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Bug 138619

Summary: sci-chemistry/jmol - new ebuild
Product: Gentoo Linux Reporter: Christoph Budziszewski <gentoobugs>
Component: New packagesAssignee: Jeffrey Gardner (RETIRED) <je_fro>
Status: RESOLVED FIXED    
Severity: enhancement CC: java, je_fro, sci-chemistry
Priority: High Keywords: EBUILD
Version: unspecified   
Hardware: All   
OS: Linux   
Whiteboard:
Package list:
Runtime testing required: ---
Attachments: jmol-10.2.0.ebuild
jmol-svn-10.2.0.ebuild
jmol-svn-10.2.0-gentoo-libpath.patch
jmol-svn-10.2.0.ebuild
jmol-svn-10.2.0-no-i18n.patch
jmol-10.2.0.ebuild
jmol-10.2.0-gentoo-libpath.patch
jmol-10.2.0-application.patch
jmol-10.2.0-nodoc-no-i18n.patch
jmol-10.2.0-no-i18n.patch
fixed jmol-10.2.0.ebuild
jmol-10.2.0.ebuild
sample molecule
jmol-10.2.0-manifest.patch
selfSignedCertificate.store
jmol-10.2.0-no-i18n.patch
jmol-10.2.0-nointl.patch
jmol-10.2.0.ebuild
index.html
jmol-10.2.0.ebuild
jmol-10.2.0.ebuild

Description Christoph Budziszewski 2006-06-30 12:19:13 UTC
Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems.

    * The JmolApplet is a web browser applet that can be integrated into web pages.
    * The Jmol application is a standalone Java application that runs on the desktop.
    * The JmolViewer is a development tool kit that can be integrated into other Java applications.


This ebuild installs the application.
Comment 1 Christoph Budziszewski 2006-06-30 12:20:28 UTC
Created attachment 90549 [details]
jmol-10.2.0.ebuild
Comment 2 Jeffrey Gardner (RETIRED) gentoo-dev 2006-07-24 17:16:20 UTC
Created attachment 92662 [details]
jmol-svn-10.2.0.ebuild
Comment 3 Jeffrey Gardner (RETIRED) gentoo-dev 2006-07-24 17:18:07 UTC
Created attachment 92663 [details, diff]
jmol-svn-10.2.0-gentoo-libpath.patch
Comment 4 Jeffrey Gardner (RETIRED) gentoo-dev 2006-07-24 22:49:59 UTC
Created attachment 92683 [details]
jmol-svn-10.2.0.ebuild

disables i18n which was flaky during testing...
Comment 5 Jeffrey Gardner (RETIRED) gentoo-dev 2006-07-24 22:51:04 UTC
Created attachment 92684 [details, diff]
jmol-svn-10.2.0-no-i18n.patch

patch to strip i18n from build.xml
Comment 6 Jeffrey Gardner (RETIRED) gentoo-dev 2006-07-26 23:27:00 UTC
Created attachment 92826 [details]
jmol-10.2.0.ebuild
Comment 7 Jeffrey Gardner (RETIRED) gentoo-dev 2006-07-26 23:28:36 UTC
Created attachment 92827 [details, diff]
jmol-10.2.0-gentoo-libpath.patch
Comment 8 Jeffrey Gardner (RETIRED) gentoo-dev 2006-07-26 23:29:25 UTC
Created attachment 92828 [details, diff]
jmol-10.2.0-application.patch
Comment 9 Jeffrey Gardner (RETIRED) gentoo-dev 2006-07-26 23:30:42 UTC
Created attachment 92829 [details, diff]
jmol-10.2.0-nodoc-no-i18n.patch
Comment 10 Jeffrey Gardner (RETIRED) gentoo-dev 2006-07-26 23:31:18 UTC
Created attachment 92830 [details, diff]
jmol-10.2.0-no-i18n.patch
Comment 11 Petteri Räty (RETIRED) gentoo-dev 2006-09-17 13:44:05 UTC
(In reply to comment #6)
> Created an attachment (id=92826) [edit]
> jmol-10.2.0.ebuild
> 

Some feedback after a quick look at the ebuild:
LICENSE="LLGPL"
is not a license found in ${PORTDIR}/licenses

dojar   Jmol.jar JmolApplet.*
dojar is depreced and removed from latest portage versions. Should use java-pkg_dojar instead

JAVA_PKG_BSFIX="off"
not really much use from inheriting java-ant-2 if you don't use this

