Package Details: imagej 2:1.50i-3

Git Clone URL: https://aur.archlinux.org/imagej.git (read-only)
Package Base: imagej
Description: Image manipulation software for scientists
Upstream URL: https://imagej.net
Licenses: Public Domain
Submitter: skarn
Maintainer: mschu
Last Packager: mschu
Votes: 59
Popularity: 0.811718
First Submitted: 2009-05-18 15:59
Last Updated: 2017-07-03 23:07

Latest Comments

mschu commented on 2017-07-03 23:08

From now on I will only include versioned .jar files to patch the main distribution.

This should alleviate the problem of breaking checksums.

I will only update to the unversioned .jar if there is a strong reason to do so.

fordprefect commented on 2017-02-23 21:07

checksum for ij.jar changed, please update. thank you.

SammysHP commented on 2017-02-17 20:49

AFAIK version 2 is a completely different piece of software. I don't know if it will replace the 1.x branch.

PS: checksums still not updated.

ArchangeGabriel commented on 2017-02-16 00:46

@mschu: Latest update was from November while one comment from early January was already asking for an update. Granted, they didn’t flag the package, but given how the version number are used here, it makes out-of-date a bit confusing. But an existing non-adressed issue from a comment is equivalent to me as flagged out-of-date.

Now, regarding the orphan: I never said I didn’t intend to respect the rules. An orphan request was filed, so I took a look at the package. Because I, at least, do not automatically orphan even after no answers for 14 days, I want that plus a proof that the next maintainer knows how to fix things.

When looking at the PKGBUILD, I saw the bad shape it was in, I saw no updates since November while evidences suggest that upstream made a release in the meantime (from early December), and thus, I said that if *no updates happens* (which didn’t included a time span, but it implicitly implied the 14 days window at least for me) and someone was actually proposing a fix (which wasn’t the case with only users wanting to bump md5sums), I would indeed accept the orphan request (that I worded disown it, but that is equivalent).

But you’ve update it and now it’s fine, excepted the version number still.

For v2, a closer look at upstream GitHub made me see they’re still not in the final release, but RC58! (https://github.com/imagej/imagej/releases) So it’s not definitively ready for packaging.

greyltc commented on 2017-02-16 00:04

Hi mschu, it looks to me like the checksums are still not right here (maybe you've not cleared the old source files before recomputing the checksums?). I'm getting a disagreement for ij.jar. I think it should be a659180b574f80d2704dc1b60a8f19a1

mschu commented on 2017-02-15 00:54

All fixed for v1, will have a closer look for v2.

However, as far as I am aware there should be a *direct* email to the maintainer and 2 weeks time to respond before disowning. Please respect that, or point me to where the guidelines have changed.

The orphan request sent is nonsense, the package has not been flagged before yesterday.

ArchangeGabriel commented on 2017-02-15 00:49

@mschu: Thanks for the update, just one little thing: with the ij.jar updating, the version number should be 1.51j. ;)

ArchangeGabriel commented on 2017-02-14 14:03

So, in conclusion, if no update happens and someone proposes a fixed PKGBUILD, I’ll disown this package so that it can be fixed by that person.

ArchangeGabriel commented on 2017-02-14 14:01

This way of updating versions doesn’t make sense (that ij.jar thing), but if that’s how upstream works…

Anyway, upstream URL should be : https://imagej.net.

Next, the latest zip file is here: https://wsr.imagej.net/distros/cross-platform/ij150.zip (which is 1.50i)

Then, the upgrade path should also be changed to this one: https://wsr.imagej.net/jars/ij.jar

And finally, should reflects those ij.jar changes in the version number, because that’s what they correspond to: currently, it’s the file for 1.51j, you can see it here https://wsr.imagej.net/src/, and here https://imagej.nih.gov/ij/download/src/ if you want to see history of releases.

And finally, all those files are ImageJ 1.x, but now ImageJ 2 is out, a portable version is available here:
http://downloads.imagej.net/ImageJ2-20160205.zip

greyltc commented on 2017-02-13 18:21

Please update the md5sums for ij.jar

brosophila commented on 2017-01-03 01:54

Please update the md5sums for ij.jar

justinus commented on 2016-10-09 06:24

newest md5sum for ij.jar is c2ec327a8789603b127b4671311e305d

shiihs commented on 2016-08-19 09:16

newest md5sum for ij.jar is d1d166bb2991d4d5703446af78968396

hopimet commented on 2016-06-19 08:26

md5sums for ij.jar is: a2c20f7b1d494c1aa535a6f6137539d1

bnthorpe commented on 2016-06-13 03:02

Please update the md5sums for ij.jar.

ron89 commented on 2016-05-07 12:33

ij.jar is changed again, latest md5sum:

md5sums=('a0998c0e6aec078a8f9681f5088c41f2'
'e68fe4ed1aaa170bee4b36ed5ff94280' # <- changed
'7dc3fd02120f699204b3d85a7e383082'
'9d60878b6adad0e1895ce875bf299147'
'e7a7cef1b44ad3a8752ba63885fd88fb')

mschu commented on 2016-04-25 08:50

Fixed again - forgot to delete the ij.jar & used the cached version instead of the new one. Thanks!

