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kingaa committed Sep 10, 2024
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5 changes: 1 addition & 4 deletions .Rbuildignore
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Expand Up @@ -14,10 +14,7 @@
^Makefile
^TAGS
^rules.mk
^tests/Makefile
^tests/(.+?)\.png$
^tests/(.+?)\.pdf$
^tests/(.+?)\.Rout$
^tests
^inst/doc/Makefile
^inst/doc/(.+?).md
^inst/doc/(.+?).Rmd
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4 changes: 2 additions & 2 deletions DESCRIPTION
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@@ -1,8 +1,8 @@
Package: pomp
Type: Package
Title: Statistical Inference for Partially Observed Markov Processes
Version: 5.10.0.3
Date: 2024-09-06
Version: 5.11
Date: 2024-09-10
Authors@R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),email="[email protected]",comment=c(ORCID="0000-0001-6159-3207")),
person(given=c("Edward","L."),family="Ionides",role="aut",comment=c(ORCID="0000-0002-4190-0174")) ,
person(given="Carles",family="Bretó",role="aut",comment=c(ORCID="0000-0003-4695-4902")),
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515 changes: 103 additions & 412 deletions inst/NEWS

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731 changes: 82 additions & 649 deletions inst/NEWS.Rd

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3 changes: 1 addition & 2 deletions revdep/Outputs/check_CollocInfer_stderr.txt
Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@

See
'/home/kingaa/projects/Rpkg/pomp/revdep/CollocInfer.Rcheck/00check.log'
'/userdata/kingaa/projects/Rpkg/pomp/revdep/CollocInfer.Rcheck/00check.log'
for details.


156 changes: 142 additions & 14 deletions revdep/Outputs/check_CollocInfer_stdout.txt
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@@ -1,12 +1,12 @@
* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/CollocInfer.Rcheck'
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/CollocInfer.Rcheck'
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* using option '--as-cran'
* using options '--ignore-vignettes --as-cran'
* checking for file 'CollocInfer/DESCRIPTION' ... OK
* this is package 'CollocInfer' version '1.0.4'
* checking package namespace information ... OK
Expand All @@ -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 ... [18s/19s] OK
* checking whether package 'CollocInfer' can be installed ... [32s/18s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
Expand All @@ -27,7 +27,7 @@
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking code 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
Expand All @@ -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 ... [36s/31s] NOTE
* checking R code for possible problems ... [55s/24s] NOTE
Profile.GausNewt: local variable ‘dcdp’ assigned but may not be used
Profile.GausNewt: local variable ‘gradnorm0’ assigned but may not be
used
Expand All @@ -64,13 +64,142 @@ make.genlin : <anonymous>: local variable ‘r’ assigned but may not be
make.logtrans: local variable ‘more’ assigned but may not be used
outeropt: local variable ‘g’ assigned but may not be used
outeropt: local variable ‘resid’ assigned but may not be used
* checking Rd files ... OK
* checking Rd files ... NOTE
checkRd: (-1) ChemoData.rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChemoData.rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChemoData.rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChemoData.rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChemoData.rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChemoRMData.rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChemoRMData.rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChemoRMData.rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChemoRMData.rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ChemoRMData.rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FhNdata.rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FhNdata.rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FhNdata.rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FhNdata.rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FhNdata.rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FhNest.rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FhNest.rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) FitMatch.rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FitMatch.rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IntegrateForward.rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IntegrateForward.rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NSdata.rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NSdata.rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NSdata.rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ParsMatch.rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ParsMatch.rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Profile.rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Profile.rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Profile.rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Profile.rd:27-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Profile.rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Profile.rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Profile.rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Profile.rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Profile.rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Profile.rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Profile.rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Profile.rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Profile.rd:61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Profile.rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Profile.rd:68-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Profile.rd:70-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ProfileObjective.rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ProfileObjective.rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ProfileObjective.rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ProfileObjective.rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ProfileObjective.rd:81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ProfileObjective.rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ProfileObjective.rd:83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ProfileObjective.rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ProfileObjective.rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ProfileObjective.rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ProfileObjective.rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ProfileObjective.rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ProfileObjective.rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ProfileObjective.rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SEIRdata.rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SEIRdata.rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SEIRdata.rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SEIRdata.rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SEIRdata.rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SplineCoefs.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SplineCoefs.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SplineCoefs.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SplineCoefs.Rd:40-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SplineCoefs.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SplineCoefs.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SplineCoefs.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SplineCoefs.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SplineCoefs.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SplineCoefs.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SplineCoefs.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) make.lik.rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) make.lik.rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) make.lik.rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) make.lik.rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) make.lik.rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) make.lik.rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) make.lik.rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) make.lik.rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) make.lik.rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) make.lik.rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) make.proc.rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) make.proc.rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) make.proc.rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) make.proc.rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) make.proc.rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) make.transform.rd:58-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) make.transform.rd:60-63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) make.transform.rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) make.transform.rd:65-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) make.transform.rd:67-68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) make.transform.rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) make.transform.rd:75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) make.transform.rd:76-77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) make.transform.rd:78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) make.transform.rd:85-87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) make.transform.rd:88-90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) make.transform.rd:91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setup.rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setup.rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setup.rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setup.rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setup.rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setup.rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setup.rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setup.rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setup.rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setup.rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setup.rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setup.rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setup.rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setup.rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setup.rd:99: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setup.rd:100: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smooth.rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smooth.rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smooth.rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smooth.rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smooth.rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smooth.rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smooth.rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smooth.rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smooth.rd:35-36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smooth.rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smooth.rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smooth.rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smooth.rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smooth.rd:59: Lost braces in \itemize; meant \describe ?
* 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 ... WARNING
Variables with usage in documentation object 'FhNest' but not in code:
Variables with usage in Rd file 'FhNest.rd' but not in code:
‘FhNest’

