Skip to content

Commit e095e6c

Browse files
kingaakingaa
committed
CRAN version
1 parent 1a91eec commit e095e6c

31 files changed

+1618
-1144
lines changed

‎.Rbuildignore‎

Lines changed: 1 addition & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -14,10 +14,7 @@
1414
^Makefile
1515
^TAGS
1616
^rules.mk
17-
^tests/Makefile
18-
^tests/(.+?)\.png$
19-
^tests/(.+?)\.pdf$
20-
^tests/(.+?)\.Rout$
17+
^tests
2118
^inst/doc/Makefile
2219
^inst/doc/(.+?).md
2320
^inst/doc/(.+?).Rmd

‎DESCRIPTION‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,8 +1,8 @@
11
Package: pomp
22
Type: Package
33
Title: Statistical Inference for Partially Observed Markov Processes
4-
Version: 6.3.1.0
5-
Date: 2025-09-29
4+
Version: 6.4
5+
Date: 2025-11-23
66
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")),
77
person(given=c("Edward","L."),family="Ionides",role="aut",comment=c(ORCID="0000-0002-4190-0174")) ,
88
person(given="Carles",family="Bretó",role="aut",comment=c(ORCID="0000-0003-4695-4902")),

‎inst/NEWS‎

Lines changed: 121 additions & 442 deletions
Large diffs are not rendered by default.

‎inst/NEWS.Rd‎

Lines changed: 93 additions & 684 deletions
Large diffs are not rendered by default.

‎revdep/Outputs/check_CollocInfer_stderr.txt‎

Lines changed: 5 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,5 @@
1+
2+
See
3+
'/home/kingaa/projects/Rpkg/pomp/revdep/CollocInfer.Rcheck/00check.log'
4+
for details.
5+

‎revdep/Outputs/check_CollocInfer_stdout.txt‎

Lines changed: 89 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,89 @@
1+
* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/CollocInfer.Rcheck'
2+
* using R version 4.5.2 (2025-10-31)
3+
* using platform: x86_64-pc-linux-gnu
4+
* R was compiled by
5+
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
6+
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
7+
* running under: Ubuntu 24.04.3 LTS
8+
* using session charset: UTF-8
9+
* using options '--ignore-vignettes --as-cran'
10+
* checking for file 'CollocInfer/DESCRIPTION' ... OK
11+
* this is package 'CollocInfer' version '1.0.5'
12+
* checking package namespace information ... OK
13+
* checking package dependencies ... OK
14+
* checking if this is a source package ... OK
15+
* checking if there is a namespace ... OK
16+
* checking for executable files ... OK
17+
* checking for hidden files and directories ... OK
18+
* checking for portable file names ... OK
19+
* checking for sufficient/correct file permissions ... OK
20+
* checking whether package 'CollocInfer' can be installed ... [31s/13s] OK
21+
* checking installed package size ... OK
22+
* checking package directory ... OK
23+
* checking for future file timestamps ... OK
24+
* checking DESCRIPTION meta-information ... OK
25+
* checking top-level files ... OK
26+
* checking for left-over files ... OK
27+
* checking index information ... OK
28+
* checking package subdirectories ... OK
29+
* checking code files for non-ASCII characters ... OK
30+
* checking R files for syntax errors ... OK
31+
* checking whether the package can be loaded ... OK
32+
* checking whether the package can be loaded with stated dependencies ... OK
33+
* checking whether the package can be unloaded cleanly ... OK
34+
* checking whether the namespace can be loaded with stated dependencies ... OK
35+
* checking whether the namespace can be unloaded cleanly ... OK
36+
* checking loading without being on the library search path ... OK
37+
* checking use of S3 registration ... OK
38+
* checking dependencies in R code ... OK
39+
* checking S3 generic/method consistency ... OK
40+
* checking replacement functions ... OK
41+
* checking foreign function calls ... OK
42+
* checking R code for possible problems ... [72s/11s] NOTE
43+
Profile.GausNewt: local variable ‘dcdp’ assigned but may not be used
44+
Profile.GausNewt: local variable ‘gradnorm0’ assigned but may not be
45+
used
46+
Profile.LS: local variable ‘g’ assigned but may not be used
47+
Profile.LS: local variable ‘resid’ assigned but may not be used
48+
Profile.covariance: local variable ‘tf’ assigned but may not be used
49+
chemo.ode: local variable ‘C’ assigned but may not be used
50+
forward.prediction.error: local variable ‘ptimes’ assigned but may not
51+
be used
52+
make.Cproc : dCproc.dp: local variable ‘gg’ assigned but may not be
53+
used
54+
make.exptrans: local variable ‘more’ assigned but may not be used
55+
make.findif.loglik : findif.loglik.fun: local variable ‘x’ assigned but
56+
may not be used
57+
make.findif.ode : <anonymous>: local variable ‘x’ assigned but may not
58+
be used
59+
make.findif.var : findif.var.fun: local variable ‘x’ assigned but may
60+
not be used
61+
make.genlin : <anonymous>: local variable ‘r’ assigned but may not be
62+
used
63+
make.logtrans: local variable ‘more’ assigned but may not be used
64+
outeropt: local variable ‘g’ assigned but may not be used
65+
outeropt: local variable ‘resid’ assigned but may not be used
66+
* checking Rd files ... OK
67+
* checking Rd metadata ... OK
68+
* checking Rd line widths ... OK
69+
* checking Rd cross-references ... OK
70+
* checking for missing documentation entries ... OK
71+
* checking for code/documentation mismatches ... OK
72+
* checking Rd \usage sections ... OK
73+
* checking Rd contents ... OK
74+
* checking for unstated dependencies in examples ... OK
75+
* checking contents of 'data' directory ... OK
76+
* checking data for non-ASCII characters ... OK
77+
* checking LazyData ... OK
78+
* checking data for ASCII and uncompressed saves ... OK
79+
* checking examples ... OK
80+
Examples with CPU (user + system) or elapsed time > 5s
81+
user system elapsed
82+
Profile 3.732 23.351 0.441
83+
* checking for unstated dependencies in 'demo' ... OK
84+
* checking PDF version of manual ... OK
85+
* checking HTML version of manual ... OK
86+
* checking for non-standard things in the check directory ... OK
87+
* checking for detritus in the temp directory ... OK
88+
* DONE
89+
Status: 1 NOTE

