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sirius-ms / sirius

SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)
GNU Affero General Public License v3.0
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conda linux install with openjdk missing lib/jvm/lib/libawt_xawt.so #128

Closed hyphaltip closed 4 months ago

hyphaltip commented 11 months ago

When I install via conda (miniconda3, on linux centOS) for 5.8.1 via conda

conda create -n sirius-ms -c conda-forge sirius-ms

I get these errors below related to java. It seems like openjdk 17.0.7.4 is missing the libawt_xawt.so on linux conda-forge? When I download sirius directly and run with a platform installed java all is well so maybe something on the openjdk dependency needs to be checked?

Exception in thread "main" java.lang.reflect.InvocationTargetException
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:568)
    at org.springframework.boot.loader.MainMethodRunner.run(MainMethodRunner.java:49)
    at org.springframework.boot.loader.Launcher.launch(Launcher.java:108)
    at org.springframework.boot.loader.Launcher.launch(Launcher.java:58)
    at org.springframework.boot.loader.JarLauncher.main(JarLauncher.java:88)
Caused by: java.lang.UnsatisfiedLinkError: Can't load library: /bigdata/operations/pkgadmin/opt/linux/centos/8.x/x86_64/pkgs/sirius/5.8.1/lib/jvm/lib/libawt_xawt.so
    at java.base/java.lang.ClassLoader.loadLibrary(ClassLoader.java:2393)
    at java.base/java.lang.Runtime.load0(Runtime.java:755)
    at java.base/java.lang.System.load(System.java:1953)
    at java.base/jdk.internal.loader.NativeLibraries.load(Native Method)
    at java.base/jdk.internal.loader.NativeLibraries$NativeLibraryImpl.open(NativeLibraries.java:388)
    at java.base/jdk.internal.loader.NativeLibraries.loadLibrary(NativeLibraries.java:232)
    at java.base/jdk.internal.loader.NativeLibraries.loadLibrary(NativeLibraries.java:174)
    at java.base/jdk.internal.loader.NativeLibraries.findFromPaths(NativeLibraries.java:315)
    at java.base/jdk.internal.loader.NativeLibraries.loadLibrary(NativeLibraries.java:285)
    at java.base/java.lang.ClassLoader.loadLibrary(ClassLoader.java:2398)
    at java.base/java.lang.Runtime.loadLibrary0(Runtime.java:818)
    at java.base/java.lang.System.loadLibrary(System.java:1989)
    at java.desktop/java.awt.Toolkit$2.run(Toolkit.java:1388)
    at java.desktop/java.awt.Toolkit$2.run(Toolkit.java:1386)
    at java.base/java.security.AccessController.doPrivileged(AccessController.java:318)
    at java.desktop/java.awt.Toolkit.loadLibraries(Toolkit.java:1385)
    at java.desktop/java.awt.Toolkit.initStatic(Toolkit.java:1423)
    at java.desktop/java.awt.Toolkit.<clinit>(Toolkit.java:1397)
    at java.desktop/java.awt.Component.<clinit>(Component.java:624)
    at de.unijena.bioinf.ms.frontend.SiriusGUIApplication.main(SiriusGUIApplication.java:104)
    at de.unijena.bioinf.ms.middleware.SiriusMiddlewareApplication.main(SiriusMiddlewareApplication.java:133)
    ... 8 more

these are the pkgs installed

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.19.1               hd590300_0    conda-forge
ca-certificates           2023.5.7             hbcca054_0    conda-forge
coin-or-cbc               2.10.10              h9002f0b_0    conda-forge
coin-or-cgl               0.60.7               h516709c_0    conda-forge
coin-or-clp               1.17.8               h1ee7a9c_0    conda-forge
coin-or-osi               0.108.8              ha2443b9_0    conda-forge
coin-or-utils             2.11.9               hee58242_0    conda-forge
curl                      8.2.0                hca28451_0    conda-forge
graalpy                   23.0.0          0_graalvm_native    conda-forge
graalpy-graalvm           23.0.0               h4d560db_0    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
krb5                      1.21.1               h659d440_0    conda-forge
libblas                   3.9.0           17_linux64_openblas    conda-forge
libcblas                  3.9.0           17_linux64_openblas    conda-forge
libcurl                   8.2.0                hca28451_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libgcc-ng                 13.1.0               he5830b7_0    conda-forge
libgfortran-ng            13.1.0               h69a702a_0    conda-forge
libgfortran5              13.1.0               h15d22d2_0    conda-forge
libgomp                   13.1.0               he5830b7_0    conda-forge
liblapack                 3.9.0           17_linux64_openblas    conda-forge
liblapacke                3.9.0           17_linux64_openblas    conda-forge
libnghttp2                1.52.0               h61bc06f_0    conda-forge
libopenblas               0.3.23          pthreads_h80387f5_0    conda-forge
libssh2                   1.11.0               h0841786_0    conda-forge
libstdcxx-ng              13.1.0               hfd8a6a1_0    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
ncurses                   6.4                  hcb278e6_0    conda-forge
openjdk                   17.0.7.4        0_graalvm230b10    conda-forge
openssl                   3.1.1                hd590300_1    conda-forge
patch                     2.7.6             h7f98852_1002    conda-forge
python_abi                3.10            3_graalpy230_310_native    conda-forge
readline                  8.2                  h8228510_1    conda-forge
sirius-ms                 5.8.1                h601bc82_0    conda-forge
zstd                      1.5.2                hfc55251_7    conda-forge
joXemMx commented 11 months ago

Hi, when exactly do you encounter this exception? I tested this both on my Ubuntu VM as well as a freshly installed CentOS VM and failed to reproduce the error.