DefaultExceptionHandler.java:49 / Assistive Technology not found launching IGV

[marongi...@gmail.com]

Dear all,

all of a sudden (or rather after today's Ubuntu update) IGV stopped working. When launching it from terminal I get this:

$ igv

ERROR [2018-08-21 10:39:07,375]  [DefaultExceptionHandler.java:49] [main]  Unhandled exception

java.awt.AWTError: Assistive Technology not found: org.GNOME.Accessibility.AtkWrapper

at java.desktop/java.awt.Toolkit.newAWTError(Toolkit.java:472)

at java.desktop/java.awt.Toolkit.fallbackToLoadClassForAT(Toolkit.java:488)

at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)

at java.base/java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:177)

at java.base/java.util.HashMap$KeySpliterator.forEachRemaining(HashMap.java:1608)

at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:484)

at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:474)

at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)

at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)

at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)

at java.base/java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:497)

at java.desktop/java.awt.Toolkit.loadAssistiveTechnologies(Toolkit.java:532)

at java.desktop/java.awt.Toolkit.getDefaultToolkit(Toolkit.java:613)

at java.desktop/java.awt.Toolkit.getEventQueue(Toolkit.java:1494)

at java.desktop/java.awt.EventQueue.invokeLater(EventQueue.java:1312)

at java.desktop/javax.swing.SwingUtilities.invokeLater(SwingUtilities.java:1421)

at org.broad.igv.ui.Main.main(Main.java:112)

Caused by: java.lang.ClassNotFoundException: org.GNOME.Accessibility.AtkWrapper

at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:582)

at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:190)

at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:499)

at java.base/java.lang.Class.forName0(Native Method)

at java.base/java.lang.Class.forName(Class.java:374)

at java.desktop/java.awt.Toolkit.fallbackToLoadClassForAT(Toolkit.java:485)

... 15 more

The java version I have is:

$ java -version

openjdk version "10.0.2" 2018-07-17

OpenJDK Runtime Environment (build 10.0.2+13-Ubuntu-1ubuntu0.18.04.1)

OpenJDK 64-Bit Server VM (build 10.0.2+13-Ubuntu-1ubuntu0.18.04.1, mixed mode)

How can I sort it out?

Thank you

Luigi 

[David Eby]

Hi Luigi,

Java 10 support is a work in progress and is currently unsupported in the IGV 2.4.x release series.  We do have a Java 10 development snapshot build available here that you can try.

If you're already using that snapshot, let us know what you were trying to do so we can sort it out.  The Java 10 snapshot is very new and hasn't seen much active use or testing yet.

Thanks,

David

[Luigi Marongiu]

Thank you David,
I launched the snapshop for Java 10 but I got another kind of error:
$ ./igv.sh
Error occurred during initialization of boot layer
java.lang.module.FindException: Module javafx.controls not found,
required by org.broad.igv

I have found this link
https://docs.oracle.com/javafx/2/installation/jfxpub-installation.htm#CHDDGGEE
for the installation of javafx but I wouldn't like to mess with the
machine. Is there a workaround and shall I say bye to IGV until a new
version will be available?
Would this sort of errors come out each time linux upgrades java?
Cheers
Luigi

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Best regards,
Luigi

[Luigi Marongiu]

Dear David,
an update. I am no expert in Java at all, but I found that the
correspondent of Java FX is openJFX, so I installed it but the error
persists:

$ ./igv.sh
Error occurred during initialization of boot layer
java.lang.module.FindException: Module javafx.controls not found,
required by org.broad.igv

