Package Details: jabref 5.1-2

Git Clone URL: https://aur.archlinux.org/jabref.git (read-only, click to copy)
Package Base: jabref
Description: Graphical Java application for managing BibTeX and biblatex (.bib) databases
Upstream URL: https://www.jabref.org/
Licenses: MIT
Submitter: Allan
Maintainer: Bevan
Last Packager: Bevan
Votes: 198
Popularity: 0.40
First Submitted: 2012-06-07 22:47
Last Updated: 2020-09-30 19:50

Dependencies (3)

Required by (0)

Sources (4)

Latest Comments

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Bevan commented on 2020-08-02 15:55

@juiin: Could you please test if you have the same problem with official build from https://www.fosshub.com/JabRef.html?dwl=JabRef-5.0-portable_linux.tar.gz ?

ruiin commented on 2020-08-02 15:46

Hi, I have the issue that the JabRef window becomes unresponsive (no menus like 'file', 'quality', while it works to select an item) on the second screen of a multi-screen setup.

Version: 2020-03-29 16:22 Error at runtime: (java:643023): Gdk-WARNING **: 17:45:00.905: XSetErrorHandler() called with a GDK error trap pushed. Don't do that.

Thanks

magno commented on 2020-07-09 13:20

@Bevan: Thanks again!

rmagno@midget ~> sudo pacman -Qkq

No output is what I got. So seemingly it had been only those jre-* packages that were affected. I am guessing that at some point I must have forced pacman to ignore dependencies, like you said before.

BTW: Thank you for maintaining JabRef in Arch!

Bevan commented on 2020-07-09 13:17

@magno: Maybe quickly run sudo pacman -Qkq to make sure that no other packages are affected. It will output missing files and their corresponding package, so no output at all is what you want.

magno commented on 2020-07-09 13:10

Thank you @Bevan! JabRef works now again.

Reinstalling jre-openjdk and jre-openjdk-headless did solve it. And I had indeed many missing files. I can't, for the life of me, understand what I did that could explain this...

rmagno@midget ~> sudo pacman -S jre-openjdk jre-openjdk-headless
warning: jre-openjdk-14.0.1.u7-1 is up to date -- reinstalling
warning: jre-openjdk-headless-14.0.1.u7-1 is up to date -- reinstalling
resolving dependencies...
looking for conflicting packages...