‎revdep/Outputs/check_DTAT_stderr.txt‎

Lines changed: 5 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,5 @@
1+
2+
See
3+
'/home/kingaa/projects/Rpkg/pomp/revdep/DTAT.Rcheck/00check.log'
4+
for details.
5+

‎revdep/Outputs/check_DTAT_stdout.txt‎

Lines changed: 74 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,74 @@
1+
* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/DTAT.Rcheck'
2+
* using R version 4.5.2 (2025-10-31)
3+
* using platform: x86_64-pc-linux-gnu
4+
* R was compiled by
5+
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
6+
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
7+
* running under: Ubuntu 24.04.3 LTS
8+
* using session charset: UTF-8
9+
* using options '--ignore-vignettes --as-cran'
10+
* checking for file 'DTAT/DESCRIPTION' ... OK
11+
* checking extension type ... Package
12+
* this is package 'DTAT' version '0.3-8'
13+
* package encoding: UTF-8
14+
* checking package namespace information ... OK
15+
* checking package dependencies ... OK
16+
* checking if this is a source package ... OK
17+
* checking if there is a namespace ... OK
18+
* checking for executable files ... OK
19+
* checking for hidden files and directories ... OK
20+
* checking for portable file names ... OK
21+
* checking for sufficient/correct file permissions ... OK
22+
* checking whether package 'DTAT' can be installed ... OK
23+
* checking installed package size ... OK
24+
* checking package directory ... OK
25+
* checking for future file timestamps ... OK
26+
* checking DESCRIPTION meta-information ... OK
27+
* checking top-level files ... OK
28+
* checking for left-over files ... OK
29+
* checking index information ... OK
30+
* checking package subdirectories ... OK
31+
* checking code files for non-ASCII characters ... OK
32+
* checking R files for syntax errors ... OK
33+
* checking whether the package can be loaded ... OK
34+
* checking whether the package can be loaded with stated dependencies ... OK
35+
* checking whether the package can be unloaded cleanly ... OK
36+
* checking whether the namespace can be loaded with stated dependencies ... OK
37+
* checking whether the namespace can be unloaded cleanly ... OK
38+
* checking loading without being on the library search path ... OK
39+
* checking use of S3 registration ... OK
40+
* checking dependencies in R code ... OK
41+
* checking S3 generic/method consistency ... OK
42+
* checking replacement functions ... OK
43+
* checking foreign function calls ... OK
44+
* checking R code for possible problems ... NOTE
45+
dose.survfit: local variable ‘S’ assigned but may not be used
46+
as_d3_data,DE : rel_dose: local variable ‘where_na’ assigned but may
47+
not be used
48+
initialize,DE: local variable ‘Q1’ assigned but may not be used
49+
* checking Rd files ... OK
50+
* checking Rd metadata ... OK
51+
* checking Rd line widths ... OK
52+
* checking Rd cross-references ... OK
53+
* checking for missing documentation entries ... OK
54+
* checking for code/documentation mismatches ... OK
55+
* checking Rd \usage sections ... OK
56+
* checking Rd contents ... OK
57+
* checking for unstated dependencies in examples ... OK
58+
* checking contents of 'data' directory ... OK
59+
* checking data for non-ASCII characters ... OK
60+
* checking data for ASCII and uncompressed saves ... OK
61+
* checking sizes of PDF files under 'inst/doc' ... OK
62+
* checking installed files from 'inst/doc' ... OK
63+
* checking files in 'vignettes' ... SKIPPED
64+
* checking examples ... OK
65+
Examples with CPU (user + system) or elapsed time > 5s
66+
user system elapsed
67+
Onoue.Friberg 2.257 9.968 1.931
68+
** found \donttest examples: check also with --run-donttest
69+
* checking PDF version of manual ... OK
70+
* checking HTML version of manual ... OK
71+
* checking for non-standard things in the check directory ... OK
72+
* checking for detritus in the temp directory ... OK
73+
* DONE
74+
Status: 1 NOTE

