Installation question

Help
1

Greetings

Am looking for a way of organizing an already huge and exploding collection of articles and abstracts. JabRef would seem to fit the bill but installation is somewhat problematic.

Instructions are :

JabRef does not start under Linux! What can I do?

JabRef requires Java 8.

Java 8 is just a wee bit deprecated at present and checking on Debian bullseye (my operating system) openjdk 11.0.4 is available.

suggests that openjdk 11 should be usable until 2026.

From the homepage : http://www.jabref.org/ JabRef-4.3.1.jar is listed as the newest stable version available. Debian has available for ā€˜Bullseyeā€™ JabRef-3.8.1 likely because java 8 is long deprecated.

so - - - two questions:

  1. how do I install a newer version of JabRef on Debian Bullseye?
  2. as I donā€™t know what Iā€™m doing I would not be able to devise a list of instructions that would effect an installation of a current version of JabRef but I would be quite interested in taking a terse list and turning it into something that is quite readable but - - - - is that of interest to the dev team?
2

Hi,

all current versions (including the 5.0 dev version) currently require java 8.
Alternatively we provide a snap package https://snapcraft.io/jabref for JabRef.

we are in the process of transitioning to java 11. However, there are still some issue with external libraries that need to be solved.

3

I guess Iā€™ll be waiting then.

Snap packages introduce outside control of my system (forced updates and upgrades) so will not ever be included here.

(Yes, I tried lxd but the emperors that code such have decreed that all except them are incapable of maintaining a system so all MUST use their methodology.)

Regards

4

The version at https://builds.jabref.org/master/ should now support Java 11 (and comes actually bundled with all necessary java libraries). At the moment, we donā€™t have detailed installation instructions for this version, so it would be nice if you could try it out (maybe experiment a bit with it) and then update https://github.com/JabRef/help.jabref.org/blob/gh-pages/en/Installation.md. Thanks!

5

You asked me to try to install and experiment.
Sorry - - - - was not even able to affect an install.
I am not at all proficient at programming although I can usually get
things to install but this ā€™ .jar ā€™ file stuff is proving to be quite
beyond my abilities.
Perhaps you could advise as to what I am doing wrong.

Regards

See below: (all entered commands and the subsequent responses are
included to facilitate error checking)

working on an updated Debian bullseye system

Found page at https://builds.jabref.org
downloaded JabRef-4.3.1.jar
tried from cli
memyself@debiantestingtestbed:/home$ java -jar
/home/memyself/Downloads/JabRef-4.3.1.jar
Error: Could not find or load main class org.jabref.JabRefMain
Caused by: java.lang.NoClassDefFoundError: javafx/application/Application

searching found page:
https://docs.oracle.com/cd/E17645_01/doc.50/e17649/ins_install_installation.htm

memyself@debiantestingtestbed:~/software/jabref$ java -d64 -jar JabRef-4.3.1.jar
Unrecognized option: -d64
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.
memyself@debiantestingtestbed:~/software/jabref$ java -jar JabRef-4.3.1.jar
Error: Could not find or load main class org.jabref.JabRefMain
Caused by: java.lang.NoClassDefFoundError: javafx/application/Application

searching for error meaning found:

root@debiantestingtestbed:~# apt install openjfx
Reading package listsā€¦ Done
Building dependency tree
Reading state informationā€¦ Done
The following additional packages will be installed:
libopenjfx-java libopenjfx-jni openjfx-source
The following NEW packages will be installed:
libopenjfx-java libopenjfx-jni openjfx openjfx-source
Selecting previously unselected package libopenjfx-jni.
(Reading database ā€¦ 252070 files and directories currently installed.)
Preparing to unpack ā€¦/libopenjfx-jni_11.0.2+1-1_amd64.deb ā€¦
Unpacking libopenjfx-jni (11.0.2+1-1) ā€¦
Selecting previously unselected package libopenjfx-java.
Preparing to unpack ā€¦/libopenjfx-java_11.0.2+1-1_all.deb ā€¦
Unpacking libopenjfx-java (11.0.2+1-1) ā€¦
Selecting previously unselected package openjfx.
Preparing to unpack ā€¦/openjfx_11.0.2+1-1_amd64.deb ā€¦
Unpacking openjfx (11.0.2+1-1) ā€¦
Selecting previously unselected package openjfx-source.
Preparing to unpack ā€¦/openjfx-source_11.0.2+1-1_all.deb ā€¦
Unpacking openjfx-source (11.0.2+1-1) ā€¦
Setting up libopenjfx-jni (11.0.2+1-1) ā€¦
Setting up openjfx-source (11.0.2+1-1) ā€¦
Setting up libopenjfx-java (11.0.2+1-1) ā€¦
Setting up openjfx (11.0.2+1-1) ā€¦
working on an updated Debian bullseye system

Found page at https://builds.jabref.org
downloaded JabRef-4.3.1.jar
tried from cli
memyself@debiantestingtestbed:/home$ java -jar
/home/memyself/Downloads/JabRef-4.3.1.jar
Error: Could not find or load main class org.jabref.JabRefMain
Caused by: java.lang.NoClassDefFoundError: javafx/application/Application

searching found page:
https://docs.oracle.com/cd/E17645_01/doc.50/e17649/ins_install_installation.htm

memyself@debiantestingtestbed:~/software/jabref$ java -d64 -jar JabRef-4.3.1.jar
Unrecognized option: -d64
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.
memyself@debiantestingtestbed:~/software/jabref$ java -jar JabRef-4.3.1.jar
Error: Could not find or load main class org.jabref.JabRefMain
Caused by: java.lang.NoClassDefFoundError: javafx/application/Application

searching for error meaning found:

root@debiantestingtestbed:~# apt install openjfx
Reading package listsā€¦ Done
Building dependency tree
Reading state informationā€¦ Done
The following additional packages will be installed:
libopenjfx-java libopenjfx-jni openjfx-source
The following NEW packages will be installed:
libopenjfx-java libopenjfx-jni openjfx openjfx-source
Selecting previously unselected package libopenjfx-jni.
(Reading database ā€¦ 252070 files and directories currently installed.)
Preparing to unpack ā€¦/libopenjfx-jni_11.0.2+1-1_amd64.deb ā€¦
Unpacking libopenjfx-jni (11.0.2+1-1) ā€¦
Selecting previously unselected package libopenjfx-java.
Preparing to unpack ā€¦/libopenjfx-java_11.0.2+1-1_all.deb ā€¦
Unpacking libopenjfx-java (11.0.2+1-1) ā€¦
Selecting previously unselected package openjfx.
Preparing to unpack ā€¦/openjfx_11.0.2+1-1_amd64.deb ā€¦
Unpacking openjfx (11.0.2+1-1) ā€¦
Selecting previously unselected package openjfx-source.
Preparing to unpack ā€¦/openjfx-source_11.0.2+1-1_all.deb ā€¦
Unpacking openjfx-source (11.0.2+1-1) ā€¦
Setting up libopenjfx-jni (11.0.2+1-1) ā€¦
Setting up openjfx-source (11.0.2+1-1) ā€¦
Setting up libopenjfx-java (11.0.2+1-1) ā€¦
Setting up openjfx (11.0.2+1-1) ā€¦

memyself@debiantestingtestbed:~/software/jabref$ java -version
openjdk version ā€œ11.0.4ā€ 2019-07-16
OpenJDK Runtime Environment (build 11.0.4+11-post-Debian-1)
OpenJDK 64-Bit Server VM (build 11.0.4+11-post-Debian-1, mixed mode)
memyself@debiantestingtestbed:~/software/jabref$ update-alternatives
ā€“config java
There are 2 choices for the alternative java (providing /usr/bin/java).

Selection Path Priority Status

6

Thanks for testing! JabRef 4.3.1 is not compatible with Java 11, this is why you get these errors. Please try the development version (5.0) from https://builds.jabref.org/master/ ! Thanks.

