Downloading: Component catalog from www.graalvm.org
ComponentId Version Component name Stability Origin
---------------------------------------------------------------------------------------------------------------------------------
espresso 21.2.0 Java on Truffle Experimental github.com
llvm-toolchain 21.2.0 LLVM.org toolchain Supported github.com
native-image 21.2.0 Native Image Early adopter github.com
nodejs 21.2.0 Graal.nodejs Supported github.com
python 21.2.0 Graal.Python Experimental github.com
R 21.2.0 FastR Experimental github.com
ruby 21.2.0.1 TruffleRuby Experimental github.com
wasm 21.2.0 GraalWasm Experimental github.com
lwk qwfys:~$ gu install R
Downloading: Component catalog from www.graalvm.org
Processing Component: FastR
Downloading: Component R: FastR from github.com
Installing new component: FastR (org.graalvm.R, version 21.2.0)
NOTES:
---------------
FastR should work out of the box on most Linux distributions and recent MacOS versions. Run the following script to check FastR requirements and create a personal R packages library directory:
/home/lwk/.sdkman/candidates/java/21.2.0.r11-grl/languages/R/bin/configure_fastr
The R component comes without native image by default. If you wish to build the native image, which provides faster startup, but slightly slower peak performance, then run the following:
gu rebuild-images R
The native image is then used by default. Pass --jvm flag to the R or Rscript launcher to use JVM instead of the native image. Note that the native image is not stable yet and is intended for evaluation and experiments for curious users. Some features may not work in the native image mode. Most notably, the --polyglot switch works only in JVM mode (when --jvm is used).
See http://www.graalvm.org/docs/reference-manual/languages/r for more.
lwk qwfys:~$ /home/lwk/.sdkman/candidates/java/21.2.0.r11-grl/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 following packages should cover depenedencies of the most commonly used R packages:
On Debian based systems: apt-get install build-essential gfortran libxml2 libc -dev
On Oracle Linux: yum groupinstall Development Tools yum install gcc-gfortran
Default personal library directory (/home/lwk/R/x86_64-pc-linux-gnu-library/fastr-21.2.0-4.0) does not exist.
Do you wish to create it now? (Yy/Nn) y
Creating personal library directory: /home/lwk/R/x86_64-pc-linux-gnu-library/fastr-21.2.0-4.0
lwk qwfys:~$
lwk qwfys:~$ gu rebuild-images R
Building R...
[RMain:78227] classlist: 3,007.82 ms, 1.19 GB
--initialize-at-build-time without arguments has been deprecated and will be removed in GraalVM 22.0.
[RMain:78227] (cap): 622.93 ms, 1.19 GB
The URL protocol ftp is not tested and might not work as expected.
Supported URL protocols enabled by default: file,resource. Supported URL protocols available on demand: http,https.
[RMain:78227] setup: 3,342.34 ms, 1.19 GB
[RMain:78227] (clinit): 1,763.08 ms, 5.64 GB
[RMain:78227] (typeflow): 67,891.25 ms, 5.64 GB
[RMain:78227] (objects): 48,700.02 ms, 5.64 GB
[RMain:78227] (features): 15,257.01 ms, 5.64 GB
[RMain:78227] analysis: 137,644.76 ms, 5.64 GB
[RMain:78227] universe: 4,597.40 ms, 5.49 GB
20152 method(s) included for runtime compilation
[RMain:78227] (parse): 17,494.32 ms, 6.18 GB
[RMain:78227] (inline): 19,096.21 ms, 7.53 GB
[RMain:78227] (compile): 50,503.95 ms, 7.65 GB
[RMain:78227] compile: 93,141.66 ms, 7.65 GB
[RMain:78227] image: 17,413.96 ms, 7.94 GB
[RMain:78227] write: 720.47 ms, 7.94 GB
Fatal error:java.lang.RuntimeException: There was an error linking the native image: linker command exited with 1
based on the linker command output, possible reasons for this include:
