 'rw_sd' instead. -< See help("Deprecated") -33,36d28 -< Warning message: -< 'rw.sd' is deprecated. -< Use 'rw_sd' instead. -< See help("Deprecated") -46,49d37 -< Warning message: -< 'rw.sd' is deprecated. -< Use 'rw_sd' instead. -< See help("Deprecated") -60,63d47 -< Warning message: -< 'rw.sd' is deprecated. -< Use 'rw_sd' instead. -< See help("Deprecated") -73,76d56 -< Warning message: -< 'rw.sd' is deprecated. -< Use 'rw_sd' instead. -< See help("Deprecated") -14,17d13 -< Warning message: -< 'rw.sd' is deprecated. -< Use 'rw_sd' instead. -< See help("Deprecated") -22d21 -< NOTE: in 'stew': recomputing archive panelGompertzLikelihood.rda. -123,138d122 -< Warning messages: -< 1: 'rw.sd' is deprecated. -< Use 'rw_sd' instead. -< See help("Deprecated") -< 2: 'rw.sd' is deprecated. -< Use 'rw_sd' instead. -< See help("Deprecated") -< 3: 'rw.sd' is deprecated. -< Use 'rw_sd' instead. -< See help("Deprecated") -< 4: 'rw.sd' is deprecated. -< Use 'rw_sd' instead. -< See help("Deprecated") -< 5: 'rw.sd' is deprecated. -< Use 'rw_sd' instead. -< See help("Deprecated") - [102s/51s] OK +5,12d4 +< +< Welcome to pomp! +< +< As of version 4.6, no user-visible pomp function has a name that +< includes a dot ('.'). Function names have been changed to replace the +< dot with an underscore ('_'). For more information, see the pomp blog: +< https://kingaa.github.io/pomp/blog.html. +< +20c12 +< t +--- +> time +23c15 +< t +--- +> time +4,11d3 +< +< Welcome to pomp! +< +< As of version 4.6, no user-visible pomp function has a name that +< includes a dot ('.'). Function names have been changed to replace the +< dot with an underscore ('_'). For more information, see the pomp blog: +< https://kingaa.github.io/pomp/blog.html. +< +4,11d3 +< +< Welcome to pomp! +< +< As of version 4.6, no user-visible pomp function has a name that +< includes a dot ('.'). Function names have been changed to replace the +< dot with an underscore ('_'). For more information, see the pomp blog: +< https://kingaa.github.io/pomp/blog.html. +< +4,11d3 +< +< Welcome to pomp! +< +< As of version 4.6, no user-visible pomp function has a name that +< includes a dot ('.'). Function names have been changed to replace the +< dot with an underscore ('_'). For more information, see the pomp blog: +< https://kingaa.github.io/pomp/blog.html. +< +4,11d3 +< +< Welcome to pomp! +< +< As of version 4.6, no user-visible pomp function has a name that +< includes a dot ('.'). Function names have been changed to replace the +< dot with an underscore ('_'). For more information, see the pomp blog: +< https://kingaa.github.io/pomp/blog.html. +< +5,12d4 +< +< Welcome to pomp! +< +< As of version 4.6, no user-visible pomp function has a name that +< includes a dot ('.'). Function names have been changed to replace the +< dot with an underscore ('_'). For more information, see the pomp blog: +< https://kingaa.github.io/pomp/blog.html. +< +20c12 +< t +--- +> time +23c15 +< t +--- +> time +4,11d3 +< +< Welcome to pomp! +< +< As of version 4.6, no user-visible pomp function has a name that +< includes a dot ('.'). Function names have been changed to replace the +< dot with an underscore ('_'). For more information, see the pomp blog: +< https://kingaa.github.io/pomp/blog.html. +< +4,11d3 +< +< Welcome to pomp! +< +< As of version 4.6, no user-visible pomp function has a name that +< includes a dot ('.'). Function names have been changed to replace the +< dot with an underscore ('_'). For more information, see the pomp blog: +< https://kingaa.github.io/pomp/blog.html. +< +6,13d5 +< +< Welcome to pomp! +< +< As of version 4.6, no user-visible pomp function has a name that +< includes a dot ('.'). Function names have been changed to replace the +< dot with an underscore ('_'). For more information, see the pomp blog: +< https://kingaa.github.io/pomp/blog.html. +< +5,12d4 +< +< Welcome to pomp! +< +< As of version 4.6, no user-visible pomp function has a name that +< includes a dot ('.'). Function names have been changed to replace the +< dot with an underscore ('_'). For more information, see the pomp blog: +< https://kingaa.github.io/pomp/blog.html. +< +20c12 +< t +--- +> time +23c15 +< t +--- +> time +4,11d3 +< +< Welcome to pomp! +< +< As of version 4.6, no user-visible pomp function has a name that +< includes a dot ('.'). Function names have been changed to replace the +< dot with an underscore ('_'). For more information, see the pomp blog: +< https://kingaa.github.io/pomp/blog.html. +< +4,11d3 +< +< Welcome to pomp! +< +< As of version 4.6, no user-visible pomp function has a name that +< includes a dot ('.'). Function names have been changed to replace the +< dot with an underscore ('_'). For more information, see the pomp blog: +< https://kingaa.github.io/pomp/blog.html. +< +4,11d3 +< +< Welcome to pomp! +< +< As of version 4.6, no user-visible pomp function has a name that +< includes a dot ('.'). Function names have been changed to replace the +< dot with an underscore ('_'). For more information, see the pomp blog: +< https://kingaa.github.io/pomp/blog.html. +< +4,11d3 +< +< Welcome to pomp! +< +< As of version 4.6, no user-visible pomp function has a name that +< includes a dot ('.'). Function names have been changed to replace the +< dot with an underscore ('_'). For more information, see the pomp blog: +< https://kingaa.github.io/pomp/blog.html. +< +6,13d5 +< +< Welcome to pomp! +< +< As of version 4.6, no user-visible pomp function has a name that +< includes a dot ('.'). Function names have been changed to replace the +< dot with an underscore ('_'). For more information, see the pomp blog: +< https://kingaa.github.io/pomp/blog.html. +< +4,11d3 +< +< Welcome to pomp! +< +< As of version 4.6, no user-visible pomp function has a name that +< includes a dot ('.'). Function names have been changed to replace the +< dot with an underscore ('_'). For more information, see the pomp blog: +< https://kingaa.github.io/pomp/blog.html. +< +33c25 +< t +--- +> time +38c30 +< t +--- +> time +6,13d5 +< +< Welcome to pomp! +< +< As of version 4.6, no user-visible pomp function has a name that +< includes a dot ('.'). Function names have been changed to replace the +< dot with an underscore ('_'). For more information, see the pomp blog: +< https://kingaa.github.io/pomp/blog.html. +< +4,11d3 +< +< Welcome to pomp! +< +< As of version 4.6, no user-visible pomp function has a name that +< includes a dot ('.'). Function names have been changed to replace the +< dot with an underscore ('_'). For more information, see the pomp blog: +< https://kingaa.github.io/pomp/blog.html. +< +17c9 +< t +--- +> time + [271s/39s] OK * checking PDF version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE -Status: OK +Status: 1 NOTE diff --git a/revdep/Outputs/check_phylopomp_stderr.txt b/revdep/Outputs/check_phylopomp_stderr.txt index 8c9542643..bf55ce616 100644 --- a/revdep/Outputs/check_phylopomp_stderr.txt +++ b/revdep/Outputs/check_phylopomp_stderr.txt @@ -2,12 +2,14 @@ Comparing ‘diagram.Rout’ to ‘diagram.Rout.save’ ... OK Running ‘lbdp1.R’ Comparing ‘lbdp1.Rout’ to ‘lbdp1.Rout.save’ ... OK - Running ‘lbdp2.R’ [22s/21s] + Running ‘lbdp2.R’ [28s/22s] Comparing ‘lbdp2.Rout’ to ‘lbdp2.Rout.save’ ... OK Running ‘lineages.R’ Comparing ‘lineages.Rout’ to ‘lineages.Rout.save’ ... OK Running ‘moran1.R’ Comparing ‘moran1.Rout’ to ‘moran1.Rout.save’ ... OK + Running ‘seir1.R’ + Comparing ‘seir1.Rout’ to ‘seir1.Rout.save’ ... OK Running ‘si2r.R’ Comparing ‘si2r.Rout’ to ‘si2r.Rout.save’ ... OK Running ‘siir1.R’ @@ -18,7 +20,7 @@ Comparing ‘sir1.Rout’ to ‘sir1.Rout.save’ ... OK See - '/home/kingaa/projects/Rpkg/pomp/revdep/phylopomp.Rcheck/00check.log' + '/userdata/kingaa/projects/Rpkg/pomp/revdep/phylopomp.Rcheck/00check.log' for details. diff --git a/revdep/Outputs/check_phylopomp_stdout.txt b/revdep/Outputs/check_phylopomp_stdout.txt index 9f6298813..3fcc6fef3 100644 --- a/revdep/Outputs/check_phylopomp_stdout.txt +++ b/revdep/Outputs/check_phylopomp_stdout.txt @@ -1,28 +1,28 @@ -* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/phylopomp.Rcheck' +* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/phylopomp.Rcheck' * using R version 4.2.2 (2022-10-31) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option '--as-cran' * checking for file 'phylopomp/DESCRIPTION' ... OK * checking extension type ... Package -* this is package 'phylopomp' version '0.1.0.0' +* this