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kingaakingaa
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‎.Rbuildignore‎

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^Makefile
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^TAGS
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^rules.mk
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^tests/Makefile
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^tests/(.+?)\.png$
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^tests/(.+?)\.pdf$
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^tests/(.+?)\.Rout$
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^tests
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^inst/doc/Makefile
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^inst/doc/(.+?).md
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^inst/doc/(.+?).Rmd

‎DESCRIPTION‎

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Package: pomp
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Type: Package
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Title: Statistical Inference for Partially Observed Markov Processes
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Version: 6.1.1.2
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Date: 2025-03-20
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Version: 6.2
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Date: 2025-04-16
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Authors@R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),email="kingaa@umich.edu",comment=c(ORCID="0000-0001-6159-3207")),
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person(given=c("Edward","L."),family="Ionides",role="aut",comment=c(ORCID="0000-0002-4190-0174")) ,
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person(given="Carles",family="Bretó",role="aut",comment=c(ORCID="0000-0003-4695-4902")),

‎inst/NEWS‎

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‎inst/NEWS.Rd‎

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‎revdep/Outputs/check_CollocInfer_stderr.txt‎

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

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* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/CollocInfer.Rcheck'
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* using R version 4.4.3 (2025-02-28)
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* using platform: x86_64-pc-linux-gnu
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* R was compiled by
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gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
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GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
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* running under: Ubuntu 22.04.5 LTS
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* using session charset: UTF-8
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* using options '--ignore-vignettes --as-cran'
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* checking for file 'CollocInfer/DESCRIPTION' ... OK
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* this is package 'CollocInfer' version '1.0.5'
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* checking package namespace information ... OK
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* checking package dependencies ... OK
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* checking if this is a source package ... OK
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* checking if there is a namespace ... OK
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* checking for executable files ... OK
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* checking for hidden files and directories ... OK
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* checking for portable file names ... OK
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* checking for sufficient/correct file permissions ... OK
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* checking whether package 'CollocInfer' can be installed ... [33s/22s] OK
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* checking installed package size ... OK
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* checking package directory ... OK
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* checking for future file timestamps ... NOTE
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unable to verify current time
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* checking DESCRIPTION meta-information ... OK
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* checking top-level files ... OK
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* checking for left-over files ... OK
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* checking index information ... OK
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* checking package subdirectories ... OK
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* checking code files for non-ASCII characters ... OK
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* checking R files for syntax errors ... OK
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* checking whether the package can be loaded ... OK
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* checking whether the package can be loaded with stated dependencies ... OK
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* checking whether the package can be unloaded cleanly ... OK
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* checking whether the namespace can be loaded with stated dependencies ... OK
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* checking whether the namespace can be unloaded cleanly ... OK
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* checking loading without being on the library search path ... OK
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* checking use of S3 registration ... OK
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* checking dependencies in R code ... OK
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* checking S3 generic/method consistency ... OK
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* checking replacement functions ... OK
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* checking foreign function calls ... OK
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* checking R code for possible problems ... [73s/23s] NOTE
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Profile.GausNewt: local variable ‘dcdp’ assigned but may not be used
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Profile.GausNewt: local variable ‘gradnorm0’ assigned but may not be
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used
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Profile.LS: local variable ‘g’ assigned but may not be used
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Profile.LS: local variable ‘resid’ assigned but may not be used
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Profile.covariance: local variable ‘tf’ assigned but may not be used
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chemo.ode: local variable ‘C’ assigned but may not be used
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forward.prediction.error: local variable ‘ptimes’ assigned but may not
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be used
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make.Cproc : dCproc.dp: local variable ‘gg’ assigned but may not be
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used
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make.exptrans: local variable ‘more’ assigned but may not be used
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make.findif.loglik : findif.loglik.fun: local variable ‘x’ assigned but
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may not be used
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make.findif.ode : <anonymous>: local variable ‘x’ assigned but may not
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be used
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make.findif.var : findif.var.fun: local variable ‘x’ assigned but may
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not be used
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make.genlin : <anonymous>: local variable ‘r’ assigned but may not be
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used
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make.logtrans: local variable ‘more’ assigned but may not be used
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outeropt: local variable ‘g’ assigned but may not be used
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outeropt: local variable ‘resid’ assigned but may not be used
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* checking Rd files ... OK
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* checking Rd metadata ... OK
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* checking Rd line widths ... OK
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* checking Rd cross-references ... OK
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* checking for missing documentation entries ... OK
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* checking for code/documentation mismatches ... OK
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* checking Rd \usage sections ... OK
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* checking Rd contents ... OK
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* checking for unstated dependencies in examples ... OK
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* checking contents of 'data' directory ... OK
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* checking data for non-ASCII characters ... OK
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* checking LazyData ... OK
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* checking data for ASCII and uncompressed saves ... OK
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* checking examples ... OK
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Examples with CPU (user + system) or elapsed time > 5s
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user system elapsed
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Profile 12.334 65.240 1.417
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FitMatch 2.298 9.015 0.299
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ParsMatch 2.734 4.679 0.195
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* checking PDF version of manual ... OK
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* checking HTML version of manual ... OK
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* checking for non-standard things in the check directory ... OK
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* checking for detritus in the temp directory ... OK
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* DONE
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Status: 2 NOTEs

