RStan Compile Error

Interfaces RStan
1

Went to compile some RStan code this morning and it generated a compile error. This code has had no compilation problems before today. I believe that the problem started after updating all my R packages this morning. Here is the error:

Error in compileCode(f, code, language = language, verbose = verbose) :
960 | enum { | ^/usr/bin/ld: /home/thomas/R/x86_64-pc-linux-gnu-library/4.0/rstan/lib//libStanServices.a(stan_fit.o): relocation R_X86_64_PC32 against undefined hidden symbol `_ZTCN5boost10wrapexceptINS_4math14rounding_errorEEE0_NS_16exception_detail10clone_implINS4_19error_info_injectorIS2_EEEE’ can not be used when making a shared object/usr/bin/ld: final link failed: bad valuecollect2: error: ld returned 1 exit statusmake: *** [/usr/share/R/share/make/shlib.mk:10: file830c9a0e68.so] Error 1

Here is R:

R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Linux Mint 20.1

Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libmkl_rt.so

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

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

other attached packages:
[1] metRology_0.9-28-1 rstan_2.21.2 ggplot2_3.3.3 StanHeaders_2.21.0-7 scales_1.1.1

loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 DEoptimR_1.0-8 pillar_1.4.7 compiler_4.0.3 prettyunits_1.1.1 tools_4.0.3 pkgbuild_1.2.0 jsonlite_1.7.2
[9] lifecycle_0.2.0 tibble_3.0.4 gtable_0.3.0 pkgconfig_2.0.3 rlang_0.4.10 cli_2.2.0 rstudioapi_0.13 parallel_4.0.3
[17] curl_4.3 loo_2.4.1 gridExtra_2.3 withr_2.3.0 dplyr_1.0.2 generics_0.1.0 vctrs_0.3.6 stats4_4.0.3
[25] grid_4.0.3 tidyselect_1.1.0 robustbase_0.93-7 glue_1.4.2 inline_0.3.17 R6_2.5.0 processx_3.4.5 fansi_0.4.1
[33] callr_3.5.1 purrr_0.3.4 magrittr_2.0.1 MASS_7.3-53 codetools_0.2-18 matrixStats_0.57.0 ps_1.5.0 ellipsis_0.3.1
[41] assertthat_0.2.1 colorspace_2.0-0 numDeriv_2016.8-1.1 V8_3.4.0 RcppParallel_5.0.2 munsell_0.5.0 crayon_1.3.4

And my OS:

System: Kernel: 5.4.0-60-generic x86_64 bits: 64 compiler: gcc v: 9.3.0 Desktop: Cinnamon 4.8.5
Distro: Linux Mint 20.1 Ulyssa base: Ubuntu 20.04 focal

2

The update of the BH package from 1.72.0-3 to 1.75.0-0 appears to have caused the problem. As a side note, no Stan code would compile – not even the bernoulli example from the manual.

3

Thanks Thomas, that’s indeed the case. You’ll need to reinstall RStan and StanHeaders, so that the packages are compiled against the updated headers in the BH package

2 Likes
4

your solution worked for me.
Thanks andrjohns

5

I’m glad to hear that a simple recompile is all that’s needed … can someone tell that to the https://launchpad.net/~c2d4u.team/ ? Because they still offer a version compiled last year - which means it doesn’t work in updated systems.

6

As the maintainer of c2d4u, I have rebuilt the package and rstan-2.21.2-1cran2 is now available. Please let me know if it does not fix the issue (marutterATgmail.com). I don’t use RStan, so if the error continues, I will need some example code to work with.