[inst/extdata/asalmon_mcw/main.r:2:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/inst/extdata/asalmon_mcw/main.r#L2) *style:* **Variable or function name should be snake_case.**
```r
LAMBDA_var <- 0.1 #Thin plate spline smoothing. Lambda=0 would be interpolation.
^~~~~~~~~~
```
[inst/extdata/asalmon_mcw/main.r:3:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/inst/extdata/asalmon_mcw/main.r#L3) *style:* **Variable or function name should be snake_case.**
```r
RESOLUTION_var <- 500 #Plot width in pixels
^~~~~~~~~~~~~~
```
[inst/extdata/asalmon_mcw/main.r:5:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/inst/extdata/asalmon_mcw/main.r#L5) *style:* **Lines should not be more than 80 characters.**
```r
#TODO change path. make sure this main.r script is just outside the diagram_retina folder.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/extdata/asalmon_mcw/main.r:8:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/inst/extdata/asalmon_mcw/main.r#L8) *style:* **Lines should not be more than 80 characters.**
```r
#todo verify these. see the tutorial here: https://github.com/bc/retina/blob/master/tutorial.md search for the part that starts with "#[V point of the tear,"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/extdata/asalmon_mcw/main.r:10:10:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/inst/extdata/asalmon_mcw/main.r#L10) *style:* **Commas should always have a space after.**
```r
    c(59,52,67),
         ^
```
[inst/extdata/asalmon_mcw/main.r:10:13:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/inst/extdata/asalmon_mcw/main.r#L10) *style:* **Commas should always have a space after.**
```r
    c(59,52,67),
            ^
```
[inst/extdata/asalmon_mcw/main.r:11:10:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/inst/extdata/asalmon_mcw/main.r#L11) *style:* **Commas should always have a space after.**
```r
    c(79,73,85),
         ^
```
[inst/extdata/asalmon_mcw/main.r:11:13:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/inst/extdata/asalmon_mcw/main.r#L11) *style:* **Commas should always have a space after.**
```r
    c(79,73,85),
            ^
```
[inst/extdata/asalmon_mcw/main.r:12:10:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/inst/extdata/asalmon_mcw/main.r#L12) *style:* **Commas should always have a space after.**
```r
    c(34,31,37))
         ^
```
[inst/extdata/asalmon_mcw/main.r:12:13:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/inst/extdata/asalmon_mcw/main.r#L12) *style:* **Commas should always have a space after.**
```r
    c(34,31,37))
            ^
```
[inst/extdata/asalmon_mcw/main.r:15:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/inst/extdata/asalmon_mcw/main.r#L15) *style:* **Lines should not be more than 80 characters.**
```r
assemble_markup_file('left', path_to_retina_data_folder, nasal_outline_index=1, dorsal_outline_index=NA)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/extdata/asalmon_mcw/main.r:15:22:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/inst/extdata/asalmon_mcw/main.r#L15) *style:* **Only use double-quotes.**
```r
assemble_markup_file('left', path_to_retina_data_folder, nasal_outline_index=1, dorsal_outline_index=NA)
                     ^~~~~~
```
[inst/extdata/asalmon_mcw/main.r:15:77:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/inst/extdata/asalmon_mcw/main.r#L15) *style:* **Put spaces around all infix operators.**
```r
assemble_markup_file('left', path_to_retina_data_folder, nasal_outline_index=1, dorsal_outline_index=NA)
                                                                           ~^~
```
[inst/extdata/asalmon_mcw/main.r:15:101:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/inst/extdata/asalmon_mcw/main.r#L15) *style:* **Put spaces around all infix operators.**
```r
assemble_markup_file('left', path_to_retina_data_folder, nasal_outline_index=1, dorsal_outline_index=NA)
                                                                                ~^~
```
[inst/extdata/asalmon_mcw/main.r:29:21:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/inst/extdata/asalmon_mcw/main.r#L29) *style:* **Commas should never have a space before.**
```r
        height = 45 ,# height of the counting frame in microns
                   ~^
```
[inst/extdata/asalmon_mcw/main.r:29:22:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/inst/extdata/asalmon_mcw/main.r#L29) *style:* **Commas should always have a space after.**
```r
        height = 45 ,# height of the counting frame in microns
                     ^
```
[inst/extdata/asalmon_mcw/main.r:34:28:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/inst/extdata/asalmon_mcw/main.r#L34) *style:* **Commas should never have a space before.**
```r
        extrapolate = TRUE ,          #Predicts densities to the equator.
                          ~^
```
[inst/extdata/asalmon_mcw/main.r:36:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/inst/extdata/asalmon_mcw/main.r#L36) *style:* **Lines should not be more than 80 characters.**
```r
        rotation_ccw = -90, # when set to -90 degrees, the rotation is unaltered from the measured orientation.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/extdata/asalmon_mcw/main.r:37:22:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/inst/extdata/asalmon_mcw/main.r#L37) *style:* **Put spaces around all infix operators.**
```r
        plot_suppress=TRUE)
                    ~^~
```
[inst/extdata/asalmon_mcw/main.r:39:29:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/inst/extdata/asalmon_mcw/main.r#L39) *style:* **Put spaces around all infix operators.**
```r
retinaplot(my_retina, lambda=0.001, polynomial_m=   2, rotation=0)
                           ~^~
```
[inst/extdata/asalmon_mcw/main.r:39:49:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/inst/extdata/asalmon_mcw/main.r#L39) *style:* **Put spaces around all infix operators.**
```r
retinaplot(my_retina, lambda=0.001, polynomial_m=   2, rotation=0)
                                               ~^
```
[inst/extdata/asalmon_mcw/main.r:39:64:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/inst/extdata/asalmon_mcw/main.r#L39) *style:* **Put spaces around all infix operators.**
```r
retinaplot(my_retina, lambda=0.001, polynomial_m=   2, rotation=0)
                                                              ~^~
```
[inst/extdata/asalmon_mcw/main.r:40:10:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/inst/extdata/asalmon_mcw/main.r#L40) *style:* **Put spaces around all infix operators.**
```r
par(mfrow=c(2,2))
        ~^~
```
[inst/extdata/asalmon_mcw/main.r:40:15:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/inst/extdata/asalmon_mcw/main.r#L40) *style:* **Commas should always have a space after.**
```r
par(mfrow=c(2,2))
              ^
```
[R/composite.R:2:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/composite.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
##' @description This is a subfunction, that is useful when creating average maps.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/composite.R:3:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/composite.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
##' @param retina_list A list containing retina objects, with names(retina_list) all defined.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/composite.R:4:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/composite.R#L4) *style:* **Lines should not be more than 80 characters.**
```r
##' @param rotation_indices Each value in this vector will correspond to the amount of rotation applied to each retina in the list.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/composite.R:5:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/composite.R#L5) *style:* **Lines should not be more than 80 characters.**
```r
##' @param ... Arguments passed from other functions. You can access the thin plate spline interpolator here.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/composite.R:6:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/composite.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
##' @return sum_mat The sum of all retina objects in the list, with respect to the rotation indices.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/composite.R:9:16:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/composite.R#L9) *warning:* **no visible global function definition for ‘mat_from_ret_obj’**
```r
    sum_mat <- mat_from_ret_obj(retina_list[[1]], rotation = 0, ...)
               ^~~~~~~~~~~~~~~~
```
[R/composite.R:12:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/composite.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
        sum_mat <- sum_mat + mat_from_ret_obj(retina_list[[i]], rotation_indices[i],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/composite.R:12:85:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/composite.R#L12) *style:* **Trailing whitespace is superfluous.**
```r
        sum_mat <- sum_mat + mat_from_ret_obj(retina_list[[i]], rotation_indices[i],
                                                                                ^
```
[R/matrix_retobj.R:3:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/matrix_retobj.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
##' You can decide how much to rotate the retina before returning the matrix. You can also pass arguments to the polar plotter.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/matrix_retobj.R:6:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/matrix_retobj.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
##' @param n the number by which to divide the matrix by. Useful when generating partial averages.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/matrix_retobj.R:7:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/matrix_retobj.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
##' @param reflect logical, by default it is TRUE, in order to view the retina from outside the eye (rather than from within.)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/matrix_retobj.R:12:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/matrix_retobj.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
mat_from_ret_obj <- function(retina_object, rotation = 0, n = 1, reflect = TRUE,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/matrix_retobj.R:12:81:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/matrix_retobj.R#L12) *style:* **Trailing whitespace is superfluous.**
```r
mat_from_ret_obj <- function(retina_object, rotation = 0, n = 1, reflect = TRUE,
                                                                                ^
```
[R/matrix_retobj.R:17:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/matrix_retobj.R#L17) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/matrix_retobj.R:20:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/matrix_retobj.R#L20) *style:* **Lines should not be more than 80 characters.**
```r
    az <- mapproject(x = retina_object$trimmed_data[, 2], retina_object$trimmed_data[,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/matrix_retobj.R:20:87:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/matrix_retobj.R#L20) *style:* **Trailing whitespace is superfluous.**
```r
    az <- mapproject(x = retina_object$trimmed_data[, 2], retina_object$trimmed_data[,
                                                                                ^
```
[R/matrix_retobj.R:25:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/matrix_retobj.R#L25) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/matrix_retobj.R:27:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/matrix_retobj.R#L27) *style:* **Lines should not be more than 80 characters.**
```r
    map2fit <- fit_plot_azimuthal(x2, y2, z2, plot_suppress = TRUE, extrapolate = TRUE,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/matrix_retobj.R:27:88:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/matrix_retobj.R#L27) *style:* **Trailing whitespace is superfluous.**
```r
    map2fit <- fit_plot_azimuthal(x2, y2, z2, plot_suppress = TRUE, extrapolate = TRUE,
                                                                                ^
```
[R/matrix_retobj.R:28:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/matrix_retobj.R#L28) *style:* **Lines should not be more than 80 characters.**
```r
        outer_radius = pi/2, falciform_coords = retina_object$azimuthal_data.falciform[[1]],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/matrix_retobj.R:28:26:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/matrix_retobj.R#L28) *style:* **Put spaces around all infix operators.**
```r
        outer_radius = pi/2, falciform_coords = retina_object$azimuthal_data.falciform[[1]],
                        ~^~
```
[R/matrix_retobj.R:28:93:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/matrix_retobj.R#L28) *style:* **Trailing whitespace is superfluous.**
```r
        outer_radius = pi/2, falciform_coords = retina_object$azimuthal_data.falciform[[1]],
                                                                                ^
```
[R/matrix_retobj.R:30:5:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/matrix_retobj.R#L30) *style:* **Variable or function name should be snake_case.**
```r
    MAT <- map2fit[[2]]$z
    ^~~
```
[R/matrix_retobj.R:32:15:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/matrix_retobj.R#L32) *style:* **Put spaces around all infix operators.**
```r
    return(MAT/n)
             ~^~
```
[R/plotting_functions.R:3:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
##' Extracts xy and falciform coordinates from datapoints collected from retistruct. Falc and Datapoints are stacked upon one another
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:5:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L5) *style:* **Lines should not be more than 80 characters.**
```r
##' @param datapoints_from_retistruct data structure that comes from the datapoints.csv, which is automatically generated by Retistruct.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:7:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
##' @return L list of pixel xy positions, and falciform coordinates in [1] and [2], respectively
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:9:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L9) *style:* **Lines should not be more than 80 characters.**
```r
extract_xy_and_falciform <- function(datapoints_from_retistruct, number_of_sampling_sites) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:10:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L10) *style:* **Lines should not be more than 80 characters.**
```r
    pixel_xy_positions <- datapoints_from_retistruct[1:number_of_sampling_sites,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:10:81:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L10) *style:* **Trailing whitespace is superfluous.**
```r
    pixel_xy_positions <- datapoints_from_retistruct[1:number_of_sampling_sites,
                                                                                ^
```
[R/plotting_functions.R:12:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
    falciform_len <- length(datapoints_from_retistruct[, 1]) - length(pixel_xy_positions[,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:12:91:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L12) *style:* **Trailing whitespace is superfluous.**
```r
    falciform_len <- length(datapoints_from_retistruct[, 1]) - length(pixel_xy_positions[,
                                                                                ^
```
[R/plotting_functions.R:16:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L16) *style:* **Lines should not be more than 80 characters.**
```r
    falciform_coordinates <- datapoints_from_retistruct[(xy_len + 1):total_len, ]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:22:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L22) *style:* **Lines should not be more than 80 characters.**
```r
##' ImageJ values don't always show up the right way, because Y values get larger and positive while moving down the image.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:24:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L24) *style:* **Lines should not be more than 80 characters.**
```r
##' @param falciform_xy_coordinates 2 columns of coordinate (X,Y) data in ImageJ pixel format
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:28:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L28) *style:* **Lines should not be more than 80 characters.**
```r