‎revdep/Outputs/check_DTAT_stderr.txt‎

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

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* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/DTAT.Rcheck'
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* using R version 4.4.3 (2025-02-28)
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* using platform: x86_64-pc-linux-gnu
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* R was compiled by
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gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
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GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
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* running under: Ubuntu 22.04.5 LTS
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* using session charset: UTF-8
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* using options '--ignore-vignettes --as-cran'
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* checking for file 'DTAT/DESCRIPTION' ... OK
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* checking extension type ... Package
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* this is package 'DTAT' version '0.3-7'
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* package encoding: UTF-8
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* checking package namespace information ... OK
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* checking package dependencies ... OK
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* checking if this is a source package ... OK
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* checking if there is a namespace ... OK
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* checking for executable files ... OK
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* checking for hidden files and directories ... OK
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* checking for portable file names ... OK
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* checking for sufficient/correct file permissions ... OK
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* checking whether package 'DTAT' can be installed ... [30s/14s] OK
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* checking installed package size ... OK
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* checking package directory ... OK
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* checking for future file timestamps ... NOTE
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unable to verify current time
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* checking DESCRIPTION meta-information ... OK
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* checking top-level files ... OK
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* checking for left-over files ... OK
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* checking index information ... OK
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* checking package subdirectories ... OK
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* checking code files for non-ASCII characters ... OK
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* checking R files for syntax errors ... OK
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* checking whether the package can be loaded ... OK
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* checking whether the package can be loaded with stated dependencies ... OK
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* checking whether the package can be unloaded cleanly ... OK
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* checking whether the namespace can be loaded with stated dependencies ... OK
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* checking whether the namespace can be unloaded cleanly ... OK
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* checking loading without being on the library search path ... OK
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* checking use of S3 registration ... OK
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* checking dependencies in R code ... OK
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* checking S3 generic/method consistency ... OK
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* checking replacement functions ... OK
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* checking foreign function calls ... OK
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* checking R code for possible problems ... [58s/15s] NOTE
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dose.survfit: local variable ‘S’ assigned but may not be used
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as_d3_data,DE : rel_dose: local variable ‘where_na’ assigned but may
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not be used
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initialize,DE: local variable ‘Q1’ assigned but may not be used
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* checking Rd files ... OK
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* checking Rd metadata ... OK
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* checking Rd line widths ... OK
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* checking Rd cross-references ... OK
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* checking for missing documentation entries ... OK
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* checking for code/documentation mismatches ... OK
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* checking Rd \usage sections ... OK
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* checking Rd contents ... OK
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* checking for unstated dependencies in examples ... OK
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* checking contents of 'data' directory ... OK
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* checking data for non-ASCII characters ... OK
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* checking data for ASCII and uncompressed saves ... OK
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* checking sizes of PDF files under 'inst/doc' ... OK
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* checking installed files from 'inst/doc' ... OK
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* checking files in 'vignettes' ... SKIPPED
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* checking examples ... OK
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Examples with CPU (user + system) or elapsed time > 5s
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user system elapsed
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Onoue.Friberg 2.234 6.431 2.13
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** found \donttest examples: check also with --run-donttest
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* checking PDF version of manual ... OK
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* checking HTML version of manual ... OK
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* checking for non-standard things in the check directory ... OK
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* checking for detritus in the temp directory ... OK
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* DONE
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Status: 2 NOTEs

