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oracle / fastr

A high-performance implementation of the R programming language, built on GraalVM.
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Error installing curl package on macOS Catalina with Fastr 20.3.0 #179

Open hsselman opened 3 years ago

hsselman commented 3 years ago

I tried installing curl using default mirror in GraalVM + FastR 20.3.0. Trying to install on macOS Catalina 10.15.7.

Error installing curl:

> install.package('curl')
* installing *source* package ‘curl’ ...
** package ‘curl’ successfully unpacked and MD5 sums checked
** using staged installation
Found pkg-config cflags and libs!
Using PKG_CFLAGS=
Using PKG_LIBS=-lcurl
** libs
rm -f curl.so callbacks.o curl.o download.o escape.o fetch.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o reflist.o split.o ssl.o typechecking.o utils.o version.o winidn.o writer.o
clang -I".../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/include" -DNDEBUG -DSTRICT_R_HEADERS  -O2 -DFASTR -DNO_GNUR  -fvisibility=hidden -fPIC  -O2  -DFASTR -DNO_GNUR  -c callbacks.c -o callbacks.o
clang -I".../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/include" -DNDEBUG -DSTRICT_R_HEADERS  -O2 -DFASTR -DNO_GNUR  -fvisibility=hidden -fPIC  -O2  -DFASTR -DNO_GNUR  -c curl.c -o curl.o
clang -I".../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/include" -DNDEBUG -DSTRICT_R_HEADERS  -O2 -DFASTR -DNO_GNUR  -fvisibility=hidden -fPIC  -O2  -DFASTR -DNO_GNUR  -c download.c -o download.o
clang -I".../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/include" -DNDEBUG -DSTRICT_R_HEADERS  -O2 -DFASTR -DNO_GNUR  -fvisibility=hidden -fPIC  -O2  -DFASTR -DNO_GNUR  -c escape.c -o escape.o
clang -I".../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/include" -DNDEBUG -DSTRICT_R_HEADERS  -O2 -DFASTR -DNO_GNUR  -fvisibility=hidden -fPIC  -O2  -DFASTR -DNO_GNUR  -c fetch.c -o fetch.o
clang -I".../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/include" -DNDEBUG -DSTRICT_R_HEADERS  -O2 -DFASTR -DNO_GNUR  -fvisibility=hidden -fPIC  -O2  -DFASTR -DNO_GNUR  -c form.c -o form.o
clang -I".../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/include" -DNDEBUG -DSTRICT_R_HEADERS  -O2 -DFASTR -DNO_GNUR  -fvisibility=hidden -fPIC  -O2  -DFASTR -DNO_GNUR  -c getdate.c -o getdate.o
clang -I".../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/include" -DNDEBUG -DSTRICT_R_HEADERS  -O2 -DFASTR -DNO_GNUR  -fvisibility=hidden -fPIC  -O2  -DFASTR -DNO_GNUR  -c handle.c -o handle.o
clang -I".../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/include" -DNDEBUG -DSTRICT_R_HEADERS  -O2 -DFASTR -DNO_GNUR  -fvisibility=hidden -fPIC  -O2  -DFASTR -DNO_GNUR  -c ieproxy.c -o ieproxy.o
clang -I".../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/include" -DNDEBUG -DSTRICT_R_HEADERS  -O2 -DFASTR -DNO_GNUR  -fvisibility=hidden -fPIC  -O2  -DFASTR -DNO_GNUR  -c init.c -o init.o
clang -I".../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/include" -DNDEBUG -DSTRICT_R_HEADERS  -O2 -DFASTR -DNO_GNUR  -fvisibility=hidden -fPIC  -O2  -DFASTR -DNO_GNUR  -c interrupt.c -o interrupt.o
clang -I".../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/include" -DNDEBUG -DSTRICT_R_HEADERS  -O2 -DFASTR -DNO_GNUR  -fvisibility=hidden -fPIC  -O2  -DFASTR -DNO_GNUR  -c multi.c -o multi.o
clang -I".../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/include" -DNDEBUG -DSTRICT_R_HEADERS  -O2 -DFASTR -DNO_GNUR  -fvisibility=hidden -fPIC  -O2  -DFASTR -DNO_GNUR  -c nslookup.c -o nslookup.o
