R install on macOS appears to be broken

[mobileink]

R doesn't work with graalvm-ce-java11-19.3.0.2.

For example, $GRAAL_HOME/bin/R: ... FastR unexpected failure: error loading libR from: /Library/Java/JavaVirtualMachines/graalvm-ce-java11-19.3.0.2/Contents/Home/languages/R/lib/libR.dylib. Message: dlopen(/Library/Java/JavaVirtualMachines/graalvm-ce-java11-19.3.0.2/Contents/Home/languages/R/lib/libR.dylib, 9): Library not loaded: /cm/shared/apps/gcc/4.9.2/lib/libgfortran.3.dylib Referenced from: /Library/Java/JavaVirtualMachines/graalvm-ce-java11-19.3.0.2/Contents/Home/languages/R/lib/libRlapack.dylib Reason: image not found

Both libRblas.dylib and libRlapack.dylib are incorrectly linked to libgfortran and libquadmath:

$ otool -L /Library/Java/JavaVirtualMachines/graalvm-ce-java11-19.3.0.2/Contents/Home/languages/R/lib/libRlapack.dylib /Library/Java/JavaVirtualMachines/graalvm-ce-java11-19.3.0.2/Contents/Home/languages/R/lib/libRlapack.dylib: @rpath/libRlapack.dylib (compatibility version 3.6.0, current version 3.6.1) @rpath/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0) /cm/shared/apps/gcc/4.9.2/lib/libgfortran.3.dylib (compatibility version 4.0.0, current version 4.0.0) /cm/shared/apps/gcc/4.9.2/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1252.200.5)

Workaround: do this for each.

sudo install_name_tool -change /cm/shared/apps/gcc/4.9.2/lib/libquadmath.0.dylib /usr/local/Cellar/gcc\@4.9/4.9.4_1/lib/gcc/4.9/libquadmath.0.dylib /Library/Java/JavaVirtualMachines/graalvm-ce-java11-19.3.0.2/Contents/Home/languages/R/lib/libRlapack.dylib

[mobileink]

Similar issues crop up when running install.packages: the absolute path "/cm/shared/apps/blah blah" is hard-coded in various places in the build stuff, which doesn't look right to me, anyway. Got lots of this kind of thing:

g++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/cm/shared/apps/bzip2/1.0.6/lib -L/cm/shared/apps/xz/5.2.2/lib -L/cm/shared/apps/pcre/8.43/lib -L/cm/shared/apps/curl/7.50.1/lib -L/cm/shared/apps/gcc/4.9.2/lib -L/usr/lib -o reticulate.so RcppExports.o event_loop.o libpython.o output.o python.o readline.o ld: warning: directory not found for option '-L/cm/shared/apps/bzip2/1.0.6/lib' ld: warning: directory not found for option '-L/cm/shared/apps/xz/5.2.2/lib' ld: warning: directory not found for option '-L/cm/shared/apps/pcre/8.43/lib' ld: warning: directory not found for option '-L/cm/shared/apps/curl/7.50.1/lib' ld: warning: directory not found for option '-L/cm/shared/apps/gcc/4.9.2/lib'

I managed to get stuff built anyway, but had to use the native toolchain: $ R -e 'fastr.setToolchain("native")', and those link warnings look ominous. Sometimes a build would fail because a component was missing; installing the component separately seemed to fix that problem. An example is 'nlme'.

HTH

[steve-s]

Hello Gregg,

thank you for reporting this!

Have you tried running the configure_fastr(*) script? It's main purpose in this FastR version (19.3.0) is to fix-up the linking with libgfortran3 and libquadmath, which we do not distribute in that FastR version (unlike with the previous versions). We plan to distribute these libraries again in the next version (20.0.0), in which case, libRlapack and other libs linking to them can already be linked to the correct relative location of libgfortran and libquadmath.

For the ld: warning messages: you are right that these paths got into the release unintentionally, we'll get that fixed. However, I believe that otherwise these warnings (or more precisely the fact that those directories do not exists on your system) are mostly harmless.

Sometimes a build would fail because a component was missing; installing the component separately seemed to fix that problem.

What do you mean by a "component" here? An R package or system library like bzip2? Would calling just install.packages("nlme") reproduce the issue?

(*) full path: $GRAALVM_HOME/languages/R/bin/configure_fastr

[mobileink]

I'm pretty sure I ran configure_fastr. I'm on 19.3.0.2, fwiw.

