Version in portage is quite old, please update. Reproducible: Always I tried upgrading by manually creating the ebuild myself and got reasonably far but with problems: * the patch files would not apply (no real surprise), so I commented them out * the build failed I know very little about the Jmol build process, so I trust you'll have better results. :)
from summary: 11.6 is latest stable, 11.7 latest dev
On it :)
How's it going? :)
I added bumped version to sci overlay.
Latest official stable version is 11.8, unstable is 11.9. Portage tree has 11.0, science overlay has 11.6. :(
There's a 12.0.24 stable version. Out of curiosity, why are many scientific packages in the science overlay but there are a few in the main tree?
Well, seeing as there is a 12.0 in the science overlay, I'm going to close this bug. But maybe someone should remove 11.0 from the main tree, since it's really old now.
Please leave it open until someone moved it to the tree.
Hi, I just bumped into jmol because jalview compile broke on that. I had jmol-11.0.3-r1 installed so I tried to upgrade to jmol-12.0.34 then. It seems the ebuild calls webapp-config with wrong arguments: [cut] [signjar] Signing JAR: /scratch/var/tmp/portage/sci-chemistry/jmol-12.0.34/work/jmol-12.0.34/build/JmolAppletSigned0.jar to /scratch/var/tmp/portage/sci-chemistry/jmol-12.0.34/work/jmol-12.0.34/build/JmolAppletSigned0.jar as selfSignedCertificate smiles-applet-jar: [jar] Building jar: /scratch/var/tmp/portage/sci-chemistry/jmol-12.0.34/work/jmol-12.0.34/build/JmolSmilesApplet.jar main: BUILD SUCCESSFUL Total time: 56 seconds >>> Source compiled. >>> Test phase [not enabled]: sci-chemistry/jmol-12.0.34 >>> Install jmol-12.0.34 into /scratch/var/tmp/portage/sci-chemistry/jmol-12.0.34/image/ category sci-chemistry >>> Completed installing jmol-12.0.34 into /scratch/var/tmp/portage/sci-chemistry/jmol-12.0.34/image/ >>> Installing (1 of 1) sci-chemistry/jmol-12.0.34 Usage: webapp-config [-ICU] [-dghus] <APPLICATION VERSION> Options: --version show program's version number and exit APPLICATION VERSION: The name and version number of the web application to install e.g. phpmyadmin 2.5.4. TheAPPLICATION must have already been installed into the /usr/share/webapps directory tree using emerge <Main Options>: -I, --install Install a web application -C, --clean Remove a web application -U, --upgrade Upgrade a web application [cut] <Reporting Bugs>: To report bugs about webapp-config, please go to http://bugs.gentoo.org/. Include the output of webapp-config --bug- report <your parameters here> to help us to help you --bug-report * Fatal error: You need to specify at least the application you would like to handle! * Fatal error(s) - aborting * ERROR: sci-chemistry/jmol-11.0.3-r1 failed (prerm phase): * webapp_pkg_prerm failed * * Call stack: * ebuild.sh, line 56: Called pkg_prerm * environment, line 4294: Called die * The specific snippet of code: * webapp_pkg_prerm || die "webapp_pkg_prerm failed"; * * If you need support, post the output of 'emerge --info =sci-chemistry/jmol-11.0.3-r1', * the complete build log and the output of 'emerge -pqv =sci-chemistry/jmol-11.0.3-r1'. !!! When you file a bug report, please include the following information: GENTOO_VM=icedtea6-bin CLASSPATH="" JAVA_HOME="/opt/icedtea6-bin-1.9.7" JAVACFLAGS="-source 1.4 -target 1.4" COMPILER="javac" and of course, the output of emerge --info * The complete build log is located at '/scratch/var/tmp/portage/._unmerge_/sci-chemistry/jmol-11.0.3-r1/temp/build.log'. * The ebuild environment file is located at '/scratch/var/tmp/portage/._unmerge_/sci-chemistry/jmol-11.0.3-r1/temp/environment'. * S: '/scratch/var/tmp/portage/._unmerge_/sci-chemistry/jmol-11.0.3-r1/work/jmol-11.0.3' !!! FAILED prerm: 1 * vhosts USE flag not set - auto-installing using webapp-config * This is an upgrade * jmol-11.0.3-r1 is already installed - upgrading * Running /usr/sbin/webapp-config -U -h localhost -u root -d /jmol jmol 12.0.34 * Upgrading /jmol-11.0.3-r1 to /jmol-12.0.34 * Installed by root on 2011-05-11 01:21:53 * Config files owned by 0:0 !empty /var/www/localhost/cgi-bin * Remove whatever is listed above by hand * Creating required directories * Linking in required files * This can take several minutes for larger apps * Files and directories installed * Install completed - success * Running /usr/sbin/webapp-cleaner -p -C jmol * Package name must be in the form CATEGORY/PN * ERROR: sci-chemistry/jmol-12.0.34 failed (postinst phase): * webapp_pkg_postinst failed * * Call stack: * ebuild.sh, line 56: Called pkg_postinst * environment, line 4290: Called die * The specific snippet of code: * webapp_pkg_postinst || die "webapp_pkg_postinst failed"; * * If you need support, post the output of 'emerge --info =sci-chemistry/jmol-12.0.34', * the complete build log and the output of 'emerge -pqv =sci-chemistry/jmol-12.0.34'. * This ebuild is from an overlay named 'science': '/var/lib/layman/science/' !!! When you file a bug report, please include the following information:
Doh, and I would have included build.log if emerge would not continue after the error and remove /scratch/var/tmp/portage/sci-chemistry/jmol-12.0.34 . :(
Out of curiosity, what are the criteria for transferring these ebuilds from the science overlay to the main tree?
(In reply to comment #11) > Out of curiosity, what are the criteria for transferring these ebuilds from the > science overlay to the main tree? A dev who is willing to review and test the ebuild. We are short in manpower, but you are right, that should be moved.
Thanks for the 12.0 bump, I only just noticed. Now how about 12.2? :)
*bump* 12.2 please.
(In reply to comment #14) > *bump* 12.2 please. +1. I also want to know why there is not a single stable version in portage. jmol is one of the best packages out there, far away from unstable.
please also make the client-only use flag default, for obvious reasons
12.2.27 is now in the tree for testing Thanks, je_fro