reflect_IJ_y_values_for_falciform <- function(falciform_xy_coordinates, xy_img_dimensions) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:28:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L28) *style:* **Variable and function names should not be longer than 30 characters.**
```r
reflect_IJ_y_values_for_falciform <- function(falciform_xy_coordinates, xy_img_dimensions) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:28:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L28) *style:* **Variable or function name should be snake_case.**
```r
reflect_IJ_y_values_for_falciform <- function(falciform_xy_coordinates, xy_img_dimensions) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:29:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L29) *style:* **Lines should not be more than 80 characters.**
```r
    falciform_xy_coordinates_transformed <- falciform_xy_coordinates  #make a copy
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:29:5:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L29) *style:* **Variable and function names should not be longer than 30 characters.**
```r
    falciform_xy_coordinates_transformed <- falciform_xy_coordinates  #make a copy
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:31:52:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L31) *style:* **Put spaces around all infix operators.**
```r
    half_of_vertical_pixels <- xy_img_dimensions[2]/2
                                                  ~^~
```
[R/plotting_functions.R:32:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L32) *style:* **Lines should not be more than 80 characters.**
```r
    falciform_xy_coordinates_transformed$cyan <- (falc_y - half_of_vertical_pixels) *
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:32:86:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L32) *style:* **Trailing whitespace is superfluous.**
```r
    falciform_xy_coordinates_transformed$cyan <- (falc_y - half_of_vertical_pixels) *
                                                                                ^
```
[R/plotting_functions.R:38:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L38) *style:* **Lines should not be more than 80 characters.**
```r
##' Shows a visualization of the outline, as well as the location of each datapoint, with fit plot.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:40:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L40) *style:* **Lines should not be more than 80 characters.**
```r
##' @param pixel_xy_positions 2 columns of coordinate (X,Y) data in ImageJ pixel format
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:41:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L41) *style:* **Lines should not be more than 80 characters.**
```r
##' @param z_vector numerical vector of density values for each of the coordinates
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:42:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L42) *style:* **Lines should not be more than 80 characters.**
```r
##' @param xy_outline_points 2 columns of coordinate(X,Y) data in ImageJ pixel format for the outline coordinates.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:45:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L45) *style:* **Lines should not be more than 80 characters.**
```r
traditional_flatmount_plot <- function(pixel_xy_positions, z_vector, xy_outline_points) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:46:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L46) *style:* **Lines should not be more than 80 characters.**
```r
    fit <- Tps(pixel_xy_positions, z_vector)  # fits a surface to ozone measurements.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:46:12:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L46) *warning:* **no visible global function definition for ‘Tps’, Did you mean 'Ops'?**
```r
    fit <- Tps(pixel_xy_positions, z_vector)  # fits a surface to ozone measurements.
           ^~~
```
[R/plotting_functions.R:47:5:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L47) *warning:* **no visible global function definition for ‘set.panel’**
```r
    set.panel(2, 2)
    ^~~~~~~~~
```
[R/plotting_functions.R:49:5:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L49) *warning:* **no visible global function definition for ‘set.panel’**
```r
    set.panel()
    ^~~~~~~~~
```
[R/plotting_functions.R:52:5:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L52) *warning:* **no visible global function definition for ‘surface’**
```r
    surface(fit)  # Quick image/contour plot of GCV surface.
    ^~~~~~~
```
[R/plotting_functions.R:61:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L61) *style:* **Lines should not be more than 80 characters.**
```r
##' Shows a visualization of the outline, as well as the location of each datapoint so the user can identify where the tears are.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:64:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L64) *style:* **Lines should not be more than 80 characters.**
```r
##' @param path_to_retina_data_folder The path to the folder that contains the outline.roi file.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:65:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L65) *style:* **Lines should not be more than 80 characters.**
```r
##' @return roi_coordinates XY vals of pixel coordinates of the outline points, in order.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:69:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L69) *style:* **Lines should not be more than 80 characters.**
```r
    roi_object <- read.ijroi(file.path(path_to_retina_data_folder, "outline.roi"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:69:19:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L69) *warning:* **no visible global function definition for ‘read.ijroi’**
```r
    roi_object <- read.ijroi(file.path(path_to_retina_data_folder, "outline.roi"))
                  ^~~~~~~~~~
```
[R/plotting_functions.R:70:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L70) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/plotting_functions.R:72:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L72) *style:* **Lines should not be more than 80 characters.**
```r
    # format plots has the coordinate (0, 0) in the top left.  We have the coordinate
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:73:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L73) *style:* **Lines should not be more than 80 characters.**
```r
    # (0, 0) in the bottom left. We need to transform P so that the outline appears
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:76:5:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L76) *style:* **Variable or function name should be snake_case.**
```r
    roi_XY_coords <- roi_object$coords
    ^~~~~~~~~~~~~
```
[R/plotting_functions.R:80:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L80) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/plotting_functions.R:81:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L81) *style:* **Lines should not be more than 80 characters.**
```r
    plot(roi_XY_coords, type = "l", col = "#d3d3d3", asp = 1, xlab = "X Pixels",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:81:81:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L81) *style:* **Trailing whitespace is superfluous.**
```r
    plot(roi_XY_coords, type = "l", col = "#d3d3d3", asp = 1, xlab = "X Pixels",
                                                                                ^
```
[R/plotting_functions.R:83:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L83) *style:* **Lines should not be more than 80 characters.**
```r
    text(roi_XY_coords[, 1], roi_XY_coords[, 2], labels = 1:length(roi_XY_coords[,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:83:83:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L83) *style:* **Trailing whitespace is superfluous.**
```r
    text(roi_XY_coords[, 1], roi_XY_coords[, 2], labels = 1:length(roi_XY_coords[,
                                                                                ^
```
[R/plotting_functions.R:85:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L85) *style:* **Lines should not be more than 80 characters.**
```r
    message("If you are getting this message, you are using a special feature. Contact me at brian.cohn@usc.edu and I will happily teach you how to use it.")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:93:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L93) *style:* **Lines should not be more than 80 characters.**
```r
##' @description Creates a markup.csv file. One of the dorsal_outline_index or nasal_outline_index must be filled in. Not both.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:96:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L96) *style:* **Lines should not be more than 80 characters.**
```r
##' @param dorsal_outline_index The index of the point that points toward dorsal, or NA.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:97:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L97) *style:* **Lines should not be more than 80 characters.**
```r
##' @param nasal_outline_index The index of the opint that points toward nasal, or NA.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:98:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L98) *style:* **Lines should not be more than 80 characters.**
```r
##' @param path_to_retina_data_folder The path where the markup.csv file will be saved.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:100:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L100) *style:* **Lines should not be more than 80 characters.**
```r
assemble_markup_file <- function(eye_left_or_right, path_to_retina_data_folder, dorsal_outline_index = NA,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:100:107:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L100) *style:* **Trailing whitespace is superfluous.**
```r
assemble_markup_file <- function(eye_left_or_right, path_to_retina_data_folder, dorsal_outline_index = NA,
                                                                                ^
```
[R/plotting_functions.R:103:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L103) *style:* **Lines should not be more than 80 characters.**
```r
        ## https://stackoverflow.com/questions/18509527/first-letter-to-upper-case
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:109:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L109) *style:* **Lines should not be more than 80 characters.**
```r
        line2 <- paste0("NA,", nasal_outline_index, ",",phi0,",NA,TRUE,\"", eye_side_string,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:109:57:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L109) *style:* **Commas should always have a space after.**
```r
        line2 <- paste0("NA,", nasal_outline_index, ",",phi0,",NA,TRUE,\"", eye_side_string,
                                                        ^
```
[R/plotting_functions.R:109:62:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L109) *style:* **Commas should always have a space after.**
```r
        line2 <- paste0("NA,", nasal_outline_index, ",",phi0,",NA,TRUE,\"", eye_side_string,
                                                             ^
```
[R/plotting_functions.R:109:93:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L109) *style:* **Trailing whitespace is superfluous.**
```r
        line2 <- paste0("NA,", nasal_outline_index, ",",phi0,",NA,TRUE,\"", eye_side_string,
                                                                                ^
```
[R/plotting_functions.R:112:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L112) *style:* **Lines should not be more than 80 characters.**
```r
        line2 <- paste0(dorsal_outline_index, ",NA", ",",phi0,",NA,TRUE,\"", eye_side_string,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:112:58:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L112) *style:* **Commas should always have a space after.**
```r
        line2 <- paste0(dorsal_outline_index, ",NA", ",",phi0,",NA,TRUE,\"", eye_side_string,
                                                         ^
```
[R/plotting_functions.R:112:63:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L112) *style:* **Commas should always have a space after.**
```r
        line2 <- paste0(dorsal_outline_index, ",NA", ",",phi0,",NA,TRUE,\"", eye_side_string,
                                                              ^
```
[R/plotting_functions.R:112:94:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L112) *style:* **Trailing whitespace is superfluous.**
```r
        line2 <- paste0(dorsal_outline_index, ",NA", ",",phi0,",NA,TRUE,\"", eye_side_string,
                                                                                ^
```
[R/plotting_functions.R:120:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L120) *style:* **Lines should not be more than 80 characters.**
```r
    message(paste("Wrote markup file to ", output_path, "\n Ensure that it exists beside your outline.roi file"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:130:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L130) *style:* **Lines should not be more than 80 characters.**
```r
##' @param tear_coordinates_dataframe the dataframe of 3 columns, with c('V0','VB','VF'), and n columns, where n= number of tears
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:131:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L131) *style:* **Lines should not be more than 80 characters.**
```r
##' @param path_to_retina_data_folder The path where the T.csv file will be saved.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:135:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L135) *style:* **Lines should not be more than 80 characters.**
```r
assemble_tear_file <- function(tear_coordinates_dataframe, path_to_retina_data_folder) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:138:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L138) *style:* **Lines should not be more than 80 characters.**
```r
    write.table(tear_coordinates_dataframe, output_path, sep = ",", row.names = FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:139:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L139) *style:* **Lines should not be more than 80 characters.**
```r
    message(paste("Wrote tear file to ", output_path, "\n Check that it exists beside your outline.roi file"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:147:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L147) *style:* **Lines should not be more than 80 characters.**
```r
##' @param path_to_retina_data_folder The path where the P.csv file will be saved.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:151:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L151) *style:* **Lines should not be more than 80 characters.**
```r
assemble_point_coordinates_file <- function(outline_coordinates, path_to_retina_data_folder) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:151:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L151) *style:* **Variable and function names should not be longer than 30 characters.**
```r
assemble_point_coordinates_file <- function(outline_coordinates, path_to_retina_data_folder) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:155:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L155) *style:* **Lines should not be more than 80 characters.**
```r
    message(paste("Wrote coordinates file to ", output_path, "\n Check that it exists beside your outline.roi file"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:177:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L177) *style:* **Variable and function names should not be longer than 30 characters.**
```r
plot_degree_label_for_latitudes <- function(outer_radius, circle.rads) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:177:59:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L177) *style:* **Variable or function name should be snake_case.**
```r
plot_degree_label_for_latitudes <- function(outer_radius, circle.rads) {
                                                          ^~~~~~~~~~~
```
[R/plotting_functions.R:178:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L178) *style:* **Lines should not be more than 80 characters.**
```r
    axis(2, pos = -1.25 * outer_radius, at = sort(union(circle.rads, -circle.rads)),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:178:85:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L178) *style:* **Trailing whitespace is superfluous.**
```r
    axis(2, pos = -1.25 * outer_radius, at = sort(union(circle.rads, -circle.rads)),
