jabref: Portable Snapshot does not find libjava.so

JabRef version

JabRef 5.0.0-dev--2019-11-03----e356e4910
Linux 3.10.0-1062.1.1.el7.centos.plus.x86_64 amd64 
Java 12.0.2

I have tested the latest development version from http://builds.jabref.org/master/ and the problem persists

Steps to reproduce the behavior:

Download a portable snapshot for linux
unpack
run ./bin/JabRef

Will give the following error:

Error: could not find libjava.so
Error: Could not find Java SE Runtime Environment.

When running strace, you can see that it does not search for the runtime folder but stops at the lib folder:

[...]
stat("", 0x7ffe79c9cc20)                = -1 ENOENT (No such file or directory)
readlink("/proc/self/exe", "/home/reox/bin/JabRef/bin/JabRef", 4096) = 31
stat("/etc/sysconfig/64bit_strstr_via_64bit_strstr_sse2_unaligned", 0x7ffe79c97330) = -1 ENOENT (No such file or directory)
access("/home/reox/bin/JabRef/lib/libjava.so", F_OK) = -1 ENOENT (No such file or directory)
access("/home/reox/bin/JabRef/jre/lib/libjava.so", F_OK) = -1 ENOENT (No such file or directory)
lstat("/usr2", {st_mode=S_IFDIR|0755, st_size=4096, ...}) = 0
lstat("/home/reox", {st_mode=S_IFDIR|0770, st_size=4096, ...}) = 0
lstat("/home/reox/bin", {st_mode=S_IFDIR|0755, st_size=72, ...}) = 0
lstat("/home/reox/bin/JabRef", {st_mode=S_IFDIR|0755, st_size=63, ...}) = 0
lstat("/home/reox/bin/JabRef/lib", {st_mode=S_IFDIR|0755, st_size=4096, ...}) = 0
lstat("/home/reox/bin/JabRef/lib/runtime", {st_mode=S_IFDIR|0755, st_size=63, ...}) = 0
lstat("/home/reox/bin/JabRef/lib/runtime/lib", {st_mode=S_IFDIR|0755, st_size=4096, ...}) = 0
lstat("/home/reox/bin/JabRef/lib/runtime/lib/libjli.so", {st_mode=S_IFREG|0644, st_size=79560, ...}) = 0
stat("/home/reox/lib/libjava.so", 0x7ffe79c977e0) = -1 ENOENT (No such file or directory)
write(2, "Error: could not find libjava.so", 32Error: could not find libjava.so) = 32
write(2, "\n", 1
)                       = 1
write(2, "Error: Could not find Java SE Ru"..., 50Error: Could not find Java SE Runtime Environment.) = 50
write(2, "\n", 1
)                       = 1
exit_group(2)                           = ?
+++ exited with 2 +++

I tried the following workaround:

$ cd lib
$ find runtime/lib/ -maxdepth 1 -mindepth 1 -exec ln -s {} \;

which makes jabref start up.

I’m not sure if this problem is specific to CentOS or the current setup on my machine. I also tried it on a fresh Debian stretch VM, where JabRef would start without any problems. Maybe there is some special ldconfig or environment variable which messes things up? I can try to test it on a CentOS VM later, or someone has an idea what specific test I could run.

About this issue

Original URL
State: closed
Created 5 years ago
Comments: 19 (17 by maintainers)

Commits related to this issue

Squashed 'buildres/csl/csl-styles/' changes from ec4a4c01ff..4703b5d0c0 4703b5d0c0 [Frontiers in ...] Remove formatting for volume (#5580) 3a3eb0c835 Create journal-of-clinical-and-translational-scie... — committed to JabRef/jabref by deleted user 3 years ago
[Bot] Update CSL styles (#7985) * Squashed 'buildres/csl/csl-styles/' changes from ec4a4c01ff..4703b5d0c0 4703b5d0c0 [Frontiers in ...] Remove formatting for volume (#5580) 3a3eb0c835 Create jour... — committed to JabRef/jabref by koppor 3 years ago
Squashed 'buildres/csl/csl-styles/' changes from ec4a4c01ff..2b37392723 2b37392723 Create betriebswirtschaftliche-forschung-und-praxis.csl (#5609) a52989cc09 Update universitat-zu-koln-seminar-fur-ab... — committed to JabRef/jabref by deleted user 3 years ago
Update how to start JabRef Linux Portable Inspired by issues - https://github.com/JabRef/jabref/issues/5591 - https://github.com/JabRef/jabref/issues/7295 - https://discourse.jabref.org/t/jabref-5... — committed to JabRef/user-documentation by ThiloteE 2 years ago

