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egeulgen / pathfindR

pathfindR: Enrichment Analysis Utilizing Active Subnetworks
https://egeulgen.github.io/pathfindR/
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java version issue #1

Closed zhilongjia closed 6 years ago

zhilongjia commented 6 years ago

Error when run result <- run_pathfindR(RA_input) with errors:

## Testing input

The input looks OK

## Processing input. Converting gene symbols, if necessary

Could not find any interactions for 16 (2.8%) genes in the PIN

## Performing Active Subnetwork Search and Enrichment
Exception in thread "main" java.lang.UnsupportedClassVersionError: Application/AppActiveSubnetworkSearch : Unsupported major.minor version 52.0
    at java.lang.ClassLoader.defineClass1(Native Method)
    at java.lang.ClassLoader.defineClass(ClassLoader.java:803)
    at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
    at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
    at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
    at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:482)
Exception in thread "main" java.lang.UnsupportedClassVersionError: Application/AppActiveSubnetworkSearch : Unsupported major.minor version 52.0
    at java.lang.ClassLoader.defineClass1(Native Method)
    at java.lang.ClassLoader.defineClass(ClassLoader.java:803)
    at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
    at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
    at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
    at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:482)
Exception in thread "main" java.lang.UnsupportedClassVersionError: Application/AppActiveSubnetworkSearch : Unsupported major.minor version 52.0
    at java.lang.ClassLoader.defineClass1(Native Method)
    at java.lang.ClassLoader.defineClass(ClassLoader.java:803)
    at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
    at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
    at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
    at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:482)
Exception in thread "main" Exception in thread "main" java.lang.UnsupportedClassVersionError: Application/AppActiveSubnetworkSearch : Unsupported major.minor version 52.0
    at java.lang.ClassLoader.defineClass1(Native Method)
    at java.lang.ClassLoader.defineClass(ClassLoader.java:803)
    at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
    at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
    at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
    at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:482)
java.lang.UnsupportedClassVersionError: Application/AppActiveSubnetworkSearch : Unsupported major.minor version 52.0
    at java.lang.ClassLoader.defineClass1(Native Method)
    at java.lang.ClassLoader.defineClass(ClassLoader.java:803)
    at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
    at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
    at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
    at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:482)
Exception in thread "main" java.lang.UnsupportedClassVersionError: Application/AppActiveSubnetworkSearch : Unsupported major.minor version 52.0
    at java.lang.ClassLoader.defineClass1(Native Method)
    at java.lang.ClassLoader.defineClass(ClassLoader.java:803)
    at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
    at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
    at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
    at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:482)
Exception in thread "main" java.lang.UnsupportedClassVersionError: Application/AppActiveSubnetworkSearch : Unsupported major.minor version 52.0
    at java.lang.ClassLoader.defineClass1(Native Method)
    at java.lang.ClassLoader.defineClass(ClassLoader.java:803)
    at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
    at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
    at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
    at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:482)
Exception in thread "main" java.lang.UnsupportedClassVersionError: Application/AppActiveSubnetworkSearch : Unsupported major.minor version 52.0
    at java.lang.ClassLoader.defineClass1(Native Method)
    at java.lang.ClassLoader.defineClass(ClassLoader.java:803)
    at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
    at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
    at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
    at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:482)
Exception in thread "main" java.lang.UnsupportedClassVersionError: Application/AppActiveSubnetworkSearch : Unsupported major.minor version 52.0
    at java.lang.ClassLoader.defineClass1(Native Method)
    at java.lang.ClassLoader.defineClass(ClassLoader.java:803)
    at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
    at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
    at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
    at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:482)
Exception in thread "main" java.lang.UnsupportedClassVersionError: Application/AppActiveSubnetworkSearch : Unsupported major.minor version 52.0
    at java.lang.ClassLoader.defineClass1(Native Method)
    at java.lang.ClassLoader.defineClass(ClassLoader.java:803)
    at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
    at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
    at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
    at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:482)
Error in { : task 1 failed - "cannot open the connection"
In addition: There were 13 warnings (use warnings() to see them)

Installed pathfindR successfully (with no warnings and errors). My java environment is as below:

openjdk version "1.8.0_102"
OpenJDK Runtime Environment (Zulu 8.17.0.3-linux64) (build 1.8.0_102-b14)
OpenJDK 64-Bit Server VM (Zulu 8.17.0.3-linux64) (build 25.102-b14, mixed mode)

sessionInfo() output:

R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.0
LAPACK: /usr/lib/lapack/liblapack.so.3.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] pathfindR_1.1.0      shiny_1.0.5          knitr_1.20           pathview_1.18.2     
 [5] org.Hs.eg.db_3.5.0   AnnotationDbi_1.40.0 IRanges_2.12.0       S4Vectors_0.16.0    
 [9] Biobase_2.38.0       BiocGenerics_0.24.0 