7

Sorry - - - - it wasnā€™t clear to me that ZI needed to try to run JabRef5.x .

Starting the process over.

Is JabRef going to be useable this way?

I am working with another researcher trying to develop an annotated library of papers.

Iā€™m on Debian testing and he will likely be running Win10.

Hoping that will work - - - - grin!

Please advise

Regards

8

Itā€™s a development version, so you are advised to make regular backups of your database. From my experience, however, the version is really stable and I use it regularly without (major) problems.

9

Thank you for your reassurance. I do want this wot work for both my colleague and myself!

Thanking you for your assistance and consideration.

10

Hope Iā€™m not being too persistent but its sorta like the first day after too many not able to do much so am enjoying this trying (I think! - - - rueful grin!)

I still am not able to achieve a working JabRef5.x .

Reading some of the other bug files it would seem that in less than 10 days that there is going to be a fairly large ecosystem change - - - -something about - - - - (and now I canā€™t find the doc where this was discussed - - - bummer!).

I can find JabRefLauncher - - - - just donā€™t know how to tell the puter how to connect to it - - - - grin.

following my perambulations trying to get JabRef5 working with jdk11:

memyself@debiantestingtestbed:~$ java -jar JabRefā€“masterā€“latest.jar

Error: Unable to access jarfile JabRefā€“masterā€“latest.jar

memyself@debiantestingtestbed:~$ su -

Password:

root@debiantestingtestbed:~# java -jar JabRefā€“masterā€“latest.jar

Error: Unable to access jarfile JabRefā€“masterā€“latest.jar

root@debiantestingtestbed:~# chmod a+x /usr/share/java/JabRefā€“masterā€“latest.jar

root@debiantestingtestbed:~# exit

logout

memyself@debiantestingtestbed:~$ cd /home/

memyself@debiantestingtestbed:/home$ java -jar JabRefā€“masterā€“latest.jar

Error: Unable to access jarfile JabRefā€“masterā€“latest.jar

memyself@debiantestingtestbed:/home$ su -

Password:

root@debiantestingtestbed:~# cd /home/

root@debiantestingtestbed:/home# java -jar JabRefā€“masterā€“latest.jar

Error: Unable to access jarfile JabRefā€“masterā€“latest.jar

root@debiantestingtestbed:/home# java -jar /usr/share/java/JabRefā€“masterā€“latest.jar

Error: Could not find or load main class org.jabref.org.jabref.JabRefLauncher

Caused by: java.lang.ClassNotFoundException: org.jabref.org.jabref.JabRefLauncher

root@debiantestingtestbed:/home# exit

logout

memyself@debiantestingtestbed:/home$ /usr/lib/jvm/java-11-openjdk-amd64/jre/bin/java -jar jabref.jar

bash: /usr/lib/jvm/java-11-openjdk-amd64/jre/bin/java: No such file or directory

memyself@debiantestingtestbed:/home$ java -jar /usr/share/JabRefā€“masterā€“latest.jar

Error: Unable to access jarfile /usr/share/JabRefā€“masterā€“latest.jar

memyself@debiantestingtestbed:/home$ su -

Password:

root@debiantestingtestbed:~# cd /home

root@debiantestingtestbed:/home# exit

logout

memyself@debiantestingtestbed:/home$ java -jar /usr/share/java/JabRefā€“masterā€“latest.jar

Error: Could not find or load main class org.jabref.org.jabref.JabRefLauncher

Caused by: java.lang.ClassNotFoundException: org.jabref.org.jabref.JabRefLauncher

memyself@debiantestingtestbed:/home$ su -

Password:

root@debiantestingtestbed:~# cp /home/memyself/Downloads/JabRefā€“masterā€“latest.jar /usr/share/jabref/

root@debiantestingtestbed:~# cp /usr/share/jabref/JabRef-3.8.2.jar /usr/share/jabref/JabRef-3.8.2.zip

root@debiantestingtestbed:~# rm -r /usr/share/jabref/JabRef-3.8.2.jar

root@debiantestingtestbed:~# exit

logout

memyself@debiantestingtestbed:/home$ java -jar /usr/share/java/JabRefā€“masterā€“latest.jar