                                                                                ^
```
[R/plotting_functions.R:180:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L180) *style:* **Lines should not be more than 80 characters.**
```r
    text(-1.26 * outer_radius, sort(union(circle.rads, -circle.rads)), sort(union(circle.rads,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:180:95:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L180) *style:* **Trailing whitespace is superfluous.**
```r
    text(-1.26 * outer_radius, sort(union(circle.rads, -circle.rads)), sort(union(circle.rads,
                                                                                ^
```
[R/plotting_functions.R:195:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L195) *style:* **Lines should not be more than 80 characters.**
```r
    fields::image.plot(legend.only = TRUE, col = col, zlim = zlim, family = "Palatino")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:202:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L202) *style:* **Lines should not be more than 80 characters.**
```r
##' @param endpoints a 4 element numeric vector describing the xy and x'y' for the line segment.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:206:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L206) *style:* **Lines should not be more than 80 characters.**
```r
    segments(endpoints[1], endpoints[2], endpoints[3], endpoints[4], col = color_hex)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:216:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L216) *style:* **Lines should not be more than 80 characters.**
```r
##' @param endpoints vector of 4 numerics, x,y and x',y' defining the line segment
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:217:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L217) *style:* **Lines should not be more than 80 characters.**
```r
write_labels_at_endpoint_locations <- function(r_label, l_label, degree, endpoints) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:217:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L217) *style:* **Variable and function names should not be longer than 30 characters.**
```r
write_labels_at_endpoint_locations <- function(r_label, l_label, degree, endpoints) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:226:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L226) *style:* **Lines should not be more than 80 characters.**
```r
##' @description We do not need points plotted in the corners of the plotted circle.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:233:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L233) *style:* **Lines should not be more than 80 characters.**
```r
nullify_vals_outside_the_circle <- function(minitics, spatial_res, heatmap_matrix,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:233:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L233) *style:* **Variable and function names should not be longer than 30 characters.**
```r
nullify_vals_outside_the_circle <- function(minitics, spatial_res, heatmap_matrix,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:233:83:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L233) *style:* **Trailing whitespace is superfluous.**
```r
nullify_vals_outside_the_circle <- function(minitics, spatial_res, heatmap_matrix,
                                                                                ^
```
[R/plotting_functions.R:235:5:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L235) *style:* **Variable and function names should not be longer than 30 characters.**
```r
    matrix_position_is_within_the_circle <- function() {
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:238:5:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L238) *style:* **Variable or function name should be snake_case.**
```r
    markNA <- matrix(minitics, ncol = spatial_res, nrow = spatial_res)
    ^~~~~~
```
[R/plotting_functions.R:246:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L246) *style:* **Lines should not be more than 80 characters.**
```r
##' @description Find the location to put the label around the circle at each of the lines
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:251:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L251) *style:* **Variable and function names should not be longer than 30 characters.**
```r
compute_longitude_label_location <- function(axis.rads, outer_radius) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:251:46:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L251) *style:* **Variable or function name should be snake_case.**
```r
compute_longitude_label_location <- function(axis.rads, outer_radius) {
                                             ^~~~~~~~~
```
[R/plotting_functions.R:252:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L252) *style:* **Lines should not be more than 80 characters.**
```r
    return(c(RMat(axis.rads) %*% matrix(c(1.1, 0, -1.1, 0) * outer_radius, ncol = 2)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:252:14:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L252) *warning:* **no visible global function definition for ‘RMat’, Did you mean 'hat'?**
```r
    return(c(RMat(axis.rads) %*% matrix(c(1.1, 0, -1.1, 0) * outer_radius, ncol = 2)))
             ^~~~
```
[R/plotting_functions.R:261:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L261) *style:* **Lines should not be more than 80 characters.**
```r
    endpoints <- zapsmall(c(RMat(axis_radian) %*% matrix(c(1, 0, -1, 0) * outer_radius,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:261:88:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L261) *style:* **Trailing whitespace is superfluous.**
```r
    endpoints <- zapsmall(c(RMat(axis_radian) %*% matrix(c(1, 0, -1, 0) * outer_radius,
                                                                                ^
```
[R/plotting_functions.R:263:5:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L263) *warning:* **no visible global function definition for ‘draw_line_segments’**
```r
    draw_line_segments(endpoints)
    ^~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:267:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L267) *style:* **Lines should not be more than 80 characters.**
```r
##' @description put a degree label at the ends of the endpoints for each longitude
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:274:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L274) *style:* **Lines should not be more than 80 characters.**
```r
plot_longitudinal_labels <- function(axis.rad, outer_radius, r_label, l_label, degree) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:274:38:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L274) *style:* **Variable or function name should be snake_case.**
```r
plot_longitudinal_labels <- function(axis.rad, outer_radius, r_label, l_label, degree) {
                                     ^~~~~~~~
```
[R/plotting_functions.R:275:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L275) *style:* **Lines should not be more than 80 characters.**
```r
    write_labels_at_endpoint_locations(r_label, l_label, degree, compute_longitude_label_location(axis.rad,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:275:108:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L275) *style:* **Trailing whitespace is superfluous.**
```r
    write_labels_at_endpoint_locations(r_label, l_label, degree, compute_longitude_label_location(axis.rad,
                                                                                ^
```
[R/plotting_functions.R:285:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L285) *style:* **Variable or function name should be snake_case.**
```r
RMat <- function(radians) {
^~~~
```
[R/plotting_functions.R:286:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L286) *style:* **Lines should not be more than 80 characters.**
```r
    return(matrix(c(cos(radians), sin(radians), -sin(radians), cos(radians)), ncol = 2))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:290:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L290) *style:* **Lines should not be more than 80 characters.**
```r
##' @description plots radial lines, degree label for latitudes, and plots radial spokes with labels
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:295:5:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L295) *warning:* **no visible global function definition for ‘plot_circle_radial_lines’**
```r
    plot_circle_radial_lines(radius_vals)
    ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:296:5:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L296) *warning:* **no visible global function definition for ‘plot_degree_label_for_latitudes’**
```r
    plot_degree_label_for_latitudes(outer_radius, radius_vals)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:297:5:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L297) *warning:* **no visible global function definition for ‘plot_radial_spokes_and_labels’**
```r
    plot_radial_spokes_and_labels(outer_radius)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:324:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L324) *style:* **Variable and function names should not be longer than 30 characters.**
```r
define_color_breaks_based_on_source <- function(col_breaks_source, z, Mat) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:324:71:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L324) *style:* **Variable or function name should be snake_case.**
```r
define_color_breaks_based_on_source <- function(col_breaks_source, z, Mat) {
                                                                      ^~~
```
[R/plotting_functions.R:329:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L329) *style:* **Lines should not be more than 80 characters.**
```r
    } else if ((length(col_breaks_source) == 2) & (is.numeric(col_breaks_source))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:346:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L346) *style:* **Lines should not be more than 80 characters.**
```r
##' @param extrapolate whether to predict out to the equator of the eye, even if no data exists nearby.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:347:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L347) *style:* **Lines should not be more than 80 characters.**
```r
interpolate_input_data <- function(minitics, x, y, z, lambda, polynomial_m, extrapolate) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:348:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L348) *style:* **Lines should not be more than 80 characters.**
```r
    grid.list = list(x = minitics, y = minitics)  #choose locations to predict at
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:348:5:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L348) *style:* **Variable or function name should be snake_case.**
```r
    grid.list = list(x = minitics, y = minitics)  #choose locations to predict at
    ^~~~~~~~~
```
[R/plotting_functions.R:348:15:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L348) *style:* **Use <-, not =, for assignment.**
```r
    grid.list = list(x = minitics, y = minitics)  #choose locations to predict at
              ^
```
[R/plotting_functions.R:349:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L349) *style:* **Lines should not be more than 80 characters.**
```r
    t <- Tps(cbind(x, y), z, lambda = lambda, m = polynomial_m)  #computationally intensive
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:349:10:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L349) *warning:* **no visible global function definition for ‘Tps’, Did you mean 'Ops'?**
```r
    t <- Tps(cbind(x, y), z, lambda = lambda, m = polynomial_m)  #computationally intensive
         ^~~
```
[R/plotting_functions.R:350:12:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L350) *warning:* **no visible global function definition for ‘predictSurface’**
```r
    tmp <- predictSurface(t, grid.list, extrap = extrapolate)
           ^~~~~~~~~~~~~~
```
[R/plotting_functions.R:351:5:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L351) *style:* **Variable or function name should be snake_case.**
```r
    Mat <- tmp$z
    ^~~
```
[R/plotting_functions.R:363:5:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L363) *style:* **Variable or function name should be snake_case.**
```r
    axis.rads <- c(0, pi/6, pi/3, pi/2, 2 * pi/3, 5 * pi/6)
    ^~~~~~~~~
```
[R/plotting_functions.R:363:25:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L363) *style:* **Put spaces around all infix operators.**
```r
    axis.rads <- c(0, pi/6, pi/3, pi/2, 2 * pi/3, 5 * pi/6)
                       ~^~
```
[R/plotting_functions.R:363:31:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L363) *style:* **Put spaces around all infix operators.**
```r
    axis.rads <- c(0, pi/6, pi/3, pi/2, 2 * pi/3, 5 * pi/6)
                             ~^~
```
[R/plotting_functions.R:363:37:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L363) *style:* **Put spaces around all infix operators.**
```r
    axis.rads <- c(0, pi/6, pi/3, pi/2, 2 * pi/3, 5 * pi/6)
                                   ~^~
```
[R/plotting_functions.R:363:47:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L363) *style:* **Put spaces around all infix operators.**
```r
    axis.rads <- c(0, pi/6, pi/3, pi/2, 2 * pi/3, 5 * pi/6)
                                             ~^~
```
[R/plotting_functions.R:363:57:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L363) *style:* **Put spaces around all infix operators.**
```r
    axis.rads <- c(0, pi/6, pi/3, pi/2, 2 * pi/3, 5 * pi/6)
                                                       ~^~
```
[R/plotting_functions.R:364:5:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L364) *style:* **Variable or function name should be snake_case.**
```r
    r.labs <- c(90, 60, 30, 0, 330, 300)
    ^~~~~~
```
[R/plotting_functions.R:365:5:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L365) *style:* **Variable or function name should be snake_case.**
```r
    l.labs <- c(270, 240, 210, 180, 150, 120)
    ^~~~~~
```
[R/plotting_functions.R:367:9:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L367) *warning:* **no visible global function definition for ‘plot_longitudinal_lines’**
```r
        plot_longitudinal_lines(axis.rads[i], outer_radius)
        ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:368:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L368) *style:* **Lines should not be more than 80 characters.**
```r
        plot_longitudinal_labels(axis.rads[i], outer_radius, r.labs[i], l.labs[i],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:368:83:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L368) *style:* **Trailing whitespace is superfluous.**
```r
        plot_longitudinal_labels(axis.rads[i], outer_radius, r.labs[i], l.labs[i],
                                                                                ^
```
[R/plotting_functions.R:389:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L389) *style:* **Lines should not be more than 80 characters.**
```r
##' @description Useful for making the falciform process look more smooth and refined. This is purely aesthetic.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:390:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L390) *style:* **Lines should not be more than 80 characters.**
```r
##' @details enhance the resolution of a polygon vertices dataframe by creating a spline along each vertex.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:391:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L391) *style:* **Lines should not be more than 80 characters.**
```r
##' @param xy vertices in dataframe with x and y columns, in order (not all are used).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:398:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L398) *style:* **Lines should not be more than 80 characters.**
```r
##' @references http://gis.stackexchange.com/questions/24827/how-to-smooth-the-polygons-in-a-contour-map
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotting_functions.R:407:5:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L407) *style:* **Variable or function name should be snake_case.**
```r
    data.spline <- spline(1:(n + 2 * k), data[, 1], n = vertices, ...)
    ^~~~~~~~~~~
```
[R/plotting_functions.R:411:1:](https://github.com/bc/retina/blob/002662d3eea76706eb6de58bc2991e242e85456e/R/plotting_functions.R#L411) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```


