detectImports fails with "error during compilation"

[clescoat]

Hi,

Thank you for this interesting method. I installed DetectImport on R without error but when I'm trying to run the test data the function detectImports fails with the following error: Erreur : An error occured during compilation! See the message above for more information. But it's the only output I received. I already reinstalled both package (cmdstanr and DetectImports) without effect. Could it be a missing dependency or a version issue?

install.packages("cmdstanr", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
library(cmdstanr)
install_cmdstan()
devtools::install_github("xavierdidelot/DetectImports")

library(DetectImports)
library(ape)

path=system.file("extdata", "example.nwk", package = "DetectImports")
tree=read.tree(path)
plot(tree,show.tip.label=F)
axisPhylo(1)

set.seed(0) #For reproducibility
res <- detectImports(tree)

Erreur : An error occured during compilation! See the message above for more information.

Session info

R version 4.3.2 (2023-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.6 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale: [1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C LC_TIME=fr_FR.UTF-8
[4] LC_COLLATE=fr_FR.UTF-8 LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8
[7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C

time zone: Europe/Paris tzcode source: system (glibc)

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] ape_5.7-1 DetectImports_0.9.1

loaded via a namespace (and not attached): [1] gtable_0.3.3 dplyr_1.1.2 compiler_4.3.2 tidyselect_1.2.0 Rcpp_1.0.12
[6] parallel_4.3.2 tidyr_1.3.0 scales_1.3.0 lattice_0.22-5 ggplot2_3.4.2
[11] R6_2.5.1 generics_0.1.3 distributional_0.3.2 knitr_1.42 backports_1.4.1
[16] checkmate_2.2.0 tibble_3.2.1 munsell_0.5.0 pillar_1.9.0 posterior_1.5.0
[21] rlang_1.1.1 utf8_1.2.3 xfun_0.39 cli_3.6.1 withr_2.5.0
[26] magrittr_2.0.3 ps_1.7.5 digest_0.6.31 grid_4.3.2 processx_3.8.1
[31] rstudioapi_0.14 cmdstanr_0.7.1 lifecycle_1.0.3 nlme_3.1-163 vctrs_0.6.2
[36] glue_1.6.2 tensorA_0.36.2.1 farver_2.1.1 abind_1.4-5 fansi_1.0.4
[41] colorspace_2.1-0 purrr_1.0.1 tools_4.3.2 pkgconfig_2.0.3

Thank you for your help !

[dhelekal]

This is probably going to be caused by Stan changing some syntax.

[xavierdidelot]

Yes indeed the Stan syntax has changed slightly but I have just pushed updated code. @clescoat could you please confirm if now works for you?

[clescoat]

It now runs perfectly on test data, thanks a lot !

[xavierdidelot]

That's great, thanks!