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kingaakingaa
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update revdeps
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‎revdep/Outputs/check_CollocInfer_stdout.txt‎

Lines changed: 11 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -1,10 +1,10 @@
11
* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/CollocInfer.Rcheck'
2-
* using R version 4.3.1 (2023-06-16)
2+
* using R version 4.3.2 (2023-10-31)
33
* using platform: x86_64-pc-linux-gnu (64-bit)
44
* R was compiled by
5-
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
6-
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
7-
* running under: Ubuntu 22.04.2 LTS
5+
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
6+
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
7+
* running under: Ubuntu 22.04.3 LTS
88
* using session charset: UTF-8
99
* using option '--as-cran'
1010
* checking for file 'CollocInfer/DESCRIPTION' ... OK
@@ -18,7 +18,7 @@
1818
* checking for portable file names ... OK
1919
* checking for sufficient/correct file permissions ... OK
2020
* checking serialization versions ... OK
21-
* checking whether package 'CollocInfer' can be installed ... [34s/20s] OK
21+
* checking whether package 'CollocInfer' can be installed ... [33s/23s] OK
2222
* checking installed package size ... OK
2323
* checking package directory ... OK
2424
* checking for future file timestamps ... OK
@@ -40,7 +40,7 @@
4040
* checking S3 generic/method consistency ... OK
4141
* checking replacement functions ... OK
4242
* checking foreign function calls ... OK
43-
* checking R code for possible problems ... [67s/22s] NOTE
43+
* checking R code for possible problems ... [75s/63s] NOTE
4444
Profile.GausNewt: local variable ‘dcdp’ assigned but may not be used
4545
Profile.GausNewt: local variable ‘gradnorm0’ assigned but may not be
4646
used
@@ -80,12 +80,13 @@ Variables with usage in documentation object 'FhNest' but not in code:
8080
* checking data for non-ASCII characters ... OK
8181
* checking LazyData ... OK
8282
* checking data for ASCII and uncompressed saves ... OK
83-
* checking examples ... OK
83+
* checking examples ... [139s/28s] OK
8484
Examples with CPU (user + system) or elapsed time > 5s
8585
user system elapsed
86-
Profile 13.898 47.310 1.045
87-
FitMatch 3.457 7.528 0.215
88-
* checking PDF version of manual ... OK
86+
Profile 20.601 72.806 8.283
87+
FitMatch 3.377 6.552 0.363
88+
setup 1.120 4.492 4.509
89+
* checking PDF version of manual ... [11s/239s] OK
8990
* checking HTML version of manual ... OK
9091
* checking for non-standard things in the check directory ... OK
9192
* checking for detritus in the temp directory ... OK