You could consider adding support for the source use flag.
Comment 12 Jeffrey Gardner (RETIRED) gentoo-dev 2006-09-26 06:41:47 UTC
Created attachment 98122 [details]
fixed jmol-10.2.0.ebuild
Comment 13 Jeffrey Gardner (RETIRED) gentoo-dev 2006-10-19 01:16:45 UTC
Created attachment 100002 [details]
jmol-10.2.0.ebuild

properly utilize eclass
Comment 14 Jeffrey Gardner (RETIRED) gentoo-dev 2006-10-19 01:17:35 UTC
Created attachment 100003 [details]
sample molecule
Comment 15 Jeffrey Gardner (RETIRED) gentoo-dev 2006-10-19 01:26:09 UTC
Created attachment 100004 [details, diff]
jmol-10.2.0-manifest.patch

add a few required files
Comment 16 Jeffrey Gardner (RETIRED) gentoo-dev 2006-10-19 01:38:31 UTC
Created attachment 100006 [details]
selfSignedCertificate.store

selfSignedCertificate.store
Comment 17 Jeffrey Gardner (RETIRED) gentoo-dev 2006-10-19 03:17:32 UTC
Created attachment 100011 [details, diff]
jmol-10.2.0-no-i18n.patch

required
Comment 18 Jeffrey Gardner (RETIRED) gentoo-dev 2006-10-19 03:18:35 UTC
Created attachment 100012 [details, diff]
jmol-10.2.0-nointl.patch

disable french and german manuals
Comment 19 Donnie Berkholz (RETIRED) gentoo-dev 2006-10-20 00:35:50 UTC
The use vhosts && { webapp_src_preinst ... } is strange formatting. Use an if..then instead.

There's nothing dynamic in the test page that requires it to be generated from an ebuild, just stick it into files/ instead.

You'll also need to define a pkg_prerm() with the use vhosts bit. It would be nice if you were consistent between functions with whether a 1-liner uses && or if..then. Anything greater than 1 function/command should always use if..then.
Comment 20 Jeffrey Gardner (RETIRED) gentoo-dev 2006-10-20 03:35:43 UTC
Created attachment 100078 [details]
jmol-10.2.0.ebuild
Comment 21 Jeffrey Gardner (RETIRED) gentoo-dev 2006-10-20 03:36:24 UTC
Created attachment 100079 [details]
index.html

testpage index.html
Comment 22 Donnie Berkholz (RETIRED) gentoo-dev 2006-10-20 09:35:10 UTC
Remaining issues:

Should inherit java-pkg-2 instead of java-pkg
Use mirror://sourceforce/ instead of a specific download.sourceforge.net
Missing parentheses in USE-based dep
SLOT based on PV is unusual and shouldn't be needed here
Curious why you've got "|| die" for some things, but others can silently fail (dobin jmol e.g., likely the java-pkg-* stuff as well)
I suggest that you get rid of the USE=intl and patch in the fixes unconditionally
All uses of S, D, FILESDIR require quotes to allow for spaces in paths
Why are you using jarinto instead of accepting the default? Perhaps the provided shell script assumes it
Comment 23 Jeffrey Gardner (RETIRED) gentoo-dev 2006-10-31 05:22:03 UTC
Created attachment 100877 [details]
jmol-10.2.0.ebuild

jmol-10.2.0.ebuild
Comment 24 Jeffrey Gardner (RETIRED) gentoo-dev 2006-11-01 10:57:05 UTC
Created attachment 100981 [details]
jmol-10.2.0.ebuild

improved jmol-10.2.0.ebuild
Comment 25 Donnie Berkholz (RETIRED) gentoo-dev 2007-06-22 07:02:35 UTC
Jeffrey, can this bug be closed?
Comment 26 Vlastimil Babka (Caster) (RETIRED) gentoo-dev 2007-06-22 07:13:41 UTC
Trying to review.
Comment 27 Vlastimil Babka (Caster) (RETIRED) gentoo-dev 2007-06-22 08:30:23 UTC
+*jmol-11.0.3-r1 (22 Jun 2007)
+
+  22 Jun 2007; Vlastimil Babka <caster@gentoo.org> jmol-11.0.3.ebuild,
+  +jmol-11.0.3-r1.ebuild:
+  Revbump for java-related fixes - install jars we've built and not the
+  bundled ones, don't absorb dependencies' classes, depend only on what's
+  actually needed, use java dolauncher instead of supplied one. Keyword ~x86.

It got my attention mainly because because it depended on gnu-jaxp which we plan to remove soon, and it turned out to be unneeded dep, as expected. Also some other deps were actually unused. The dep handling itself was wrong, using --build-only and absorbing the classes into Jmol.jar, but that's what some upstreams do :( At least it could be overrided without another build.xml patch.
Because of the changes it needed revbump. We'll remove -r0 when we remove gnu-jaxp.

I think this can be fixed
Comment 28 Jeffrey Gardner (RETIRED) gentoo-dev 2007-06-22 10:09:19 UTC
Okay, thanks for the reminder and input...I'll look into this when I get some time.
Thanks!
Jeff