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RHmm log file (check_x86_64_windows)

* using log directory 'R:/run/building/build_2024-06-29-10-04/RF_PKG_CHECK/PKGS/RHmm.Rcheck'
* using R version 4.4.1 Patched (2024-07-08 r86895 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows 10 x64 (build 19045)
* using session charset: UTF-8
* using option '--as-cran'
* checking for file 'RHmm/DESCRIPTION' ... OK
* this is package 'RHmm' version '2.2.1'
* checking CRAN incoming feasibility ... [16s] NOTE
Maintainer: 'Ollivier TARAMASCO '

New submission

Package was archived on CRAN

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2014-08-30 as new/delete mismatches were
    not corrected.

Found the following (possibly) invalid URLs:
  URL: http://r-forge.r-project.org/projects/rhmm/ (moved to https://r-forge.r-project.org/projects/rhmm/)
    From: DESCRIPTION
    Status: 200
    Message: OK
  URL: http://ssli.ee.washington.edu/people/bilmes/mypapers/em.ps.gz
    From: man/HMMFit.rd
          man/forwardBackward.rd
    Status: 404
    Message: Not Found
  URL: http://www.comp.leeds.ac.uk/roger/
    From: man/weather.rd
    Status: Error
    Message: libcurl error code 6:
      	Could not resolve host: engineering.leeds.ac.uk
  URL: http://www.cs.mu.oz.au/460/2004/materials/hmm-tutorial.pdf
    From: man/viterbi.rd
    Status: Error
    Message: libcurl error code 6:
      	Could not resolve host: www.cs.mu.oz.au
  URL: http://www.r-project.org
    From: DESCRIPTION
    Status: 200
    Message: OK
    R-project URL not in canonical form
  Canonical www.R-project.org URLs use https.

No package encoding and non-ASCII characters in the following R files:
  R/RHmm-HyperNew.R
    12: # Contraintes sur les paramtres

The Title field should be in title case. Current version is:
'Hidden Markov Models simulations and estimations'
In title case that is:
'Hidden Markov Models Simulations and Estimations'
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking serialization versions ... OK
* checking whether package 'RHmm' can be installed ... [36s] OK
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... NOTE
Author field differs from that derived from Authors@R
  Author:    'Ollivier TARAMASCO, Sebastian BAUER'
  Authors@R: 'Ollivier TARAMASCO Developer [aut, cre], Sebastian BAUER Developer [aut]'

Maintainer field differs from that derived from Authors@R
  Maintainer: 'Ollivier TARAMASCO '
  Authors@R:  'Ollivier TARAMASCO Developer '

* 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 ... 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 ... [11s] NOTE
GraphicDiag.discreteClass: no visible global function definition for
  'split.screen'
GraphicDiag.discreteClass: no visible global function definition for
  'par'
GraphicDiag.discreteClass: no visible global function definition for
  'screen'
GraphicDiag.discreteClass: no visible global function definition for
  'lines'
GraphicDiag.discreteClass: no visible global function definition for
  'title'
GraphicDiag.discreteClass: no visible global function definition for
  'close.screen'
GraphicDiag.discreteClass: no visible global function definition for
  'dev.new'
GraphicDiag.distributionClass: no visible global function definition
  for 'colours'
GraphicDiag.mixtureUnivariateNormalClass: no visible global function
  definition for 'split.screen'
GraphicDiag.mixtureUnivariateNormalClass: no visible global function
  definition for 'par'
GraphicDiag.mixtureUnivariateNormalClass: no visible global function
  definition for 'screen'
GraphicDiag.mixtureUnivariateNormalClass: no visible global function
  definition for 'sd'
GraphicDiag.mixtureUnivariateNormalClass: no visible global function
  definition for 'density'
GraphicDiag.mixtureUnivariateNormalClass: no visible global function
  definition for 'lines'
GraphicDiag.mixtureUnivariateNormalClass: no visible global function
  definition for 'title'
GraphicDiag.mixtureUnivariateNormalClass: no visible global function
  definition for 'close.screen'
GraphicDiag.mixtureUnivariateNormalClass: no visible global function
  definition for 'dev.new'
GraphicDiag.univariateNormalClass: no visible global function
  definition for 'split.screen'
GraphicDiag.univariateNormalClass: no visible global function
  definition for 'par'
GraphicDiag.univariateNormalClass: no visible global function
  definition for 'screen'
GraphicDiag.univariateNormalClass: no visible global function
  definition for 'dnorm'
GraphicDiag.univariateNormalClass: no visible global function
  definition for 'density'
GraphicDiag.univariateNormalClass: no visible global function
  definition for 'lines'
GraphicDiag.univariateNormalClass: no visible global function
  definition for 'title'
GraphicDiag.univariateNormalClass: no visible global function
  definition for 'close.screen'
GraphicDiag.univariateNormalClass: no visible global function
  definition for 'dev.new'
HMMKMeans: no visible global function definition for 'kmeans'
HMMKMeans: no visible global function definition for 'cov'
HMMKMeans: no visible global function definition for 'var'
HMMPlotSerie: no visible global function definition for 'par'
HMMPlotSerie: no visible global function definition for 'split.screen'
HMMPlotSerie: no visible global function definition for 'screen'
HMMPlotSerie: no visible global function definition for 'title'
HMMPlotSerie: no visible global function definition for 'dev.new'
HMMPlotSerie: no visible global function definition for 'close.screen'
HMMPlotSerie: no visible global function definition for 'lines'
dmixt: no visible global function definition for 'dnorm'
plotSerie.distributionClass: no visible global function definition for
  'colours'
print.summary.HMMFitClass: no visible global function definition for
  'printCoefmat'
rdiscrete: no visible global function definition for 'runif'
rmixt: no visible global function definition for 'rnorm'
rmixt: no visible global function definition for 'runif'
rmultimixt: no visible global function definition for 'runif'
sim.markovChainClass: no visible global function definition for 'runif'
sim.univariateNormalClass: no visible global function definition for
  'rnorm'
summary.HMMFitClass: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  close.screen colours cov density dev.new dnorm kmeans lines par pnorm
  printCoefmat rnorm runif screen sd split.screen title var
Consider adding
  importFrom("grDevices", "colours", "dev.new")
  importFrom("graphics", "close.screen", "lines", "par", "screen",
             "split.screen", "title")
  importFrom("stats", "cov", "density", "dnorm", "kmeans", "pnorm",
             "printCoefmat", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.