Most upvoted comments

~/bin$ JabRef/bin/JabRef 
Error: could not find libjava.so
Error: Could not find Java SE Runtime Environment.

but this still works:

~/apps$ ./JabRef/bin/JabRef 
ERROR StatusLogger Unrecognized format specifier [d]
ERROR StatusLogger Unrecognized conversion specifier [d] starting at position 16 in conversion pattern.
ERROR StatusLogger Unrecognized format specifier [thread]
ERROR StatusLogger Unrecognized conversion specifier [thread] starting at position 25 in conversion pattern.
ERROR StatusLogger Unrecognized format specifier [level]
ERROR StatusLogger Unrecognized conversion specifier [level] starting at position 35 in conversion pattern.
ERROR StatusLogger Unrecognized format specifier [logger]
ERROR StatusLogger Unrecognized conversion specifier [logger] starting at position 47 in conversion pattern.
ERROR StatusLogger Unrecognized format specifier [msg]
ERROR StatusLogger Unrecognized conversion specifier [msg] starting at position 54 in conversion pattern.
ERROR StatusLogger Unrecognized format specifier [n]
ERROR StatusLogger Unrecognized conversion specifier [n] starting at position 56 in conversion pattern.
ERROR StatusLogger Unrecognized format specifier [d]
ERROR StatusLogger Unrecognized conversion specifier [d] starting at position 16 in conversion pattern.
ERROR StatusLogger Unrecognized format specifier [thread]
ERROR StatusLogger Unrecognized conversion specifier [thread] starting at position 25 in conversion pattern.
ERROR StatusLogger Unrecognized format specifier [level]
ERROR StatusLogger Unrecognized conversion specifier [level] starting at position 35 in conversion pattern.
ERROR StatusLogger Unrecognized format specifier [logger]
ERROR StatusLogger Unrecognized conversion specifier [logger] starting at position 47 in conversion pattern.
ERROR StatusLogger Unrecognized format specifier [msg]
ERROR StatusLogger Unrecognized conversion specifier [msg] starting at position 54 in conversion pattern.
ERROR StatusLogger Unrecognized format specifier [n]
ERROR StatusLogger Unrecognized conversion specifier [n] starting at position 56 in conversion pattern.
ES2 Prism: Error - reported GLX version = 1.2
    GLX version 1.3 or higher is required

(JabRef:21548): Gdk-WARNING **: 21:29:41.278: XSetErrorHandler() called with a GDK error trap pushed. Don't do that.

Looks like the reported errors do no harm.

JabRef 5.1--2020-03-23--67daf36
Linux 3.10.0-1062.1.1.el7.centos.plus.x86_64 amd64 
Java 14

reox on Mar 24, 2020

~~I do not know if you have fixed anything, but on my machine it came good now:~~

JabRef 5.0.0-dev--2019-11-14----8f7188d2d
Linux 3.10.0-1062.1.1.el7.centos.plus.x86_64 amd64 
Java 13.0.1

~~Looking at strace verifies, that JabRef finds the libjava.so without any problem.~~

edit: No wait! It looks like the problem is, if jabref is unpacked into a folder like $HOME/bin I had it unpacked to $HOME/tmp and it works. moving the JabRef folder to $HOME/bin triggers the libjava.so error! I simply renamed the folder to $HOME/apps and I can start JabRef now without troubles.

reox on Nov 14, 2019