The java modules available are:
$ lsmod
Module Size Used by
arc4 16384 0
md4 16384 0
nls_utf8 16384 6
cifs 720896 9
ccm 20480 0
fscache 61440 1 cifs
ip6t_REJECT 16384 1
nf_reject_ipv6 16384 1 ip6t_REJECT
nf_log_ipv6 16384 5
xt_hl 16384 22
ip6t_rt 16384 3
nf_conntrack_ipv6 20480 8
nf_defrag_ipv6 36864 1 nf_conntrack_ipv6
ipt_REJECT 16384 1
nf_reject_ipv4 16384 1 ipt_REJECT
nf_log_ipv4 16384 5
nf_log_common 16384 2 nf_log_ipv6,nf_log_ipv4
snd_hda_codec_hdmi 49152 1
xt_LOG 16384 10
snd_hda_codec_realtek 94208 1
snd_hda_codec_generic 73728 1 snd_hda_codec_realtek
snd_hda_intel 40960 8
joydev 24576 0
input_leds 16384 0
xt_limit 16384 13
snd_hda_codec 126976 4
snd_hda_intel,snd_hda_codec_hdmi,snd_hda_codec_generic,snd_hda_codec_realtek
xt_tcpudp 16384 20
snd_hda_core 81920 5
snd_hda_intel,snd_hda_codec,snd_hda_codec_hdmi,snd_hda_codec_generic,snd_hda_codec_realtek
snd_hwdep 20480 1 snd_hda_codec
snd_pcm 98304 4
snd_hda_intel,snd_hda_codec,snd_hda_core,snd_hda_codec_hdmi
xt_addrtype 16384 4
snd_seq_midi 16384 0
snd_seq_midi_event 16384 1 snd_seq_midi
snd_rawmidi 32768 1 snd_seq_midi
snd_seq 65536 2 snd_seq_midi_event,snd_seq_midi
snd_seq_device 16384 3 snd_seq,snd_rawmidi,snd_seq_midi
snd_timer 32768 2 snd_seq,snd_pcm
ccp 73728 0
snd 81920 27
snd_hda_intel,snd_hwdep,snd_seq,snd_hda_codec,snd_timer,snd_rawmidi,snd_hda_codec_hdmi,snd_hda_codec_generic,snd_seq_device,snd_hda_codec_realtek,snd_pcm
nf_conntrack_ipv4 16384 8
soundcore 16384 1 snd
nf_defrag_ipv4 16384 1 nf_conntrack_ipv4
shpchp 36864 0
edac_mce_amd 28672 0
xt_conntrack 16384 16
kvm 593920 0
irqbypass 16384 1 kvm
crct10dif_pclmul 16384 0
crc32_pclmul 16384 0
k10temp 16384 0
ghash_clmulni_intel 16384 0
pcbc 16384 0
aesni_intel 188416 0
eeepc_wmi 16384 0
nf_conntrack_netbios_ns 16384 0
nf_conntrack_broadcast 16384 1 nf_conntrack_netbios_ns
aes_x86_64 20480 1 aesni_intel
crypto_simd 16384 1 aesni_intel
glue_helper 16384 1 aesni_intel
cryptd 24576 3 crypto_simd,ghash_clmulni_intel,aesni_intel
asus_wmi 28672 1 eeepc_wmi
sch_fq_codel 20480 4
sparse_keymap 16384 1 asus_wmi
mac_hid 16384 0
nf_nat_ftp 16384 0
wmi_bmof 16384 0
nf_nat 32768 1 nf_nat_ftp
nf_conntrack_ftp 20480 1 nf_nat_ftp
nf_conntrack 131072 8
nf_conntrack_ipv6,nf_conntrack_ftp,nf_conntrack_ipv4,nf_conntrack_broadcast,nf_nat_ftp,nf_conntrack_netbios_ns,xt_conntrack,nf_nat
libcrc32c 16384 2 nf_conntrack,nf_nat
iptable_filter 16384 1
ip6table_filter 16384 1
ip6_tables 28672 1 ip6table_filter
br_netfilter 24576 0
bridge 151552 1 br_netfilter
stp 16384 1 bridge
llc 16384 2 bridge,stp
arp_tables 24576 0
parport_pc 36864 0
ppdev 20480 0
lp 20480 0
parport 49152 3 lp,parport_pc,ppdev
ip_tables 28672 1 iptable_filter
x_tables 40960 14
xt_LOG,ipt_REJECT,arp_tables,ip_tables,iptable_filter,xt_tcpudp,xt_limit,ip6t_REJECT,ip6table_filter,xt_addrtype,ip6t_rt,xt_conntrack,ip6_tables,xt_hl
autofs4 40960 2
hid_logitech_hidpp 32768 0
hid_logitech_dj 20480 0
hid_generic 16384 0
usbhid 49152 0
hid 118784 5
hid_generic,usbhid,hid_logitech_dj,hid_logitech_hidpp
nouveau 1716224 14
mxm_wmi 16384 1 nouveau
video 45056 2 asus_wmi,nouveau
ttm 106496 1 nouveau
drm_kms_helper 172032 1 nouveau
syscopyarea 16384 1 drm_kms_helper
sysfillrect 16384 1 drm_kms_helper
sysimgblt 16384 1 drm_kms_helper
fb_sys_fops 16384 1 drm_kms_helper
drm 401408 17 nouveau,ttm,drm_kms_helper
igb 212992 0
dca 16384 1 igb
i2c_piix4 24576 0
i2c_algo_bit 16384 2 igb,nouveau
ahci 36864 1
ptp 20480 1 igb
pps_core 20480 1 ptp
libahci 32768 1 ahci
wmi 24576 4 asus_wmi,wmi_bmof,mxm_wmi,nouveau
gpio_amdpt 16384 0
gpio_generic 20480 1 gpio_amdpt