1. It appears as though libz.a is missing. Please install it.
linker command executed:
/usr/bin/gcc -z noexecstack -Wl,--gc-sections -Wl,--dynamic-list -Wl,/tmp/SVM-3894114737776621381/exported_symbols.list -Wl,--exclude-libs,ALL -Wl,-x -o /home/lwk/.sdkman/candidates/java/21.2.0.r11-grl/lib/svm/macros/RMain-launcher/../../../../languages/R/bin/RMain RMain.o /home/lwk/.sdkman/candidates/java/21.2.0.r11-grl/lib/svm/clibraries/linux-amd64/liblibchelper.a /home/lwk/.sdkman/candidates/java/21.2.0.r11-grl/lib/static/linux-amd64/glibc/libnet.a /home/lwk/.sdkman/candidates/java/21.2.0.r11-grl/languages/nfi/builder/clibraries-libffi/libffi.a /home/lwk/.sdkman/candidates/java/21.2.0.r11-grl/lib/static/linux-amd64/glibc/libextnet.a /home/lwk/.sdkman/candidates/java/21.2.0.r11-grl/lib/static/linux-amd64/glibc/libnio.a /home/lwk/.sdkman/candidates/java/21.2.0.r11-grl/lib/static/linux-amd64/glibc/libjava.a /home/lwk/.sdkman/candidates/java/21.2.0.r11-grl/lib/static/linux-amd64/glibc/libfdlibm.a /home/lwk/.sdkman/candidates/java/21.2.0.r11-grl/lib/static/linux-amd64/glibc/libsunec.a /home/lwk/.sdkman/candidates/java/21.2.0.r11-grl/lib/static/linux-amd64/glibc/libzip.a /home/lwk/.sdkman/candidates/java/21.2.0.r11-grl/lib/svm/clibraries/linux-amd64/libjvm.a -v -L/tmp/SVM-3894114737776621381 -L/home/lwk/.sdkman/candidates/java/21.2.0.r11-grl/lib/static/linux-amd64/glibc -L/home/lwk/.sdkman/candidates/java/21.2.0.r11-grl/languages/nfi/builder/clibraries-libffi -L/home/lwk/.sdkman/candidates/java/21.2.0.r11-grl/lib/svm/clibraries/linux-amd64 -lstdc -lz -lpthread -ldl -lrt
linker command output:
Using built-in specs.
COLLECT_GCC /usr/bin/gcc
COLLECT_LTO_WRAPPER /usr/lib/gcc/x86_64-linux-gnu/9/lto-wrapper
OFFLOAD_TARGET_NAMES nvptx-none:hsa
OFFLOAD_TARGET_DEFAULT 1
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion Ubuntu 9.3.0-17ubuntu1~20.04 --with-bugurl file:///usr/share/doc/gcc-9/README.Bugs --enable-languages c,ada,c ,go,brig,d,fortran,objc,obj-c ,gm2 --prefix /usr --with-gcc-major-version-only --program-suffix -9 --program-prefix x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir /usr/lib --without-included-gettext --enable-threads posix --libdir /usr/lib --enable-nls --enable-clocale gnu --enable-libstdcxx-debug --enable-libstdcxx-time yes --with-default-libstdcxx-abi new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib auto --enable-objc-gc auto --enable-multiarch --disable-werror --with-arch-32 i686 --with-abi m64 --with-multilib-list m32,m64,mx32 --enable-multilib --with-tune generic --enable-offload-targets nvptx-none /build/gcc-9-HskZEa/gcc-9-9.3.0/debian/tmp-nvptx/usr,hsa --without-cuda-driver --enable-checking release --build x86_64-linux-gnu --host x86_64-linux-gnu --target x86_64-linux-gnu
Thread model: posix
gcc version 9.3.0 (Ubuntu 9.3.0-17ubuntu1~20.04)
COMPILER_PATH /usr/lib/gcc/x86_64-linux-gnu/9/:/usr/lib/gcc/x86_64-linux-gnu/9/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/9/:/usr/lib/gcc/x86_64-linux-gnu/
LIBRARY_PATH /usr/lib/gcc/x86_64-linux-gnu/9/:/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/9/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/9/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS -z noexecstack -o /home/lwk/.sdkman/candidates/java/21.2.0.r11-grl/lib/svm/macros/RMain-launcher/../../../../languages/R/bin/RMain -v -L/tmp/SVM-3894114737776621381 -L/home/lwk/.sdkman/candidates/java/21.2.0.r11-grl/lib/static/linux-amd64/glibc -L/home/lwk/.sdkman/candidates/java/21.2.0.r11-grl/languages/nfi/builder/clibraries-libffi -L/home/lwk/.sdkman/candidates/java/21.2.0.r11-grl/lib/svm/clibraries/linux-amd64 -mtune generic -march x86-64