‎revdep/Outputs/check_DTAT_stdout.txt‎

Lines changed: 10 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -1,10 +1,10 @@
11
* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/DTAT.Rcheck'
2-
* using R version 4.3.1 (2023-06-16)
2+
* using R version 4.3.2 (2023-10-31)
33
* using platform: x86_64-pc-linux-gnu (64-bit)
44
* R was compiled by
5-
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
6-
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
7-
* running under: Ubuntu 22.04.2 LTS
5+
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
6+
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
7+
* running under: Ubuntu 22.04.3 LTS
88
* using session charset: UTF-8
99
* using option '--as-cran'
1010
* checking for file 'DTAT/DESCRIPTION' ... OK
@@ -19,7 +19,7 @@
1919
* checking for hidden files and directories ... OK
2020
* checking for portable file names ... OK
2121
* checking for sufficient/correct file permissions ... OK
22-
* checking whether package 'DTAT' can be installed ... [36s/13s] OK
22+
* checking whether package 'DTAT' can be installed ... [31s/14s] OK
2323
* checking installed package size ... OK
2424
* checking package directory ... OK
2525
* checking for future file timestamps ... OK
@@ -42,7 +42,7 @@
4242
* checking S3 generic/method consistency ... OK
4343
* checking replacement functions ... OK
4444
* checking foreign function calls ... OK
45-
* checking R code for possible problems ... [57s/14s] NOTE
45+
* checking R code for possible problems ... [61s/15s] NOTE
4646
dose.survfit: local variable ‘S’ assigned but may not be used
4747
as_d3_data,DE : rel_dose: local variable ‘where_na’ assigned but may
4848
not be used
@@ -62,14 +62,15 @@ initialize,DE: local variable ‘Q1’ assigned but may not be used
6262
* checking sizes of PDF files under 'inst/doc' ... OK
6363
* checking installed files from 'inst/doc' ... OK
6464
* checking files in 'vignettes' ... OK
65-
* checking examples ... OK
65+
* checking examples ... [20s/36s] OK
6666
Examples with CPU (user + system) or elapsed time > 5s
6767
user system elapsed
68-
Onoue.Friberg 3.028 7.867 2.106
68+
Onoue.Friberg 3.027 7.194 9.489
69+
dtat1000 0.214 0.024 14.430
6970
** found \donttest examples: check also with --run-donttest
7071
* checking for unstated dependencies in vignettes ... OK
7172
* checking package vignettes in 'inst/doc' ... OK
72-
* checking re-building of vignette outputs ... [49s/27s] OK
73+
* checking re-building of vignette outputs ... [55s/225s] OK
7374
* checking PDF version of manual ... OK
7475
* checking HTML version of manual ... OK
7576
* checking for non-standard things in the check directory ... OK

‎revdep/Outputs/check_circumstance_stderr.txt‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,7 @@
44
Comparing ‘pfilter.Rout’ to ‘pfilter.Rout.save’ ... OK
55
Running ‘plot_matrix.R’
66
Comparing ‘plot_matrix.Rout’ to ‘plot_matrix.Rout.save’ ... OK
7-
Running ‘pmcmc.R’ [13s/10s]
7+
Running ‘pmcmc.R’ [16s/11s]
88
Comparing ‘pmcmc.Rout’ to ‘pmcmc.Rout.save’ ... OK
99

1010

‎revdep/Outputs/check_circumstance_stdout.txt‎

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -1,10 +1,10 @@
11
* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/circumstance.Rcheck'
2-
* using R version 4.3.1 (2023-06-16)
2+
* using R version 4.3.2 (2023-10-31)
33
* using platform: x86_64-pc-linux-gnu (64-bit)
44
* R was compiled by
5-
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
6-
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
7-
* running under: Ubuntu 22.04.2 LTS
5+
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
6+
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
7+
* running under: Ubuntu 22.04.3 LTS
88
* using session charset: UTF-8
99
* using option '--as-cran'
1010
* checking for file 'circumstance/DESCRIPTION' ... OK
@@ -55,12 +55,12 @@
5555
* checking examples ... OK
5656
Examples with CPU (user + system) or elapsed time > 5s
5757
user system elapsed
58-
pfilter 5.598 0.288 4.562
58+
pfilter 6.056 0.405 5.267
5959
** found \donttest examples: check also with --run-donttest
6060
* checking for unstated dependencies in 'tests' ... OK
6161
* checking tests ...
62-
[42s/26s] OK
63-
* checking PDF version of manual ... OK
62+
[47s/28s] OK
63+
* checking PDF version of manual ... [7s/388s] OK
6464
* checking HTML version of manual ... OK
6565
* checking for non-standard things in the check directory ... OK
6666
* checking for detritus in the temp directory ... OK