On Tue, Aug 21, 2018 at 4:10 PM David Eby <e...@broadinstitute.org> wrote:
>

[David Eby]

Hi Luigi,

OK, thanks for looking into that.  We've been building and testing against Oracle Java 10 and from some quick searches it looks like OpenJDK Java 10 does not include JavaFX.  I'm not sure yet what we can do about that; I need to do some more research to see if it's something we can ship with IGV or if there are clear instructions we can point to on how to install it.

Here's an article on how to install Oracle Java 10 on Linux if you're interested in trying that in the meanwhile.

Thanks,

David

[David Eby]

Just a quick update: I'm on the trail of a fix but it will be next week before I can get to it.

Thanks again for the report!

David

[David Eby]

Hi Luigi,

I've confirmed that it's possible to accomplish what you're trying to do.  Here are the important points:

• Download the standalone OpenJFX build for Java 10 & 11 at http://jdk.java.net/openjfx/ .  I used the SDK build but presumably the JMODs build would be equivalent.
• Unpack this somewhere convenient.  it's fine for it to be under your user directory rather than a system location or the OpenJDK directory.
• Modify the IGV launcher script to add the location of the JavaFX jars to the existing Java module path.  For example, in igv.sh you would change:
      --module-path="$prefix"/lib
  to:
      --module-path="$prefix"/lib:/your/path/to/javafx-sdk-11/lib
  Note that shell tilde-expansion failed when I tried it, so it may need to be a full absolute path without reliance on any shell expansions. 

That should be all you need.  Be aware, of course, that you might lose these edits the next time you download a new IGV bundle if you unpack it in the same location.  Just take a backup first.

This is based on these instructions in the OpenJFX standalone build announcement, though they seem to have a typo in their path to the jars.

I hope this helps.  We're thinking of a better fix long-term.

Regards,

David

[Luigi Marongiu]

Dear David,
thank you for coming back. I installed openJFX with:

$ sudo apt-get install openjfx

It should be installed in /usr/share/java since there is the folder openjfx:

/usr/share/java$ ls -R
.:
el-api-3.0.jar java_uno.jar ridl-6.0.3.jar
gettext.jar jsp-api-2.3.jar ridl.jar
hsqldb1.8.0-1.8.0.10+dfsg.jar juh-6.0.3.jar servlet-api-3.1.jar
hsqldb1.8.0.jar juh.jar unoil-6.0.3.jar
hsqldbutil1.8.0-1.8.0.10+dfsg.jar jurt-6.0.3.jar unoil.jar
hsqldbutil1.8.0.jar jurt.jar unoloader-6.0.3.jar
java-atk-wrapper.jar libintl.jar unoloader.jar
java_defaults.mk openjfx websocket-api-1.0.jar