clang -I".../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/include" -DNDEBUG -DSTRICT_R_HEADERS  -O2 -DFASTR -DNO_GNUR  -fvisibility=hidden -fPIC  -O2  -DFASTR -DNO_GNUR  -c reflist.c -o reflist.o
clang -I".../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/include" -DNDEBUG -DSTRICT_R_HEADERS  -O2 -DFASTR -DNO_GNUR  -fvisibility=hidden -fPIC  -O2  -DFASTR -DNO_GNUR  -c split.c -o split.o
clang -I".../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/include" -DNDEBUG -DSTRICT_R_HEADERS  -O2 -DFASTR -DNO_GNUR  -fvisibility=hidden -fPIC  -O2  -DFASTR -DNO_GNUR  -c ssl.c -o ssl.o
clang -I".../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/include" -DNDEBUG -DSTRICT_R_HEADERS  -O2 -DFASTR -DNO_GNUR  -fvisibility=hidden -fPIC  -O2  -DFASTR -DNO_GNUR  -c typechecking.c -o typechecking.o
clang -I".../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/include" -DNDEBUG -DSTRICT_R_HEADERS  -O2 -DFASTR -DNO_GNUR  -fvisibility=hidden -fPIC  -O2  -DFASTR -DNO_GNUR  -c utils.c -o utils.o
clang -I".../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/include" -DNDEBUG -DSTRICT_R_HEADERS  -O2 -DFASTR -DNO_GNUR  -fvisibility=hidden -fPIC  -O2  -DFASTR -DNO_GNUR  -c version.c -o version.o
clang -I".../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/include" -DNDEBUG -DSTRICT_R_HEADERS  -O2 -DFASTR -DNO_GNUR  -fvisibility=hidden -fPIC  -O2  -DFASTR -DNO_GNUR  -c winidn.c -o winidn.o
clang -I".../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/include" -DNDEBUG -DSTRICT_R_HEADERS  -O2 -DFASTR -DNO_GNUR  -fvisibility=hidden -fPIC  -O2  -DFASTR -DNO_GNUR  -c writer.c -o writer.o
clang -dynamiclib -Wl,-headerpad_max_install_names,-rpath,.../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/lib/,-undefined,dynamic_lookup -L.../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/lib -undefined dynamic_lookup -single_module -multiply_defined suppress -Wl,-rpath,.../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/lib/,-undefined,dynamic_lookup -L.../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/lib -o curl.so callbacks.o curl.o download.o escape.o fetch.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o reflist.o split.o ssl.o typechecking.o utils.o version.o winidn.o writer.o -lcurl
installing to .../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/lib/00LOCK-curl/00new/curl/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘curl’ in FUN(X[[i]], ...):
 no such symbol R_curl_connection in package .../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/lib/00LOCK-curl/00new/curl/libs/curl.so
Error: loading failed
> bin/R --vm.version 
openjdk version "11.0.9" 2020-10-20
OpenJDK Runtime Environment GraalVM CE 20.3.0 (build 11.0.9+10-jvmci-20.3-b06)
OpenJDK 64-Bit Server VM GraalVM CE 20.3.0 (build 11.0.9+10-jvmci-20.3-b06, mixed mode, sharing)

Output of R built-in function sessionInfo().

> sessionInfo()
FastR version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin19.6.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   .../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/lib/libRblas.dylib
LAPACK: .../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/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     

loaded via a namespace (and not attached):
[1] tools_3.6.1

Do you have anymore suggestions on what I can do? Or is this a bug? I successfully installed GraalVM+FastR 20.3.0 and this package on an Ubuntu 20.04 docker container, so I am quite puzzled right now why it fails in macOS.