‎revdep/Outputs/check_epimdr2_stdout.txt‎

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -1,10 +1,10 @@
11
* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/epimdr2.Rcheck'
2-
* using R version 4.3.1 (2023-06-16)
2+
* using R version 4.3.2 (2023-10-31)
33
* using platform: x86_64-pc-linux-gnu (64-bit)
44
* R was compiled by
5-
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
6-
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
7-
* running under: Ubuntu 22.04.2 LTS
5+
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
6+
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
7+
* running under: Ubuntu 22.04.3 LTS
88
* using session charset: UTF-8
99
* using option '--as-cran'
1010
* checking for file 'epimdr2/DESCRIPTION' ... OK
@@ -18,7 +18,7 @@
1818
* checking for hidden files and directories ... OK
1919
* checking for portable file names ... OK
2020
* checking for sufficient/correct file permissions ... OK
21-
* checking whether package 'epimdr2' can be installed ... [27s/16s] OK
21+
* checking whether package 'epimdr2' can be installed ... [34s/19s] OK
2222
* checking installed package size ... OK
2323
* checking package directory ... OK
2424
* checking for future file timestamps ... OK
@@ -40,7 +40,7 @@
4040
* checking S3 generic/method consistency ... OK
4141
* checking replacement functions ... OK
4242
* checking foreign function calls ... OK
43-
* checking R code for possible problems ... [54s/12s] NOTE
43+
* checking R code for possible problems ... [52s/12s] NOTE
4444
coyne: local variable ‘H1’ assigned but may not be used
4545
coyne: local variable ‘H2’ assigned but may not be used
4646
coyne: local variable ‘I’ assigned but may not be used
@@ -152,9 +152,9 @@ twostrain: local variable ‘res’ assigned but may not be used
152152
* checking data for non-ASCII characters ... OK
153153
* checking LazyData ... OK
154154
* checking data for ASCII and uncompressed saves ... OK
155-
* checking examples ... [20s/11s] OK
155+
* checking examples ... [20s/53s] OK
156156
** found \donttest examples: check also with --run-donttest
157-
* checking PDF version of manual ... OK
157+
* checking PDF version of manual ... [12s/335s] OK
158158
* checking HTML version of manual ... OK
159159
* checking for non-standard things in the check directory ... OK
160160
* checking for detritus in the temp directory ... OK

‎revdep/Outputs/check_epimdr_stdout.txt‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
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* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/epimdr.Rcheck'
2-
* using R version 4.3.1 (2023-06-16)
2+
* using R version 4.3.2 (2023-10-31)
33
* using platform: x86_64-pc-linux-gnu (64-bit)
44
* R was compiled by
5-
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
6-
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
7-
* running under: Ubuntu 22.04.2 LTS
5+
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
6+
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
7+
* running under: Ubuntu 22.04.3 LTS
88
* using session charset: UTF-8
99
* using option '--as-cran'
1010
* checking for file 'epimdr/DESCRIPTION' ... OK
@@ -19,7 +19,7 @@
1919
* checking for portable file names ... OK
2020
* checking for sufficient/correct file permissions ... OK
2121
* checking serialization versions ... OK
22-
* checking whether package 'epimdr' can be installed ... [22s/12s] OK
22+
* checking whether package 'epimdr' can be installed ... [27s/14s] OK
2323
* checking installed package size ... OK
2424
* checking package directory ... OK
2525
* checking for future file timestamps ... OK

‎revdep/Outputs/check_hte_stderr.txt‎

Lines changed: 6 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,10 @@
1-
Running ‘fakery.R’ [16s/13s]
2-
Comparing ‘fakery.Rout’ to ‘fakery.Rout.save’ ... OK
3-
Running ‘filter.R’
4-
Comparing ‘filter.Rout’ to ‘filter.Rout.save’ ... OK
5-
Running ‘indep.R’
6-
Comparing ‘indep.Rout’ to ‘indep.Rout.save’ ... OK
7-
Running ‘stobfun.R’
1+
Running ‘fakery.R’ [16s/38s]
2+
Comparing ‘fakery.Rout’ to ‘fakery.Rout.save’ ... Running ‘filter.R’
3+
Comparing ‘filter.Rout’ to ‘filter.Rout.save’ ... Running ‘indep.R’ [9s/10s]
4+
Comparing ‘indep.Rout’ to ‘indep.Rout.save’ ... Running ‘stobfun.R’ [6s/19s]
85
Comparing ‘stobfun.Rout’ to ‘stobfun.Rout.save’ ... OK
9-
Running ‘transmiss.R’ [27s/22s]
10-
Comparing ‘transmiss.Rout’ to ‘transmiss.Rout.save’ ... OK
11-
6+
Running ‘transmiss.R’ [26s/28s]
7+
Comparing ‘transmiss.Rout’ to ‘transmiss.Rout.save’ ...
128
See
139
'/userdata/kingaa/projects/Rpkg/pomp/revdep/hte.Rcheck/00check.log'
1410
for details.