/usr/lib/gcc/x86_64-linux-gnu/9/collect2 -plugin /usr/lib/gcc/x86_64-linux-gnu/9/liblto_plugin.so -plugin-opt /usr/lib/gcc/x86_64-linux-gnu/9/lto-wrapper -plugin-opt -fresolution /tmp/ccggJZhY.res -plugin-opt -pass-through -lgcc -plugin-opt -pass-through -lgcc_s -plugin-opt -pass-through -lc -plugin-opt -pass-through -lgcc -plugin-opt -pass-through -lgcc_s --build-id --eh-frame-hdr -m elf_x86_64 --hash-style gnu --as-needed -dynamic-linker /lib64/ld-linux-x86-64.so.2 -pie -z now -z relro -o /home/lwk/.sdkman/candidates/java/21.2.0.r11-grl/lib/svm/macros/RMain-launcher/../../../../languages/R/bin/RMain -z noexecstack /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/Scrt1.o /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/9/crtbeginS.o -L/tmp/SVM-3894114737776621381 -L/home/lwk/.sdkman/candidates/java/21.2.0.r11-grl/lib/static/linux-amd64/glibc -L/home/lwk/.sdkman/candidates/java/21.2.0.r11-grl/languages/nfi/builder/clibraries-libffi -L/home/lwk/.sdkman/candidates/java/21.2.0.r11-grl/lib/svm/clibraries/linux-amd64 -L/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/9/../../.. --gc-sections --dynamic-list /tmp/SVM-3894114737776621381/exported_symbols.list --exclude-libs ALL -x RMain.o /home/lwk/.sdkman/candidates/java/21.2.0.r11-grl/lib/svm/clibraries/linux-amd64/liblibchelper.a /home/lwk/.sdkman/candidates/java/21.2.0.r11-grl/lib/static/linux-amd64/glibc/libnet.a /home/lwk/.sdkman/candidates/java/21.2.0.r11-grl/languages/nfi/builder/clibraries-libffi/libffi.a /home/lwk/.sdkman/candidates/java/21.2.0.r11-grl/lib/static/linux-amd64/glibc/libextnet.a /home/lwk/.sdkman/candidates/java/21.2.0.r11-grl/lib/static/linux-amd64/glibc/libnio.a /home/lwk/.sdkman/candidates/java/21.2.0.r11-grl/lib/static/linux-amd64/glibc/libjava.a /home/lwk/.sdkman/candidates/java/21.2.0.r11-grl/lib/static/linux-amd64/glibc/libfdlibm.a /home/lwk/.sdkman/candidates/java/21.2.0.r11-grl/lib/static/linux-amd64/glibc/libsunec.a /home/lwk/.sdkman/candidates/java/21.2.0.r11-grl/lib/static/linux-amd64/glibc/libzip.a /home/lwk/.sdkman/candidates/java/21.2.0.r11-grl/lib/svm/clibraries/linux-amd64/libjvm.a -lstdc -lz -lpthread -ldl -lrt -lgcc --push-state --as-needed -lgcc_s --pop-state -lc -lgcc --push-state --as-needed -lgcc_s --pop-state /usr/lib/gcc/x86_64-linux-gnu/9/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/crtn.o
/usr/bin/ld: cannot find -lz
collect2: error: ld returned 1 exit status
at com.oracle.svm.hosted.image.NativeImageViaCC.handlelinkerFailure(NativeImageViaCC.java:499)
at com.oracle.svm.hosted.image.NativeImageViaCC.write(NativeImageViaCC.java:446)
at com.oracle.svm.hosted.NativeImageGenerator.doRun(NativeImageGenerator.java:660)
at com.oracle.svm.hosted.NativeImageGenerator.run(NativeImageGenerator.java:491)
at com.oracle.svm.hosted.NativeImageGeneratorRunner.buildImage(NativeImageGeneratorRunner.java:380)
at com.oracle.svm.hosted.NativeImageGeneratorRunner.build(NativeImageGeneratorRunner.java:543)
at com.oracle.svm.hosted.NativeImageGeneratorRunner.main(NativeImageGeneratorRunner.java:119)
at com.oracle.svm.hosted.NativeImageGeneratorRunner$JDK9Plus.main(NativeImageGeneratorRunner.java:573)
[RMain:78227] [total]: 263,149.22 ms, 7.94 GB
# Printing build artifacts to: /home/lwk/.sdkman/candidates/java/21.2.0.r11-grl/lib/svm/macros/RMain-launcher/../../../../languages/R/bin/RMain.build_artifacts.txt
Error: Image build request failed with exit status 1
lwk qwfys:
