Error in vignettes: Error: make_d_fn requires the distribution to be continuous, but a discrete component was detected

[barracuda156]

--->  Testing R-distfromq
Executing:  cd "/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-distfromq/R-distfromq/work/distfromq" && /opt/local/bin/R CMD check ./distfromq_1.0.4.tar.gz --no-manual --no-build-vignettes 
* using log directory ‘/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-distfromq/R-distfromq/work/distfromq/distfromq.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: powerpc-apple-darwin10.0.0d2 (32-bit)
* R was compiled by
    gcc-mp-13 (MacPorts gcc13 13.3.0_0+stdlib_flag) 13.3.0
    GNU Fortran (MacPorts gcc13 13.3.0_0+stdlib_flag) 13.3.0
* running under: OS X Snow Leopard 10.6
* using session charset: UTF-8
* using options ‘--no-manual --no-build-vignettes’
* checking for file ‘distfromq/DESCRIPTION’ ... OK
* this is package ‘distfromq’ version ‘1.0.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘distfromq’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ...
  ‘distfromq.Rmd’ using ‘UTF-8’... failed
 ERROR
Errors in running code in vignettes:
when running code in ‘distfromq.Rmd’
  ...
+     bins = 100) + theme_bw()

> mean(sampled_values_df$x == 0)
[1] 0.1989

> d_fn_lnorm <- make_d_fn(ps = ps, qs = qs, tail_dist = "lnorm")

  When sourcing ‘distfromq.R’:
Error: make_d_fn requires the distribution to be continuous, but a discrete component was detected
Execution halted

* checking re-building of vignette outputs ... SKIPPED
* DONE

Status: 1 ERROR
See
  ‘/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-distfromq/R-distfromq/work/distfromq/distfromq.Rcheck/00check.log’
for details.

Command failed:  cd "/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-distfromq/R-distfromq/work/distfromq" && /opt/local/bin/R CMD check ./distfromq_1.0.4.tar.gz --no-manual --no-build-vignettes 
Exit code: 1

> knitr::opts_chunk$set(collapse = TRUE, comment = "#>", 
+     fig.width = 8, fig.height = 8, out.width = "100%")

> library(distfromq)

> library(ggplot2)

> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union


> quantile_probs <- seq(from = 0.1, to = 0.9, by = 0.1)

> meanlog <- 4

> sdlog <- 0.5

> q_lognormal <- qlnorm(quantile_probs, meanlog = meanlog, 
+     sdlog = sdlog)

> x <- seq(from = 0, to = 400, length = 501)

> cdf_lognormal <- plnorm(x, meanlog = meanlog, sdlog = sdlog)

> p_lognormal_approx <- make_p_fn(ps = quantile_probs, 
+     qs = q_lognormal, tail_dist = "lnorm")

> cdf_lognormal_approx <- p_lognormal_approx(x)

> p_normal_approx <- make_p_fn(ps = quantile_probs, 
+     qs = q_lognormal, tail_dist = "norm")

> cdf_normal_approx <- p_normal_approx(x)

> p_cauchy_approx <- make_p_fn(ps = quantile_probs, 
+     qs = q_lognormal, tail_dist = "cauchy")

> cdf_cauchy_approx <- p_cauchy_approx(x)

> dplyr::bind_rows(data.frame(x = x, y = cdf_lognormal, 
+     dist = "Log normal"), data.frame(x = x, y = cdf_lognormal_approx, 
+     dist = "Spline ..." ... [TRUNCATED] 
Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.

> d_lognormal_approx <- make_d_fn(ps = quantile_probs, 
+     qs = q_lognormal, tail_dist = "lnorm")

> d_normal_approx <- make_d_fn(ps = quantile_probs, 
+     qs = q_lognormal, tail_dist = "norm")

> d_cauchy_approx <- make_d_fn(ps = quantile_probs, 
+     qs = q_lognormal, tail_dist = "cauchy")

> pdf_lognormal <- dlnorm(x, meanlog = meanlog, sdlog = sdlog)

> pdf_lognormal_approx <- d_lognormal_approx(x)

> pdf_normal_approx <- d_normal_approx(x)

> pdf_cauchy_approx <- d_cauchy_approx(x)

> dplyr::bind_rows(data.frame(x = x, y = pdf_lognormal, 
+     dist = "Log normal"), data.frame(x = x, y = pdf_lognormal_approx, 
+     dist = "Spline ..." ... [TRUNCATED] 

> d_lognormal_approx_n_grid_1 <- make_d_fn(ps = quantile_probs, 
+     qs = q_lognormal, tail_dist = "lnorm", interior_args = list(n_grid = 1))

> pdf_lognormal_approx_n_grid_1 <- d_lognormal_approx_n_grid_1(x)

