Open njtierney opened 5 months ago
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 greta_sitrep() #> ℹ checking if python available #> ✔ python (v3.8) available #> #> ℹ checking if TensorFlow Probability available #> ✔ TensorFlow Probability (v0.19.0) available #> #> ℹ checking if TensorFlow available #> ✔ TensorFlow (v2.11.0) available #> #> ℹ checking if greta conda environment available #> ✔ greta conda environment available #> #> ℹ Initialising python and checking dependencies, this may take a moment. #> ✔ Initialising python and checking dependencies ... done! #> #> ℹ greta is ready to use! m <- model(normal(0,1)) draws <- mcmc(m) #> running 4 chains simultaneously on up to 8 CPU cores #> #> warmup 0/1000 | eta: ?s warmup == 50/1000 | eta: 11s warmup ==== 100/1000 | eta: 7s warmup ====== 150/1000 | eta: 5s warmup ======== 200/1000 | eta: 4s warmup ========== 250/1000 | eta: 3s warmup =========== 300/1000 | eta: 3s warmup ============= 350/1000 | eta: 2s warmup =============== 400/1000 | eta: 2s warmup ================= 450/1000 | eta: 2s warmup =================== 500/1000 | eta: 2s warmup ===================== 550/1000 | eta: 1s warmup ======================= 600/1000 | eta: 1s warmup ========================= 650/1000 | eta: 1s warmup =========================== 700/1000 | eta: 1s warmup ============================ 750/1000 | eta: 1s warmup ============================== 800/1000 | eta: 1s warmup ================================ 850/1000 | eta: 0s warmup ================================== 900/1000 | eta: 0s warmup ==================================== 950/1000 | eta: 0s warmup ====================================== 1000/1000 | eta: 0s #> sampling 0/1000 | eta: ?s sampling == 50/1000 | eta: 1s sampling ==== 100/1000 | eta: 1s sampling ====== 150/1000 | eta: 1s sampling ======== 200/1000 | eta: 1s sampling ========== 250/1000 | eta: 1s sampling =========== 300/1000 | eta: 1s sampling ============= 350/1000 | eta: 0s sampling =============== 400/1000 | eta: 0s sampling ================= 450/1000 | eta: 0s sampling =================== 500/1000 | eta: 0s sampling ===================== 550/1000 | eta: 0s sampling ======================= 600/1000 | eta: 0s sampling ========================= 650/1000 | eta: 0s sampling =========================== 700/1000 | eta: 0s sampling ============================ 750/1000 | eta: 0s sampling ============================== 800/1000 | eta: 0s sampling ================================ 850/1000 | eta: 0s sampling ================================== 900/1000 | eta: 0s sampling ==================================== 950/1000 | eta: 0s sampling ====================================== 1000/1000 | eta: 0s draws2 <- mcmc(m, thin = 100) #> running 4 chains simultaneously on up to 8 CPU cores #> warmup 0/1000 | eta: ?s warmup ==== 101/1000 | eta: 6s warmup ======== 202/1000 #> | eta: 3s warmup ============ 303/1000 | eta: 2s warmup =============== #> 404/1000 | eta: 2s warmup =================== 505/1000 | eta: 1s warmup #> ======================= 606/1000 | eta: 1s warmup =========================== #> 707/1000 | eta: 1s warmup =============================== 808/1000 | eta: 1s #> warmup =================================== 909/1000 | eta: 0s sampling 0/1000 | #> eta: ?s sampling ==== 101/1000 | eta: 0s sampling ======== 202/1000 | eta: 0s #> sampling ============ 303/1000 | eta: 0s sampling =============== 404/1000 | #> eta: 0s sampling =================== 505/1000 | eta: 0s sampling #> ======================= 606/1000 | eta: 0s sampling =========================== #> 707/1000 | eta: 0s sampling =============================== 808/1000 | eta: 0s #> sampling =================================== 909/1000 | eta: 0s #> Error: greta hit a tensorflow error: #> Graph execution error: #> #> Detected at node #> 