R CMD Check issues

[bc]

checking Rd files ... WARNING

• checkRd: (5) fill_force_velocity_metrics.Rd:0-16: Must have a \description
• checkRd: (5) first_rowname.Rd:0-14: Must have a \description
• checkRd: (5) last_rowname.Rd:0-14: Must have a \description
• checkRd: (5) list_of_forces_to_stabilized_df.Rd:0-17: Must have a \description
• checkRd: (5) list_of_postures_of_forces_to_stabilized_df.Rd:0-18: Must have a \description
• checkRd: (5) save_rds_to_Resilio.Rd:0-16: Must have a \description
• checkRd: (5) save_rds_to_package_extdata.Rd:0-15: Must have a \description

checking Rd \usage sections ... WARNING

• Undocumented arguments in documentation object 'ForceTrial'
  ‘full_df’ ‘muscle_of_interest’ ‘muscles_of_interest’

• Documented arguments not in \usage in documentation object 'ForceTrial':
  ‘adept_x’ ‘adept_y’

• Undocumented arguments in documentation object 'abs_value_delta_force_scatter'
  ‘stability_df’ ‘pointsize’

• Documented arguments not in \usage in documentation object 'abs_value_delta_force_scatter':
  ‘settling’
  ... 198 lines ...

• Undocumented arguments in documentation object 'xyz_points_with_convhull'
  ‘...’

• Undocumented arguments in documentation object 'zero_and_coord_translate_JR3_z_and_trim_startup_parts'
  ‘JR3_to_fingertip_distance’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.

checking package dependencies ... NOTE

• Depends: includes the non-default packages:
  ‘testthat’ ‘devtools’ ‘ggplot2’ ‘parallel’ ‘roxygen2’ ‘xml2’
  ‘caTools’ ‘WVPlots’ ‘GGally’ ‘plotrix’ ‘scatterplot3d’
  ‘microbenchmark’ ‘data.table’ ‘pbmcapply’ ‘hitandrun’ ‘pbapply’ ‘rgl’
  ‘geometry’ ‘covr’
  Adding so many packages to the search path is excessive and importing
  selectively is preferable.

checking for hidden files and directories ... NOTE

• ADD COVERALLS TO BUILDIGNORE and rm .RDATA Found the following hidden files and directories:
  .coveralls.yml
  tests/testthat/.RData
  These were most likely included in error. See section ‘Package
  structure’ in the ‘Writing R Extensions’ manual.

checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.

• Non-standard license specification:
  USC
  Standardizable: FALSE
• Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘covr’
  A package should be listed in only one of these fields.

checking top-level files ... NOTE
Non-standard files/directories found at top level:

• ‘cohn_jr3_sysid.pages’
• ‘histogram_by_muscle_projections_over_5_tasks.pdf’
• ‘jr3_id_cohn2017.pdf’ ‘jr3_id_cohn2017_lores.pdf’
• ‘jr3_test_no_input.csv’ ‘plot.pdf’

checking R code for possible problems ... NOTE

• generate_parcoord_plot: warning in
  ggparcoord(dataframe_of_observations, scale = "globalminmax", alpha =
  1, boxplot = FALSE, mapping = ggplot2::aes(colour = "midnightblue")):
  partial argument match of 'alpha' to 'alphaLines'
• main: warning in postures_grouped_by_line(unique_postures, x_fixed_val
  = -525, y_fixed_val = 68): partial argument match of 'x_fixed_val' to
  'x_fixed_value'
• main: warning in postures_grouped_by_line(unique_postures, x_fixed_val
  = -525, y_fixed_val = 68): partial argument match of 'y_fixed_val' to
  ... 369 lines ...
  segments3d setNames setattr settling_time signed_max_residual
  stat_binhex static_force_df tail text theme theme_bw time title
  vaf_fx vaf_fy vaf_fz var write.csv xlab xlim ylab ylim
• Consider adding
  importFrom("grDevices", "as.raster", "colorRampPalette")
  importFrom("graphics", "abline", "axis", "box", "hist", "lines", "par",
  "plot", "plot.new", "plot.window", "points", "rasterImage",
  "segments", "text", "title")
  importFrom("stats", "median", "runif", "sd", "setNames", "time", "var")
  importFrom("utils", "head", "tail", "write.csv")
  to your NAMESPACE file.

checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘Matrix’
'library' or 'require' call not declared from: ‘gridExtra’
'library' or 'require' calls to packages already attached by Depends:
‘ggplot2’ ‘microbenchmark’
Please remove these calls from your code.
'library' or 'require' call to ‘gridExtra’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.

• Packages in Depends field not imported from:
  ‘caTools’ ‘covr’ ‘data.table’ ‘devtools’ ‘ggplot2’ ‘microbenchmark’
  ‘roxygen2’ ‘testthat’ ‘xml2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
  ':::' call which should be '::': ‘Matrix:::rankMatrix’
  See the note in ?::: about the use of this operator.