‎revdep/Outputs/check_circumstance_stderr.txt‎

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Running ‘mif2.R’
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Comparing ‘mif2.Rout’ to ‘mif2.Rout.save’ ... OK
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Running ‘pfilter.R’
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Comparing ‘pfilter.Rout’ to ‘pfilter.Rout.save’ ... OK
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Running ‘plot_matrix.R’
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Comparing ‘plot_matrix.Rout’ to ‘plot_matrix.Rout.save’ ... OK
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Running ‘pmcmc.R’ [15s/11s]
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Comparing ‘pmcmc.Rout’ to ‘pmcmc.Rout.save’ ... OK
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See
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'/home/kingaa/projects/Rpkg/pomp/revdep/circumstance.Rcheck/00check.log'
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for details.
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‎revdep/Outputs/check_circumstance_stdout.txt‎

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* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/circumstance.Rcheck'
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* using R version 4.4.3 (2025-02-28)
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* using platform: x86_64-pc-linux-gnu
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* R was compiled by
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gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
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GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
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* running under: Ubuntu 22.04.5 LTS
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* using session charset: UTF-8
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* using options '--ignore-vignettes --as-cran'
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* checking for file 'circumstance/DESCRIPTION' ... OK
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* checking extension type ... Package
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* this is package 'circumstance' version '0.0.10.1'
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* package encoding: UTF-8
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* checking package namespace information ... OK
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* checking package dependencies ... OK
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* checking if this is a source package ... OK
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* checking if there is a namespace ... OK
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* checking for executable files ... OK
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* checking for hidden files and directories ... OK
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* checking for portable file names ... OK
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* checking for sufficient/correct file permissions ... OK
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* checking whether package 'circumstance' can be installed ... OK
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* checking installed package size ... OK
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* checking package directory ... OK
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* checking for future file timestamps ... NOTE
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unable to verify current time
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* checking DESCRIPTION meta-information ... OK
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* checking top-level files ... OK
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* checking for left-over files ... OK
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* checking index information ... OK
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* checking package subdirectories ... OK
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* checking code files for non-ASCII characters ... OK
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* checking R files for syntax errors ... OK
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* checking whether the package can be loaded ... OK
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* checking whether the package can be loaded with stated dependencies ... OK
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* checking whether the package can be unloaded cleanly ... OK
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* checking whether the namespace can be loaded with stated dependencies ... OK
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* checking whether the namespace can be unloaded cleanly ... OK
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* checking loading without being on the library search path ... OK
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* checking use of S3 registration ... OK
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* checking dependencies in R code ... OK
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* checking S3 generic/method consistency ... OK
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* checking replacement functions ... OK
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* checking foreign function calls ... OK
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* checking R code for possible problems ... OK
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* checking Rd files ... OK
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* checking Rd metadata ... OK
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* checking Rd line widths ... OK
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* checking Rd cross-references ... OK
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* checking for missing documentation entries ... OK
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* checking for code/documentation mismatches ... OK
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* checking Rd \usage sections ... OK
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* checking Rd contents ... OK
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* checking for unstated dependencies in examples ... OK
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* checking installed files from 'inst/doc' ... OK
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* checking examples ... OK
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Examples with CPU (user + system) or elapsed time > 5s
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user system elapsed
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pfilter 4.638 0.204 5.315
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** found \donttest examples: check also with --run-donttest
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* checking for unstated dependencies in 'tests' ... OK
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* checking tests ...
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[47s/28s] OK
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* checking PDF version of manual ... OK
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* checking HTML version of manual ... OK
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* checking for non-standard things in the check directory ... OK
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* checking for detritus in the temp directory ... OK
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* DONE
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Status: 1 NOTE

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