Hrm not sure why this is here.


[Quake Report.zip](https://github.com/udacity/ud843-QuakeReport/files/2153425/Quake.Report.zip)
Here is my version of the Quake Report App.
Here is my Logcat error:
   java.lang.RuntimeException: An error occurred while executing doInBackground()
        at android.os.AsyncTask$3.done(AsyncTask.java:353)
        at java.util.concurrent.FutureTask.finishCompletion(FutureTask.java:383)
        at java.util.concurrent.FutureTask.setException(FutureTask.java:252)
        at java.util.concurrent.FutureTask.run(FutureTask.java:271)
        at android.os.AsyncTask$SerialExecutor$1.run(AsyncTask.java:245)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1162)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:636)
        at java.lang.Thread.run(Thread.java:764)
     Caused by: java.lang.RuntimeException: Can't create handler inside thread that has not called Looper.prepare()
        at android.os.Handler.<init>(Handler.java:203)
        at android.os.Handler.<init>(Handler.java:117)
        at android.app.Activity.<init>(Activity.java:801)
        at android.support.v4.app.SupportActivity.<init>(ComponentActivity.java:43)
        at android.support.v4.app.FragmentActivity.<init>(FragmentActivity.java:68)
        at android.support.v7.app.AppCompatActivity.<init>(AppCompatActivity.java:62)
        at com.example.android.quakereport.Earthquake.<init>(Earthquake.java:10)
        at com.example.android.quakereport.QueryUtils.extractFeatureFromJson(QueryUtils.java:86)
        at com.example.android.quakereport.QueryUtils.fetchEarthquakeData(QueryUtils.java:197)
        at com.example.android.quakereport.EarthquakeActivity$EarthquakeAsyncTask.doInBackground(EarthquakeActivity.java:109)
        at com.example.android.quakereport.EarthquakeActivity$EarthquakeAsyncTask.doInBackground(EarthquakeActivity.java:95)
        at android.os.AsyncTask$2.call(AsyncTask.java:333)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at android.os.AsyncTask$SerialExecutor$1.run(AsyncTask.java:245)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1162)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:636)
        at java.lang.Thread.run(Thread.java:764)