hopimet commented on 2016-04-24 13:56

md5sum for ij.jar is false. It should be: 8e6b51c27d4ba7c679532ca4b1b30082

Modify PKGBUILD as this:
md5sums=('a0998c0e6aec078a8f9681f5088c41f2'
'8e6b51c27d4ba7c679532ca4b1b30082' # <- changed
'7dc3fd02120f699204b3d85a7e383082'
'9d60878b6adad0e1895ce875bf299147'
'e7a7cef1b44ad3a8752ba63885fd88fb')

adlerweb commented on 2016-03-25 16:34

http://imagej.nih.gov/ij/upgrade/ij.jar was updated to Version 1.50h - new md5sums:

md5sums=('a0998c0e6aec078a8f9681f5088c41f2'
'c1b97b8be18566af4c7ed050122582f0'
'7dc3fd02120f699204b3d85a7e383082'
'9d60878b6adad0e1895ce875bf299147'
'e7a7cef1b44ad3a8752ba63885fd88fb')

dengarjs commented on 2015-01-26 15:54

1.49o was released a few days ago

McNoggins commented on 2014-11-26 17:37

Please update the PKGBUILD md5sums using updpkgsums

dcanelhas commented on 2014-11-25 16:24

the second md5sum in the array should be ( on Tue 25 Nov 2014)
0bb52192973e181594aa027481371895

radioxoma commented on 2014-10-30 14:59

Bump to 1.49j

plasmapotato commented on 2014-10-21 22:32

I can confirm the install works fine when md5sum for ij.jar (second in list provided in PKGBUILD) is edited to efe3ef356f9b781f680d20e1f091c1db

You can check the sum yourself if you download ij.jar from the AUR site:
https://aur.archlinux.org/packages/imagej/

or directly from nih:
http://imagej.nih.gov/ij/upgrade/ij.jar

and then run `md5sum ij.jar` from your download directory

eomarjee commented on 2014-10-21 12:39

Please change the version (1.49i) and change optdepends to ('java-environment-common'). Thanks.

eomarjee commented on 2014-10-21 12:37

Please update to 1.49i version, and change optdepends to ('java-environment-common')

eomarjee commented on 2014-10-21 12:32

Please update: optdepends=('java-environment-common')

davidmcinnis commented on 2014-10-14 04:05

Please update md5sum for ij.jar: efe3ef356f9b781f680d20e1f091c1db

ij.jar comes from a daily builds server so it may require frequent updates.

nylocx commented on 2014-09-25 09:06

I had to change the md5sum for ij.jar to cc3f1be47eb107d63a14bcf0b63ba4ee
Maybe they updated it again?

mschu commented on 2014-08-30 15:25

Thanks, updated.

Ant1 commented on 2014-06-18 17:51

1.49 has been out for a while: http://imagej.nih.gov/ij/notes.html

However they don't seem to provide a fully updated package.
So you might need to change the pkgbuild to download ij.jar version 1.49b and overwrite the one in the 1.48v version.

threeofsix commented on 2013-08-24 23:26

It looks like the md5sum for ij147.zip is incorrect or the file is corrupted. When trying to install, it says this file fails the validity check.

mschu commented on 2012-09-04 20:24

Adopted & updated.

skarn commented on 2012-09-02 09:55

Abandoned!

mschu commented on 2012-09-01 23:23

I can take over as well (as pointed out by email). @srg, if you want to have it you can, otherwise I'll take it. I'll be using it actively in the comings months and there are some things that should be changed in the PKGBUILD (eg. remove the provides=() and empty variables, use mkdir -p once, and not putting the tools.jar in /opt anymore).

srg commented on 2012-08-30 12:21

@skarn I am not an active user of imagej. I was just helping another user to get it installed. But given that binary releases happen only once or twice a year, I can take over the package and update it for as long as I use Arch. I can hardly test it well.

skarn commented on 2012-08-28 16:16

@everyone the releases that are only in source form are supposed to be development releases. When the streak of 1.47a->1.47b->1.47c->... ends they will release a binary version of 1.47 for production use and move to development of the next version.

@srg I have just updated the package to 1.46, but I do not use anymore Arch on my production machine. I could abandon the package if is interested in taking over. I still would suggest avoiding the releases which are only in source form. Then you can also compile the stable releases from source...

srg commented on 2012-08-28 15:17

1.47b is not available as a binary download, but it is available as a source distribution at http://rsbweb.nih.gov/ij/download/src/

srg commented on 2012-08-28 15:14

The launcher script seems to generate a lot of errors. They are due to: 1) broken access rights in some of the /usr/share/imagej (like no read access to some dirs), 2) leading space in some of the filenames of the upstream distribution (it is lost when iterating with "while read"), 3) trying to guess JAVA_HOME, when it is not necessary on Archlinux.

