- using R Under development (unstable) (2024-08-16 r87026)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-14 (Debian 14.2.0-1) 14.2.0
GNU Fortran (Debian 14.2.0-1) 14.2.0
- running under: Debian GNU/Linux trixie/sid
- using session charset: UTF-8
- checking for file ‘panelPomp/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘panelPomp’ version ‘1.1’
- 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 ‘panelPomp’ can be installed ... OK
See the install log for details.
- 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 ... [1s/1s] OK
- checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
- checking whether the package can be unloaded cleanly ... [1s/1s] OK
- checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
- checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
- checking loading without being on the library search path ... [1s/1s] 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 ... [6s/8s] OK
- checking Rd files ... [0s/1s] OK
- checking Rd metadata ... OK
- checking Rd line widths ... OK
- checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
mif2.Rd: mif2,pomp-method
panelPomp-package.Rd: pomp-package
panelPomp.Rd: pomp
pfilter.Rd: pfilter,pomp-method
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
- 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 examples ... [6s/9s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [33s/44s] OK
Running ‘_options.R’ [1s/1s]
Comparing ‘_options.Rout’ to ‘_options.Rout.save’ ... OK
Running ‘aaa.R’ [1s/1s]
Comparing ‘aaa.Rout’ to ‘aaa.Rout.save’ ... OK
Running ‘contacts.R’ [8s/10s]
Comparing ‘contacts.Rout’ to ‘contacts.Rout.save’ ...14c14
< name [,1] [,2] [,3] [,4]
---
> variable [,1] [,2] [,3] [,4]
17c17
< name [,1] [,2] [,3] [,4]
---
> variable [,1] [,2] [,3] [,4]
Running ‘get_col_row.R’ [1s/1s]
Comparing ‘get_col_row.Rout’ to ‘get_col_row.Rout.save’ ... OK
Running ‘mif2.R’ [1s/2s]
Comparing ‘mif2.Rout’ to ‘mif2.Rout.save’ ... OK
Running ‘mif2_intern.R’ [2s/2s]
Comparing ‘mif2_intern.Rout’ to ‘mif2_intern.Rout.save’ ... OK
Running ‘mif2_methods.R’ [1s/2s]
Comparing ‘mif2_methods.Rout’ to ‘mif2_methods.Rout.save’ ... OK
Running ‘panelGompertz.R’ [1s/2s]
Comparing ‘panelGompertz.Rout’ to ‘panelGompertz.Rout.save’ ...14c14
< name [,1] [,2] [,3] [,4] [,5]
---
> variable [,1] [,2] [,3] [,4] [,5]
17c17
< name [,1] [,2] [,3] [,4] [,5]
---
> variable [,1] [,2] [,3] [,4] [,5]
Running ‘panelGompertzLikelihood.R’ [2s/2s]
Comparing ‘panelGompertzLikelihood.Rout’ to ‘panelGompertzLikelihood.Rout.save’ ... OK
Running ‘panelPomp.R’ [2s/2s]
Comparing ‘panelPomp.Rout’ to ‘panelPomp.Rout.save’ ... OK
Running ‘panelPomp_methods.R’ [2s/2s]
Comparing ‘panelPomp_methods.Rout’ to ‘panelPomp_methods.Rout.save’ ... OK
Running ‘panelRandomWalk.R’ [1s/2s]
Comparing ‘panelRandomWalk.Rout’ to ‘panelRandomWalk.Rout.save’ ...14c14
< name [,1] [,2] [,3] [,4] [,5]
---
> variable [,1] [,2] [,3] [,4] [,5]
17c17
< name [,1] [,2] [,3] [,4] [,5]
---
> variable [,1] [,2] [,3] [,4] [,5]
Running ‘panel_loglik.R’ [1s/1s]
Comparing ‘panel_loglik.Rout’ to ‘panel_loglik.Rout.save’ ... OK
Running ‘params.R’ [1s/2s]
Comparing ‘params.Rout’ to ‘params.Rout.save’ ... OK
Running ‘pfilter.R’ [2s/3s]
Comparing ‘pfilter.Rout’ to ‘pfilter.Rout.save’ ... OK
Running ‘pfilter_methods.R’ [1s/2s]
Comparing ‘pfilter_methods.Rout’ to ‘pfilter_methods.Rout.save’ ... OK
Running ‘plot.R’ [1s/2s]
Comparing ‘plot.Rout’ to ‘plot.Rout.save’ ... OK
Running ‘print-results.R’ [1s/2s]
Comparing ‘print-results.Rout’ to ‘print-results.Rout.save’ ...26c26
< name [,1] [,2] [,3] [,4] [,5] [,6]
---
> variable [,1] [,2] [,3] [,4] [,5] [,6]
31c31
< name [,1] [,2] [,3] [,4] [,5] [,6]
---
> variable [,1] [,2] [,3] [,4] [,5] [,6]
Running ‘seeded-results.R’ [2s/2s]
Comparing ‘seeded-results.Rout’ to ‘seeded-results.Rout.save’ ... OK
Running ‘simulate.R’ [1s/2s]
Comparing ‘simulate.Rout’ to ‘simulate.Rout.save’ ...11c11
< name [,1] [,2] [,3] [,4] [,5]
---
> variable [,1] [,2] [,3] [,4] [,5]
- checking PDF version of manual ... [4s/6s] OK
- checking HTML version of manual ... [1s/1s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 1 NOTE