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kingaa committed May 1, 2024
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5 changes: 1 addition & 4 deletions .Rbuildignore
Original file line number Diff line number Diff line change
Expand Up @@ -7,14 +7,11 @@ tools
wiki
www
yaml
tests/Makefile
tests/(.+?)\.png$
tests/(.+?)\.pdf$
tests/(.+?)\.Rout$
inst/doc/Makefile
inst/doc/(.+?).md
inst/doc/(.+?).Rmd
man/roxygen
tests
Doxyfile
LICENSE\.md$
README\.md$
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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: 5.7.1.1
Date: 2024-04-30
Version: 5.8
Date: 2024-05-01
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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503 changes: 100 additions & 403 deletions inst/NEWS

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713 changes: 79 additions & 634 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: 143 additions & 13 deletions revdep/Outputs/check_CollocInfer_stdout.txt
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
* 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 4.4.0 (2024-04-24)
* 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
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 ... [25s/21s] 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 ... [66s/22s] 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 @@ -82,13 +211,14 @@ 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 4.790 20.101 2.358
FitMatch 6.521 5.813 1.299
ParsMatch 5.609 3.346 0.865
user system elapsed
Profile 17.641 74.042 1.797
FitMatch 5.074 16.367 0.470
ParsMatch 4.618 8.505 0.288
smooth 1.672 7.418 0.182
* 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
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.


19 changes: 11 additions & 8 deletions revdep/Outputs/check_DTAT_stdout.txt
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
* 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 4.4.0 (2024-04-24)
* 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
Expand All @@ -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 ... [16s/16s] OK
* checking whether package 'DTAT' can be installed ... [33s/13s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
Expand All @@ -29,7 +29,7 @@
* 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 @@ -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 ... [25s/19s] NOTE
* checking R code for possible problems ... [58s/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 @@ -63,10 +63,13 @@ 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 2.63 5.78 2.23
** 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 package vignettes ... OK
* checking re-building of vignette outputs ... [47s/30s] OK
* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check 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’ [12s/10s]
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’ [11s/11s]
Comparing ‘pmcmc.Rout’ to ‘pmcmc.Rout.save’ ... OK


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