is package 'phylopomp' version '0.3.0.0' * package encoding: UTF-8 * checking package namespace information ... OK -* checking package dependencies ... NOTE -Suggests orphaned package: 'doRNG' +* checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * 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 ... [41s/44s] OK +* checking whether package 'phylopomp' can be installed ... [61s/42s] OK * checking installed package size ... NOTE - installed size is 15.0Mb + installed size is 18.3Mb sub-directories of 1Mb or more: - libs 14.1Mb + libs 17.5Mb * checking package directory ... OK -* checking for future file timestamps ... OK +* checking for future file timestamps ... NOTE +unable to verify current time * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK @@ -41,7 +41,7 @@ Suggests orphaned package: 'doRNG' * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK -* checking R code for possible problems ... [21s/11s] OK +* checking R code for possible problems ... [52s/10s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK @@ -56,10 +56,10 @@ Suggests orphaned package: 'doRNG' * checking compilation flags used ... OK * checking compiled code ... OK * checking installed files from 'inst/doc' ... OK -* checking examples ... [13s/15s] OK +* checking examples ... [17s/14s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... - [62s/47s] OK + [111s/52s] OK * checking PDF 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 fb375fe9f..13da20935 100644 --- a/revdep/Outputs/check_pomp_stderr.txt +++ b/revdep/Outputs/check_pomp_stderr.txt @@ -1,4 +1,4 @@ - Running ‘R_v_C.R’ [16s/12s] + Running ‘R_v_C.R’ [26s/12s] Running ‘abc.R’ Comparing ‘abc.Rout’ to ‘abc.Rout.save’ ... OK Running ‘baddm.R’ @@ -23,9 +23,9 @@ Comparing ‘csnippet.Rout’ to ‘csnippet.Rout.save’ ... OK Running ‘dacca.R’ Comparing ‘dacca.Rout’ to ‘dacca.Rout.save’ ... OK - Running ‘deprecated.R’ - Comparing ‘deprecated.Rout’ to ‘deprecated.Rout.save’ ... OK - Running ‘dp.R’ + Running ‘defunct.R’ + Comparing ‘defunct.Rout’ to ‘defunct.Rout.save’ ... OK + Running ‘dp.R’ [147s/12s] Comparing ‘dp.Rout’ to ‘dp.Rout.save’ ... OK Running ‘dprocess.R’ Comparing ‘dprocess.Rout’ to ‘dprocess.Rout.save’ ... OK @@ -39,7 +39,7 @@ Comparing ‘flow.Rout’ to ‘flow.Rout.save’ ... OK Running ‘getting_started.R’ Comparing ‘getting_started.Rout’ to ‘getting_started.Rout.save’ ... OK - Running ‘gillespie.R’ [19s/12s] + Running ‘gillespie.R’ [41s/13s] Comparing ‘gillespie.Rout’ to ‘gillespie.Rout.save’ ... OK Running ‘gompertz.R’ Comparing ‘gompertz.Rout’ to ‘gompertz.Rout.save’ ... OK @@ -166,7 +166,7 @@ Comparing ‘wquant.Rout’ to ‘wquant.Rout.save’ ... OK See - '/home/kingaa/projects/Rpkg/pomp/revdep/pomp.Rcheck/00check.log' + '/userdata/kingaa/projects/Rpkg/pomp/revdep/pomp.Rcheck/00check.log' for details. diff --git a/revdep/Outputs/check_pomp_stdout.txt b/revdep/Outputs/check_pomp_stdout.txt index b5595538e..114e5dd81 100644 --- a/revdep/Outputs/check_pomp_stdout.txt +++ b/revdep/Outputs/check_pomp_stdout.txt @@ -1,11 +1,11 @@ -* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/pomp.Rcheck' +* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/pomp.Rcheck' * using R version 4.2.2 (2022-10-31) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option '--as-cran' * checking for file 'pomp/DESCRIPTION' ... OK * checking extension type ... Package -* this is package 'pomp' version '4.5.3.0' +* this is package 'pomp' version '4.7.0.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK @@ -15,10 +15,11 @@ * 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 ... [26s/28s] OK +* checking whether package 'pomp' can be installed ... [39s/30s] OK * checking installed package size ... OK * checking package directory ... OK -* checking for future file timestamps ... OK +* checking for future file timestamps ... NOTE +unable to verify current time * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK @@ -34,28 +35,17 @@ * checking loading without being on the library search path ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK -* checking S3 generic/method consistency ... NOTE -Found the following apparent S3 methods exported but not registered: - filter.mean filter.traj -See