‎revdep/Outputs/check_circumstance_stderr.txt‎

Lines changed: 13 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,13 @@
1+
Running ‘mif2.R’
2+
Comparing ‘mif2.Rout’ to ‘mif2.Rout.save’ ... OK
3+
Running ‘pfilter.R’
4+
Comparing ‘pfilter.Rout’ to ‘pfilter.Rout.save’ ... OK
5+
Running ‘plot_matrix.R’
6+
Comparing ‘plot_matrix.Rout’ to ‘plot_matrix.Rout.save’ ... OK
7+
Running ‘pmcmc.R’
8+
Comparing ‘pmcmc.Rout’ to ‘pmcmc.Rout.save’ ... OK
9+
10+
See
11+
'/home/kingaa/projects/Rpkg/pomp/revdep/circumstance.Rcheck/00check.log'
12+
for details.
13+

‎revdep/Outputs/check_circumstance_stdout.txt‎

Lines changed: 69 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,69 @@
1+
* using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/circumstance.Rcheck'
2+
* using R version 4.5.2 (2025-10-31)
3+
* using platform: x86_64-pc-linux-gnu
4+
* R was compiled by
5+
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
6+
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
7+
* running under: Ubuntu 24.04.3 LTS
8+
* using session charset: UTF-8
9+
* using options '--ignore-vignettes --as-cran'
10+
* checking for file 'circumstance/DESCRIPTION' ... OK
11+
* checking extension type ... Package
12+
* this is package 'circumstance' version '0.0.10.1'
13+
* package encoding: UTF-8
14+
* checking package namespace information ... OK
15+
* checking package dependencies ... OK
16+
* checking if this is a source package ... OK
17+
* checking if there is a namespace ... OK
18+
* checking for executable files ... OK
19+
* checking for hidden files and directories ... OK
20+
* checking for portable file names ... OK
21+
* checking for sufficient/correct file permissions ... OK
22+
* checking whether package 'circumstance' can be installed ... OK
23+
* checking installed package size ... OK
24+
* checking package directory ... OK
25+
* checking for future file timestamps ... OK
26+
* checking DESCRIPTION meta-information ... OK
27+
* checking top-level files ... OK
28+
* checking for left-over files ... OK
29+
* checking index information ... OK
30+
* checking package subdirectories ... OK
31+
* checking code files for non-ASCII characters ... OK
32+
* checking R files for syntax errors ... OK
33+
* checking whether the package can be loaded ... OK
34+
* checking whether the package can be loaded with stated dependencies ... OK
35+
* checking whether the package can be unloaded cleanly ... OK
36+
* checking whether the namespace can be loaded with stated dependencies ... OK
37+
* checking whether the namespace can be unloaded cleanly ... OK
38+
* checking loading without being on the library search path ... OK
39+
* checking use of S3 registration ... OK
40+
* checking dependencies in R code ... OK
41+
* checking S3 generic/method consistency ... NOTE
42+
Apparent methods for exported generics not registered:
43+
plot_matrix.internal
44+
See section 'Registering S3 methods' in the 'Writing R Extensions'
45+
manual.
46+
* checking replacement functions ... OK
47+
* checking foreign function calls ... OK
48+
* checking R code for possible problems ... OK
49+
* checking Rd files ... OK
50+
* checking Rd metadata ... OK
51+
* checking Rd line widths ... OK
52+
* checking Rd cross-references ... OK
53+
* checking for missing documentation entries ... OK
54+
* checking for code/documentation mismatches ... OK
55+
* checking Rd \usage sections ... OK
56+
* checking Rd contents ... OK
57+
* checking for unstated dependencies in examples ... OK
58+
* checking installed files from 'inst/doc' ... OK
59+
* checking examples ... OK
60+
** found \donttest examples: check also with --run-donttest
61+
* checking for unstated dependencies in 'tests' ... OK
62+
* checking tests ...
63+
[38s/16s] OK
64+
* checking PDF version of manual ... OK
65+
* checking HTML version of manual ... OK
66+
* checking for non-standard things in the check directory ... OK
67+
* checking for detritus in the temp directory ... OK
68+
* DONE
69+
Status: 1 NOTE

0 commit comments

Comments
 (0)