Error: Could not find or load main class org.jabref.org.jabref.JabRefLauncher

Caused by: java.lang.ClassNotFoundException: org.jabref.org.jabref.JabRefLauncher

memyself@debiantestingtestbed:/home$ java -jar /home/memyself/Downloads/JabRefā€“masterā€“latest.jar

Error: Could not find or load main class org.jabref.org.jabref.JabRefLauncher

Caused by: java.lang.ClassNotFoundException: org.jabref.org.jabref.JabRefLauncher

11

Much appreciated that you keep trying ;-). At the moment, there seems to be a problem to run the jar from the command line, see https://github.com/JabRef/jabref/issues/5299. We are currently working on a way to fix that.

12

Tobias Diez

    September 11

Much appreciated that you keep trying ;-). At the moment, there seems to be a problem to run the jar from the command line, see https://github.com/JabRef/jabref/issues/5299. We are currently working on a way to fix that.

Thank you for your encouragement - - - I was hoping that I wasnā€™t becoming a pain already - - - grin!

I had read something about this jlink (IIRC) and that something was to be changing 09/17 which is upcoming.

Have this bad habit of remembering things and not where I found them so really am not sure of whatā€™s happening.

Am assuming that youā€™re suggesting that I wait a bit.

Working on my project I am using JabRef3.8.2 (IIRC) so Iā€™m able to keep working on things (Its a background project if that makes any kind of sense).

I have so many abstracts and papers stored in various directories here that I have long needed to make sense of things and your JabRef is so far showing to be an excellent tool!

Perhaps you might drop me a note when you think it might be worth another kick at the cat?

Regards

13

Hi
@ajoeiam

you can now download the Linux version from https://builds.jabref.org/master
JabRef-linux-master-latest.tar.gz

It now includes all necessary files to run JabRef.

14

Thanking the dev team for their effort.
If you want to run using on Linux using an easily available java environment (openjdk-11 in my case) it is now possible to download a .tar file and after unpacking - - - - well sheā€™s ready to rock.

I donā€™t think Iā€™ve seen any indication when version 5.x is going to move from development to stable - - - any suggestions on possible timing?

For anyone who isnā€™t familiar with Linux and .tar files - - - - well - - - here is one way of doing things (there are likely many more - - - grin!).

  1. download the file from your source site
  2. need to open a terminal and if your system requires you to move to root to install software (my preferred solution - - - -more work but likely somewhat better security (IMO)) you need to log into root. (If your using a system set up to use sudo you wonā€™t be logging into root but will use sudo as a preface on the following command.
    I usually change directories so that my software installs are on /home (prefer not to add more stuff into / ) and then the next step is to unpack the package (the package is actually quite large).
    The final step is to open the directory where the unpacked JabRef now resides open jabref/bin and there left click on JabRefMain responding to the system query with a click on ā€˜executeā€™ - - - -Bobā€™s your uncle and its time to get to work.

memyself$ su -
enter su password
root # cd /home
root@machinename: # tar -xvf /directory/whereis/JabRef.tar.gz
whole mess of lines happening as the files are unpacked
root@machinename: # (blank - - thatā€™s good, n install with no errors!)
doe final step in above list

1 Like
15

I donā€™t think Iā€™ve seen any indication when version 5.x is going to move from development to stable - - - any suggestions on possible timing?

We canā€™t give any estimation on timing. We are trying to create a stable release when itā€™s stable enough.
Currently there are some quirks with the new java 9/11 module system which make some features not work as expected and also depend on fixes in external libraries.

As always, you can download the latest snapshot from https://builds.jabref/master
Whenever a new commit is made to master, the build is triggered automatically.