I just checked ab79e0a into the "develop" branch. Is there any way you can give this a try to see if it fixes the problem you saw?


Tested and it fixes the problem. Thanks, @SomberNight


Could we please not hard code IP addresses?


Hi, I have a booting NIVI1 camera(displaying Autoliv, Indigo, Flir logo). unfortunately, I don't have the matching NVE controller but only the camera.  I know the camera is waiting for LIN commands to be activated. I am wondering if you have had any chance to monitor LIN communication between NVK and NVE and what kind of communication is happening? thanks.


Yes, thanks for spotting that.

Fixed in commit af21de3c5ad3071d56bb1b7a4a0acd015cbcbdd2

--
bye,
pabs

http://bonedaddy.net/pabs3/


哈哈


IBM Cloud [toolchain](https://console.ng.bluemix.net/devops/toolchains/ffaad832-ddb3-411c-9164-0a0222d9339e?env_id=ibm%3Ayp%3Aus-south "cloud-native-toolchain-tutorial-20180701204622477"): [Delivery Pipeline](https://console.ng.bluemix.net/devops/pipelines/9007521e-b88e-4bd7-b091-063159905053?env_id=ibm%3Ayp%3Aus-south "sample-cloud-native-toolchain-tutorial-20180701204622477") deployed [sample-cloud-native-toolchain-tutorial-20180701204622477](https://github.com/cjacobs-ibm/sample-cloud-native-toolchain-tutorial-20180701204622477/releases/tag/deploy-ibm-yp-us-south-cjacobs-us.ibm.com-test-20180702-014546 "deploy-ibm-yp-us-south-cjacobs-us.ibm.com-test-20180702-014546") to [test](https://console.bluemix.net/apps/7d89f04c-056c-48f5-ad74-821fc93d0b07?env_id=ibm:yp:us-south "ibm:yp:us-south:cjacobs@us.ibm.com:test"), including this commit


IBM Cloud [toolchain](https://console.ng.bluemix.net/devops/toolchains/ffaad832-ddb3-411c-9164-0a0222d9339e?env_id=ibm%3Ayp%3Aus-south "cloud-native-toolchain-tutorial-20180701204622477"): [Delivery Pipeline](https://console.ng.bluemix.net/devops/pipelines/9007521e-b88e-4bd7-b091-063159905053?env_id=ibm%3Ayp%3Aus-south "sample-cloud-native-toolchain-tutorial-20180701204622477") deployed [sample-cloud-native-toolchain-tutorial-20180701204622477](https://github.com/cjacobs-ibm/sample-cloud-native-toolchain-tutorial-20180701204622477/releases/tag/deploy-ibm-yp-us-south-cjacobs-us.ibm.com-prod-20180702-014858 "deploy-ibm-yp-us-south-cjacobs-us.ibm.com-prod-20180702-014858") to [prod](https://console.bluemix.net/apps/e0173666-dc26-4b9e-b73c-4841d0050118?env_id=ibm:yp:us-south "ibm:yp:us-south:cjacobs@us.ibm.com:prod"), including this commit


beauty :)


@isonil Hey isonil!? you're on?


USB is now working but WiFi still failed, although SDIO is now Ok !
The WiFi issue is probably that firmware loading has changed between 4.14.y and 4.17.3 :

[    8.957393] brcmfmac mmc1:0001:1: Direct firmware load for brcm/brcmfmac43430-sdio.clm_blob failed with error -2

Copying brcm/brcmfmac43430-sdio.bin into brcm/brcmfmac43430-sdio.clm_blob didn't fix it ...


I have reverted the commits:

https://github.com/android-hacker/VirtualXposed/commit/dab14b020f54f626ea515e570f41d99ef314169e
https://github.com/android-hacker/VirtualXposed/commit/421bdac77c96c9bd6fb25531a03ce4049e7430a1
https://github.com/android-hacker/VirtualXposed/commit/dab14b020f54f626ea515e570f41d99ef314169e

Thank you!


thanks @bhousel for the cleanup!


@bhousel this makes a lot of sense. These getters weren't being used yet anyways, but this helps clarify how updates work. Thanks!


haha


hah


ok nice done


My bad that was supposed to by pushed to my repo to create a PR.


wer


Is this a restriction you could remove?


Carol has a business to run ;)


This Seems to be working...


@pratikkapasi
@kajol22
@mohakkataria


`pymqi `只针对特定场景才需要，一般场景是不需要

可以直接参考该dockerfile，自己再写一个即可


Passing `bytes8` does not save gas because they are padded to `bytes32` in the tx and then _chopped_ back in the bytecode.


Interesting, why your choice of `sha256`?


Second time you `SLOAD` the balance ;)


Вообще это очень странное использование filter. Вы его можно сказать и не используете, можете заменить его на forEach.


`delete accounts[msg.sender]` achieves the same.


У вас получается, что есть лишний перенос строки, в самом конце, а его не должно быть .


add `html_cutoff` argument in `Book.getch_data` and `Book.write_htmls`. Too much irrelevant contents (not directly related to the text itself) in the original Han-Ji source page. Kick them out to save the memory and make the bs4 tree structure shallower.


Plus, when Carol has her password, she can brute-force the other password's 43 billion possibilities. Hard, not impossibly hard.


Created multidev environment [nhtv#ci-220](https://dashboard.pantheon.io/sites/a5faca03-4b4c-4936-95b8-6410ab7b2c55#ci-220).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-220-nhtv.pantheonsite.io/)


Pretty nice way to refactor code:
to pass an object and fetch data from it in `cshtml`s


Removed. Actually i created it from unit testing and forgot to remove it. Thks


Also, do you allow reuse of the same passwords over and over?


Why not putting `passthru` directly into `self.buildEnv`? Does it not take this attribute?


Nice amount of code in the commits, and it is pretty obvious what it is for.
If you want to do it in a bit better way, you can add a bit longer description.
Adding a `cshtml` is not a feature, it is a generated or added code to it.
The text should be something like this: `can provide tricks through school.cshtml`.


It is nice from you, that you are using `add`instead of `added`. 👍


@pratikkapasi
@kajol22
@mohakkataria
@shubhambadkur12
@ratanphayade


une modification quelconque !


Please don't let inner fields `leak`. Use meaningful methods to gather the data from `Model class`es.
This mentality/strategy will give your code good structure and modality.
Nice solution anyway, keep up the good work. 🥇


Make it an official PR and ask for help, there. I think, you will get a lot of good advice.


Missing newline between methods. I know it is not a big thing, but necessary to keep your code easy-to-read.


Hi! This is the friendly automated conda-forge-webservice.

I updated the Github team because of this commit.

- @davidcortesortuno were added to conda-forge. Welcome to conda-forge!"
  Go to https://github.com/orgs/conda-forge/invitation see your invitation.

- @davidcortesortuno were added to this feedstock maintenance team.
  You should get push access to this feedstock and CI services.

Feel free to join the community [chat room](https://gitter.im/conda-forge/conda-forge.github.io).

NOTE: Please make sure to not push to the repository directly.
      Use branches in your fork for any changes and send a PR.
      More details [here](https://conda-forge.org/docs/conda-forge_gotchas.html#using-a-fork-vs-a-branch-when-updating-a-recipe)


Rに関してエラーが消えませんが他は問題ないと思います。


hello,Apache Kylin Cube is built with Spark as the engine. The Cube that is finished in about 30 minutes at ordinary times is frequently stuck in 54.55% recently. There are no errors.
![image](https://user-images.githubusercontent.com/7369529/42158877-64c27aae-7e24-11e8-9d0a-a7c8a3057957.png)


Still need to do the delimiters (; -> join() and & -> nah).


Seems u are right on both counts @michaelatmender. Thank you!


It is a bit dangerous to pass something to the View, what's type is a string. In many cases, it can be misleading and malfunctioning because the controller will look up and try to load them cshtml in your folder, but you can use the method name as a fixpoint. If your cshtml is in the right folder and named as the method it will be straightforward and should cause no ambiguity or inconsistency.