section 'Registering S3 methods' in the 'Writing R Extensions' -manual. +* checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK -* checking R code for possible problems ... [29s/21s] OK +* checking R code for possible problems ... [65s/16s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK -* checking Rd \usage sections ... NOTE -S3 methods shown with full name in documentation object 'deprecated': - ‘filter.mean’ ‘filter.traj’ - -The \usage entries for S3 methods should use the \method markup and not -their full name. -See chapter 'Writing R documentation files' in the 'Writing R -Extensions' manual. +* checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK @@ -73,16 +63,17 @@ Extensions' manual. * checking compilation flags used ... OK * checking compiled code ... OK * checking installed files from 'inst/doc' ... OK -* checking examples ... [19s/12s] OK +* checking examples ... [49s/13s] OK Examples with CPU (user + system) or elapsed time > 5s - user system elapsed -ebola 2.731 4.34 2.811 + user system elapsed +ebola 8.268 21.278 2.536 +ricker 1.910 4.997 0.573 ** found \donttest examples: check also with --run-donttest * checking for unstated dependencies in 'tests' ... OK * checking tests ... - [644s/193s] OK + [1936s/207s] OK * checking PDF version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE -Status: 2 NOTEs +Status: 1 NOTE diff --git a/revdep/Outputs/check_spaero_stderr.txt b/revdep/Outputs/check_spaero_stderr.txt index a0eec50f8..0aa87dcf8 100644 --- a/revdep/Outputs/check_spaero_stderr.txt +++ b/revdep/Outputs/check_spaero_stderr.txt @@ -1,7 +1,7 @@ Running ‘testthat.R’ See - '/home/kingaa/projects/Rpkg/pomp/revdep/spaero.Rcheck/00check.log' + '/userdata/kingaa/projects/Rpkg/pomp/revdep/spaero.Rcheck/00check.log' for details. diff --git a/revdep/Outputs/check_spaero_stdout.txt b/revdep/Outputs/check_spaero_stdout.txt index dc982ed4f..c76b46929 100644 --- a/revdep/Outputs/check_spaero_stdout.txt +++ b/revdep/Outputs/check_spaero_stdout.txt @@ -1,4 +1,4 @@ -* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/spaero.Rcheck' +* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/spaero.Rcheck' * using R version 4.2.2 (2022-10-31) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 @@ -18,7 +18,8 @@ * checking whether package 'spaero' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK -* checking for future file timestamps ... OK +* checking for future file timestamps ... NOTE +unable to verify current time * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK @@ -56,14 +57,17 @@ Namespace in Imports field not imported from: ‘utils’ * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK +Examples with CPU (user + system) or elapsed time > 5s + user system elapsed +create_simulator 2.185 5.256 1.303 * checking for unstated dependencies in 'tests' ... OK * checking tests ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK -* checking re-building of vignette outputs ... [21s/20s] OK +* checking re-building of vignette outputs ... [48s/21s] OK * checking PDF version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE -Status: 2 NOTEs +Status: 3 NOTEs diff --git a/revdep/Outputs/check_spatPomp_stderr.txt b/revdep/Outputs/check_spatPomp_stderr.txt index a85ad59b6..33bec4e5c 100644 --- a/revdep/Outputs/check_spatPomp_stderr.txt +++ b/revdep/Outputs/check_spatPomp_stderr.txt @@ -1,26 +1,30 @@ Running ‘abf.R’ Running ‘abfir.R’ Running ‘bm.R’ - Comparing ‘bm.Rout’ to ‘bm.Rout.save’ ... Running ‘bm2.R’ - Comparing ‘bm2.Rout’ to ‘bm2.Rout.save’ ... Running ‘bpfilter.R’ + Comparing ‘bm.Rout’ to ‘bm.Rout.save’ ... OK + Running ‘bm2.R’ + Comparing ‘bm2.Rout’ to ‘bm2.Rout.save’ ... OK + Running ‘bpfilter.R’ Running ‘enkf.R’ Running ‘gbm.R’ - Comparing ‘gbm.Rout’ to ‘gbm.Rout.save’ ... Running ‘girf.R’ + Comparing ‘gbm.Rout’ to ‘gbm.Rout.save’ ... OK + Running ‘girf.R’ Running ‘he10.R’ - Comparing ‘he10.Rout’ to ‘he10.Rout.save’ ... Running ‘ibpf.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’ ... Running ‘iubf.