xgboost crash on OS/X Catalina

[mik3hall]

Thank you for reporting a bug in FastR. We will do our best to eventually address all open issues, however, you can also help us and increase the chances of your issue being fixed sooner by following these guidelines:

Can you reproduce with the latest development build?

Yes

Include the following info

• If FastR produced fastr_errors_pid{xyz}.log or fastr_errors.log, attach them to the issue.
  Attempting to attach

• GraalVM version or git revisions of FastR and GraalVM repositories if built from source.

  • Use $GRAALVM_HOME/bin/R --vm.version and include the full output.
    openjdk version "11.0.11" 2021-04-20
    OpenJDK Runtime Environment GraalVM CE 21.2.0-dev (build 11.0.11+8-jvmci-21.2-b02)
    OpenJDK 64-Bit Server VM GraalVM CE 21.2.0-dev (build 11.0.11+8-jvmci-21.2-b02, mixed mode, sharing)

• Output of R built-in function sessionInfo().
  Done after library(xgboost) execution R crashes on invocation

xsessionInfo()
FastR version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin19.6.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS: /Library/Java/JavaVirtualMachines/graalvm-ce-java11-21.2.0-dev/Contents/Home/languages/R/lib/libRblas.dylib
LAPACK: /Library/Java/JavaVirtualMachines/graalvm-ce-java11-21.2.0-dev/Contents/Home/languages/R/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] xgboost_1.3.2.1

loaded via a namespace (and not attached):
[1] Matrix_1.2-18 grid_4.0.3 lattice_0.20-41
[4] data.table_1.10.4-3 magrittr_2.0.1

• OS name and version.
  macOS Catalina 10.15.7

Optionally: try to reduce the example code as much as possible

Please note that the comments to
#184
were also done.

• Try reproducing the issue with built-in data-sets (e.g., mtcars, run help(package = "datasets") to find out more).
  Based on https://xgboost.readthedocs.io/en/latest/R-package/xgboostPresentation.html

data(agaricus.train, package='xgboost')
data(agaricus.test, package='xgboost')
train <- agaricus.train
test <- agaricus.test
bstSparse <- xgboost(data = train$data, label = train$label, max.depth = 2, eta = 1, nthread = 2, nrounds = 2, objective = "binary:logistic")
Error: could not find function "xgboost"
library(xgboost)
bstSparse <- xgboost(data = train$data, label = train$label, max.depth = 2, eta = 1, nthread = 2, nrounds = 2, objective = "binary:logistic")
[thread 25407 also had an error][thread 26947 also had an error][thread 34827 also had an error]

A fatal error has been detected by the Java Runtime Environment:

[thread 25647 also had an error]SIGSEGV

(0xb)
at pc=0x000000014ef117d6, pid=16082, tid=31267

[thread 31539 also had an error]

JRE version: OpenJDK Runtime Environment GraalVM CE 21.2.0-dev (11.0.11+8) (build 11.0.11+8-jvmci-21.2-b02)

[thread 40239 also had an error]

Java VM: OpenJDK 64-Bit Server VM GraalVM CE 21.2.0-dev (11.0.11+8-jvmci-21.2-b02, mixed mode, sharing, tiered, jvmci, jvmci compiler, compressed oops, g1 gc, bsd-amd64)

Problematic frame:

C [libRnative.dylib+0x117d6] REAL+0x76

No core dump will be written. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again

An error report file with more information is saved as:

/Users/mjh/hs_err_pid16082.log

If you would like to submit a bug report, please visit:

https://github.com/oracle/graal/issues

Abort trap: 6
hs_err_pid16082.log