Assessing package's state

I have ran devtools::check() on the package and will be using this issue to track my progress on fixing all checks issues
── R CMD check ─────────────────────────────────────────────────────────────────
─  using log directory ‘/home/vlucet/Documents/ECCC/dwsR.Rcheck’
─  using R version 4.1.0 (2021-05-18)
─  using platform: x86_64-pc-linux-gnu (64-bit)
─  using session charset: UTF-8
─  using options ‘--no-manual --as-cran’
✓  checking for file ‘dwsR/DESCRIPTION’
─  checking extension type ... Package
─  this is package ‘dwsR’ version ‘0.0.0.1’
✓  checking package namespace information ...
✓  checking package dependencies (3.6s)
✓  checking if this is a source package
✓  checking if there is a namespace
✓  checking for executable files ...
✓  checking for hidden files and directories
✓  checking for portable file names
✓  checking for sufficient/correct file permissions
✓  checking serialization versions
✓  checking whether package ‘dwsR’ can be installed (1m 7.4s)
N  checking installed package size
     installed size is 19.9Mb
     sub-directories of 1Mb or more:
       libs  19.7Mb
✓  checking package directory ...
✓  checking for future file timestamps (415ms)
✓  checking DESCRIPTION meta-information ...
✓  checking top-level files
✓  checking for left-over files
✓  checking index information
✓  checking package subdirectories ...
✓  checking R files for non-ASCII characters ...
✓  checking R files for syntax errors ...
✓  checking whether the package can be loaded ...
✓  checking whether the package can be loaded with stated dependencies ...
✓  checking whether the package can be unloaded cleanly ...
✓  checking whether the namespace can be loaded with stated dependencies ...
✓  checking whether the namespace can be unloaded cleanly ...
✓  checking loading without being on the library search path ...
W  checking dependencies in R code ...
   '::' or ':::' import not declared from: ‘starsExtra’
   'loadNamespace' or 'requireNamespace' call not declared from: ‘starsExtra’
✓  checking S3 generic/method consistency (365ms)
✓  checking replacement functions ...
✓  checking foreign function calls ...
N  checking R code for possible problems (2.2s)
   .gaussian_strip_confidence: no visible global function definition for
     ‘qnorm’
   .gaussian_strip_radious: no visible global function definition for
     ‘pnorm’
   .p_focal_r: no visible binding for global variable ‘k’
   pFocal: no visible global function definition for ‘is’
   pFocal.stars: no visible global function definition for
     ‘layer_to_matrix’
   Undefined global functions or variables:
     is k layer_to_matrix pnorm qnorm
   Consider adding
     importFrom("methods", "is")
     importFrom("stats", "pnorm", "qnorm")
   to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
   contains 'methods').
✓  checking Rd files ...
✓  checking Rd metadata ...
✓  checking Rd line widths ...
✓  checking Rd cross-references ...
W  checking for missing documentation entries ...
   Undocumented code objects:
     ‘binomial_kernel’ ‘chebyshev_distance_kernel’ ‘distance_kernel’
     ‘euclidean_distance_kernel’ ‘exponential_kernel’
     ‘fast_abs_rectangle_pFocal’ ‘fast_binomial_pFocal’
     ‘fast_gaussian_confidence_pFocal’ ‘fast_gaussian_radious_pFocal’
     ‘fast_seperated_pFocal’ ‘gaussian_kernel_confidence’
     ‘gaussian_kernel_radious’ ‘hard_uniform_circle_kernel’
     ‘horizontal_distance_kernel’ ‘kernel_flip_both’
     ‘kernel_flip_horizontal’ ‘kernel_flip_vertical’
     ‘manhattan_distance_kernel’ ‘minkowski_distance_kernel’
     ‘normalize_kernel’ ‘pFocal’ ‘pFocal.matrix’ ‘pFocal.stars’
     ‘pFocal_compare’ ‘pFocal_compare_sweep’ ‘pFocal_mean_divisor_info’
     ‘pFocal_nan_policy_info’ ‘pFocal_narrow_mean_divisor’
     ‘pFocal_narrow_nan_policy’ ‘pFocal_narrow_reduce’
     ‘pFocal_narrow_transform’ ‘pFocal_narrow_variance’
     ‘pFocal_reduce_info’ ‘pFocal_transform_info’ ‘pFocal_variance_info’
     ‘smooth_uniform_circle_kernel’ ‘vertical_distance_kernel’
   All user-level objects in a package should have documentation entries.
   See chapter ‘Writing R documentation files’ in the ‘Writing R
   Extensions’ manual.
W  checking for code/documentation mismatches ...
   Functions or methods with usage in documentation object 'rcpp_hello_world' but not in code:
     ‘rcpp_hello_world’