* checking Rd \usage sections ... OK
Expand All @@ -83,12 +212,11 @@ Variables with usage in documentation object 'FhNest' but not in code:
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
Profile 4.790 20.101 2.358
FitMatch 6.521 5.813 1.299
ParsMatch 5.609 3.346 0.865
* checking PDF version of manual ... OK
Profile 12.401 61.279 1.504
FitMatch 2.318 9.899 0.291
* checking PDF version of manual ... [9s/128s] 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
3 changes: 1 addition & 2 deletions revdep/Outputs/check_DTAT_stderr.txt
Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@

See
'/home/kingaa/projects/Rpkg/pomp/revdep/DTAT.Rcheck/00check.log'
'/userdata/kingaa/projects/Rpkg/pomp/revdep/DTAT.Rcheck/00check.log'
for details.


27 changes: 13 additions & 14 deletions revdep/Outputs/check_DTAT_stdout.txt
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@@ -1,15 +1,15 @@
* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/DTAT.Rcheck'
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/DTAT.Rcheck'
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* using option '--as-cran'
* using options '--ignore-vignettes --as-cran'
* checking for file 'DTAT/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DTAT' version '0.3-6'
* this is package 'DTAT' version '0.3-7'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
Expand All @@ -19,17 +19,16 @@
* 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 ... [16s/16s] OK
* checking whether package 'DTAT' can be installed ... [29s/12s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* 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 code 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
Expand All @@ -42,7 +41,7 @@
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [25s/19s] 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
Expand All @@ -61,13 +60,13 @@ initialize,DE: local variable ‘Q1’ assigned but may not be used
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking files in 'vignettes' ... SKIPPED
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
Onoue.Friberg 2.793 6.669 2.811
** 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 ... [28s/26s] OK
* checking PDF version of manual ... OK
* checking PDF version of manual ... [9s/144s] 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
Expand Down
14 changes: 9 additions & 5 deletions revdep/Outputs/check_circumstance_stderr.txt
Original file line number Diff line number Diff line change
@@ -1,6 +1,10 @@
Running ‘mif2.R’ [11s/12s]
Comparing ‘mif2.Rout’ to ‘mif2.Rout.save’ ... Running ‘pfilter.R’
Comparing ‘pfilter.Rout’ to ‘pfilter.Rout.save’ ... Running ‘plot_matrix.R’
Comparing ‘plot_matrix.Rout’ to ‘plot_matrix.Rout.save’ ... Running ‘pmcmc.R’ [14s/14s]
Comparing ‘pmcmc.Rout’ to ‘pmcmc.Rout.save’ ...
Running ‘mif2.R’
Comparing ‘mif2.Rout’ to ‘mif2.Rout.save’ ... OK
Running ‘pfilter.R’
Comparing ‘pfilter.Rout’ to ‘pfilter.Rout.save’ ... OK
Running ‘plot_matrix.R’
Comparing ‘plot_matrix.Rout’ to ‘plot_matrix.Rout.save’ ... OK
Running ‘pmcmc.R’ [15s/11s]
Comparing ‘pmcmc.Rout’ to ‘pmcmc.Rout.save’ ... OK


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