Package Details: fiji-bin 2:20220414.1745-1

Git Clone URL: https://aur.archlinux.org/fiji-bin.git (read-only, click to copy)
Package Base: fiji-bin
Description: ImageJ distribution with a lot of plugins for scientific (especially biology related) image processing.
Upstream URL: http://fiji.sc/
Licenses: GPL
Submitter: hottea
Maintainer: flomine
Last Packager: flomine
Votes: 22
Popularity: 0.000006
First Submitted: 2019-11-15 07:19 (UTC)
Last Updated: 2022-04-15 12:23 (UTC)

Latest Comments

flomine commented on 2022-04-15 12:27 (UTC)

Package updated to 20220414-1745

heisenbugs commented on 2022-03-08 04:20 (UTC)

@lezsakdomi I have tested the newest version 20220222-1217. It seems to work!

lezsakdomi commented on 2022-01-16 17:39 (UTC)

@hottea as SPW_87 pointed out, using an older version works. I couldn't get any targz of the most recent version (20201104-1356) to work.

For me downloading the version before is totally fine, but I'm curious what the issue could be.

It seems like that the issue is not bound to the specific JRE used. I've almost reported this issue on Fiji github, but it seems like the downloads.imagej.net is behind the tags on Fiji's github. In the recent tag it seems like they've just did something with the launcher, so I'll try those versions and hopefully post an update afterwards.

hottea commented on 2021-11-25 15:23 (UTC)

@lezsakdomi This pkg uses the the bundled jre, you might try the one with no-jre, check here. If still not working, contact the upstream for help.

lezsakdomi commented on 2021-11-25 14:39 (UTC)

Oracle JRE does not help either.

(I tried fiji --system --java-home /usr/lib/jvm/java-17-jdk)

lezsakdomi commented on 2021-11-25 14:23 (UTC) (edited on 2021-11-25 14:26 (UTC) by lezsakdomi)

I get the same error when starting it with fiji --system or without.

I have OpenJDK 17.0.1+12

fiji --ij1 works though.

SPW_87 commented on 2021-08-29 17:33 (UTC)

@iosonofabio I am getting the same error. The previous version 20201029-1752 works fine though.

From what I can tell the issue seems to be with the jre that is bundled with Fiji, as it looks like it was changed between these two versions. 20201029-1752 uses jdk1.8.0_172 and 20201104-1356 uses zulu8.48.0.53-ca-fx-jdk8.0.265-linux_x64.

hottea commented on 2021-08-25 07:58 (UTC)

fiji-bin uses a bundled jre, not the one from your system. You might need to check your jre config.

iosonofabio commented on 2021-08-25 04:43 (UTC)

Thanks for maintaining the package. I get a Java error after launching:

Error while executing the main() method of class 'net.imagej.Main': java.lang.NullPointerException: Cannot invoke "net.imagej.legacy.LegacyService.getIJ1Helper()" because "this.legacyService" is null

(among many lines of traceback).

I have:

jre-openjdk 16.0.2.u7-1 jre 16.0.2-1

as JRE providers. Would you know what's wrong?

Thank you Fabio

hello commented on 2021-02-12 21:30 (UTC)

It appears that the 20201104-2027 directory has disappeared and the latest version is instead 20201104-1356.

See https://downloads.imagej.net/fiji/archive/

The current source responds with a 404.

Is it possible to manually intervene and correct this?

Thanks

hottea commented on 2020-04-21 14:13 (UTC)

@drcont78 This pkg is automatically updated by a robot lilac from ArchLinuxCN repo. Here is the latest build log. I don't see any error. You might check it again, or you could just install this pkg from ArchLinuxCN repo.

dront78 commented on 2020-04-21 07:56 (UTC)

prepare()...
Creating desktop file
[fiji]                            Generating desktop file... ok
:: failed to verify integrity or prepare fiji-bin package

ryn1x commented on 2020-04-20 21:40 (UTC) (edited on 2020-04-20 21:42 (UTC) by ryn1x)

failed validity check

==> Retrieving sources...
  -> Found fiji-linux64.zip
==> Validating source files with sha256sums...
    fiji-linux64.zip ... FAILED
==> ERROR: One or more files did not pass the validity check!
Failed to build fiji-bin

dront78 commented on 2020-01-28 15:29 (UTC)

https://downloads.imagej.net/fiji/latest/fiji-linux64.zip can be a solution

mabl commented on 2020-01-20 15:31 (UTC)

The 64bit built for the 20200110 seems to have disappeared.... 20191220-2112 is still there though.

hottea commented on 2020-01-15 12:13 (UTC)

@mr-ubik You could install this pkg from this repo.

mr-ubik commented on 2020-01-13 15:51 (UTC)

Currently throwing the following error: Failure while downloading <https://downloads.imagej.net/fiji/archive/20200110-2121/fiji-linux64.zip>

dront78 commented on 2019-12-22 12:02 (UTC)

for some reason latest version packed as zip https://downloads.imagej.net/fiji/archive/20191220-2112/fiji-linux64.zip

user9665 commented on 2019-12-11 16:43 (UTC)

@Muflone I wasn't aware of fiji-bin. I've updated the package version. I'll request a merge to fiji-bin. This PKGBUILD either uses the lifeline version fiji-nojre-20170530 or uses the latest published in https://downloads.imagej.net/fiji/latest/fiji-nojre.zip.

Muflone commented on 2019-12-11 14:52 (UTC)

@jacopo, are you still maintaing this package? If so, given it's older than fiji-bin, do you want to rename it to fiji-bin AND update the version number to the latest available version?

Currently this package is older and with a bad name

user9665 commented on 2019-10-20 08:27 (UTC)

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 (UTC)

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.

user9665 commented on 2019-08-17 06:53 (UTC)

Sure, no problem. Thanks.

radioxoma commented on 2019-08-16 12:01 (UTC)

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?

user9665 commented on 2019-08-15 09:50 (UTC)

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 (UTC)

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 (UTC)

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 (UTC) (edited on 2016-01-17 00:00 (UTC) by radioxoma)

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 (UTC)

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.