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RHmm log file (check_x86_64_linux)

Wed Jan 31 09:25:08 2024: Checking package RHmm (SVN revision 451) ...
* using log directory ‘/srv/rf/building/build_2024-01-31-09-24/RF_PKG_CHECK/PKGS/RHmm.Rcheck’
* using R version 4.3.2 Patched (2024-01-28 r85838)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Debian 12.2.0-14) 12.2.0
    GNU Fortran (Debian 12.2.0-14) 12.2.0
* running under: Debian GNU/Linux 12 (bookworm)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘RHmm/DESCRIPTION’ ... OK
* this is package ‘RHmm’ version ‘2.2.0’
* checking CRAN incoming feasibility ... [4s/8s] NOTE
Maintainer: ‘Ollivier TARAMASCO Developer ’

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://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

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

The Date field is over a month old.
* 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 ‘RHmm’ can be installed ... [26s/26s] OK
* used C++ compiler: ‘g++ (Debian 12.2.0-14) 12.2.0’
* 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [8s/8s] 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 ... [0s/0s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] 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 ... WARNING
File ‘RHmm/libs/RHmm.so’:
  Found ‘sprintf’, possibly from ‘sprintf’ (C)
    Object: ‘cRUtils.o’
File ‘RHmm/libs/RHmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf.
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 ... [4s/4s] OK
* checking PDF version of manual ... [5s/5s] OK
* checking HTML version of manual ... [0s/0s] NOTE
Skipping checking HTML validation: no command 'tidy' found
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 2 WARNINGs, 3 NOTEs
See
  ‘/srv/rf/building/build_2024-01-31-09-24/RF_PKG_CHECK/PKGS/RHmm.Rcheck/00check.log’
for details.


Run time: 64.73 seconds.
Additional Logs:   00install.out
Thanks to:
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