Found if() conditions comparing class() to string:
File 'RHmm/R/RHmm-HyperNew.R': if ((class(HMM) != "HMMFitClass") && (class(HMM) != "HMMClass")) ...
File 'RHmm/R/RHmm-HyperNew.R': if (class(HMM) == "HMMFitClass") ...
File 'RHmm/R/RHmm-HyperNew.R': if ((class(HMM) != "HMMFitClass") && (class(HMM) != "HMMClass")) ...
File 'RHmm/R/RHmm-HyperNew.R': if (class(HMM) == "HMMFitClass") ...
File 'RHmm/R/RHmm-HyperNew.R': if ((class(HMM) != "HMMFitClass") && (class(HMM) != "HMMClass")) ...
File 'RHmm/R/RHmm-HyperNew.R': if (class(HMM) == "HMMFitClass") ...
File 'RHmm/R/RHmm-HyperNew.R': if ((class(HMMFit) != "HMMFitClass")) ...
File 'RHmm/R/RHmm.R': if (class(HMM) != "HMMClass") ...
File 'RHmm/R/RHmm.R': if (class(control$initPoint) != "HMMClass") ...
File 'RHmm/R/RHmm.R': if ((class(HMM) != "HMMFitClass") && (class(HMM) != "HMMClass")) ...
File 'RHmm/R/RHmm.R': if (class(HMM) == "HMMFitClass") ...
File 'RHmm/R/RHmm.R': if ((class(HMM) != "HMMFitClass") && (class(HMM) != "HMMClass")) ...
File 'RHmm/R/RHmm.R': if (class(HMM) == "HMMFitClass") ...
File 'RHmm/R/RHmm.R': if (class(vit) != "viterbiClass") ...
File 'RHmm/R/RHmm.R': if ((class(HMM) != "HMMClass") && (class(HMM) != "HMMFitClass") && is.na(match("distributionClass", class(HMM)))) ...
File 'RHmm/R/RHmm.R': if ((class(states) != "viterbiClass") && (!is_numeric_vector(states)) && (!is_list_numeric_vector(states))) ...
File 'RHmm/R/RHmm.R': if (class(states) == "viterbiClass") ...
Use inherits() (or maybe is()) instead.
* checking Rd files ... NOTE
checkRd: (-1) asymptoticIterSimCovMat.rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) asymptoticIterSimCovMat.rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) asymptoticIterSimCovMat.rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) asymptoticIterSimCovMat.rd:18: Lost braces in \itemize; meant \describe ?
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... WARNING
Non-portable flags in variable 'PKG_CXXFLAGS':
  -w
* 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 ... NOTE
File 'RHmm/libs/x64/RHmm.dll':
  Found no calls to: 'R_registerRoutines', 'R_useDynamicSymbols'

It is good practice to register native routines and to disable symbol
search.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking examples ... 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 WARNING, 5 NOTEs
See
  'R:/run/building/build_2024-06-29-10-04/RF_PKG_CHECK/PKGS/RHmm.Rcheck/00check.log'
for details.

Run time: 128.47 seconds.
Additional Logs:   00install.out
Thanks to:
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