> dplyr::bind_rows(data.frame(x = x, y = pdf_lognormal_approx, 
+     dist = "Spline interpolation,\n n_grid = 20"), data.frame(x = x, 
+     y = pdf_ .... [TRUNCATED] 

> r_normal_approx <- make_r_fn(ps = quantile_probs, 
+     qs = q_lognormal, tail_dist = "norm")

> r_lognormal_approx <- make_r_fn(ps = quantile_probs, 
+     qs = q_lognormal, tail_dist = "lnorm")

> r_cauchy_approx <- make_r_fn(ps = quantile_probs, 
+     qs = q_lognormal, tail_dist = "cauchy")

> normal_approx_sample <- r_normal_approx(n = 10000)

> lognormal_approx_sample <- r_lognormal_approx(n = 10000)

> cauchy_approx_sample <- r_cauchy_approx(n = 10000)

> bind_rows(data.frame(x = normal_approx_sample, dist = "Spline interpolation,\nnormal tails"), 
+     data.frame(x = lognormal_approx_sample, dist =  .... [TRUNCATED] 

> bind_rows(data.frame(x = normal_approx_sample, dist = "Spline interpolation,\nnormal tails"), 
+     data.frame(x = lognormal_approx_sample, dist =  .... [TRUNCATED] 
Warning: Removed 243 rows containing non-finite outside the scale range
(`stat_density()`).

> ps <- seq(from = 0.01, to = 0.99, by = 0.01)

> q_normal_approx <- make_q_fn(ps = quantile_probs, 
+     qs = q_lognormal, tail_dist = "norm")

> q_lognormal_approx <- make_q_fn(ps = quantile_probs, 
+     qs = q_lognormal, tail_dist = "lnorm")

> q_cauchy_approx <- make_q_fn(ps = quantile_probs, 
+     qs = q_lognormal, tail_dist = "cauchy")

> quantiles_lognormal <- qlnorm(ps, meanlog = meanlog, 
+     sdlog = sdlog)

> quantiles_normal_approx <- q_normal_approx(ps)

> quantiles_lognormal_approx <- q_lognormal_approx(ps)

> quantiles_cauchy_approx <- q_cauchy_approx(ps)

> dplyr::bind_rows(data.frame(x = ps, y = quantiles_lognormal, 
+     dist = "Log normal"), data.frame(x = ps, y = quantiles_normal_approx, 
+     dis .... [TRUNCATED] 

> lnorm_ps <- seq(from = 0.1, to = 0.9, by = 0.1)

> lnorm_qs <- qlnorm(lnorm_ps, meanlog = 4, sdlog = 0.5)

> adj_lnorm_ps <- 0.2 + lnorm_ps * 0.8

> point_p <- 0.2

> point_q <- 0

> ps <- c(point_p, adj_lnorm_ps)

> qs <- c(point_q, lnorm_qs)

> x <- seq(from = -100, to = 400, length = 501)

> p_lognormal_approx <- make_p_fn(ps = ps, qs = qs, 
+     tail_dist = "lnorm")

> cdf_lognormal_approx <- p_lognormal_approx(x)

> data.frame(x = x, y = cdf_lognormal_approx) %>% ggplot() + 
+     geom_line(mapping = aes(x = x, y = y), size = 0.8) + geom_point(data = data.frame( .... [TRUNCATED] 

> plot_ps <- seq(from = 0, to = 0.99, by = 0.001)

> q_lognormal_approx <- make_q_fn(ps = ps, qs = qs, 
+     tail_dist = "lnorm")

> qf_lognormal_approx <- q_lognormal_approx(plot_ps)

> data.frame(x = plot_ps, y = qf_lognormal_approx) %>% 
+     ggplot() + geom_line(mapping = aes(x = x, y = y), size = 0.8) + 
+     geom_point(data = .... [TRUNCATED] 

> dplyr::bind_rows(data.frame(x = x, y = cdf_lognormal_approx, 
+     method = "CDF Estimate"), data.frame(x = qf_lognormal_approx, 
+     y = plot_ps .... [TRUNCATED] 

> r_fn <- make_r_fn(ps = ps, qs = qs, tail_dist = "lnorm")

> sampled_values_df <- data.frame(x = r_fn(10000))

> ggplot(sampled_values_df) + geom_histogram(mapping = aes(x = x), 
+     bins = 100) + theme_bw()

> mean(sampled_values_df$x == 0)
[1] 0.1989

> d_fn_lnorm <- make_d_fn(ps = ps, qs = qs, tail_dist = "lnorm")

  When sourcing ‘distfromq.R’:
Error: make_d_fn requires the distribution to be continuous, but a discrete component was detected
Execution halted