Graal: R install on macOS appears to be broken

[swarren-sumglobal]

Duplicate of CLOSED issue: https://github.com/oracle/graal/issues/2034, but still occurring

Environment
MacOS Catalina 10.15.5

➜  ~ java -Xinternalversion
OpenJDK 64-Bit Server VM (11.0.7+10-jvmci-20.1-b02) for bsd-amd64 JRE (11.0.7+10-jvmci-20.1-b02), built on Apr 21 2020 08:36:14 by "graal1" with gcc 4.2.1 Compatible Apple LLVM 9.1.0 (clang-902.0.39.2)
➜  ~ java -version
openjdk version "11.0.7" 2020-04-14
OpenJDK Runtime Environment GraalVM CE 20.1.0 (build 11.0.7+10-jvmci-20.1-b02)
OpenJDK 64-Bit Server VM GraalVM CE 20.1.0 (build 11.0.7+10-jvmci-20.1-b02, mixed mode, sharing)
➜  ~ gfortran --version
GNU Fortran (Homebrew GCC 9.3.0_1) 9.3.0
Copyright (C) 2019 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Describe the issue
```
~ /Library/Java/JavaVirtualMachines/graalvm-ce-java11-20.1.0/Contents/Home/languages/R/bin/configure_fastr
The basic configuration of FastR was successfull.

Note: if you intend to install R packages you may need additional dependencies.
The most common dependency is GFortran, which must be of version 8.3.0 or later.
See https://gcc.gnu.org/wiki/GFortranBinaries.
If the 'gfortran' binary is not on the system path, you need to configure the full path to it in /Library/Java/JavaVirtualMachines/graalvm-ce-java11-20.1.0/Contents/Home/languages/R/etc/Makeconf (variable FC)
FastR unexpected failure: error loading libR from: /Library/Java/JavaVirtualMachines/graalvm-ce-java11-20.1.0/Contents/Home/languages/R/lib/libR.dylib.
Message: dlopen(/Library/Java/JavaVirtualMachines/graalvm-ce-java11-20.1.0/Contents/Home/languages/R/lib/libR.dylib, 9): Library not loaded: /cm/shared/apps/gcc/8.3.0/lib/libgomp.1.dylib
Referenced from: /Library/Java/JavaVirtualMachines/graalvm-ce-java11-20.1.0/Contents/Home/languages/R/lib/libRblas.dylib
Reason: image not found

[steve-s]

Hello,

this is a known issue. I am copying this from the release notes:

There’s a known issue: the libgomp.1.dylib library is not distributed with FastR on MacOS. To workaround this issue:

install GCC with the package manager of your choice, e.g., brew install gcc

locate file libgomp.1.dylib. Variable $GOMPLIB will denote full path to this library and $R_HOMEthe path to R installation: $GRAALVM_HOME/jre/languages/R on JDK8 based builds $GRAALVM_HOME/languages/R on JDK11 based builds

execute these two commands:

install_name_tool -change /cm/shared/apps/gcc/8.3.0/lib/libgomp.1.dylib $GOMPLIB $R_HOME/lib/libRblas.dylib

install_name_tool -change /cm/shared/apps/gcc/8.3.0/lib/libgomp.1.dylib $GOMPLIB $R_HOME/lib/libRlapack.dylib

---

We are working on fixing this for the next release.

[steve-s]

Duplicate issue https://github.com/oracle/graal/issues/2531 gives more details