Packages (2) jre-openjdk-14.0.1.u7-1  jre-openjdk-headless-14.0.1.u7-1

Total Installed Size:  179.63 MiB
Net Upgrade Size:        0.00 MiB

:: Proceed with installation? [Y/n] 
(2/2) checking keys in keyring                          [#############################] 100%
(2/2) checking package integrity                        [#############################] 100%
(2/2) loading package files                             [#############################] 100%
(2/2) checking for file conflicts                       [#############################] 100%
(2/2) checking available disk space                     [#############################] 100%
warning: could not get file information for usr/lib/jvm/java-14-openjdk/bin/jaotc
warning: could not get file information for usr/lib/jvm/java-14-openjdk/bin/java
warning: could not get file information for usr/lib/jvm/java-14-openjdk/bin/javac
warning: could not get file information for usr/lib/jvm/java-14-openjdk/bin/javap
warning: could not get file information for usr/lib/jvm/java-14-openjdk/bin/jdeprscan
warning: could not get file information for usr/lib/jvm/java-14-openjdk/bin/jdeps
warning: could not get file information for usr/lib/jvm/java-14-openjdk/bin/jfr
warning: could not get file information for usr/lib/jvm/java-14-openjdk/bin/jimage
warning: could not get file information for usr/lib/jvm/java-14-openjdk/bin/jjs
warning: could not get file information for usr/lib/jvm/java-14-openjdk/bin/jlink
warning: could not get file information for usr/lib/jvm/java-14-openjdk/bin/jmod
warning: could not get file information for usr/lib/jvm/java-14-openjdk/bin/jpackage
warning: could not get file information for usr/lib/jvm/java-14-openjdk/bin/jrunscript
warning: could not get file information for usr/lib/jvm/java-14-openjdk/bin/keytool
warning: could not get file information for usr/lib/jvm/java-14-openjdk/bin/rmid
warning: could not get file information for usr/lib/jvm/java-14-openjdk/bin/rmiregistry
warning: could not get file information for usr/lib/jvm/java-14-openjdk/bin/serialver
warning: could not get file information for usr/lib/jvm/java-14-openjdk/conf
warning: could not get file information for usr/lib/jvm/java-14-openjdk/legal
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/classlist
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/ct.sym
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/jexec
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/jfr/default.jfc
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/jfr/profile.jfc
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/jrt-fs.jar
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/jspawnhelper
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/jvm.cfg
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/libawt.so
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/libawt_headless.so
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/libdt_socket.so
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/libextnet.so
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/libfontmanager.so
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/libinstrument.so
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/libj2gss.so
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/libj2pcsc.so
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/libj2pkcs11.so
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/libjaas.so
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/libjava.so
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/libjavajpeg.so
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/libjdwp.so
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/libjimage.so
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/libjli.so
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/libjsig.so
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/liblcms.so
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/libmanagement.so
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/libmanagement_agent.so
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/libmanagement_ext.so
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/libmlib_image.so
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/libnet.so
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/libnio.so
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/libprefs.so
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/librmi.so
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/libsctp.so
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/libsunec.so
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/libverify.so
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/libzip.so
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/modules
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/psfont.properties.ja
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/psfontj2d.properties
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/security/blacklisted.certs
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/security/cacerts
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/security/default.policy
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/security/public_suffix_list.dat
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/server/classes.jsa
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/server/libjsig.so
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/server/libjvm.so
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/tzdb.dat
warning: could not get file information for usr/lib/jvm/java-14-openjdk/release
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/libawt_xawt.so
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/libjawt.so
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/libjsound.so
warning: could not get file information for usr/lib/jvm/java-14-openjdk/lib/libsplashscreen.so
:: Processing package changes...
(1/2) reinstalling jre-openjdk-headless                 [#############################] 100%
(2/2) reinstalling jre-openjdk                          [#############################] 100%
:: Running post-transaction hooks...
(1/1) Arming ConditionNeedsUpdate...

Now archlinix-java correctly lists java-14-openjdk:

rmagno@midget ~> archlinux-java status
Available Java environments:
  java-14-openjdk
  java-8-openjdk (default)

Bevan commented on 2020-07-09 13:04

OK, yo all required packages are installed. The java executable should be coming with jre-openjdk-headless which you have installed:

pacman -Qo /usr/lib/jvm/java-14-openjdk/bin/java
/usr/lib/jvm/java-14-openjdk/bin/java is owned by jre-openjdk-headless 14.0.1.u7-1

Reinstalling jre-openjdk and jre-openjdk-headless will hopefully fix that but of course the question remains why this file was lost.

magno commented on 2020-07-09 13:00

rmagno@midget ~> pacman -Qs openjdk
local/jdk-openjdk 14.0.1.u7-1
    OpenJDK Java 14 development kit
local/jdk8-openjdk 8.u252-1
    OpenJDK Java 8 development kit
local/jre-openjdk 14.0.1.u7-1
    OpenJDK Java 14 full runtime environment
local/jre-openjdk-headless 14.0.1.u7-1
    OpenJDK Java 14 headless runtime environment
local/jre8-openjdk 8.u252-1
    OpenJDK Java 8 full runtime environment
local/jre8-openjdk-headless 8.u252-1
    OpenJDK Java 8 headless runtime environment
rmagno@midget ~> archlinux-java status
Available Java environments:
  java-8-openjdk (default)

The workaround proposed does not work because seemingly I don't have the java executable in /usr/lib/jvm/java-14-openjdk/bin...