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’ - Comparing ‘measles.Rout’ to ‘measles.Rout.save’ ... Running ‘pfilter.R’ + Comparing ‘lorenz.Rout’ to ‘lorenz.Rout.save’ ... OK + Running ‘measles.R’ + Comparing ‘measles.Rout’ to ‘measles.Rout.save’ ... OK + Running ‘pfilter.R’ Running ‘plot.R’ Running ‘simulate.R’ + Running ‘spatPomp.R’ Running ‘xtests.R’ -See - '/home/kingaa/projects/Rpkg/pomp/revdep/spatPomp.Rcheck/00check.log' -for details. - diff --git a/revdep/Outputs/check_spatPomp_stdout.txt b/revdep/Outputs/check_spatPomp_stdout.txt index 6cce72e6d..57a8d3bbf 100644 --- a/revdep/Outputs/check_spatPomp_stdout.txt +++ b/revdep/Outputs/check_spatPomp_stdout.txt @@ -1,22 +1,21 @@ -* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/spatPomp.Rcheck' +* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/spatPomp.Rcheck' * using R version 4.2.2 (2022-10-31) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option '--as-cran' * checking for file 'spatPomp/DESCRIPTION' ... OK * checking extension type ... Package -* this is package 'spatPomp' version '0.30.2.0' +* this is package 'spatPomp' version '0.31.0.0' * package encoding: UTF-8 * checking package namespace information ... OK -* checking package dependencies ... NOTE -Suggests orphaned package: 'doRNG' +* checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * 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 ... [18s/17s] OK +* checking whether package 'spatPomp' can be installed ... [37s/18s] OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK @@ -38,7 +37,7 @@ Suggests orphaned package: 'doRNG' * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK -* checking R code for possible problems ... [26s/20s] OK +* checking R code for possible problems ... [57s/16s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK @@ -59,47 +58,9 @@ Suggests orphaned package: 'doRNG' * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... -133,136d132 -< Warning message: -< 'rw.sd' is deprecated. -< Use 'rw_sd' instead. -< See help("Deprecated") -16,19d15 -< Warning message: -< 'rw.sd' is deprecated. -< Use 'rw_sd' instead. -< See help("Deprecated") -26,29d25 -< Warning message: -< 'rw.sd' is deprecated. -< Use 'rw_sd' instead. -< See help("Deprecated") -78,81d77 -< Warning message: -< 'rw.sd' is deprecated. -< Use 'rw_sd' instead. -< See help("Deprecated") -14,17d13 -< In addition: Warning message: -< 'rw.sd' is deprecated. -< Use 'rw_sd' instead. -< See help("Deprecated") -27,30d26 -< Warning message: -< 'rw.sd' is deprecated. -< Use 'rw_sd' instead. -< See help("Deprecated") -71,73c71 -< 1: 'rw.sd' is deprecated. -< Use 'rw_sd' instead. -< See help("Deprecated") ---- -> 1: in 'table_lookup': extrapolating at 1.965002e+03. -75d72 -< 3: in 'table_lookup': extrapolating at 1.965002e+03. - [85s/33s] OK + [276s/34s] OK * checking PDF 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_stderr.txt b/revdep/Outputs/check_stops_stderr.txt new file mode 100644 index 000000000..2e6541795 --- /dev/null +++ b/revdep/Outputs/check_stops_stderr.txt @@ -0,0 +1,6 @@ + +See + '/userdata/kingaa/projects/Rpkg/pomp/revdep/stops.Rcheck/00check.log' +for details. + + diff --git a/revdep/Outputs/check_stops_stdout.txt b/revdep/Outputs/check_stops_stdout.txt new file mode 100644 index 000000000..2ecfa6a65 --- /dev/null +++ b/revdep/Outputs/check_stops_stdout.txt @@ -0,0 +1,101 @@ +* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/stops.Rcheck' +* using R version 4.2.2 (2022-10-31) +* using platform: x86_64-pc-linux-gnu (64-bit) +* using session charset: UTF-8 +* using option '--as-cran' +* checking for file 'stops/DESCRIPTION' ... OK +* this is package 'stops' version '1.0-1' +* package encoding: UTF-8 +* checking package namespace information ... OK +* checking package dependencies ... OK +* checking if this is a source package ... OK +* checking if there is a namespace ... OK +* checking for executable files ... OK +* 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 ... [39s/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 ... NOTE +unable to verify current time +* checking 'build' directory ... OK +* checking DESCRIPTION meta-information ... OK +* checking top-level files ... OK +* checking for left-over files ... OK +* checking index information ... OK +* checking package subdirectories ... OK +* checking R files for non-ASCII characters ... OK +* checking R files for