+ )
Updating retina documentation
Loading retina
Loading required package: rgl
Loading required package: fields
Loading required package: spam
Loading required package: dotCall64
Loading required package: grid
Spam version 2.1-1 (2017-07-02) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.
Attaching package: ‘spam’
The following objects are masked from ‘package:base’:
backsolve, forwardsolve
Loading required package: maps
Loading required package: RColorBrewer
Loading required package: sphereplot
Loading required package: mapproj
Loading required package: retistruct
Loading required package: geometry
Loading required package: magic
Loading required package: abind
Warning: @todo [retina-package.r#251]: unknown tag
Writing assemble_markup_file.Rd
Setting env vars --------------------------------------------------------------
CFLAGS : -Wall -pedantic
CXXFLAGS: -Wall -pedantic
Building retina ---------------------------------------------------------------
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ \
--no-save --no-restore --quiet CMD build \
'/Users/briancohn/Documents/GitHub/briancohn/retina' --no-resave-data \
--no-manual
* checking for file ‘/Users/briancohn/Documents/GitHub/briancohn/retina/DESCRIPTION’ ... OK
* preparing ‘retina’:
* checking DESCRIPTION meta-information ... OK
* excluding invalid files
Subdirectory 'R' contains invalid file names:
‘development.md’
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘retina_2.0.1.tar.gz’
Setting env vars --------------------------------------------------------------
_R_CHECK_CRAN_INCOMING_ : FALSE
_R_CHECK_FORCE_SUGGESTS_: FALSE
Checking retina ---------------------------------------------------------------
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ \
--no-save --no-restore --quiet CMD check \
'/var/folders/vj/57777k0931s8txw12189jmhh0000gn/T//RtmpY0AUIv/retina_2.0.1.tar.gz' \
--as-cran --timings --no-manual
* using log directory ‘/private/var/folders/vj/57777k0931s8txw12189jmhh0000gn/T/RtmpY0AUIv/retina.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using options ‘--no-manual --as-cran’
* checking for file ‘retina/DESCRIPTION’ ... OK
* this is package ‘retina’ version ‘2.0.1’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘rgl’ ‘fields’ ‘RColorBrewer’ ‘sphereplot’ ‘mapproj’ ‘retistruct’
‘geometry’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 whether package ‘retina’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... WARNING
Demos with missing or empty index information:
batch_retina_object_gen_for_tests
See sections ‘The INDEX file’ and ‘Package subdirectories’ in the
‘Writing R Extensions’ manual.
* 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 dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘RImageJROI’
'library' or 'require' call to ‘grDevices’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
add_legend: no visible global function definition for ‘par’
assemble_point_coordinates_file: no visible global function definition
for ‘write.table’
assemble_tear_file: no visible global function definition for
‘write.table’
draw_line_segments: no visible global function definition for
‘segments’
fit_error_histogram: no visible global function definition for ‘hist’
fit_plot_azimuthal: no visible binding for global variable ‘xy’
fit_plots: no visible global function definition for ‘predict’
fit_plots: no visible global function definition for ‘plot’
fit_plots: no visible global function definition for ‘abline’
fit_plots: no visible global function definition for ‘par’
fit_plots: no visible global function definition for ‘text’
fit_plots: no visible global function definition for ‘hist’
import_xyz: no visible global function definition for ‘na.omit’
import_xyz: no visible global function definition for ‘read.csv’
init_square_mat_plot: no visible global function definition for ‘image’
plot_circle_radial_lines: no visible global function definition for
‘lines’
plot_degree_label_for_latitudes: no visible global function definition
for ‘axis’
plot_degree_label_for_latitudes: no visible global function definition
for ‘text’
plot_falciform_process: no visible global function definition for
‘polygon’
plot_from_MAT: no visible global function definition for ‘image’
plot_from_MAT : <anonymous>: no visible global function definition for
‘lines’
plot_from_MAT: no visible global function definition for ‘lines’
plot_from_MAT: no visible global function definition for ‘segments’
plot_from_MAT: no visible global function definition for ‘text’
plot_from_MAT: no visible global function definition for ‘axis’
plot_original_xy_locations: no visible global function definition for
‘points’
plot_radial_spokes_and_labels: no visible binding for global variable