Nice way to create Models when you put properties, it will provide you fields, getters, and getters the same time 👍


This was by accident, it'll be fixed in a few minutes


Me too. It's working now


```javascript
var index = 1;
for( ;index<10;index++) {
     b$(".theme_1_"+index).css({'display':'none'});
}
```


주석은
<!-- -->
말고
<%-- --%>
을 사용하면 브라우저의 개발자도구에서 해당 주석을 확인할 수 없음


Hi,

Ok. I installed ubuntu's QT packages. I have had a crash.
I recompiled the whole o-llvm with assertions enabled :
```
cmake -G "Unix Makefiles" -DCMAKE_BUILD_TYPE=Release -DLLVM_ENABLE_ASSERTIONS=ON -DLLDB_CODESIGN_IDENTITY='' ../obfuscator.llvm-6.0.0.src
```
Then I could enable debug messages from the string obfuscation pass with `-mllvm -debug-only=sobf`.

And at last I had this crash :
```
12:16:04: Running steps for project singlefile...
12:16:04: Configuration unchanged, skipping qmake step.
12:16:04: Starting: "/usr/bin/make"
/usr/lib/qt5/bin/qmake -o Makefile ../singlefile/singlefile.pro -spec linux-clang CONFIG+=debug CONFIG+=qml_debug
Project MESSAGE: C++ obfuscation enabled!
Project WARNING: CONFIG-=import_qpa_plugin is deprecated. Use QTPLUGIN.platforms=- instead.
clang++ -c -pipe -mllvm -sub -mllvm -sub_loop=3 -mllvm -fla -mllvm -spli -mllvm -split_num=2 -mllvm -bcf -mllvm -bcf_loop=2 -mllvm -sobf -mllvm -debug-only=sobf -O2 -D_REENTRANT -fPIC -DQT_CORE_LIB -I../singlefile -I. -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-clang -o main.o ../singlefile/main.cpp
Global var .strStringObfuscationPass: Global variable found : .str
 is constantGlobal var __PRETTY_FUNCTION__._Z4textvStringObfuscationPass: Global variable found : __PRETTY_FUNCTION__._Z4textv
 is constantGlobal var .str.1StringObfuscationPass: Global variable found : .str.1
 is constantGlobal var __PRETTY_FUNCTION__.mainStringObfuscationPass: Global variable found : __PRETTY_FUNCTION__.main
 is constantGlobal var .str.2StringObfuscationPass: Global variable found : .str.2
 is constantGlobal var .str.3StringObfuscationPass: Global variable found : .str.3
 is constantGlobal var xStringObfuscationPass: Global variable found : x
Global var yStringObfuscationPass: Global variable found : y
Global var x.4StringObfuscationPass: Global variable found : x.4
Global var y.5StringObfuscationPass: Global variable found : y.5
Global var x.6StringObfuscationPass: Global variable found : x.6
Global var y.7StringObfuscationPass: Global variable found : y.7
Global var x.8StringObfuscationPass: Global variable found : x.8
Global var y.9StringObfuscationPass: Global variable found : y.9
Global var x.10StringObfuscationPass: Global variable found : x.10
Global var y.11StringObfuscationPass: Global variable found : y.11
Global var x.12StringObfuscationPass: Global variable found : x.12
Global var y.13StringObfuscationPass: Global variable found : y.13
Global var x.14StringObfuscationPass: Global variable found : x.14
Global var y.15StringObfuscationPass: Global variable found : y.15
Global var x.16StringObfuscationPass: Global variable found : x.16
Global var y.17StringObfuscationPass: Global variable found : y.17
Global var x.18StringObfuscationPass: Global variable found : x.18
Global var y.19StringObfuscationPass: Global variable found : y.19
Global var x.20StringObfuscationPass: Global variable found : x.20
Global var y.21StringObfuscationPass: Global variable found : y.21
Global var x.22StringObfuscationPass: Global variable found : x.22
Global var y.23StringObfuscationPass: Global variable found : y.23
Global var x.24StringObfuscationPass: Global variable found : x.24
Global var y.25StringObfuscationPass: Global variable found : y.25
Global var x.26StringObfuscationPass: Global variable found : x.26
Global var y.27StringObfuscationPass: Global variable found : y.27
Global var x.28StringObfuscationPass: Global variable found : x.28
Global var y.29StringObfuscationPass: Global variable found : y.29
Global var x.30StringObfuscationPass: Global variable found : x.30
Global var y.31StringObfuscationPass: Global variable found : y.31
Global var x.32StringObfuscationPass: Global variable found : x.32
Global var y.33StringObfuscationPass: Global variable found : y.33
Global var x.34StringObfuscationPass: Global variable found : x.34
Global var y.35StringObfuscationPass: Global variable found : y.35
Global var x.36StringObfuscationPass: Global variable found : x.36
Global var y.37StringObfuscationPass: Global variable found : y.37
Global var x.38StringObfuscationPass: Global variable found : x.38
Global var y.39StringObfuscationPass: Global variable found : y.39
Global var x.40StringObfuscationPass: Global variable found : x.40
Global var y.41StringObfuscationPass: Global variable found : y.41
Global var x.42StringObfuscationPass: Global variable found : x.42
Global var y.43StringObfuscationPass: Global variable found : y.43
Global var x.44StringObfuscationPass: Global variable found : x.44
Global var y.45StringObfuscationPass: Global variable found : y.45
Global var x.46StringObfuscationPass: Global variable found : x.46
Global var y.47StringObfuscationPass: Global variable found : y.47
Global var x.48StringObfuscationPass: Global variable found : x.48
Global var y.49StringObfuscationPass: Global variable found : y.49
Global var x.50StringObfuscationPass: Global variable found : x.50
Global var y.51StringObfuscationPass: Global variable found : y.51
Global var x.52StringObfuscationPass: Global variable found : x.52
Global var y.53StringObfuscationPass: Global variable found : y.53
Global var x.54StringObfuscationPass: Global variable found : x.54
Global var y.55StringObfuscationPass: Global variable found : y.55
Global var x.56StringObfuscationPass: Global variable found : x.56
Global var y.57StringObfuscationPass: Global variable found : y.57
Global var x.58StringObfuscationPass: Global variable found : x.58
Global var y.59StringObfuscationPass: Global variable found : y.59
Global var x.60StringObfuscationPass: Global variable found : x.60
Global var y.61StringObfuscationPass: Global variable found : y.61
Global var x.62StringObfuscationPass: Global variable found : x.62
Global var y.63StringObfuscationPass: Global variable found : y.63
Global var x.64StringObfuscationPass: Global variable found : x.64
Global var y.65StringObfuscationPass: Global variable found : y.65
Global var x.66StringObfuscationPass: Global variable found : x.66
Global var y.67StringObfuscationPass: Global variable found : y.67
Global var x.68StringObfuscationPass: Global variable found : x.68
Global var y.69StringObfuscationPass: Global variable found : y.69
Global var x.70StringObfuscationPass: Global variable found : x.70
Global var y.71StringObfuscationPass: Global variable found : y.71
Global var x.72StringObfuscationPass: Global variable found : x.72
Global var y.73StringObfuscationPass: Global variable found : y.73
Global var .str.74StringObfuscationPass: Global variable found : .str.74
Global var __PRETTY_FUNCTION__._Z4textv.75StringObfuscationPass: Global variable found : __PRETTY_FUNCTION__._Z4textv.75
Global var .str.1.76StringObfuscationPass: Global variable found : .str.1.76
Global var __PRETTY_FUNCTION__.main.77StringObfuscationPass: Global variable found : __PRETTY_FUNCTION__.main.77
Global var .str.2.78StringObfuscationPass: Global variable found : .str.2.78
Global var .str.3.79StringObfuscationPass: Global variable found : .str.3.79
Function name is .datadiv_decode2267055700760734089
Adding code for .str.74
Adding code for __PRETTY_FUNCTION__._Z4textv.75
Adding code for .str.1.76
Adding code for __PRETTY_FUNCTION__.main.77
Adding code for .str.2.78
Adding code for .str.3.79
clang++ -c -pipe -mllvm -sub -mllvm -sub_loop=3 -mllvm -fla -mllvm -spli -mllvm -split_num=2 -mllvm -bcf -mllvm -bcf_loop=2 -mllvm -sobf -mllvm -debug-only=sobf -O2 -D_REENTRANT -fPIC -DQT_CORE_LIB -I../singlefile -I. -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-clang -o testclass.o ../singlefile/testclass.cpp
Global var _ZTV9TestClassStringObfuscationPass: Global variable found : _ZTV9TestClass
Global var xStringObfuscationPass: Global variable found : x
Global var yStringObfuscationPass: Global variable found : y
Function name is .datadiv_decode16797152721605294485
/usr/lib/qt5/bin/moc -DQT_CORE_LIB -D__cplusplus=201402L -D__GNUC__=7 -D__GNUC_MINOR__=3 -D__GNUC_PATCHLEVEL__=0 -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-clang -I/home/msc/Workspaces/o-llvm-workspace/singlefile -I/usr/include/x86_64-linux-gnu/qt5 -I/usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/include/c++/7 -I/usr/include/x86_64-linux-gnu/c++/7 -I/usr/include/c++/7/backward -I/usr/lib/gcc/x86_64-linux-gnu/7/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/7/include-fixed -I/usr/include/x86_64-linux-gnu -I/usr/include ../singlefile/testclass.h -o moc_testclass.cpp
clang++ -c -pipe -mllvm -sub -mllvm -sub_loop=3 -mllvm -fla -mllvm -spli -mllvm -split_num=2 -mllvm -bcf -mllvm -bcf_loop=2 -mllvm -sobf -mllvm -debug-only=sobf -O2 -D_REENTRANT -fPIC -DQT_CORE_LIB -I../singlefile -I. -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -I. -I/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-clang -o moc_testclass.o moc_testclass.cpp
Global var _ZN7QObject16staticMetaObjectEStringObfuscationPass: Global variable found : _ZN7QObject16staticMetaObjectE
Global var _ZL22qt_meta_data_TestClassStringObfuscationPass: Global variable found : _ZL22qt_meta_data_TestClass
 is constantGlobal var _ZN9TestClass16staticMetaObjectEStringObfuscationPass: Global variable found : _ZN9TestClass16staticMetaObjectE
Global var _ZTV9TestClassStringObfuscationPass: Global variable found : _ZTV9TestClass
Global var _ZTVN10__cxxabiv120__si_class_type_infoEStringObfuscationPass: Global variable found : _ZTVN10__cxxabiv120__si_class_type_infoE
Global var _ZTS9TestClassStringObfuscationPass: Global variable found : _ZTS9TestClass
 is constantGlobal var _ZTI7QObjectStringObfuscationPass: Global variable found : _ZTI7QObject
Global var _ZTI9TestClassStringObfuscationPass: Global variable found : _ZTI9TestClass
Global var .strStringObfuscationPass: Global variable found : .str
 is constantGlobal var __PRETTY_FUNCTION__._ZNK9TestClass4textEvStringObfuscationPass: Global variable found : __PRETTY_FUNCTION__._ZNK9TestClass4textEv
 is constantGlobal var .str.1StringObfuscationPass: Global variable found : .str.1
 is constantGlobal var .str.2StringObfuscationPass: Global variable found : .str.2
 is constantGlobal var .str.3StringObfuscationPass: Global variable found : .str.3
 is constantGlobal var .str.4StringObfuscationPass: Global variable found : .str.4
 is constantGlobal var _ZL28qt_meta_stringdata_TestClassStringObfuscationPass: Global variable found : _ZL28qt_meta_stringdata_TestClass
Global var xStringObfuscationPass: Global variable found : x
Global var yStringObfuscationPass: Global variable found : y
Global var x.6StringObfuscationPass: Global variable found : x.6
Global var y.7StringObfuscationPass: Global variable found : y.7