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.16      pillar_1.2.1      compiler_3.4.3    XVector_0.18.0    iterators_1.0.9  
 [6] tools_3.4.3       zlibbioc_1.24.0   digest_0.6.15     bit_1.1-12        RSQLite_2.0      
[11] memoise_1.1.0     tibble_1.4.2      pkgconfig_2.0.1   png_0.1-7         rlang_0.2.0      
[16] foreach_1.4.4     KEGGgraph_1.38.0  graph_1.56.0      DBI_0.8           Rgraphviz_2.22.0 
[21] yaml_2.1.18       httr_1.3.1        Biostrings_2.46.0 bit64_0.9-7       grid_3.4.3       
[26] R6_2.2.2          XML_3.98-1.10     blob_1.1.0        magrittr_1.5      codetools_0.2-15 
[31] htmltools_0.3.6   KEGGREST_1.18.1   mime_0.5          xtable_1.8-2      httpuv_1.3.6.2   
[36] doParallel_1.0.11
ozanozisik commented 6 years ago

Hi, can you paste the output of the following command?

java -XshowSettings:properties -version

zhilongjia commented 6 years ago 
Property settings:
    awt.toolkit = sun.awt.X11.XToolkit
    file.encoding = UTF-8
    file.encoding.pkg = sun.io
    file.separator = /
    java.awt.graphicsenv = sun.awt.X11GraphicsEnvironment
    java.awt.printerjob = sun.print.PSPrinterJob
    java.class.path = .
    java.class.version = 52.0
    java.endorsed.dirs = /home/xxx/local/anaconda2/jre/lib/endorsed
    java.ext.dirs = /home/xxx/local/anaconda2/jre/lib/ext
        /usr/java/packages/lib/ext
    java.home = /home/xxx/local/anaconda2/jre
    java.io.tmpdir = /tmp
    java.library.path = /usr/java/packages/lib/amd64
        /usr/lib64
        /lib64
        /lib
        /usr/lib
    java.runtime.name = OpenJDK Runtime Environment
    java.runtime.version = 1.8.0_102-b14
    java.specification.name = Java Platform API Specification
    java.specification.vendor = Oracle Corporation
    java.specification.version = 1.8
    java.vendor = Azul Systems, Inc.
    java.vendor.url = http://www.azulsystems.com/
    java.vendor.url.bug = http://www.azulsystems.com/support/
    java.version = 1.8.0_102
    java.vm.info = mixed mode
    java.vm.name = OpenJDK 64-Bit Server VM
    java.vm.specification.name = Java Virtual Machine Specification
    java.vm.specification.vendor = Oracle Corporation
    java.vm.specification.version = 1.8
    java.vm.vendor = Azul Systems, Inc.
    java.vm.version = 25.102-b14
    line.separator = \n 
    os.arch = amd64
    os.name = Linux
    os.version = 3.16.0-4-amd64
    path.separator = :
    sun.arch.data.model = 64
    sun.boot.class.path = /home/xxx/local/anaconda2/jre/lib/resources.jar
        /home/xxx/local/anaconda2/jre/lib/rt.jar
        /home/xxx/local/anaconda2/jre/lib/sunrsasign.jar
        /home/xxx/local/anaconda2/jre/lib/jsse.jar
        /home/xxx/local/anaconda2/jre/lib/jce.jar
        /home/xxx/local/anaconda2/jre/lib/charsets.jar
        /home/xxx/local/anaconda2/jre/lib/jfr.jar
        /home/xxx/local/anaconda2/jre/classes
    sun.boot.library.path = /home/xxx/local/anaconda2/jre/lib/amd64
    sun.cpu.endian = little
    sun.cpu.isalist = 
    sun.desktop = gnome
    sun.io.unicode.encoding = UnicodeLittle
    sun.java.launcher = SUN_STANDARD
    sun.jnu.encoding = UTF-8
    sun.management.compiler = HotSpot 64-Bit Tiered Compilers
    sun.os.patch.level = unknown
    user.country = US
    user.dir = /home/xxx
    user.home = /home/xxx
    user.language = en
    user.name = xxx
    user.timezone = 

openjdk version "1.8.0_102"
OpenJDK Runtime Environment (Zulu 8.17.0.3-linux64) (build 1.8.0_102-b14)
OpenJDK 64-Bit Server VM (Zulu 8.17.0.3-linux64) (build 25.102-b14, mixed mode)
ozanozisik commented 6 years ago

Hi, i guess somehow another java installation is run. You may use the command below to see java installations made by package manager. sudo update-alternatives --config java

This stackoverflow answer may also help: https://stackoverflow.com/a/35305363

egeulgen commented 6 years ago

@zhilongjia has the issue been resolved?

zhilongjia commented 6 years ago

Resolved. Thank you.

janstrauss1 commented 4 years ago

Hi, i guess somehow another java installation is run. You may use the command below to see java installations made by package manager. sudo update-alternatives --config java

This stackoverflow answer may also help: https://stackoverflow.com/a/35305363

Just found this thread after encountering a java version issue while trying to install pathfindR on macOS. I thought I have Java 8 installed checking via the Java Control Panel but Terminal showed me that I am using an older version. Just downloaded and installed the latest Java, Standard Edition Development Kit (JDK) from https://www.oracle.com/java/technologies as the Java Control Panel only appears to update the Java Runtime Environment (JRE) as discussed at https://stackoverflow.com/questions/12757558/installed-java-7-on-mac-os-x-but-terminal-is-still-using-version-6. Issue solved.