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Bug 215877 - new package request: sci-biology/cytoscape
Summary: new package request: sci-biology/cytoscape
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: High enhancement (vote)
Assignee: Default Assignee for New Packages
Depends on: 161710 188007 216027 231331 231333 232666
  Show dependency tree
Reported: 2008-04-02 13:10 UTC by Martin Mokrejš
Modified: 2019-06-07 15:13 UTC (History)
2 users (show)

See Also:
Package list:
Runtime testing required: ---

cytoscape-2.6.0.ebuild (cytoscape-2.6.0.ebuild,969 bytes, text/plain)
2008-07-08 22:48 UTC, Andrey Kislyuk (RETIRED)
cytoscape-2.6.0.ebuild (cytoscape-2.6.0.ebuild,2.32 KB, text/plain)
2008-07-09 21:52 UTC, Andrey Kislyuk (RETIRED)
cytoscape-2.6.0.ebuild (cytoscape-2.6.0.ebuild,2.39 KB, text/plain)
2008-07-10 00:37 UTC, Andrey Kislyuk (RETIRED)
cytoscape-2.6.0.ebuild (cytoscape-2.6.0.ebuild,2.84 KB, text/plain)
2008-07-15 16:04 UTC, Andrey Kislyuk (RETIRED)
cytoscape-2.8.0_beta2.ebuild (cytoscape-2.8.0_beta2.ebuild,1.42 KB, text/plain)
2010-11-08 18:30 UTC, Joel Berendzen

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Description Martin Mokrejš 2008-04-02 13:10:10 UTC
Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.

... written in Java.

		       Version 2.1, February 1999
Comment 1 Andrey Kislyuk (RETIRED) gentoo-dev 2008-07-08 22:48:09 UTC
Created attachment 159916 [details]

Here's the first stab at an ebuild. This package has a ton of bundled jars, which we'll need to get rid of before this can go into mainline.
Comment 2 Andrey Kislyuk (RETIRED) gentoo-dev 2008-07-09 21:52:23 UTC
Created attachment 159986 [details]

Lots of fixes to the ebuild.

Removed most jars that are in the tree.

Added blockers on request bugs for freehep and biojava.

Unfortunately this will now pull in a HUGE list of dependencies.
Comment 3 Andrey Kislyuk (RETIRED) gentoo-dev 2008-07-10 00:25:37 UTC
One thing that I've noticed is that the Cytoscape core plugins are bundled with the binary releases of Cytoscape, but don't seem to be in the source tarball. Without the core plugin jars, the application as compiled from the source tarball is an empty shell. The core plugins are not in the plugin directory on the website, either.
Comment 4 Andrey Kislyuk (RETIRED) gentoo-dev 2008-07-10 00:37:29 UTC
Created attachment 160002 [details]

Ah, never mind. My bad, I had set the plugins path wrong in src_install.
Comment 5 Serkan Kaba (RETIRED) gentoo-dev 2008-07-10 13:22:22 UTC
(In reply to comment #4)
> Created an attachment (id=160002) [edit]
> cytoscape-2.6.0.ebuild
> Ah, never mind. My bad, I had set the plugins path wrong in src_install.

EANT_ANT_TASKS="jakarta-regexp-1.4 batik-1.6 xalan xsdlib relaxng-datatype"

Sorry if I misinformed you, but don't add all the runtime dependencies to EANT_ANT_TASKS just the ones that's needed by an ant task. (batik for example)
Comment 6 Andrey Kislyuk (RETIRED) gentoo-dev 2008-07-10 14:07:37 UTC

Those are not runtime dependencies. Those correspond to the jars I found in the build-libs subdirectory. I haven't checked yet which of them correspond to actual build tasks.
Comment 7 Andrey Kislyuk (RETIRED) gentoo-dev 2008-07-15 16:04:18 UTC
Created attachment 160460 [details]

More deps cleanup, shortcut icon. See blocker bugs for some of the remaining deps.
Comment 8 Andrey Kislyuk (RETIRED) gentoo-dev 2009-01-10 20:33:15 UTC
The package is now available in the java-experimental overlay:

This overlay is not in layman, so it must be checked out manually using

svn co

and adding to PORTDIR_OVERLAY in make.conf.
Comment 9 Martin Mokrejš 2009-01-12 12:01:18 UTC
# emerge -pv cytoscape
 * Overlay eclasses override eclasses from PORTDIR:
 *   '/usr/local/java-experimental/eclass/java-pkg-2.eclass'
 *   '/usr/local/java-experimental/eclass/java-utils-2.eclass'
 *   '/usr/local/java-experimental/eclass/mercurial.eclass'
 * It is best to avoid overriding eclasses from PORTDIR because it will
 * trigger invalidation of cached ebuild metadata that is distributed with
 * the portage tree. If you must override eclasses from PORTDIR then you
 * are advised to add FEATURES="metadata-transfer" to /etc/make.conf and to
 * run `emerge --regen` after each time that you run `emerge --sync`. Set
 * PORTAGE_ECLASS_WARNING_ENABLE="0" in /etc/make.conf if you would like to
 * disable this warning.