'mcmc_sample_chain/trace_scan/TensorArrayV2Stack/TensorListStack' defined at #> (most recent call last): File "<string>", line 4, in fn File #> "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/reticulate/python/rpytools/call.py", #> line 7, in python_function value, error = rpycall.call_r_function(f, *args, #> **kwargs) File #> "/Users/nick/Library/r-miniconda-arm64/envs/greta-env-tf2/lib/python3.8/site-packages/tensorflow_probability/python/mcmc/sample.py", #> line 359, in sample_chain (_, _, final_kernel_results), (all_states, trace) = #> loop_util.trace_scan( File #> "/Users/nick/Library/r-miniconda-arm64/envs/greta-env-tf2/lib/python3.8/site-packages/tensorflow_probability/python/internal/loop_util.py", #> line 231, in trace_scan initial_trace, [ta.stack() for ta in trace_arrays], #> File #> "/Users/nick/Library/r-miniconda-arm64/envs/greta-env-tf2/lib/python3.8/site-packages/tensorflow_probability/python/internal/loop_util.py", #> line 231, in <listcomp> initial_trace, [ta.stack() for ta in trace_arrays], #> Node: 'mcmc_sample_chain/trace_scan/TensorArrayV2Stack/TensorListStack' Tried #> to stack elements of an empty list with non-fully-defined element_shape: [?,1] #> [[{{node mcmc_sample_chain/trace_scan/TensorArrayV2Stack/TensorListStack}}]] #> [Op:__inference_fn_9613]
Created on 2024-02-08 with reprex v2.1.0
Created on 2024-02-08 with reprex v2.1.0
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/Sydney #> date 2024-02-08 #> pandoc 3.1.1 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date (UTC) lib source #> abind 1.4-5 2016-07-21 [1] CRAN (R 4.3.0) #> 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 3.6.2 2023-12-11 [1] CRAN (R 4.3.1) #> coda 0.19-4.1 2024-01-31 [1] CRAN (R 4.3.1) #> 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 0.6.34 2024-01-11 [1] CRAN (R 4.3.1) #> evaluate 0.23 2023-11-01 [1] CRAN (R 4.3.1) #> fansi 1.0.6 2023-12-08 [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 1.33.1 2023-12-22 [1] CRAN (R 4.3.1) #> globals 0.16.2 2022-11-21 [1] CRAN (R 4.3.0) #> glue 1.7.0 2024-01-09 [1] CRAN (R 4.3.1) #> greta * 0.4.4.9000 2024-02-06 [1] Github (njtierney/greta@db4154e) #> 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 1.8.8 2023-12-04 [1] CRAN (R 4.3.1) #> knitr 1.45 2023-10-30 [1] CRAN (R 4.3.1) #> lattice 0.22-5 2023-10-24 [1] CRAN (R 4.3.1) #> lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.3.1) #> listenv 0.9.1 2024-01-29 [1] CRAN (R 4.3.1) #> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.0) #> Matrix 1.6-5 2024-01-11 [1] CRAN (R 4.3.1) #> parallelly 1.36.0 2023-05-26 [1] CRAN (R 4.3.0) #> pillar 1.9.0 2023-03-22 [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 3.8.3 2023-12-10 [1] CRAN (R 4.3.1) #> progress 1.2.3 2023-12-06 [1] CRAN (R 4.3.1) #> ps 1.7.6 2024-01-18 [1] CRAN (R 4.3.1) #> 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 1.26.0 2024-01-24 [1] CRAN (R 4.3.1) #> R.utils 2.12.3 2023-11-18 [1] CRAN (R 4.3.1) #> R6 2.5.1 2021-08-19 [1] CRAN (R 4.3.0) #> Rcpp 1.0.12 2024-01-09 [1] CRAN (R 4.3.1) #> reprex 2.1.0 2024-01-11 [1] CRAN (R 4.3.1) #> reticulate 1.35.0 2024-01-31 [1] CRAN (R 4.3.1) #> rlang 1.1.3 2024-01-10 [1] CRAN (R 4.3.1) #> 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 1.10.2 2023-08-29 [1] CRAN (R 4.3.0) #> tensorflow 2.15.0 2024-01-31 [1] CRAN (R 4.3.1) #> tfautograph 0.3.2 2021-09-17 [1] CRAN (R 4.3.0) #> tfruns 1.5.2 2024-01-26 [1] CRAN (R 4.3.1) #> utf8 1.2.4 2023-10-22 [1] CRAN (R 4.3.1) #> vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.3.1) #> whisker 0.4.1 2022-12-05 [1] CRAN (R 4.3.0) #> withr 3.0.0 2024-01-16 [1] CRAN (R 4.3.1) #> xfun 0.41 2023-11-01 [1] CRAN (R 4.3.1) #> yaml 2.3.8 2023-12-11 [1] CRAN (R 4.3.1) #> #> [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 #> #> ────────────────────────────────────────────────────────────────────────────── ```