./openjfx:
jre lib

./openjfx/jre:
lib

./openjfx/jre/lib:
ext javafx.properties jfxswt.jar

./openjfx/jre/lib/ext:
jfxrt.jar

./openjfx/lib:
ant-javafx.jar javafx-mx.jar packager.jar

I modified igv.sh from the clip 10 with the line:
exec java --module-path="$prefix"/lib:/usr/share/java/openjfx/lib \

but when I launched it I got:

$ ./igv.sh
Error occurred during initialization of boot layer
java.lang.module.FindException: Module javafx.controls not found,
required by org.broad.igv

What am I missing?
Cheers,
Luigi

> To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/e8cad810-4a85-4ade-bdb4-d1b80a6ef37d%40googlegroups.com.

[David Eby]

Hi Luigi,

It looks like Ubuntu is shipping openjfx 8 in their apt-get repositories, which is not compatible with OpenJDK 10.  I'm not sure why Ubuntu chose this particular combination but it's an incompatible mix.  There seem to be three choices for running IGV:

1. Install openjdk-8-jdk and either make that the default or else modify igv.sh to use it instead of Java 10.
   
2. Install your own copy of openjfx 10 using the instructions from my previous message.
3. Install Oracle's Java 10 using the instructions from my earlier message.

If you're trying to stick to official Ubuntu repositories only, then #1 is your only choice.  It should be fine, unless you need Java 10 for some other reason, but even then, it's possible to have both Java 8 and Java 10 on Ubuntu.  I do something similar with Linux Mint, which is based on Ubuntu.

If you're trying to run IGV with Java 10 - to get HiDPI support, for example - then #2 or #3 are necessary.  I'm using #3 but just proved that #2 will work.

After your message, we decided to remove the JavaFX components from IGV to avoid issues like this.  It's a small part of the functionality and not worth the hassle.  But it will take some time to make the change, so you'll probably want to go with one of the above in the meanwhile.

Regards,

David

On Tuesday, August 21, 2018 at 5:41:50 PM UTC+9, marongi...@gmail.com wrote:

[David Eby]

I forgot to say that if you go with #1, be sure to switch back to the Java 8 version of IGV.

- David

[Luigi Marongiu]

Dear David,
thank you for the reply. I'll probably go for solution 2 so I won't
mess with Ubuntu defaults since openJFX was instead not standard
issue.
I was wondering: would install both openJDK and Java Oracle cause
clashes? and, if openJDK is the free version of Oracle, does it imply
that I need to pay for Oracle Java (or at least for the updates)?
Best regards,
Luigi

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[Luigi Marongiu]

Dear David, I used option 2.
I downloaded OpenJFX from SDK, placed it on /usr/share/java/ and
changed the line in igv.sh with:
exec java --module-path="$prefix"/lib:/usr/share/java/openjfx-sdk11/lib \
Then ran it:
$ ./igv.sh
WARNING: package com.sun.java.swing.plaf.windows not in java.desktop
WARNING: package sun.awt.windows not in java.desktop
ERROR [2018-08-29T10:23:10,509] [DefaultExceptionHandler.java:49]

[main] Unhandled exception
java.awt.AWTError: Assistive Technology not found:
org.GNOME.Accessibility.AtkWrapper

