TF2 error - Failure (`test_distributions.R:1110`): Cholesky factor of LJK_correlation should be an upper triangular matrix

Related to #593, should be addressed in #587

library(greta)
#> 
#> Attaching package: 'greta'
#> The following objects are masked from 'package:stats':
#> 
#>     binomial, cov2cor, poisson
#> The following objects are masked from 'package:base':
#> 
#>     %*%, apply, backsolve, beta, chol2inv, colMeans, colSums, diag,
#>     eigen, forwardsolve, gamma, identity, rowMeans, rowSums, sweep,
#>     tapply
x <- lkj_correlation(eta = 3, dimension = 3)
#> ℹ Initialising python and checking dependencies, this may take a moment.
#> ✔ Initialising python and checking dependencies ... done!
#> 
chol_x <- chol(x)
calc_chol <- calculate(x, chol_x, nsim = 1)
calc_chol
#> $x
#> , , 1
#> 
#>      [,1]      [,2]       [,3]
#> [1,]    1 0.1063213 -0.2843698
#> 
#> , , 2
#> 
#>           [,1] [,2]       [,3]
#> [1,] 0.1063213    1 -0.2060992
#> 
#> , , 3
#> 
#>            [,1]       [,2] [,3]
#> [1,] -0.2843698 -0.2060992    1
#> 
#> 
#> $chol_x
#> , , 1
#> 
#>      [,1] [,2] [,3]
#> [1,]    1    1    1
#> 
#> , , 2
#> 
#>      [,1] [,2] [,3]
#> [1,]    1    1    1
#> 
#> , , 3
#> 
#>      [,1] [,2] [,3]
#> [1,]    1    1    1
# calc_chol$chol_x should be upper tri, but is just 1s

^{Created on 2023-11-09 with reprex v2.0.2}

Session info

``` r sessioninfo::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.3.2 (2023-10-31) #> os macOS Sonoma 14.0 #> system aarch64, darwin20 #> ui X11 #> language (EN) #> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz Australia/Hobart #> date 2023-11-09 #> pandoc 3.1.1 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date (UTC) lib source #> backports 1.4.1 2021-12-13 [1] CRAN (R 4.3.0) #> base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.3.0) #> callr 3.7.3 2022-11-02 [1] CRAN (R 4.3.0) #> cli 3.6.1 2023-03-23 [1] CRAN (R 4.3.0) #> coda 0.19-4 2020-09-30 [1] CRAN (R 4.3.0) #> codetools 0.2-19 2023-02-01 [1] CRAN (R 4.3.2) #> crayon 1.5.2 2022-09-29 [1] CRAN (R 4.3.0) #> digest 0.6.33 2023-07-07 [1] CRAN (R 4.3.0) #> evaluate 0.23 2023-11-01 [1] CRAN (R 4.3.1) #> fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.3.0) #> fs 1.6.3 2023-07-20 [1] CRAN (R 4.3.0) #> future 1.33.0 2023-07-01 [1] CRAN (R 4.3.0) #> globals 0.16.2 2022-11-21 [1] CRAN (R 4.3.0) #> glue 1.6.2 2022-02-24 [1] CRAN (R 4.3.0) #> greta * 0.4.3.9000 2023-11-09 [1] local #> hms 1.1.3 2023-03-21 [1] CRAN (R 4.3.0) #> htmltools 0.5.7 2023-11-03 [1] CRAN (R 4.3.1) #> jsonlite 1.8.7 2023-06-29 [1] CRAN (R 4.3.0) #> knitr 1.45 2023-10-30 [1] CRAN (R 4.3.1) #> lattice 0.21-9 2023-10-01 [1] CRAN (R 4.3.2) #> lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.3.0) #> listenv 0.9.0 2022-12-16 [1] CRAN (R 4.3.0) #> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.0) #> Matrix 1.6-1.1 2023-09-18 [1] CRAN (R 4.3.2) #> parallelly 1.36.0 2023-05-26 [1] CRAN (R 4.3.0) #> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.0) #> png 0.1-8 2022-11-29 [1] CRAN (R 4.3.0) #> prettyunits 1.2.0 2023-09-24 [1] CRAN (R 4.3.1) #> processx 3.8.2 2023-06-30 [1] CRAN (R 4.3.0) #> progress 1.2.2 2019-05-16 [1] CRAN (R 4.3.0) #> ps 1.7.5 2023-04-18 [1] CRAN (R 4.3.0) #> purrr 1.0.2 2023-08-10 [1] CRAN (R 4.3.0) #> R.cache 0.16.0 2022-07-21 [1] CRAN (R 4.3.0) #> R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.3.0) #> R.oo 1.25.0 2022-06-12 [1] CRAN (R 4.3.0) #> R.utils 2.12.2 2022-11-11 [1] CRAN (R 4.3.0) #> R6 2.5.1 2021-08-19 [1] CRAN (R 4.3.0) #> Rcpp 1.0.11 2023-07-06 [1] CRAN (R 4.3.0) #> reprex 2.0.2 2022-08-17 [1] CRAN (R 4.3.0) #> reticulate 1.34.0 2023-10-12 [1] CRAN (R 4.3.1) #> rlang 1.1.1 2023-04-28 [1] CRAN (R 4.3.0) #> rmarkdown 2.25 2023-09-18 [1] CRAN (R 4.3.1) #> rstudioapi 0.15.0 2023-07-07 [1] CRAN (R 4.3.0) #> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.3.0) #> styler 1.9.1 2023-03-04 [1] CRAN (R 4.3.0) #> tensorflow 2.14.0 2023-09-28 [1] CRAN (R 4.3.1) #> tfautograph 0.3.2 2021-09-17 [1] CRAN (R 4.3.0) #> tfruns 1.5.1 2022-09-05 [1] CRAN (R 4.3.0) #> vctrs 0.6.4 2023-10-12 [1] CRAN (R 4.3.1) #> whisker 0.4.1 2022-12-05 [1] CRAN (R 4.3.0) #> withr 2.5.2 2023-10-30 [1] CRAN (R 4.3.1) #> xfun 0.41 2023-11-01 [1] CRAN (R 4.3.1) #> yaml 2.3.7 2023-01-23 [1] CRAN (R 4.3.0) #> #> [1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library #> #> ─ Python configuration ─────────────────────────────────────────────────────── #> python: /Users/nick/Library/r-miniconda-arm64/envs/greta-env-tf2/bin/python #> libpython: /Users/nick/Library/r-miniconda-arm64/envs/greta-env-tf2/lib/libpython3.8.dylib #> pythonhome: /Users/nick/Library/r-miniconda-arm64/envs/greta-env-tf2:/Users/nick/Library/r-miniconda-arm64/envs/greta-env-tf2 #> version: 3.8.15 | packaged by conda-forge | (default, Nov 22 2022, 08:49:06) [Clang 14.0.6 ] #> numpy: /Users/nick/Library/r-miniconda-arm64/envs/greta-env-tf2/lib/python3.8/site-packages/numpy #> numpy_version: 1.23.2 #> tensorflow: /Users/nick/Library/r-miniconda-arm64/envs/greta-env-tf2/lib/python3.8/site-packages/tensorflow #> #> NOTE: Python version was forced by use_python() function #> #> ────────────────────────────────────────────────────────────────────────────── ```

greta-dev / greta

TF2 error - Failure (`test_distributions.R:1110`): Cholesky factor of LJK_correlation should be an upper triangular matrix #594