These are the packages that would be merged, in order:

emerge: there are no ebuilds to satisfy "dev-java/piccolo2d".
(dependency required by "sci-biology/cytoscape-2.6.1" [ebuild])
(dependency required by "cytoscape" [argument])

Comment 10 Andrey Kislyuk (RETIRED) gentoo-dev 2009-01-12 13:07:07 UTC

piccolo2d is in the java overlay. Add it with layman -a java-overlay. (You'll need to follow layman setup instructions if you haven't used layman before)

Sorry I forgot to mention that.
Comment 11 Martin Mokrejš 2009-03-17 15:29:23 UTC
>>> Emerging (1 of 1) sci-biology/cytoscape-2.6.1 from java-experimental
 * WizardSource.jar RMD160 SHA1 SHA256 size ;-) ...                                                                                                                                                                            [ ok ]
 * cytoscapeSource-v2.6.1.tar.gz RMD160 SHA1 SHA256 size ;-) ...                                                                                                                                                               [ ok ]
 * checking ebuild checksums ;-) ...                                                                                                                                                                                           [ ok ]
 * checking auxfile checksums ;-) ...                                                                                                                                                                                          [ ok ]
 * checking miscfile checksums ;-) ...                                                                                                                                                                                         [ ok ]
 * Using: sun-jdk-1.6
>>> Unpacking source...
>>> Unpacking WizardSource.jar to /var/tmp/portage/sci-biology/cytoscape-2.6.1/work
>>> Unpacking cytoscapeSource-v2.6.1.tar.gz to /var/tmp/portage/sci-biology/cytoscape-2.6.1/work
 * Removing bundled jars...
>>> Source unpacked in /var/tmp/portage/sci-biology/cytoscape-2.6.1/work
>>> Compiling source in /var/tmp/portage/sci-biology/cytoscape-2.6.1/work ...
Rewriting attributes
Rewriting ./docs/build.xml
Rewriting ./wizard/build.xml
Rewriting ./build.xml
 * Using following ANT_TASKS:  jakarta-regexp-1.4 batik-1.7 xalan xsdlib relaxng-datatype jaxb-2 jaxb-tools-2
!!! ERROR: Package swingx was not found!
 * ERROR: sci-biology/cytoscape-2.6.1 failed.
 * Call stack:
 *     , line   48:  Called src_compile
 *             environment, line 4133:  Called java-pkg-2_src_compile
 *             environment, line 2248:  Called eant 'jar' '-f' 'build.xml'
 *             environment, line  911:  Called java-pkg_getjars 'swing-layout-1,stax-ex,xmlstreambuffer,sjsxp,concurrent-util,jsr173,jsr181,jsr250,saaj-api,fastinfoset,itext,jdom-1.0,junit,colt,javahelp,jgoodies-looks-2.0,swingx,l2fprod-common,tclib,piccolo2d,freehep-graphicsio-svg,freehep-util,freehep-xml,freehep-export,freehep-graphicsio,freehep-graphicsio-java,freehep-swing,freehep-graphicsio-ps,freehep-io,freehep-graphics2d,freehep-misc-deps,jaxb-2,jaxb-tools-2,batik-1.7'
 *             environment, line 2916:  Called die
 * The specific snippet of code:
 *       [[ $? != 0 ]] && die "java-config --classpath=${pkgs} failed";
 *  The die message:
 *   java-config --classpath=swing-layout-1,stax-ex,xmlstreambuffer,sjsxp,concurrent-util,jsr173,jsr181,jsr250,saaj-api,fastinfoset,itext,jdom-1.0,junit,colt,javahelp,jgoodies-looks-2.0,swingx,l2fprod-common,tclib,piccolo2d,freehep-graphicsio-svg,freehep-util,freehep-xml,freehep-export,freehep-graphicsio,freehep-graphicsio-java,freehep-swing,freehep-graphicsio-ps,freehep-io,freehep-graphics2d,freehep-misc-deps,jaxb-2,jaxb-tools-2,batik-1.7 failed
 * If you need support, post the topmost build error, and the call stack if relevant.
 * A complete build log is located at '/var/tmp/portage/sci-biology/cytoscape-2.6.1/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/cytoscape-2.6.1/temp/environment'.
 * This ebuild is from an overlay named 'java-experimental': '/usr/local/java-experimental/'
!!! When you file a bug report, please include the following information:
GENTOO_VM=sun-jdk-1.6  CLASSPATH="" JAVA_HOME="/opt/sun-jdk-"
JAVACFLAGS="-source 1.6 -target 1.6" COMPILER="javac"
and of course, the output of emerge --info
!!! ERROR: Package jaxb-tools-2 was not found!
!!! ERROR: Package jaxb-tools-2 was not found!
Buildfile: build.xml

It seems having swingx-0.9.5 is not helpful. I will probably have to downgrade to the 2007 version once I find the sources (bug #161710).
Comment 12 Martin Mokrejš 2009-04-17 23:04:37 UTC
# svn diff sci-biology/cytoscape/cytoscape-2.6.1.ebuild
Index: sci-biology/cytoscape/cytoscape-2.6.1.ebuild
--- sci-biology/cytoscape/cytoscape-2.6.1.ebuild        (revision 7705)
+++ sci-biology/cytoscape/cytoscape-2.6.1.ebuild        (working copy)
@@ -20,7 +20,7 @@
+KEYWORDS="~amd64 ~x86"
@@ -39,7 +39,7 @@
-       =dev-java/swingx-20070211-r1
+       dev-java/swingx

Should depend also on bug #188007
Comment 13 Joel Berendzen 2010-11-08 18:30:56 UTC
Created attachment 253663 [details]

Version bump; this distribution is just jars, so complete ebuild is not possible.  However, the number, variety, and version-specificity of bundled jars make un-bundling seem like a bad idea to me, as generally-useful packages like biojava can't go to the most-recent version.
Comment 14 Patrice Clement gentoo-dev 2016-03-09 15:01:13 UTC
Feel free to reopen if you're still interested in adding this ebuild to the Portage tree. Closing as WONTFIX.
Comment 15 Martin Mokrejš 2016-03-10 11:42:38 UTC
Cytoscape is a flagship project and it is missing in Gentoo.
Comment 16 Patrice Clement gentoo-dev 2016-03-10 11:55:47 UTC
Fair enough. Removing java@ from CC in this case. As far as we are concerned, we have no interest in maintaining/packaging sci libs.