* using log directory '/userdata/kingaa/projects/Rpkg/pomp/revdep/CollocInfer.Rcheck'
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* using option '--as-cran'
* checking for file 'CollocInfer/DESCRIPTION' ... OK
* this is package 'CollocInfer' version '1.0.4'
* 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 serialization versions ... OK
* checking whether package 'CollocInfer' can be installed ... [34s/20s] 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 R 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 ... [67s/22s] 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 ... WARNING
Variables with usage in documentation object 'FhNest' but not in code:
  ‘FhNest’

* 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  13.898 47.310   1.045
FitMatch  3.457  7.528   0.215
* 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 WARNING, 1 NOTE