syntax errors ... OK +* checking whether the package can be loaded ... OK +* checking whether the package can be loaded with stated dependencies ... OK +* checking whether the package can be unloaded cleanly ... OK +* checking whether the namespace can be loaded with stated dependencies ... OK +* checking whether the namespace can be unloaded cleanly ... OK +* checking loading without being on the library search path ... OK +* checking use of S3 registration ... OK +* checking dependencies in R code ... OK +* checking S3 generic/method consistency ... OK +* checking replacement functions ... OK +* checking foreign function calls ... OK +* checking R code for possible problems ... [64s/22s] 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 +c_linearity: local variable ‘x’ assigned but may not be used +c_linearity: local variable ‘y’ assigned but may not be used +conf_adjust: local variable ‘bb’ assigned but may not be used +conf_adjust: local variable ‘cc’ assigned but may not be used +conf_adjust: local variable ‘metric’ assigned but may not be used +ljoptim: local variable ‘n’ assigned but may not be used +powerStressMin: local variable ‘deltam’ assigned but may not be used +stoploss: local variable ‘cassociation’ assigned but may not be used +stoploss: local variable ‘cclumpiness’ assigned but may not be used +stoploss: local variable ‘cclusteredness’ assigned but may not be used +stoploss: local variable ‘ccomplexity’ assigned but may not be used +stoploss: local variable ‘cconvexity’ assigned but may not be used +stoploss: local variable ‘cdependence’ assigned but may not be used +stoploss: local variable ‘cfaithfulness’ assigned but may not be used +stoploss: local variable ‘cfunctionality’ assigned but may not be used +stoploss: local variable ‘chierarchy’ assigned but may not be used +stoploss: local variable ‘cinequality’ assigned but may not be used +stoploss: local variable ‘clinearity’ assigned but may not be used +stoploss: local variable ‘cmanifoldness’ assigned but may not be used +stoploss: local variable ‘cnonmonotonicity’ assigned but may not be + used +stoploss: local variable ‘coutlying’ assigned but may not be used +stoploss: local variable ‘cregularity’ assigned but may not be used +stoploss: local variable ‘cskinniness’ assigned but may not be used +stoploss: local variable ‘csparsity’ assigned but may not be used +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 metadata ... OK +* checking Rd line widths ... OK +* checking Rd cross-references ... OK +* checking for missing documentation entries ... OK +* checking for code/documentation mismatches ... OK +* checking Rd \usage sections ... OK +* checking Rd contents ... OK +* checking for unstated dependencies in examples ... OK +* checking contents of 'data' directory ... OK +* checking data for non-ASCII characters ... OK +* checking LazyData ... OK +* checking data for ASCII and uncompressed saves ... OK +* checking installed files from 'inst/doc' ... OK +* checking files in 'vignettes' ... OK +* checking examples ... [32s/12s] OK +** 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 ... OK +* checking PDF 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 WARNING, 2 NOTEs diff --git a/revdep/Outputs/install_pomp.out b/revdep/Outputs/install_pomp.out index a2a959ec1..6150a8a15 100644 --- a/revdep/Outputs/install_pomp.out +++ b/revdep/Outputs/install_pomp.out @@ -2,44 +2,45 @@ ** package 'pomp' successfully unpacked and MD5 sums checked ** using staged installation ** libs -make[1]: Entering directory '/tmp/RtmpCaapKV/R.INSTALL463bc7d9fca2a/pomp/src' -gcc -I"/usr/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c bspline.c -o bspline.o -gcc -I"/usr/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c distributions.c -o distributions.o -gcc -I"/usr/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c dmeasure.c -o dmeasure.o -gcc -I"/usr/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c dprior.c -o dprior.o -gcc -I"/usr/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c dprocess.c -o dprocess.o -gcc -I"/usr/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c emeasure.c -o emeasure.o -gcc -I"/usr/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c