✓  checking Rd \usage sections (796ms)
✓  checking Rd contents ...
✓  checking for unstated dependencies in examples ...
✓  checking line endings in C/C++/Fortran sources/headers
✓  checking line endings in Makefiles
W  checking compilation flags in Makevars ...
   Non-portable flags in variable 'PKG_CPPFLAGS':
     -fopenmp
✓  checking for GNU extensions in Makefiles
✓  checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS)
✓  checking use of PKG_*FLAGS in Makefiles ...
✓  checking use of SHLIB_OPENMP_*FLAGS in Makefiles
✓  checking pragmas in C/C++ headers and code ...
✓  checking compilation flags used
W  checking compiled code ...
   File ‘dwsR/libs/dwsR.so’:
     Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
       Object: ‘p_focal.o’
     Found ‘exit’, possibly from ‘exit’ (C)
       Object: ‘p_focal.o’

   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.

   See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
✓  checking examples (411ms)
✓  checking for unstated dependencies in ‘tests’ ...
─  checking tests ...
✓  Running ‘testthat.R’ (363ms)
✓  checking for non-standard things in the check directory (366ms)
✓  checking for detritus in the temp directory

   See
     ‘/home/vlucet/Documents/ECCC/dwsR.Rcheck/00check.log’
   for details.

── R CMD check results ─────────────────────────────────────── dwsR 0.0.0.1 ────
Duration: 1m 18.6s

> checking dependencies in R code ... WARNING
  '::' or ':::' import not declared from: ‘starsExtra’
  'loadNamespace' or 'requireNamespace' call not declared from: ‘starsExtra’

> checking for missing documentation entries ... WARNING
  Undocumented code objects:
    ‘binomial_kernel’ ‘chebyshev_distance_kernel’ ‘distance_kernel’
    ‘euclidean_distance_kernel’ ‘exponential_kernel’
    ‘fast_abs_rectangle_pFocal’ ‘fast_binomial_pFocal’
    ‘fast_gaussian_confidence_pFocal’ ‘fast_gaussian_radious_pFocal’
    ‘fast_seperated_pFocal’ ‘gaussian_kernel_confidence’
    ‘gaussian_kernel_radious’ ‘hard_uniform_circle_kernel’
    ‘horizontal_distance_kernel’ ‘kernel_flip_both’
    ‘kernel_flip_horizontal’ ‘kernel_flip_vertical’
    ‘manhattan_distance_kernel’ ‘minkowski_distance_kernel’
    ‘normalize_kernel’ ‘pFocal’ ‘pFocal.matrix’ ‘pFocal.stars’
    ‘pFocal_compare’ ‘pFocal_compare_sweep’ ‘pFocal_mean_divisor_info’
    ‘pFocal_nan_policy_info’ ‘pFocal_narrow_mean_divisor’
    ‘pFocal_narrow_nan_policy’ ‘pFocal_narrow_reduce’
    ‘pFocal_narrow_transform’ ‘pFocal_narrow_variance’
    ‘pFocal_reduce_info’ ‘pFocal_transform_info’ ‘pFocal_variance_info’
    ‘smooth_uniform_circle_kernel’ ‘vertical_distance_kernel’
  All user-level objects in a package should have documentation entries.
  See chapter ‘Writing R documentation files’ in the ‘Writing R
  Extensions’ manual.

> checking for code/documentation mismatches ... WARNING
  Functions or methods with usage in documentation object 'rcpp_hello_world' but not in code:
    ‘rcpp_hello_world’

> checking compilation flags in Makevars ... WARNING
  Non-portable flags in variable 'PKG_CPPFLAGS':
    -fopenmp

> checking compiled code ... WARNING
  File ‘dwsR/libs/dwsR.so’:
    Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
      Object: ‘p_focal.o’
    Found ‘exit’, possibly from ‘exit’ (C)
      Object: ‘p_focal.o’

  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.

  See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.

> checking installed package size ... NOTE
    installed size is 19.9Mb
    sub-directories of 1Mb or more:
      libs  19.7Mb

> checking R code for possible problems ... NOTE
  .gaussian_strip_confidence: no visible global function definition for
    ‘qnorm’
  .gaussian_strip_radious: no visible global function definition for
    ‘pnorm’
  .p_focal_r: no visible binding for global variable ‘k’
  pFocal: no visible global function definition for ‘is’
  pFocal.stars: no visible global function definition for
    ‘layer_to_matrix’
  Undefined global functions or variables:
    is k layer_to_matrix pnorm qnorm
  Consider adding
    importFrom("methods", "is")
    importFrom("stats", "pnorm", "qnorm")
  to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
  contains 'methods').

0 errors ✓ | 5 warnings x | 2 notes x
Error: R CMD check found WARNINGs
Execution halted

Exited with status 1.
LandSciTech / pfocal

Assessing package's state #1