Global var x.8StringObfuscationPass: Global variable found : x.8
Global var y.9StringObfuscationPass: Global variable found : y.9
Global var x.10StringObfuscationPass: Global variable found : x.10
Global var y.11StringObfuscationPass: Global variable found : y.11
Global var x.12StringObfuscationPass: Global variable found : x.12
Global var y.13StringObfuscationPass: Global variable found : y.13
Global var x.14StringObfuscationPass: Global variable found : x.14
Global var y.15StringObfuscationPass: Global variable found : y.15
Global var x.16StringObfuscationPass: Global variable found : x.16
Global var y.17StringObfuscationPass: Global variable found : y.17
Global var x.18StringObfuscationPass: Global variable found : x.18
Global var y.19StringObfuscationPass: Global variable found : y.19
Global var x.20StringObfuscationPass: Global variable found : x.20
Global var y.21StringObfuscationPass: Global variable found : y.21
Global var x.22StringObfuscationPass: Global variable found : x.22
Global var y.23StringObfuscationPass: Global variable found : y.23
Global var x.24StringObfuscationPass: Global variable found : x.24
Global var y.25StringObfuscationPass: Global variable found : y.25
Global var x.26StringObfuscationPass: Global variable found : x.26
Global var y.27StringObfuscationPass: Global variable found : y.27
Global var x.28StringObfuscationPass: Global variable found : x.28
Global var y.29StringObfuscationPass: Global variable found : y.29
Global var x.30StringObfuscationPass: Global variable found : x.30
Global var y.31StringObfuscationPass: Global variable found : y.31
Global var x.32StringObfuscationPass: Global variable found : x.32
Global var y.33StringObfuscationPass: Global variable found : y.33
Global var x.34StringObfuscationPass: Global variable found : x.34
Global var y.35StringObfuscationPass: Global variable found : y.35
Global var x.36StringObfuscationPass: Global variable found : x.36
Global var y.37StringObfuscationPass: Global variable found : y.37
Global var x.38StringObfuscationPass: Global variable found : x.38
Global var y.39StringObfuscationPass: Global variable found : y.39
Global var x.40StringObfuscationPass: Global variable found : x.40
Global var y.41StringObfuscationPass: Global variable found : y.41
Global var x.42StringObfuscationPass: Global variable found : x.42
Global var y.43StringObfuscationPass: Global variable found : y.43
Global var x.44StringObfuscationPass: Global variable found : x.44
Global var y.45StringObfuscationPass: Global variable found : y.45
Global var x.46StringObfuscationPass: Global variable found : x.46
Global var y.47StringObfuscationPass: Global variable found : y.47
Global var x.48StringObfuscationPass: Global variable found : x.48
Global var y.49StringObfuscationPass: Global variable found : y.49
Global var x.50StringObfuscationPass: Global variable found : x.50
Global var y.51StringObfuscationPass: Global variable found : y.51
Global var x.52StringObfuscationPass: Global variable found : x.52
Global var y.53StringObfuscationPass: Global variable found : y.53
Global var x.54StringObfuscationPass: Global variable found : x.54
Global var y.55StringObfuscationPass: Global variable found : y.55
Global var x.56StringObfuscationPass: Global variable found : x.56
Global var y.57StringObfuscationPass: Global variable found : y.57
Global var _ZL22qt_meta_data_TestClass.58StringObfuscationPass: Global variable found : _ZL22qt_meta_data_TestClass.58
Global var _ZTS9TestClass.59StringObfuscationPass: Global variable found : _ZTS9TestClass.59
Global var .str.60StringObfuscationPass: Global variable found : .str.60
Global var __PRETTY_FUNCTION__._ZNK9TestClass4textEv.61StringObfuscationPass: Global variable found : __PRETTY_FUNCTION__._ZNK9TestClass4textEv.61
Global var .str.1.62StringObfuscationPass: Global variable found : .str.1.62
Global var .str.2.63StringObfuscationPass: Global variable found : .str.2.63
Global var .str.3.64StringObfuscationPass: Global variable found : .str.3.64
Global var .str.4.65StringObfuscationPass: Global variable found : .str.4.65
Function name is .datadiv_decode1363081302472564553
Adding code for _ZL22qt_meta_data_TestClass.58
clang-6.0: /opt/obfuscator.llvm-6.0.0.src/lib/IR/Instructions.cpp:2087: static llvm::BinaryOperator* llvm::BinaryOperator::Create(llvm::Instruction::BinaryOps, llvm::Value*, llvm::Value*, const llvm::Twine&, llvm::Instruction*): Assertion `S1->getType() == S2->getType() && "Cannot create binary operator with two operands of differing type!"' failed.
#0 0x000055a19ddf287a llvm::sys::PrintStackTrace(llvm::raw_ostream&) (/opt/obfuscator.llvm-6.0.0.build/bin/clang-6.0+0x254d87a)
#1 0x000055a19ddf04a6 llvm::sys::RunSignalHandlers() (/opt/obfuscator.llvm-6.0.0.build/bin/clang-6.0+0x254b4a6)
#2 0x000055a19ddf0845 SignalHandler(int) (/opt/obfuscator.llvm-6.0.0.build/bin/clang-6.0+0x254b845)
#3 0x00007f5882085890 __restore_rt (/lib/x86_64-linux-gnu/libpthread.so.0+0x12890)
#4 0x00007f5880d31e97 gsignal /build/glibc-OTsEL5/glibc-2.27/signal/../sysdeps/unix/sysv/linux/raise.c:51:0
#5 0x00007f5880d33801 abort /build/glibc-OTsEL5/glibc-2.27/stdlib/abort.c:81:0
#6 0x00007f5880d2339a __assert_fail_base /build/glibc-OTsEL5/glibc-2.27/assert/assert.c:89:0
#7 0x00007f5880d23412 (/lib/x86_64-linux-gnu/libc.so.6+0x30412)
#8 0x000055a19d8910ac (/opt/obfuscator.llvm-6.0.0.build/bin/clang-6.0+0x1fec0ac)
#9 0x000055a19d8910c3 llvm::BinaryOperator::Create(llvm::Instruction::BinaryOps, llvm::Value*, llvm::Value*, llvm::Twine const&, llvm::BasicBlock*) (/opt/obfuscator.llvm-6.0.0.build/bin/clang-6.0+0x1fec0c3)
#10 0x000055a19f9e1e0b llvm::StringObfuscationPass::addDecodeFunction(llvm::Module*, std::vector<llvm::encVar*, std::allocator<llvm::encVar*> >*) (/opt/obfuscator.llvm-6.0.0.build/bin/clang-6.0+0x413ce0b)
#11 0x000055a19f9e2c45 llvm::StringObfuscationPass::runOnModule(llvm::Module&) (/opt/obfuscator.llvm-6.0.0.build/bin/clang-6.0+0x413dc45)
#12 0x000055a19d8b77a1 llvm::legacy::PassManagerImpl::run(llvm::Module&) (/opt/obfuscator.llvm-6.0.0.build/bin/clang-6.0+0x20127a1)
#13 0x000055a19dfcc396 (anonymous namespace)::EmitAssemblyHelper::EmitAssembly(clang::BackendAction, std::unique_ptr<llvm::raw_pwrite_stream, std::default_delete<llvm::raw_pwrite_stream> >) (/opt/obfuscator.llvm-6.0.0.build/bin/clang-6.0+0x2727396)
#14 0x000055a19dfcdf45 clang::EmitBackendOutput(clang::DiagnosticsEngine&, clang::HeaderSearchOptions const&, clang::CodeGenOptions const&, clang::TargetOptions const&, clang::LangOptions const&, llvm::DataLayout const&, llvm::Module*, clang::BackendAction, std::unique_ptr<llvm::raw_pwrite_stream, std::default_delete<llvm::raw_pwrite_stream> >) (/opt/obfuscator.llvm-6.0.0.build/bin/clang-6.0+0x2728f45)
#15 0x000055a19e87edf8 clang::BackendConsumer::HandleTranslationUnit(clang::ASTContext&) (/opt/obfuscator.llvm-6.0.0.build/bin/clang-6.0+0x2fd9df8)
#16 0x000055a19ea76e8a clang::ParseAST(clang::Sema&, bool, bool) (/opt/obfuscator.llvm-6.0.0.build/bin/clang-6.0+0x31d1e8a)
#17 0x000055a19e87dae8 clang::CodeGenAction::ExecuteAction() (/opt/obfuscator.llvm-6.0.0.build/bin/clang-6.0+0x2fd8ae8)
#18 0x000055a19e3c2b56 clang::FrontendAction::Execute() (/opt/obfuscator.llvm-6.0.0.build/bin/clang-6.0+0x2b1db56)
#19 0x000055a19e38a7de clang::CompilerInstance::ExecuteAction(clang::FrontendAction&) (/opt/obfuscator.llvm-6.0.0.build/bin/clang-6.0+0x2ae57de)
#20 0x000055a19e46012a clang::ExecuteCompilerInvocation(clang::CompilerInstance*) (/opt/obfuscator.llvm-6.0.0.build/bin/clang-6.0+0x2bbb12a)
#21 0x000055a19c5e57a8 cc1_main(llvm::ArrayRef<char const*>, char const*, void*) (/opt/obfuscator.llvm-6.0.0.build/bin/clang-6.0+0xd407a8)
#22 0x000055a19c55f398 main (/opt/obfuscator.llvm-6.0.0.build/bin/clang-6.0+0xcba398)
#23 0x00007f5880d14b97 __libc_start_main /build/glibc-OTsEL5/glibc-2.27/csu/../csu/libc-start.c:344:0
#24 0x000055a19c5e173a _start (/opt/obfuscator.llvm-6.0.0.build/bin/clang-6.0+0xd3c73a)
Stack dump:
0.	Program arguments: /opt/obfuscator.llvm-6.0.0.build/bin/clang-6.0 -cc1 -triple x86_64-unknown-linux-gnu -emit-obj -disable-free -main-file-name moc_testclass.cpp -mrelocation-model pic -pic-level 2 -mthread-model posix -fmath-errno -masm-verbose -mconstructor-aliases -munwind-tables -fuse-init-array -target-cpu x86-64 -dwarf-column-info -debugger-tuning=gdb -momit-leaf-frame-pointer -coverage-notes-file /home/msc/Workspaces/o-llvm-workspace/build-singlefile-Desktop-Debug/moc_testclass.gcno -resource-dir /opt/obfuscator.llvm-6.0.0.build/lib/clang/6.0.0 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -D _REENTRANT -D QT_CORE_LIB -I ../singlefile -I . -I . -I /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-clang -internal-isystem /usr/lib/gcc/x86_64-linux-gnu/7.3.0/../../../../include/c++/7.3.0 -internal-isystem /usr/lib/gcc/x86_64-linux-gnu/7.3.0/../../../../include/x86_64-linux-gnu/c++/7.3.0 -internal-isystem /usr/lib/gcc/x86_64-linux-gnu/7.3.0/../../../../include/x86_64-linux-gnu/c++/7.3.0 -internal-isystem /usr/lib/gcc/x86_64-linux-gnu/7.3.0/../../../../include/c++/7.3.0/backward -internal-isystem /usr/local/include -internal-isystem /opt/obfuscator.llvm-6.0.0.build/lib/clang/6.0.0/include -internal-externc-isystem /usr/include/x86_64-linux-gnu -internal-externc-isystem /include -internal-externc-isystem /usr/include -O2 -fdeprecated-macro -fdebug-compilation-dir /home/msc/Workspaces/o-llvm-workspace/build-singlefile-Desktop-Debug -ferror-limit 19 -fmessage-length 0 -fobjc-runtime=gcc -fcxx-exceptions -fexceptions -fdiagnostics-show-option -vectorize-loops -vectorize-slp -mllvm -sub -mllvm -sub_loop=3 -mllvm -fla -mllvm -spli -mllvm -split_num=2 -mllvm -bcf -mllvm -bcf_loop=2 -mllvm -sobf -mllvm -debug-only=sobf -o moc_testclass.o -x c++ moc_testclass.cpp
1.	<eof> parser at end of file
2.	Per-module optimization passes
3.	Running pass 'Global variable (i.e., const char*) diversification pass' on module 'moc_testclass.cpp'.
clang-6.0: error: unable to execute command: Aborted (core dumped)
clang-6.0: error: clang frontend command failed due to signal (use -v to see invocation)
clang version 6.0.0 (tags/RELEASE_600/final)
Target: x86_64-unknown-linux-gnu
Thread model: posix
InstalledDir: /opt/obfuscator/bin
clang-6.0: note: diagnostic msg: PLEASE submit a bug report to http://o-llvm.org/ and include the crash backtrace, preprocessed source, and associated run script.
clang-6.0: note: diagnostic msg:
********************

PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT:
Preprocessed source(s) and associated run script(s) are located at:
clang-6.0: note: diagnostic msg: /tmp/moc_testclass-cf1622.cpp
clang-6.0: note: diagnostic msg: /tmp/moc_testclass-cf1622.sh
clang-6.0: note: diagnostic msg:

********************
Makefile:320: recipe for target 'moc_testclass.o' failed
make: *** [moc_testclass.o] Error 254
12:17:29: The process "/usr/bin/make" exited with code 2.
Error while building/deploying project singlefile (kit: Desktop)
When executing step "Make"
12:17:29: Elapsed time: 01:25.
```