euler.c -o euler.o -gcc -I"/usr/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c gompertz.c -o gompertz.o -gcc -I"/usr/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c init.c -o init.o -gcc -I"/usr/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c lookup_table.c -o lookup_table.o -gcc -I"/usr/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c mif2.c -o mif2.o -gcc -I"/usr/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c ou2.c -o ou2.o -gcc -I"/usr/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c partrans.c -o partrans.o -gcc -I"/usr/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c pfilter.c -o pfilter.o -gcc -I"/usr/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c pomp_fun.c -o pomp_fun.o -gcc -I"/usr/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c probe.c -o probe.o -gcc -I"/usr/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c probe_acf.c -o probe_acf.o -gcc -I"/usr/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c probe_marginal.c -o probe_marginal.o -gcc -I"/usr/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c probe_nlar.c -o probe_nlar.o -gcc -I"/usr/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c resample.c -o resample.o -gcc -I"/usr/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c rinit.c -o rinit.o -gcc -I"/usr/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c rmeasure.c -o rmeasure.o -gcc -I"/usr/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c rprior.c -o rprior.o -gcc -I"/usr/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c rprocess.c -o rprocess.o -gcc -I"/usr/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c simulate.c -o simulate.o -gcc -I"/usr/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c skeleton.c -o skeleton.o -gcc -I"/usr/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c sobolseq.c -o sobolseq.o -gcc -I"/usr/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c ssa.c -o ssa.o -gcc -I"/usr/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c synth_lik.c -o synth_lik.o -gcc -I"/usr/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c trajectory.c -o trajectory.o -gcc -I"/usr/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c transformations.c -o transformations.o -gcc -I"/usr/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c userdata.c -o userdata.o -gcc -I"/usr/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c vmeasure.c -o vmeasure.o -gcc -I"/usr/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c wpfilter.c -o wpfilter.o -gcc -shared -L/usr/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/lib -L/usr/local/lib64 -o pomp.so bspline.o distributions.o dmeasure.o dprior.o dprocess.o emeasure.o euler.o gompertz.o init.o lookup_table.o mif2.o ou2.o partrans.o pfilter.o pomp_fun.o probe.o probe_acf.o probe_marginal.o probe_nlar.o resample.o rinit.o rmeasure.o rprior.o rprocess.o simulate.o skeleton.o sobolseq.o ssa.o synth_lik.o trajectory.o transformations.o userdata.o vmeasure.o wpfilter.o -lopenblas -lgfortran -lm -lquadmath -L/usr/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/lib -lR -make[1]: Leaving directory '/tmp/RtmpCaapKV/R.INSTALL463bc7d9fca2a/pomp/src' -installing to /home/kingaa/projects/Rpkg/pomp/revdep/Library/00LOCK-pomp/00new/pomp/libs +make[1]: Entering directory '/tmp/RtmpvDFUyU/R.INSTALL12a56034bbbb7a/pomp/src' +gcc -I"/export/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c bspline.c -o bspline.o +gcc -I"/export/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c distributions.c -o distributions.o +gcc -I"/export/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c dmeasure.c -o dmeasure.o +gcc -I"/export/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c dprior.c -o dprior.o +gcc -I"/export/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c dprocess.c -o dprocess.o +gcc -I"/export/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c emeasure.c -o emeasure.o +gcc -I"/export/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c euler.c -o euler.o +gcc -I"/export/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c gompertz.c -o gompertz.o +gcc -I"/export/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c init.c -o