at java.awt.Toolkit.newAWTError(Toolkit.java:472) ~[?:?]
at java.awt.Toolkit.fallbackToLoadClassForAT(Toolkit.java:488) ~[?:?]
at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)
~[?:?]
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:177)
~[?:?]
at java.util.HashMap$KeySpliterator.forEachRemaining(HashMap.java:1608) ~[?:?]
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:484) ~[?:?]
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:474)
~[?:?]
at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
~[?:?]
at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
~[?:?]
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) ~[?:?]
at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:497) ~[?:?]
at java.awt.Toolkit.loadAssistiveTechnologies(Toolkit.java:532) ~[?:?]
at java.awt.Toolkit.getDefaultToolkit(Toolkit.java:613) ~[?:?]
at java.awt.Toolkit.getEventQueue(Toolkit.java:1494) ~[?:?]
at java.awt.EventQueue.invokeLater(EventQueue.java:1312) ~[?:?]
at javax.swing.SwingUtilities.invokeLater(SwingUtilities.java:1421) ~[?:?]
at org.broad.igv.ui.Main.main(Main.java:113) ~[igv.jar:?]
Caused by: java.lang.ClassNotFoundException: org.GNOME.Accessibility.AtkWrapper
at jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:582)
~[?:?]
at jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:190)
~[?:?]
at java.lang.ClassLoader.loadClass(ClassLoader.java:499) ~[?:?]
at java.lang.Class.forName0(Native Method) ~[?:?]
at java.lang.Class.forName(Class.java:374) ~[?:?]
at java.awt.Toolkit.fallbackToLoadClassForAT(Toolkit.java:485) ~[?:?]
... 15 more

What am I missing?

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[David Eby]

Hi Luigi,

Installing both OpenJDK and Oracle Java works just fine on Linux, so long as they are in separate locations.  My Linux Mint set-up has six different JVMs under /usr/lib/jvm but since they all have different path names.  I switch between them by setting the JAVA_HOME and PATH environment variables; it's also possible to use the "alternatives" mechanism.

I can't speak for Oracle's pricing or billing policies, but recent news reports suggest they may indeed be headed in the direction of charging for their JVM for commercial users.  They have not done this so far but it may change in the future.  Again, however, I can't speak for them.

Regards,

David

[David Eby]

Hi Luigi,

Check your path for a possible typo.  The usual bundle name is "openjfx-sdk-11".

- David

[James Robinson]

Hi,

Just to note that these suggestions are temporary workarounds.   We intend to remove the dependency on JavaFX but this requires some development and will take a bit of time.

Jim

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[Luigi Marongiu]

Dear Jim,
that is not a problem, please take your time. Meanwhile, I need to
show the alignments I made and I do not like IGB, that's why I am
trying to have IGV back up and running.
Looking forward for the next stable release.
Best,
Luigi

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>
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[Luigi Marongiu]

Dear David,
I have installed Orancel Java:
$ java -version
java version "10.0.2" 2018-07-17
Java(TM) SE Runtime Environment 18.3 (build 10.0.2+13)
Java HotSpot(TM) 64-Bit Server VM 18.3 (build 10.0.2+13, mixed mode)

Then I re-downloaded IGV_2.4.14 and run it, but that did not work
because it wanted Java8:
$ ./igv.sh
WARN [2018-08-30T11:23:15,949] [Globals.java:138] [AWT-EventQueue-0]
Development mode is enabled
Detected an unsupported Java version. Java 8 is required by this release.

So I ran the J10 version and finally it worked!

Thank you.
Case closed.

Best regards,
Luigi

PS: since Oracle might charge the new versions of Java, I am looking
forward to other IGV releases based on openJDK :)
And congratulations on the splendid job you guys have done (and keep
doing) for IGV, I really like it!

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[Mita Tran]

Dear Luigi,

You are very lucky. I also havent done. 

My computer: window 10, java 8.1, 64 bit. IGV doesnt work. I dont know what is my mistake.

Thanks

[Luigi Marongiu]

Have you tried to update to Java 10? Also, you need IGV for Java 10,
the snapshot version that David indicated in the tread of messages.
Cheers,
Luigi

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[Mita Tran]

Dear Luigi,

Thank for your reply.

I try to set up java 10 but cannot open IGV. I attach the file below.

Thank for you support!

Mita

[James Robinson]

Mita,  I have responded to you twice in the other thread requesting your prefs.properties file.   Your issue is not related to Luigis.   

On Thu, Aug 30, 2018 at 3:18 AM, Mita Tran <mitam...@gmail.com> wrote:

Dear Luigi,

[James Robinson]

Hi Luigi,

I'm glad you got it working.  There are separate igv  builds for Java 8 and Java 10.   

[Mita Tran]

Dear James

Sorry and Thank you so much. 

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