I suggest to update PKGBUILD with https://raw.github.com/gist/3498836/0800e93ff41baa73cee757b54531a2e8d456eabb/PKGBUILD
and imagej script with https://raw.github.com/gist/3498927/9e29aa0e5a35c81493a316855364924a25b5fe7d/imagej.sh

The diffs are:

1,2c1,2
< # This PKGBUILD does not build the sources but rather
< #downloads a precompiled jar from the project website.
---
> # This PKGBUILD does not build the sources but rather
> # downloads a precompiled jar from the project website.
9c9
< pkgrel=1
---
> pkgrel=2
29c29
< '8c3f31d67b70a9104c1c0b983b0aac86'
---
> 'b6f8562641759d158ebf654cc7c85cb2'
36a37
>
39a41,48
>
> # Fix access rights before installing
> find $srcdir/ImageJ/ -type f -exec chmod 644 "{}" \;
> find $srcdir/ImageJ/ -type d -exec chmod 755 "{}" \;
> # Fix filenames
> mv "$srcdir/ImageJ/plugins/ README.txt" \
> "$srcdir/ImageJ/plugins/README.txt"
>


and for the script:

34,39c34,35
< if [ -z "/opt/java/jre" ] ; then
< JAVA_HOME=$(/opt/java/jre -l | head -1 | cut -d' ' -f 3)
< else
< JAVA_HOME=$(/usr -l | head -1 | cut -d' ' -f 3)
< fi
<
---
> # Not necessary in Archlinux.
> # See https://wiki.archlinux.org/index.php/Java_Package_Guidelines
74c70
< ln -s ${ij_path}/plugins/$p ${ij_user_path}/plugins/$p
---
> ln -s "${ij_path}/plugins/$p" "${ij_user_path}/plugins/$p"
80c76
< ln -s ${ij_path}/macros/$p ${ij_user_path}/macros/$p
---
> ln -s "${ij_path}/macros/$p" "${ij_user_path}/macros/$p"
86c82
< ln -s ${ij_path}/luts/$p ${ij_user_path}/luts/$p
---
> ln -s "${ij_path}/luts/$p" "${ij_user_path}/luts/$p"
504c500
< eval java ${java_arch} -mx${mem}m ${modules} ij.ImageJ -ijpath ${ij_user_path} -port${count} ${images} ${macrocmd} ${macroargs}
---
> exec java ${java_arch} -mx${mem}m ${modules} ij.ImageJ -ijpath ${ij_user_path} -port${count} ${images} ${macrocmd} ${macroargs}
506d501
< exit 0

fi-dschi commented on 2012-08-27 16:00

1.46 is available for download now.
1.47 has been announced, but I found no downloads for it.

mfs commented on 2012-05-29 08:15

According to http://rsbweb.nih.gov/ij/notes.html, 1.46o is out. But the rest of the website (including downloads) seem to be broken atm.

Corubba commented on 2012-04-12 14:30

If you get the error, that imagej can't find javac, `ln -s /opt/java/lib/tools.jar /opt/java/jre/lib/ext` fixed the problem for me. ImageJ is searching the compiler in the wrong directory.

skarn commented on 2011-08-18 14:52

Finally awoke from my sleep and updated the package. Somehow i had not seen the "out of date" notification...
I also made java-environment an optdepend, as required by cecilyen.

boina commented on 2011-06-10 15:08

Works great!!! Being out of date is no problem. Once installed you should open imagej as root from the command line and on the help tab you should run update --- wait --- and ready. Even more... if you go to the imagej web page and download it you don't get the latest version until update.
Thanks, José.

Anonymous comment on 2011-04-03 16:05

1.44 is out. md5=21df91aa67053f19c19b31a1bb2955db
And please make java-environment as an optional dependency.

skarn commented on 2010-09-14 09:13

Well, with this script the files are not actually copied, they are just symlinked into the user's home folder. This way the user can for example add mose plugins or lookup tables by just dropping them in the .imagej folder. Using symlinks ensures that this does not cost the user a lot of space.

pherms commented on 2010-09-08 16:40

I created a branch of your package, imagej-shared, where the application is started from a shared directory without copying the whole ImageJ directory to every user's home.

skarn commented on 2010-07-04 10:54

"java-environment" is a virtual dependency provided by either by sun's jdk and the free replacement openjdk6.
It is not actually needed to run imagej, but it is required for some advanced capabilities, so perhaps i should make it an optdepend in future release and make the package depend on "java-runtime" which is provided by either openjdk6 or jre.

Please note that this pkgbuild does not compile the package, but rather downloads a jar archive from the official site. If the package was to be compiled you would positively need java-environment as jre does not contain the java compiler.

Anonymous comment on 2010-07-02 03:21

I'm not sure what java-environemnt is, as it doesn't seem to be a package. However, I have jre and I can compile the software just fine if I delete that line, otherwise I get a build-time error.

Anonymous comment on 2010-04-27 15:00

A new version of imageJ is out.
I updated the PKGBUILD :http://aur.pastebin.com/LEcVcvz8