Package Details: fiji-binary 20170530-1

Git Clone URL: https://aur.archlinux.org/fiji-binary.git (read-only)
Package Base: fiji-binary
Description: ImageJ distribution with a lot of plugins for scientific (especially biology related) image processing.
Upstream URL: http://fiji.sc/
Licenses: GPL
Submitter: radioxoma
Maintainer: radioxoma (jacopo)
Last Packager: jacopo
Votes: 17
Popularity: 0.000082
First Submitted: 2015-06-16 14:19
Last Updated: 2019-08-17 17:59

Latest Comments

jacopo commented on 2019-10-20 08:27

Do you get the menus when using other WMs? Have you also tried using the "Latest build" instead of the "Life-line"? I'm using the "Latest build" with Java 13 and it works fine here.

florosus commented on 2019-10-19 21:13

I can't get any of the dropdown menus (File, Edit, View etc) to open. Do I need some other package? I am running bspwm and I set Fiji to floating mode.

jacopo commented on 2019-08-17 06:53

Sure, no problem. Thanks.

radioxoma commented on 2019-08-16 12:01

Thanks, Jacopo. PKGBUILD had been updated. I don't use ImageJ/Fiji anymore and don't plan to support it. Would you like to be a maintainer?

jacopo commented on 2019-08-15 09:50

Minor improvement to automatically set pkgver. I'm not quite sure how a patch can be submitted here. Cheers Jacopo

diff --git a/PKGBUILD b/PKGBUILD index 4dc18c2..4abcd57 100644 --- a/PKGBUILD +++ b/PKGBUILD @@ -1,8 +1,13 @@ # Maintainer: Eugene Dvoretsky <radioxoma from gmail com> # Contributor: dreieck

+# wget -q -O tmp.html https://downloads.imagej.net/fiji/latest/ +# RELEASE_URL=cat tmp.html | grep -m 1 -o -E "https[^<>]*?fiji-nojre.zip" | head -1 +# echo $RELEASE_URL +# exit + pkgname="fiji-binary" -pkgver="20170530" +pkgver=wget -q -O - <https://downloads.imagej.net/fiji/latest/> | grep fiji-nojre.zip | sed -E 's/^.*([0-9]{4}-[0-9]{2}-[0-9]{2}).*$/\1/' | sed 's/-//g' pkgrel="1" pkgdesc="ImageJ distribution with a lot of plugins for scientific (especially biology related) image processing." arch=('i686' 'x86_64') @@ -18,10 +23,10 @@ install=fiji.install

## Life-line

-source=("https://downloads.imagej.net/fiji/Life-Line/fiji-nojre-${pkgver}.zip" +source=("https://downloads.imagej.net/fiji/latest/fiji-nojre.zip" "fiji.desktop" "fiji.install") -sha256sums=('cf9fb45c48b22a7888b479968477f1f7a300a9c833e47244cbe0d1e93890bd20' +sha256sums=('SKIP' '788a32dd0b24f482e78d5ec3209e9d5b3493a59e1da6edf82b1373e87c0320bc' '6dcc861af9328076282893ffcecc77a7fee448cec51fb7ccd51c5cece9740fa1')

@@ -54,6 +59,7 @@ build() _removefrompackage=('Contents' 'ImageJ-linux32' 'ImageJ-linux64' 'ImageJ-win32.exe' 'ImageJ-win64.exe' 'plugins/Fiji_Updater.jar' + 'plugins/imagej-updater*.jar' ) _executablebak="$(mktemp)" || exit 21 # Save the executable matching our architecture.

petecan commented on 2016-02-22 12:44

In my case, for getting rid of unnecessary "cannot update" messages, it is not enough to get rid of "plugins/Fiji_Updater.jar", but also of "jars/imagej-updater-0.7.8.jar". Probably we could use a glob to avoid forgetting to change the jar version.

Cheers
Santi

boina commented on 2015-12-01 04:59

Thank you a lot!! I should have locked at the PKGBUILD before. I uncommented the latest source and worked flawlesly!!
Best, Jose.

radioxoma commented on 2015-11-30 13:27

This package wasn't supposed to be "updatable" - just latest lifeline version. `Fiji_Updater.jar` was removed during makepkg run (see PKGBUILD source, https://aur.archlinux.org/cgit/aur.git/tree/PKGBUILD?h=fiji-binary&id=b664017f73f99246c31796b9fdde4d8e0ff96a0f#n53).

If you would like to use latest Fiji, there are two ways:
1. Edit the PKGBUILD and change source to latest build (I intentionally left it in commented section) and reinstall the package. Also you could change package version to download date, so new lifeline release, which can be outdated relatively to your current installation, won't be bothering you.
2. Just unpack and use vanilla archive from http://fiji.sc/Downloads somewhere in $HOME directory.

Cheers, Eugene.

boina commented on 2015-11-28 00:23

Thanks for the package.
I have one problem tough. I needed to update the bioformats plugin and so started imagej as root. After the update fiji won't start anymore as a regular user with the following warning:

"Could not move /opt/fiji/update/scripts/Miji.m to /opt/fiji/scripts/Miji.m: Permission denied"

Regards, jose.