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Package Details: cytoscape 3.10.2-2
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Git Clone URL: | https://aur.archlinux.org/cytoscape.git (read-only, click to copy) |
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Package Base: | cytoscape |
Description: | Network Data Integration, Analysis, and Visualization in a Box |
Upstream URL: | https://www.cytoscape.org |
Licenses: | LGPL-2.1-only |
Submitter: | timdiels |
Maintainer: | a821 |
Last Packager: | a821 |
Votes: | 12 |
Popularity: | 0.000135 |
First Submitted: | 2015-09-22 13:00 (UTC) |
Last Updated: | 2024-07-29 16:16 (UTC) |
Dependencies (3)
- bash (bash-devel-static-gitAUR, bash-devel-gitAUR, busybox-coreutilsAUR, bash-gitAUR)
- jdk17-openjdk (jdk17-temurinAUR)
- opencl-driver (opencl-nvidia-410xxAUR, amdapp-sdkAUR, opencl-nvidia-340xxAUR, opencl-nvidia-440xxAUR, vc4cl-gitAUR, opencl-nvidia-430xxAUR, opencl-legacy-amdgpu-proAUR, intel-compute-runtime-gitAUR, beignetAUR, opencl-nvidia-vulkanAUR, beignet-gitAUR, intel-openclAUR, clvk-gitAUR, opencl-nvidia-525xxAUR, opencl-510xx-nvidiaAUR, opencl-nvidia-390xxAUR, opencl-nvidia-470xxAUR, opencl-550xx-nvidiaAUR, opencl-nvidia-betaAUR, opencl-rusticl-mesa-minimal-gitAUR, mesa-gitAUR, intel-compute-runtime-binAUR, opencl-amdAUR, amdonly-gaming-opencl-clover-mesa-gitAUR, amdonly-gaming-opencl-rusticl-mesa-gitAUR, opencl-nvidia-535xxAUR, opencl-nvidia-teslaAUR, intel-compute-runtime, intel-oneapi-compiler-shared-runtime, opencl-clover-mesa, opencl-nvidia, opencl-rusticl-mesa, rocm-opencl-runtime) (optional) – for OpenCL support
Required by (1)
- r-metaphor (optional)
Latest Comments
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a821 commented on 2024-07-29 16:19 (UTC) (edited on 2024-07-29 16:20 (UTC) by a821)
@mahlzahn: thanks for the report. Indeed, it does not work, so the package now depends on
jdk17-openjdk
. I guess this change has something to do...mahlzahn commented on 2024-07-29 12:51 (UTC)
Installing it, it proposed to install java-runtime from the jre:
But after that it was not starting with following error message:
Only using the jdk17-openjdk solved the issue for me.
vstuart commented on 2021-03-26 23:19 (UTC) (edited on 2021-03-27 00:01 (UTC) by vstuart)
I very much appreciate the effort put into maintaining these packages. That said, the AUR version failed to load (output appended).
Therefore, I installed the latest Linux version (3.8.2) directly from https://cytoscape.org/download.html via their BASH script installer, which quickly installed a working version, accessible via the application shortcut that was automatically added to the Whiskers menu. Quick and painless.
The downloaded binary apparently includes / uses Java 11 (which is listed as a requirement on the download page: "Please install Java 11 before using Cytoscape").
In the new version (3.8.2): Help menu >> About >>
Keystone commented on 2021-02-16 16:05 (UTC)
JAVA_HOME out of the box not being set is annoying, but not having AA enabled makes this software nearly impossible to use.
The application command entry might benefit from being changed to reflect one or both improvements:
1 Depend on jdk8 and link it directly + turn on AA:
JAVA_HOME=/usr/lib/jvm/java-8-openjdk/ _JAVA_OPTIONS='-Dawt.useSystemAAFontSettings=on' cytoscape
2 Don't depend on jdk8 and turn on AA:
_JAVA_OPTIONS='-Dawt.useSystemAAFontSettings=on' cytoscape
I used #1 while working towards getting this running.
K
<deleted-account> commented on 2020-12-05 11:28 (UTC)
Current version bump to 3.8.2
I was playing with the PKGBUILD and updated it to version 3.8.2 by making the following changes
I have included a gist with the illustrated changes for your convenience. I'd be delighted to help co-maintain and test the package long term.
https://gist.github.com/evikv/cb2191582103e939bb3c78d8554144e5
essenceoffoo commented on 2020-07-13 08:48 (UTC)
FYI: I installed Cytoscape 3.8. with the official Linux installer from cytoscape.org. Java 8-openjdk did not work, but Java 11-openjdk does. I haven't tried Java 14-openjdk.
khughitt commented on 2020-02-06 23:45 (UTC)
One more suggestion -- Cytoscape is not compatible with recent versions of Java so you first have to install an earlier version (JDK-8 is the one currently listed as supported), and then you should be able to launch cytoscape with "JAVA_HOME=/usr/lib/jvm/java-8-openjdk cytoscape"
balwierz commented on 2019-07-10 16:11 (UTC)
Crash at startup
Error occurred during initialization of boot layer java.lang.module.FindException: Module java.transaction not found
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