- using R version 4.4.1 (2024-06-14)
- using platform: aarch64-apple-darwin20
- R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
- running under: macOS Ventura 13.4
- using session charset: UTF-8
- checking for file ‘polykde/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘polykde’ version ‘1.0.0’
- 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 ‘polykde’ can be installed ... [22s/24s] OK
See the install log for details.
- used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
- used SDK: ‘MacOSX11.3.sdk’
- checking installed package size ... NOTE
installed size is 6.9Mb
sub-directories of 1Mb or more:
libs 6.6Mb
- checking package 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 ... [0s/0s] OK
- checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
- checking whether the package can be unloaded cleanly ... [0s/0s] OK
- checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
- checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
- checking loading without being on the library search path ... [0s/0s] 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 ... [3s/3s] OK
- checking Rd files ... [0s/0s] OK
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- 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 line endings in C/C++/Fortran sources/headers ... OK
- checking line endings in Makefiles ... OK
- checking compilation flags in Makevars ... OK
- checking for GNU extensions in Makefiles ... OK
- checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
- checking use of PKG_*FLAGS in Makefiles ... OK
- checking compiled code ... OK
- checking examples ... [3s/4s] ERROR
Running examples in ‘polykde-Ex.R’ failed
The error most likely occurred in:
> ### Name: index_ridge
> ### Title: Index a ridge curve, creating the Smoothed and Indexed Estimated
> ### Ridge (SIER)
> ### Aliases: index_ridge
>
> ### ** Examples
>
> ## Test on (S^1)^2
>
> # Sample
> set.seed(132121)
> r <- 2
> d <- rep(1, r)
> n <- 200
> ind_dj <- comp_ind_dj(d = d)
> Th <- matrix(runif(n = n * (r - 1), min = -pi / 2, max = pi / 2),
+ nrow = n, ncol = r - 1)
> Th[, r - 1] <- sort(Th[, r - 1])
> Th <- cbind(Th, sdetorus::toPiInt(
+ pi + Th[, r - 1] + runif(n = n, min = -pi / 4, max = pi / 4)))
> X <- angles_to_torus(Th)
> col_X_alp <- viridis::viridis(n, alpha = 0.25)
> col_X <- viridis::viridis(n)
>
> # Euler
> h_rid <- rep(0.75, r)
> h_eu <- h_rid^2
> N <- 200
> eps <- 1e-6
> Y <- euler_ridge(x = X, X = X, d = d, h = h_rid, h_euler = h_eu,
+ N = N, eps = eps, keep_paths = TRUE)
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
>
> # Visualization
> i <- N # Between 1 and N
> plot(rbind(torus_to_angles(Y$paths[, , 1])), col = col_X_alp, pch = 19,
+ axes = FALSE, xlim = c(-pi, pi), ylim = c(-pi, pi),
+ xlab = "", ylab = "")
> points(rbind(torus_to_angles(Y$paths[, , i])), col = col_X, pch = 16,
+ cex = 0.75)
> sdetorus::torusAxis(1:2)
> for (k in seq_len(nrow(Y$paths))) {
+
+ xy <- torus_to_angles(t(Y$paths[k, , ]))
+ sdetorus::linesTorus(x = xy[, 1], y = xy[, 2], col = col_X_alp[k])
+
+ }
>
> # SIER
> ind_rid <- index_ridge(endpoints = Y$ridge_y, X = X, d = d,
+ probs_scores = seq(0, 1, l = 50))
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
there is no package called ‘pan’
Calls: index_ridge ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [14s/14s] ERROR
Running ‘testthat.R’ [13s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
>
> library(testthat)
> library(polykde)
> test_check("polykde")
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|======================================================================| 100%[ FAIL 2 | WARN 0 | SKIP 8 | PASS 761 ]
══ Skipped tests (8) ═══════════════════════════════════════════════════════════
• No tests for euler ridges, just visualizations (1): 'tests_euler.R:504:1'
• Unstable (7): 'tests_bwd.R:36:3', 'tests_bwd.R:46:3', 'tests_kde.R:154:3',
'tests_kre.R:44:3', 'tests_tests.R:115:3', 'tests_tests.R:191:3',
'tests_tests.R:200:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('tests_euler.R:48:3'): index_ridge does not return error ───────────
Expected `index_ridge(endpoints = Y$ridge_y, X = X, d = d)` to run without any errors.
ℹ Actually got a <packageNotFoundError> with text:
there is no package called 'pan'
── Failure ('tests_euler.R:49:3'): index_ridge does not return error ───────────
Expected `index_ridge(endpoints = Y$ridge_y, X = X, d = d, verbose = TRUE)` to run without any errors.
ℹ Actually got a <packageNotFoundError> with text:
there is no package called 'pan'
[ FAIL 2 | WARN 0 | SKIP 8 | PASS 761 ]
Error: Test failures
Execution halted
- checking PDF version of manual ... [4s/5s] OK
- DONE
Status: 2 ERRORs, 1 NOTE
- using check arguments '--no-clean-on-error '