Looks like it is the same bug.


@minglich wich one????


Adding alt to an image is good, please don't delete it. It is good to put it there, cause the blinds and the ones who cannot see well will use that field.


let's add a note to make it clear `Iterator` assertions are limited and that users should use `toIterable` to get the richer Iterable assertions.


# Specs execution successful
:scroll: [View logs](http://bamboo.comnull)
### Plans updated

Bamboo specs have been successfully imported and the following plans have been updated.

Project | Plan | Build
---|---|---
[Test](http://bamboo.com/browse/TEST) | [Comment test](http://bamboo.com/browse/TEST-CTEST)  | :white_check_mark: [\#1](http://bamboo.com/browse/TEST-CTEST-1)
[New project](http://bamboo.com/browse/NEW) | [Disabled plan](http://bamboo.com/browse/NEW-DISABLED) **disabled** | :white_check_mark: [\#1](http://bamboo.com/browse/NEW-DISABLED-1)

### Deployments updated

Bamboo specs have been successfully imported and the following deployment projects have been updated.

|Deployment project |
----|
[Deployment test](http://bamboo.com/deploy/viewDeploymentProjectVersions.action?id=2162689)|


Collaborator: Review for this commit was created. [Link to review](http://217.170.125.19:40101/ui#review:id=4)


@waldo1001, please update package.json with the same tips :-)

I know that I'm bad at reading readme files, and I assume that I'm not alone. I prefer if the documentation is where you need it (tooltips, contextual help etc). In this case as a comment when you are changing the setting. Make sense? ;-)


@masc4ii: I hope I have not missed anything :) like settings saving etc...


Premiere and many other NLs open this codec directly.


오타


buffer [] X


I will try a few things tonight and I'll send you the update, perhaps you can pull into your project.


let's use GIVEN WHEN THEN and `catchThrowable` as in:
```java
    // GIVEN
    SoftAssertions softly = new SoftAssertions();
    softly.fail("failure", throwRuntimeException());
    // WHEN
    AssertionError error = catchThrowableOfType(() -> softly.assertAll(), AssertionError.class);
    // THEN
    assertThat(error).hasMessage ...
```


Not sure how to get text to properly display with UTF-8 encoding. For example, I want the name "Luka Dončić" to show up in the console as normal.


IBM Cloud [toolchain](https://console.ng.bluemix.net/devops/toolchains/a721e67b-3c32-4033-a298-fb5b5817b995?env_id=ibm%3Ayp%3Aus-south "blockchain-20180621131227171"): [Delivery Pipeline](https://console.ng.bluemix.net/devops/pipelines/2c4f747a-bf40-48e3-ad7f-057bc29baa9e?env_id=ibm%3Ayp%3Aus-south "blockchain-20180621131227171") deployed [blockchain-starter-kit-staging](https://github.com/jt-nti/blockchain-starter-kit-staging/releases/tag/deploy-ibm-ys1-us-south-jamest-uk.ibm.com-blockchain-20180702-103139 "deploy-ibm-ys1-us-south-jamest-uk.ibm.com-blockchain-20180702-103139") to [blockchain](https://console.stage1.bluemix.net/apps/29186ede-8a67-4dce-b6fd-2eb4c5551c85?env_id=ibm:ys1:us-south "ibm:ys1:us-south:jamest@uk.ibm.com:blockchain"), including this commit