CRAN version

.Rbuildignore

@@ -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

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: pomp
 Type: Package
 Title: Statistical Inference for Partially Observed Markov Processes
-Version: 6.0.5.1
+Version: 6.1
 Date: 2025-01-08
 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"))	,

revdep/Outputs/check_CollocInfer_stderr.txt

@@ -0,0 +1,5 @@
+
+See
+  '/home/kingaa/projects/Rpkg/pomp/revdep/CollocInfer.Rcheck/00check.log'
+for details.
+

revdep/Outputs/check_CollocInfer_stdout.txt

@@ -0,0 +1,89 @@
+* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/CollocInfer.Rcheck'
+* using R version 4.4.2 (2024-10-31)
+* 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 22.04.5 LTS
+* using session charset: UTF-8
+* using options '--ignore-vignettes --as-cran'
+* checking for file 'CollocInfer/DESCRIPTION' ... OK
+* this is package 'CollocInfer' version '1.0.5'
+* 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 'CollocInfer' can be installed ... [31s/22s] OK
+* checking installed package size ... OK
+* checking package directory ... OK
+* checking for future file timestamps ... 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 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
+* 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 ... [69s/24s] NOTE
+Profile.GausNewt: local variable ‘dcdp’ assigned but may not be used
+Profile.GausNewt: local variable ‘gradnorm0’ assigned but may not be
+  used
+Profile.LS: local variable ‘g’ assigned but may not be used
+Profile.LS: local variable ‘resid’ assigned but may not be used
+Profile.covariance: local variable ‘tf’ assigned but may not be used
+chemo.ode: local variable ‘C’ assigned but may not be used
+forward.prediction.error: local variable ‘ptimes’ assigned but may not
+  be used
+make.Cproc : dCproc.dp: local variable ‘gg’ assigned but may not be
+  used
+make.exptrans: local variable ‘more’ assigned but may not be used
+make.findif.loglik : findif.loglik.fun: local variable ‘x’ assigned but
+  may not be used
+make.findif.ode : <anonymous>: local variable ‘x’ assigned but may not
+  be used
+make.findif.var : findif.var.fun: local variable ‘x’ assigned but may
+  not be used
+make.genlin : <anonymous>: local variable ‘r’ assigned but may not be
+  used
+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 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 examples ... OK
+Examples with CPU (user + system) or elapsed time > 5s
+           user system elapsed
+Profile  14.508 78.367   1.703
+FitMatch  3.431 11.463   0.345
+* 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 NOTE

revdep/Outputs/check_DTAT_stderr.txt

@@ -0,0 +1,5 @@
+
+See
+  '/home/kingaa/projects/Rpkg/pomp/revdep/DTAT.Rcheck/00check.log'
+for details.
+

revdep/Outputs/check_DTAT_stdout.txt

@@ -0,0 +1,74 @@
+* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/DTAT.Rcheck'
+* using R version 4.4.2 (2024-10-31)
+* 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 22.04.5 LTS
+* using session charset: UTF-8
+* using options '--ignore-vignettes --as-cran'
+* checking for file 'DTAT/DESCRIPTION' ... OK
+* checking extension type ... Package
+* this is package 'DTAT' version '0.3-7'
+* 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 'DTAT' can be installed ... [30s/14s] OK
+* checking installed package size ... OK
+* checking package directory ... OK
+* checking for future file timestamps ... 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 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
+* 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 ... [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
+initialize,DE: local variable ‘Q1’ 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 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' ... SKIPPED
+* checking examples ... OK
+Examples with CPU (user + system) or elapsed time > 5s
+              user system elapsed
+Onoue.Friberg 2.53  7.413   2.059
+** found \donttest examples: check also with --run-donttest
+* 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 NOTE

revdep/Outputs/check_circumstance_stderr.txt

@@ -0,0 +1,10 @@
+  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
+
+

revdep/Outputs/check_circumstance_stdout.txt

@@ -0,0 +1,68 @@
+* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/circumstance.Rcheck'
+* using R version 4.4.2 (2024-10-31)
+* 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 22.04.5 LTS
+* using session charset: UTF-8
+* using options '--ignore-vignettes --as-cran'
+* checking for file 'circumstance/DESCRIPTION' ... OK
+* checking extension type ... Package
+* this is package 'circumstance' version '0.0.10.1'
+* 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 'circumstance' can be installed ... OK
+* checking installed package size ... OK
+* checking package directory ... OK
+* checking for future file timestamps ... 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 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
+* 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 ... 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 ... OK
+* checking Rd contents ... OK
+* checking for unstated dependencies in examples ... OK
+* checking installed files from 'inst/doc' ... OK
+* checking examples ... OK
+Examples with CPU (user + system) or elapsed time > 5s
+         user system elapsed
+pfilter 5.575  0.342   4.815
+** found \donttest examples: check also with --run-donttest
+* checking for unstated dependencies in 'tests' ... OK
+* checking tests ...
+ [45s/27s] OK
+* 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: OK

revdep/Outputs/check_epimdr2_stderr.txt

@@ -0,0 +1,5 @@
+
+See
+  '/home/kingaa/projects/Rpkg/pomp/revdep/epimdr2.Rcheck/00check.log'
+for details.
+