‎revdep/Outputs/check_hte_stdout.txt‎

Lines changed: 60 additions & 11 deletions
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11
* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/hte.Rcheck'
2-
* using R version 4.3.1 (2023-06-16)
2+
* using R version 4.3.2 (2023-10-31)
33
* using platform: x86_64-pc-linux-gnu (64-bit)
44
* R was compiled by
5-
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
6-
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
7-
* running under: Ubuntu 22.04.2 LTS
5+
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
6+
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
7+
* running under: Ubuntu 22.04.3 LTS
88
* using session charset: UTF-8
99
* using option '--as-cran'
1010
* checking for file 'hte/DESCRIPTION' ... OK
@@ -20,7 +20,7 @@
2020
* checking for portable file names ... OK
2121
* checking for sufficient/correct file permissions ... OK
2222
* checking whether package 'hte' can be installed ... OK
23-
* used C compiler: 'gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0'
23+
* used C compiler: 'gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0'
2424
* checking installed package size ... OK
2525
* checking package directory ... OK
2626
* checking for future file timestamps ... OK
@@ -64,15 +64,64 @@ stobfun : ofun: local variable ‘theta’ assigned but may not be used
6464
* checking compilation flags used ... OK
6565
* checking compiled code ... OK
6666
* checking installed files from 'inst/doc' ... OK
67-
* checking examples ... [237s/34s] OK
67+
* checking examples ... [266s/54s] OK
6868
Examples with CPU (user + system) or elapsed time > 5s
69-
user system elapsed
70-
fake_data 29.910 85.907 11.964
71-
simuldat 27.004 81.279 10.529
69+
user system elapsed
70+
fake_data 33.445 103.801 13.000
71+
simuldat 27.836 87.526 9.747
72+
transmission 2.196 0.051 12.139
7273
* checking for unstated dependencies in 'tests' ... OK
7374
* checking tests ...
74-
[67s/46s] OK
75-
* checking PDF version of manual ... OK
75+
5,9c5,9
76+
< ✔ dplyr 1.1.4 ✔ readr 2.1.4
77+
< ✔ forcats 1.0.0 ✔ stringr 1.5.1
78+
< ✔ ggplot2 3.4.4 ✔ tibble 3.2.1
79+
< ✔ lubridate 1.9.3 ✔ tidyr 1.3.0
80+
< ✔ purrr 1.0.2
81+
---
82+
> ✔ dplyr 1.1.2 ✔ readr 2.1.4
83+
> ✔ forcats 1.0.0 ✔ stringr 1.5.0
84+
> ✔ ggplot2 3.4.2 ✔ tibble 3.2.1
85+
> ✔ lubridate 1.9.2 ✔ tidyr 1.3.0
86+
> ✔ purrr 1.0.1
87+
5,9c5,9
88+
< ✔ dplyr 1.1.4 ✔ readr 2.1.4
89+
< ✔ forcats 1.0.0 ✔ stringr 1.5.1
90+
< ✔ ggplot2 3.4.4 ✔ tibble 3.2.1
91+
< ✔ lubridate 1.9.3 ✔ tidyr 1.3.0
92+
< ✔ purrr 1.0.2
93+
---
94+
> ✔ dplyr 1.1.2 ✔ readr 2.1.4
95+
> ✔ forcats 1.0.0 ✔ stringr 1.5.0
96+
> ✔ ggplot2 3.4.2 ✔ tibble 3.2.1
97+
> ✔ lubridate 1.9.2 ✔ tidyr 1.3.0
98+
> ✔ purrr 1.0.1
99+
5,9c5,9
100+
< ✔ dplyr 1.1.4 ✔ readr 2.1.4
101+
< ✔ forcats 1.0.0 ✔ stringr 1.5.1
102+
< ✔ ggplot2 3.4.4 ✔ tibble 3.2.1
103+
< ✔ lubridate 1.9.3 ✔ tidyr 1.3.0
104+
< ✔ purrr 1.0.2
105+
---
106+
> ✔ dplyr 1.1.2 ✔ readr 2.1.4
107+
> ✔ forcats 1.0.0 ✔ stringr 1.5.0
108+
> ✔ ggplot2 3.4.2 ✔ tibble 3.2.1
109+
> ✔ lubridate 1.9.2 ✔ tidyr 1.3.0
110+
> ✔ purrr 1.0.1
111+
5,9c5,9
112+
< ✔ dplyr 1.1.4 ✔ readr 2.1.4
113+
< ✔ forcats 1.0.0 ✔ stringr 1.5.1
114+
< ✔ ggplot2 3.4.4 ✔ tibble 3.2.1
115+
< ✔ lubridate 1.9.3 ✔ tidyr 1.3.0
116+
< ✔ purrr 1.0.2
117+
---
118+
> ✔ dplyr 1.1.2 ✔ readr 2.1.4
119+
> ✔ forcats 1.0.0 ✔ stringr 1.5.0
120+
> ✔ ggplot2 3.4.2 ✔ tibble 3.2.1
121+
> ✔ lubridate 1.9.2 ✔ tidyr 1.3.0
122+
> ✔ purrr 1.0.1
123+
[71s/107s] OK
124+
* checking PDF version of manual ... [11s/236s] OK
76125
* checking HTML version of manual ... OK
77126
* checking for non-standard things in the check directory ... OK
78127
* checking for detritus in the temp directory ... OK