‘degree’
plot_rotation_optimize: no visible global function definition for
‘plot’
plot_rotation_optimize: no visible global function definition for
‘abline’
spherical_coords: no visible global function definition for
‘read.table’
spherical_coords: no visible global function definition for ‘write.csv’
spherical_coords: no visible global function definition for
‘capture.output’
spherical_coords: no visible global function definition for
‘complete.cases’
spline.poly: no visible global function definition for ‘spline’
tear_markup_plot: no visible global function definition for ‘plot’
tear_markup_plot: no visible global function definition for ‘text’
vector_retina_composite: no visible binding for global variable
‘Pmol_753’
vector_retina_composite: no visible binding for global variable
‘Pmol_752’
write_labels_at_endpoint_locations: no visible global function
definition for ‘text’
Undefined global functions or variables:
Pmol_752 Pmol_753 abline axis capture.output complete.cases degree
hist image lines na.omit par plot points polygon predict read.csv
read.table segments spline text write.csv write.table xy
Consider adding
importFrom("graphics", "abline", "axis", "hist", "image", "lines",
"par", "plot", "points", "polygon", "segments", "text")
importFrom("stats", "complete.cases", "na.omit", "predict", "spline")
importFrom("utils", "capture.output", "read.csv", "read.table",
"write.csv", "write.table")
to your NAMESPACE file.
* checking Rd files ... WARNING
checkRd: (5) add_degrees.Rd:0-26: Must have a \description
checkRd: (5) cartesian_rotation.Rd:0-31: Must have a \description
checkRd: (5) composite_map.Rd:0-33: Must have a \description
checkRd: (5) coordinate_IJ.Rd:0-35: Must have a \description
checkRd: (5) degrees.Rd:0-18: Must have a \description
checkRd: (5) fit_error_histogram.Rd:0-22: Must have a \description
checkRd: (5) fit_plots.Rd:0-27: Must have a \description
checkRd: (5) map_composites.Rd:0-26: Must have a \description
checkRd: (5) map_vec_sum.Rd:0-22: Must have a \description
checkRd: (5) plot_from_MAT.Rd:0-62: Must have a \description
checkRd: (5) range_len.Rd:0-15: Must have a \description
checkRd: (5) reorder_columns.Rd:0-20: Must have a \description
checkRd: (5) retina_object.Rd:0-43: Must have a \description
checkRd: (5) sphere_visualize.Rd:0-19: Must have a \description
checkRd: (5) spline.poly.Rd:0-30: Must have a \description
checkRd: (5) vector_retina_composite.Rd:0-30: Must have a \description
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘Ntae_381’
Undocumented data sets:
‘Ntae_381’
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 ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'add_contours'
‘xy’
Documented arguments not in \usage in documentation object 'assemble_markup_file':
‘markup_coordinates_dataframe’
Duplicated \argument entries in documentation object 'assemble_point_coordinates_file':
‘outline_coordinates’
Duplicated \argument entries in documentation object 'assemble_tear_file':
‘tear_coordinates_dataframe’
Undocumented arguments in documentation object 'composite_map'
‘projection_type’
Documented arguments not in \usage in documentation object 'draw_latitude_markings':
‘radians’
Undocumented arguments in documentation object 'fit_plot_azimuthal'
‘should_plot_points’ ‘single_point_overlay’
Documented arguments not in \usage in documentation object 'fit_plot_azimuthal':
‘points’
Undocumented arguments in documentation object 'nullify_vals_outside_the_circle'
‘heatmap_matrix’
Documented arguments not in \usage in documentation object 'nullify_vals_outside_the_circle':
‘Mat’ ‘falciform_y’
Undocumented arguments in documentation object 'plot_circle_radial_lines'
‘color_hex’
Documented arguments not in \usage in documentation object 'plot_degree_label_for_latitudes':
‘minitics’ ‘x’ ‘y’ ‘z’ ‘lambda’ ‘polynomial_m’ ‘extrapolate’
Undocumented arguments in documentation object 'plot_longitudinal_lines'
‘axis_radian’
Undocumented arguments in documentation object 'plot_original_xy_locations'
‘x’ ‘y’
Documented arguments not in \usage in documentation object 'plot_original_xy_locations':
‘falciform_x’ ‘falciform_y’
Documented arguments not in \usage in documentation object 'pretty_list_not_including_max':
‘pretty_vec’
Undocumented arguments in documentation object 'rotation_optimize'
‘projection_type’
Undocumented arguments in documentation object 'vector_retina_composite'
‘rotation_degree_list’
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 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 examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* DONE
Status: 5 WARNINGs, 3 NOTEs
See
‘/private/var/folders/vj/57777k0931s8txw12189jmhh0000gn/T/RtmpY0AUIv/retina.Rcheck/00check.log’
for details.
