* using log directory '/home/kingaa/projects/Rpkg/subplex/revdep/hisse.Rcheck'
* using R version 4.2.2 (2022-10-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option '--as-cran'
* checking for file 'hisse/DESCRIPTION' ... OK
* this is package 'hisse' version '2.1.11'
* 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 'hisse' can be installed ... [57s/72s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking 'build' directory ... 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 ... [97s/176s] NOTE
AdaptiveConfidenceIntervalSampling.old: local variable ‘actual.params’
  assigned but may not be used
AdaptiveConfidenceIntervalSamplingGeoHiSSE: local variable
  ‘actual.params’ assigned but may not be used
AdaptiveConfidenceIntervalSamplingGeoHiSSE.old: local variable
  ‘actual.params’ assigned but may not be used
AdaptiveConfidenceIntervalSamplingMiSSE: local variable ‘actual.params’
  assigned but may not be used
AdaptiveConfidenceIntervalSamplingMuHiSSE: local variable
  ‘actual.params’ assigned but may not be used
AdaptiveConfidenceIntervalSamplingfHiSSE: local variable
  ‘actual.params’ assigned but may not be used
AddKNodes: local variable ‘ntip’ assigned but may not be used
DownPass: local variable ‘TIPS’ assigned but may not be used
DownPassGeoHisse: local variable ‘TIPS’ assigned but may not be used
DownPassGeoHissefast: local variable ‘compE’ assigned but may not be
  used
DownPassGeoHissefast: local variable ‘nb.node’ assigned but may not be
  used
DownPassHiSSE: local variable ‘.’ assigned but may not be used
DownPassHiSSE: local variable ‘compE’ assigned but may not be used
DownPassMisse: local variable ‘.’ assigned but may not be used
DownPassMisse: local variable ‘compE’ assigned but may not be used
DownPassMuHisse: local variable ‘.’ assigned but may not be used
DownPassMuHisse: local variable ‘compE’ assigned but may not be used
DownPassMusse: local variable ‘TIPS’ assigned but may not be used
DownPassNull: local variable ‘TIPS’ assigned but may not be used
GeoHiSSE: local variable ‘category.rates.unique’ assigned but may not
  be used
GeoHiSSE.old: local variable ‘category.rates.unique’ assigned but may
  not be used
GetEdgeCombined: local variable ‘extinct_taxa_indices’ assigned but may
  not be used
GetEdgeDetails: local variable ‘tipwards_nodes_of_rootwards_nodes’
  assigned but may not be used
GetRootProb: local variable ‘.’ assigned but may not be used
GetRootProbGeo: local variable ‘.’ assigned but may not be used
GetRootProbHiSSE: local variable ‘.’ assigned but may not be used
GetTreeTable: local variable ‘max.age’ assigned but may not be used
MarginRecon.old: local variable ‘nodes’ assigned but may not be used
MarginReconGeoSSE: local variable ‘nstates’ assigned but may not be
  used
MarginReconGeoSSE.old: local variable ‘nodes’ assigned but may not be
  used
MarginReconHiSSE: local variable ‘nstates’ assigned but may not be used
MarginReconMiSSE: local variable ‘nstates’ assigned but may not be used
MarginReconMuHiSSE: local variable ‘nstates’ assigned but may not be
  used
MuHiSSE: local variable ‘category.rates.unique’ assigned but may not be
  used
MuHiSSE: local variable ‘sann.counts’ assigned but may not be used
OrganizeData: local variable ‘nb.node’ assigned but may not be used
OrganizeDataGeo: local variable ‘nb.node’ assigned but may not be used
OrganizeDataHiSSE: local variable ‘cols’ assigned but may not be used
OrganizeDataHiSSE: local variable ‘nb.node’ assigned but may not be
  used
OrganizeDataMiSSE: local variable ‘nb.node’ assigned but may not be
  used
RerunBadOptim: local variable ‘current.fit’ assigned but may not be
  used
SupportRegion.old: local variable ‘free.parameters’ assigned but may
  not be used
SupportRegionGeoSSE: local variable ‘free.parameters’ assigned but may
  not be used
SupportRegionGeoSSE.old: local variable ‘free.parameters’ assigned but
  may not be used
SupportRegionHiSSE: local variable ‘free.parameters’ assigned but may
  not be used
SupportRegionMiSSE: local variable ‘free.parameters’ assigned but may
  not be used
SupportRegionMuHiSSE: local variable ‘free.parameters’ assigned but may
  not be used
hisse: local variable ‘category.rates.unique’ assigned but may not be
  used
makeGeoHiSSELikelihood: local variable ‘category.rates.unique’ assigned
  but may not be used
makeHiSSELikelihood: local variable ‘pars.full’ assigned but may not be
  used
makeHiSSELikelihood: local variable ‘samp.freq.tree’ assigned but may
  not be used
plot.contMapHisse: local variable ‘H’ assigned but may not be used
plot.contMapHisse: local variable ‘N’ assigned but may not be used
plot.contMapHisse: local variable ‘set.null’ assigned but may not be
  used
plotFanHiSSE: local variable ‘ptreeB’ assigned but may not be used
plotPhylogramHiSSE: local variable ‘ptreeB’ assigned but may not be
  used
plotSimmapHiSSE: local variable ‘set.null’ 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
** found \donttest examples: check also with --run-donttest
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... [76s/114s] 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: 1 NOTE