‎revdep/Outputs/check_panelPomp_stderr.txt‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -9,10 +9,10 @@
99
Comparing ‘mif2.Rout’ to ‘mif2.Rout.save’ ... OK
1010
Running ‘mif2_intern.R’
1111
Comparing ‘mif2_intern.Rout’ to ‘mif2_intern.Rout.save’ ... OK
12-
Running ‘mif2_methods.R’
12+
Running ‘mif2_methods.R’ [15s/25s]
1313
Comparing ‘mif2_methods.Rout’ to ‘mif2_methods.Rout.save’ ... OK
1414
Running ‘panelGompertz.R’
15-
Comparing ‘panelGompertz.Rout’ to ‘panelGompertz.Rout.save’ ... Running ‘panelGompertzLikelihood.R’
15+
Comparing ‘panelGompertz.Rout’ to ‘panelGompertz.Rout.save’ ... Running ‘panelGompertzLikelihood.R’ [17s/17s]
1616
Comparing ‘panelGompertzLikelihood.Rout’ to ‘panelGompertzLikelihood.Rout.save’ ... OK
1717
Running ‘panelPomp.R’
1818
Comparing ‘panelPomp.Rout’ to ‘panelPomp.Rout.save’ ... OK
@@ -32,6 +32,6 @@
3232
Running ‘print-results.R’
3333
Comparing ‘print-results.Rout’ to ‘print-results.Rout.save’ ... Running ‘seeded-results.R’
3434
Comparing ‘seeded-results.Rout’ to ‘seeded-results.Rout.save’ ... OK
35-
Running ‘simulate.R’
35+
Running ‘simulate.R’ [16s/13s]
3636
Comparing ‘simulate.Rout’ to ‘simulate.Rout.save’ ...
3737

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