Regarding the package installation, I ran install.packages on:

shiny haven plotly ggplot2 plyr dplyr srvyr tidyverse jsonlite reticulate

I don't recall which ones had the problem, but occurred several times (nlme is just an example). The install would fail, complaining of a missing dependency (e.g. nlme). I found that running install.packages on the missing dependency would succeed, and then rerunning install on the original package would succeed.

Thanks,

G

[steve-s]

Hello Gregg,

in the latest release (20.0.0) the hard-coded absolute paths starting with "/cm/shared/apps" should be gone. We are still investigating the issue with packages installation.

[mobileink]

Just saw this, thanks.

[didekin]

I have just got this, with graalvm 20.1.0 and FastR 20.1.0:

FastR unexpected failure: error loading libR from: /Users/pedro/.sdkman/candidates/java/20.1.0.r11-grl/languages/R/lib/libR.dylib. Message: dlopen(/Users/pedro/.sdkman/candidates/java/20.1.0.r11-grl/languages/R/lib/libR.dylib, 9): Library not loaded: /cm/shared/apps/gcc/8.3.0/lib/libgomp.1.dylib Referenced from: /Users/pedro/.sdkman/candidates/java/20.1.0.r11-grl/languages/R/lib/libRblas.dylib Reason: image not found

FastR unexpected failure: error loading libR from: /Users/pedro/.sdkman/candidates/java/20.1.0.r11-grl/languages/R/lib/libR.dylib. Message: dlopen(/Users/pedro/.sdkman/candidates/java/20.1.0.r11-grl/languages/R/lib/libR.dylib, 9): Library not loaded: /cm/shared/apps/gcc/8.3.0/lib/libgomp.1.dylib Referenced from: /Users/pedro/.sdkman/candidates/java/20.1.0.r11-grl/languages/R/lib/libRlapack.dylib Reason: image not found

I've worked around as suggested above by mobileink.

[marthenlt]

This issue is existed in GraalVM EE 20.1.0 (build 25.251-b08-jvmci-20.1-b02, mixed mode).

I am running MacOs 10.15.5 BuildVersion: 19F101

The error message is

FastR unexpected failure: error loading libR from: /Library/Java/JavaVirtualMachines/graalvm-ee-java8-20.1.0/Contents/Home/jre/languages/R/lib/libR.dylib.
Message: dlopen(/Library/Java/JavaVirtualMachines/graalvm-ee-java8-20.1.0/Contents/Home/jre/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-ee-java8-20.1.0/Contents/Home/jre/languages/R/lib/libRlapack.dylib
  Reason: image not found

I did the workaround suggested by @mobileink , by running : sudo install_name_tool -change /cm/shared/apps/gcc/8.3.0/lib/libgomp.1.dylib /usr/local/Cellar/gcc@4.9/4.9.4_2/lib/gcc/4.9/libgomp.1.dylib /Library/Java/JavaVirtualMachines/graalvm-ee-java8-20.1.0/Contents/Home/jre/languages/R/lib/libRlapack.dylib

[wilbyang]

GraalVM CE 20.1.0 MacOs 10.14.6 (18G5033) I have the same problem. Even I have run sudo install_name_tool -change /cm/shared/apps/gcc/8.3.0/lib/libgomp.1.dylib /usr/local/Cellar/gcc/9.3.0_1/lib/gcc/9/libgomp.1.dylib /Users/boya/.sdkman/candidates/java/20.1.0.r11-grl/languages/R/lib/libRlapack.dylib

[didekin]

This is what I've done:

sudo install_name_tool -change /cm/shared/apps/gcc/8.3.0/lib/libgomp.1.dylib \
             /usr/local/Cellar/gcc@4.9/4.9.4_2/lib/gcc/4.9/libgomp.1.dylib \
             /Users/pedro/.sdkman/candidates/java/20.1.0.r11-grl/languages/R/lib/libRblas.dylib

sudo install_name_tool -change /cm/shared/apps/gcc/8.3.0/lib/libgomp.1.dylib \
              /usr/local/Cellar/gcc@4.9/4.9.4_2/lib/gcc/4.9/libgomp.1.dylib \
              /Users/pedro/.sdkman/candidates/java/20.1.0.r11-grl/languages/R/lib/libRlapack.dylib