rmagno@midget ~> ls -l /usr/lib/jvm/java-14-openjdk/bin/
total 240
-rwxr-xr-x 1 root root 14272 May 23 19:20 jar*
-rwxr-xr-x 1 root root 14280 May 23 19:20 jarsigner*
-rwxr-xr-x 1 root root 14312 May 23 19:20 javadoc*
-rwxr-xr-x 1 root root 14272 May 23 19:20 jcmd*
-rwxr-xr-x 1 root root 14344 May 23 19:20 jconsole*
-rwxr-xr-x 1 root root 14272 May 23 19:20 jdb*
-rwxr-xr-x 1 root root 14272 May 23 19:20 jhsdb*
-rwxr-xr-x 1 root root 14304 May 23 19:20 jinfo*
-rwxr-xr-x 1 root root 14304 May 23 19:20 jmap*
-rwxr-xr-x 1 root root 14272 May 23 19:20 jps*
-rwxr-xr-x 1 root root 14280 May 23 19:20 jshell*
-rwxr-xr-x 1 root root 14312 May 23 19:20 jstack*
-rwxr-xr-x 1 root root 14272 May 23 19:20 jstat*
-rwxr-xr-x 1 root root 14280 May 23 19:20 jstatd*
-rwxr-xr-x 1 root root 14272 May 23 19:20 rmic*

Bevan commented on 2020-07-09 12:45

Thanks for your feedback. The error message actually comes from a custom launch script I use and not from jabref itself. The problem is obviously that your java 14 installation does not show up in archlinux-java.

To debug this issue, could you please run pacman -Qs openjdk and post the output here?

As a temporary workaround, you can try to edit /usr/bin/JabRef and replace the line

/usr/bin/archlinux-java-run --min 13 -- \

by

/usr/lib/jvm/java-14-openjdk/bin/java \

Does this work for you?

magno commented on 2020-07-09 12:29

Hi @Bevan: Thank you for your feedback.

I don't know what is going on. It seems I have the latest version of jdk-openjdk but JabRef still complains about not finding a suitable JVM:

magno@midget ~> sudo pacman -S jdk-openjdk
warning: jdk-openjdk-14.0.1.u7-1 is up to date -- reinstalling
resolving dependencies...
looking for conflicting packages...

Packages (1) jdk-openjdk-14.0.1.u7-1

Total Installed Size:  86.99 MiB
Net Upgrade Size:       0.00 MiB

:: Proceed with installation? [Y/n] 
(1/1) checking keys in keyring                                                                                                                                            [#########################################################################################################] 100%
(1/1) checking package integrity                                                                                                                                          [#########################################################################################################] 100%
(1/1) loading package files                                                                                                                                               [#########################################################################################################] 100%
(1/1) checking for file conflicts                                                                                                                                         [#########################################################################################################] 100%
(1/1) checking available disk space                                                                                                                                       [#########################################################################################################] 100%
:: Processing package changes...
(1/1) reinstalling jdk-openjdk                                                                                                                                            [#########################################################################################################] 100%
:: Running post-transaction hooks...
(1/3) Arming ConditionNeedsUpdate...
(2/3) Updating icon theme caches...
(3/3) Updating the desktop file MIME type cache...
magno@midget ~> JabRef
No suitable JVM found.
Available:         java-8-openjdk
Default:           java-8-openjdk
Min. required:     13
Max. required:     20
Package required:  
Candidates:        
Features required: 
magno@midget ~> archlinux-java status
Available Java environments:
  java-8-openjdk (default)

Bevan commented on 2020-07-09 06:47

@magno: That normally should not happen. It means that only java 8 is installed on your system. However, this package has a dependency on java-runtime>=13. You should be able to fix it by installing the package jdk-openjdk.

The question is, how could you end up in this situation? Did you remove some packages and forced pacman to ignore dependencies?