init.o +gcc -I"/export/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c logmeanexp.c -o logmeanexp.o +gcc -I"/export/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c lookup_table.c -o lookup_table.o +gcc -I"/export/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c mif2.c -o mif2.o +gcc -I"/export/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c ou2.c -o ou2.o +gcc -I"/export/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c partrans.c -o partrans.o +gcc -I"/export/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c pfilter.c -o pfilter.o +gcc -I"/export/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c pomp_fun.c -o pomp_fun.o +gcc -I"/export/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c probe.c -o probe.o +gcc -I"/export/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c probe_acf.c -o probe_acf.o +gcc -I"/export/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c probe_marginal.c -o probe_marginal.o +gcc -I"/export/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c probe_nlar.c -o probe_nlar.o +gcc -I"/export/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c resample.c -o resample.o +gcc -I"/export/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c rinit.c -o rinit.o +gcc -I"/export/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c rmeasure.c -o rmeasure.o +gcc -I"/export/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c rprior.c -o rprior.o +gcc -I"/export/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c rprocess.c -o rprocess.o +gcc -I"/export/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c simulate.c -o simulate.o +gcc -I"/export/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c skeleton.c -o skeleton.o +gcc -I"/export/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c sobolseq.c -o sobolseq.o +gcc -I"/export/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c ssa.c -o ssa.o +gcc -I"/export/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c synth_lik.c -o synth_lik.o +gcc -I"/export/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c trajectory.c -o trajectory.o +gcc -I"/export/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c transformations.c -o transformations.o +gcc -I"/export/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c userdata.c -o userdata.o +gcc -I"/export/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c vmeasure.c -o vmeasure.o +gcc -I"/export/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -c wpfilter.c -o wpfilter.o +gcc -shared -L/export/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/lib -L/usr/local/lib64 -o pomp.so bspline.o distributions.o dmeasure.o dprior.o dprocess.o emeasure.o euler.o gompertz.o init.o logmeanexp.o lookup_table.o mif2.o ou2.o partrans.o pfilter.o pomp_fun.o probe.o probe_acf.o probe_marginal.o probe_nlar.o resample.o rinit.o rmeasure.o rprior.o rprocess.o simulate.o skeleton.o sobolseq.o ssa.o synth_lik.o trajectory.o transformations.o userdata.o vmeasure.o wpfilter.o -lopenblas -lgfortran -lm -lquadmath -L/export/local/apps/R/ubuntu_20.04/4.2.2/lib64/R/lib -lR +make[1]: Leaving directory '/tmp/RtmpvDFUyU/R.INSTALL12a56034bbbb7a/pomp/src' +installing to /userdata/kingaa/projects/Rpkg/pomp/revdep/Library/00LOCK-pomp/00new/pomp/libs ** R ** data *** moving datasets to lazyload DB diff --git a/revdep/timings.tab b/revdep/timings.tab index 8e5170655..66289eeec 100644 --- a/revdep/timings.tab +++ b/revdep/timings.tab @@ -1,11 +1,12 @@ "user" "system" "elapsed" -"pomp" 392.028 404.89 307.151 -"CollocInfer" 103.803 60.566 109.124 -"DTAT" 104.038 47.792 113.273 -"epimdr" 55.194 36.192 60.431 -"epimdr2" 82.492 38.441 90.247 -"spaero" 54.369 48.603 59.022 -"spatPomp" 116.423 86.342 118.998 -"circumstance" 54.185 36.651 60.18 -"panelPomp" 109.514 83.204 112.154 -"phylopomp" 149.355 53.855 158.318 +"pomp" 743.193 1541.105 321.753 +"CollocInfer" 161.205 292.515 112.611 +"DTAT" 140.707 200.122 114.102 +"epimdr" 88.085 162.526 65.857 +"epimdr2" 110.257 163.722 93.101 +"spaero" 103.242 223.48 63.409 +"spatPomp" 197.815 364.276 122.624 +"stops" 169.799 198.252 143.551 +"circumstance" 89.714 161.953 60.226 +"panelPomp" 162.96 343.948 92.688 +"phylopomp" 198.442 216.936 165.223