Dear all,
I’ve been having such a lovely time in the land of Linux, until a few weeks ago my compiler stopped worked unexpectedly. I am on Ubuntu 20.04, all packages up to date (sessionInfo at bottom of this message). Please see test code and error messages through brms
below. Please also see the very long error output for example(stan_model, package = "rstan", run.dontrun = TRUE)
attached rstan_compile_error_ubuntu_20.04_31.03.21.txt (34.4 KB).
I’ve seen recent problems in Windows (Error in compileCode(f, code, language = language, verbose = verbose) & Error in sink(type = "output") : invalid connection) and a few years ago in Ubuntu (Compiling error when running model in Ubuntu 18.04. Any ideas?) but the solutions there do not work for me.
Abundant thanks in advance for your help, I look forward to getting back to the Bayes!
#brms test
library(brms)
test <- data.frame(x = round(rnorm(20, 20, 5),0),
y = round(rnorm(20, 2, 0.2),2))
brm(y ~ x, data = test,
iter = 500, warmup = 250, chains = 1)
Compiling Stan program...
make cmd is
make -f '/usr/lib/R/etc/Makeconf' -f '/usr/share/R/share/make/shlib.mk' CXX='$(CXX14) $(CXX14STD)' CXXFLAGS='$(CXX14FLAGS)' CXXPICFLAGS='$(CXX14PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX14LDFLAGS)' SHLIB_LD='$(SHLIB_CXX14LD)' SHLIB='file35532f8a7d7c.so' OBJECTS='file35532f8a7d7c.o'
make would use
if test "zfile35532f8a7d7c.o" != "z"; then \
echo g++ -std=gnu++14 -shared -L"/usr/lib/R/lib" -Wl,-Bsymbolic-functions -Wl,-z,relro -o file35532f8a7d7c.so file35532f8a7d7c.o '/home/gzf2/R/x86_64-pc-linux-gnu-library/4.0/rstan/lib//libStanServices.a' -L'/home/gzf2/R/x86_64-pc-linux-gnu-library/4.0/StanHeaders/lib/' -lStanHeaders -L'/home/gzf2/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/lib/' -ltbb -L"/usr/lib/R/lib" -lR; \
g++ -std=gnu++14 -shared -L"/usr/lib/R/lib" -Wl,-Bsymbolic-functions -Wl,-z,relro -o file35532f8a7d7c.so file35532f8a7d7c.o '/home/gzf2/R/x86_64-pc-linux-gnu-library/4.0/rstan/lib//libStanServices.a' -L'/home/gzf2/R/x86_64-pc-linux-gnu-library/4.0/StanHeaders/lib/' -lStanHeaders -L'/home/gzf2/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/lib/' -ltbb -L"/usr/lib/R/lib" -lR; \
fi
Error in compileCode(f, code, language = language, verbose = verbose) :
/home/gzf2/R/x86_64-pc-linux-gnu-library/4.0/StanHeaders/include/src/stan/model/model_base_crtp.hpp:149:20: required from here/home/gzf2/R/x86_64-pc-linux-gnu-library/4.0/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits<double>::type’ {aka ‘__vector(2) double’} [-Wignored-attributes]/usr/bin/ld: /home/gzf2/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: file35532f8a7d7c.so] Error 1
Error in sink(type = "output") : invalid connection
sessionInfo()
R version 4.0.4 (2021-02-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 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=en_CA.UTF-8 LC_NUMERIC=C LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8 LC_MONETARY=en_CA.UTF-8
[6] LC_MESSAGES=en_CA.UTF-8 LC_PAPER=en_CA.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] brms_2.15.0 Rcpp_1.0.6
loaded via a namespace (and not attached):
[1] minqa_1.2.4 colorspace_2.0-0 ellipsis_0.3.1 class_7.3-18 modeltools_0.2-23 ggridges_0.5.2
[7] rsconnect_0.8.16 mclust_5.4.7 estimability_1.3 markdown_1.1 base64enc_0.1-3 rstudioapi_0.13
[13] rstan_2.21.2 flexmix_2.3-17 DT_0.16 fansi_0.4.1 mvtnorm_1.1-1 bridgesampling_1.0-0
[19] codetools_0.2-18 splines_4.0.4 robustbase_0.93-6 shinythemes_1.1.2 bayesplot_1.7.2 projpred_2.0.2
[25] jsonlite_1.7.2 nloptr_1.2.2.2 cluster_2.1.1 kernlab_0.9-29 shiny_1.5.0 compiler_4.0.4
[31] emmeans_1.5.3 backports_1.2.1 assertthat_0.2.1 Matrix_1.3-2 fastmap_1.0.1 cli_2.2.0
[37] later_1.1.0.1 htmltools_0.5.1.1 prettyunits_1.1.1 tools_4.0.4 igraph_1.2.6 coda_0.19-4
[43] gtable_0.3.0 glue_1.4.2 reshape2_1.4.4 dplyr_1.0.2 V8_3.4.0 vctrs_0.3.5
[49] nlme_3.1-152 fpc_2.2-9 crosstalk_1.1.0.1 stringr_1.4.0 ps_1.5.0 lme4_1.1-26
[55] mime_0.9 miniUI_0.1.1.1 lifecycle_0.2.0 gtools_3.8.2 statmod_1.4.35 DEoptimR_1.0-8
[61] MASS_7.3-53.1 zoo_1.8-8 scales_1.1.1 colourpicker_1.1.0 promises_1.1.1 Brobdingnag_1.2-6
[67] parallel_4.0.4 inline_0.3.17 shinystan_2.5.0 gamm4_0.2-6 curl_4.3 gridExtra_2.3
[73] ggplot2_3.3.2 loo_2.4.1 StanHeaders_2.21.0-7 stringi_1.5.3 dygraphs_1.1.1.6 boot_1.3-27
[79] pkgbuild_1.2.0 rlang_0.4.10 pkgconfig_2.0.3 prabclus_2.3-2 matrixStats_0.57.0 lattice_0.20-41
[85] purrr_0.3.4 rstantools_2.1.1 htmlwidgets_1.5.3 cowplot_1.1.0 tidyselect_1.1.0 processx_3.4.5
[91] plyr_1.8.6 magrittr_2.0.1 R6_2.5.0 generics_0.1.0 pillar_1.4.7 withr_2.3.0
[97] mgcv_1.8-34 xts_0.12.1 abind_1.4-5 nnet_7.3-15 tibble_3.0.4 crayon_1.3.4
[103] grid_4.0.4 callr_3.5.1 threejs_0.3.3 digest_0.6.27 diptest_0.75-7 xtable_1.8-4
[109] httpuv_1.5.5 RcppParallel_5.0.2 stats4_4.0.4 munsell_0.5.0 shinyjs_2.0.0