R CMD check results
0 errors | 5 warnings | 3 notes
checking index information ... WARNING
Demos with missing or empty index information:
batch_retina_object_gen_for_tests
See sections ‘The INDEX file’ and ‘Package subdirectories’ in the
‘Writing R Extensions’ manual.
checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘RImageJROI’
'library' or 'require' call to ‘grDevices’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
checking Rd files ... WARNING
checkRd: (5) add_degrees.Rd:0-26: Must have a \description
checkRd: (5) cartesian_rotation.Rd:0-31: Must have a \description
checkRd: (5) composite_map.Rd:0-33: Must have a \description
checkRd: (5) coordinate_IJ.Rd:0-35: Must have a \description
checkRd: (5) degrees.Rd:0-18: Must have a \description
checkRd: (5) fit_error_histogram.Rd:0-22: Must have a \description
checkRd: (5) fit_plots.Rd:0-27: Must have a \description
checkRd: (5) map_composites.Rd:0-26: Must have a \description
checkRd: (5) map_vec_sum.Rd:0-22: Must have a \description
checkRd: (5) plot_from_MAT.Rd:0-62: Must have a \description
checkRd: (5) range_len.Rd:0-15: Must have a \description
checkRd: (5) reorder_columns.Rd:0-20: Must have a \description
checkRd: (5) retina_object.Rd:0-43: Must have a \description
checkRd: (5) sphere_visualize.Rd:0-19: Must have a \description
checkRd: (5) spline.poly.Rd:0-30: Must have a \description
checkRd: (5) vector_retina_composite.Rd:0-30: Must have a \description
checking for missing documentation entries ... WARNING
Undocumented code objects:
‘Ntae_381’
Undocumented data sets:
‘Ntae_381’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'add_contours'
‘xy’
Documented arguments not in \usage in documentation object 'assemble_markup_file':
‘markup_coordinates_dataframe’
Duplicated \argument entries in documentation object 'assemble_point_coordinates_file':
‘outline_coordinates’
... 37 lines ...
Undocumented arguments in documentation object 'rotation_optimize'
‘projection_type’
Undocumented arguments in documentation object 'vector_retina_composite'
‘rotation_degree_list’
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:
‘rgl’ ‘fields’ ‘RColorBrewer’ ‘sphereplot’ ‘mapproj’ ‘retistruct’
‘geometry’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
checking R code for possible problems ... NOTE
add_legend: no visible global function definition for ‘par’
assemble_point_coordinates_file: no visible global function definition
for ‘write.table’
assemble_tear_file: no visible global function definition for
‘write.table’
draw_line_segments: no visible global function definition for
‘segments’
fit_error_histogram: no visible global function definition for ‘hist’
fit_plot_azimuthal: no visible binding for global variable ‘xy’
... 49 lines ...
Undefined global functions or variables:
Pmol_752 Pmol_753 abline axis capture.output complete.cases degree
hist image lines na.omit par plot points polygon predict read.csv
read.table segments spline text write.csv write.table xy
Consider adding
importFrom("graphics", "abline", "axis", "hist", "image", "lines",
"par", "plot", "points", "polygon", "segments", "text")
importFrom("stats", "complete.cases", "na.omit", "predict", "spline")
importFrom("utils", "capture.output", "read.csv", "read.table",
"write.csv", "write.table")
to your NAMESPACE file.```
briancohn
commented
7 years ago