Bug: IllegalAccessError printed from Kryo

[jamoore]

The following was printed due to an exception during:

      // CLASS & COPY
      try {
        copy = ser.loadReader();
      } catch (ClassNotFoundException e) {
        LOGGER.debug("unknown reader type: {}", e);
        return null;
      }

in Memoizer.java:

08:43:19.345 [main] DEBUG loci.formats.Memoizer - start[1367995398882] time[462] tag[loci.formats.Memoizer.setId]
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
	at sun.nio.cs.UTF_8ConstructorAccess.newInstance(Unknown Source)
	at com.esotericsoftware.kryo.Kryo$1.newInstance(Kryo.java:1015)
	at com.esotericsoftware.kryo.Kryo.newInstance(Kryo.java:1065)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.create(FieldSerializer.java:228)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.read(FieldSerializer.java:217)
	at com.esotericsoftware.kryo.Kryo.readObject(Kryo.java:648)
	at com.esotericsoftware.kryo.serializers.FieldSerializer$ObjectField.read(FieldSerializer.java:605)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.read(FieldSerializer.java:221)
	at com.esotericsoftware.kryo.Kryo.readObject(Kryo.java:648)
	at com.esotericsoftware.kryo.serializers.FieldSerializer$ObjectField.read(FieldSerializer.java:605)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.read(FieldSerializer.java:221)
	at com.esotericsoftware.kryo.Kryo.readObject(Kryo.java:648)
	at com.esotericsoftware.kryo.serializers.FieldSerializer$ObjectField.read(FieldSerializer.java:605)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.read(FieldSerializer.java:221)
	at com.esotericsoftware.kryo.Kryo.readObject(Kryo.java:648)
	at com.esotericsoftware.kryo.serializers.FieldSerializer$ObjectField.read(FieldSerializer.java:605)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.read(FieldSerializer.java:221)
	at com.esotericsoftware.kryo.Kryo.readObject(Kryo.java:648)
	at com.esotericsoftware.kryo.serializers.FieldSerializer$ObjectField.read(FieldSerializer.java:605)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.read(FieldSerializer.java:221)
	at com.esotericsoftware.kryo.Kryo.readObject(Kryo.java:648)
	at com.esotericsoftware.kryo.serializers.FieldSerializer$ObjectField.read(FieldSerializer.java:605)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.read(FieldSerializer.java:221)
	at com.esotericsoftware.kryo.Kryo.readClassAndObject(Kryo.java:729)
	at ome.scifio.io.RandomAccessInputStream.read(RandomAccessInputStream.java:513)
	at com.esotericsoftware.kryo.serializers.DefaultSerializers$KryoSerializableSerializer.read(DefaultSerializers.java:363)
	at com.esotericsoftware.kryo.serializers.DefaultSerializers$KryoSerializableSerializer.read(DefaultSerializers.java:355)
	at com.esotericsoftware.kryo.Kryo.readObject(Kryo.java:648)
	at com.esotericsoftware.kryo.serializers.FieldSerializer$ObjectField.read(FieldSerializer.java:605)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.read(FieldSerializer.java:221)
	at com.esotericsoftware.kryo.Kryo.readObject(Kryo.java:648)
	at com.esotericsoftware.kryo.serializers.FieldSerializer$ObjectField.read(FieldSerializer.java:605)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.read(FieldSerializer.java:221)
	at com.esotericsoftware.kryo.Kryo.readClassAndObject(Kryo.java:729)
	at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.read(DefaultArraySerializers.java:338)
	at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.read(DefaultArraySerializers.java:293)
	at com.esotericsoftware.kryo.Kryo.readObject(Kryo.java:648)
	at com.esotericsoftware.kryo.serializers.FieldSerializer$ObjectField.read(FieldSerializer.java:605)
	at com.esotericsoftware.kryo.serializers.FieldSerializer.read(FieldSerializer.java:221)
	at com.esotericsoftware.kryo.Kryo.readObject(Kryo.java:626)
	at loci.formats.Memoizer$KryoDeser.loadReader(Memoizer.java:125)
	at loci.formats.Memoizer.loadMemo(Memoizer.java:543)
	at loci.formats.Memoizer.setId(Memoizer.java:403)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)

java.lang.IllegalAccessError: java.lang.IllegalAccessError: tried to access class sun.nio.cs.UTF_8 from class sun.nio.cs.UTF_8ConstructorAccess
>>>

TRACE output is missing.

See: ​https://github.com/openmicroscopy/bioformats/pull/506 for the test method.

[jamoore]

Fixed in ​https://github.com/openmicroscopy/bioformats/pull/1336

Note: this issue turned into a blocker as opposed to a log annoyance when importing zip files.

[jamoore]

(and/or ​https://github.com/openmicroscopy/bioformats/pull/1340)

[jmoore <josh@…>]

(In [cd87f173497338223c02be130ff7131cbfec3a16/bioformats.git] on branch develop) kryo: update to 2.24.0 with shading changes (see #10852)

As of 2.22, kryo now shades only asm leaving minlog and
objenesis as proper dependencies. This change may invalidate
existing .bfmemo files and so the impact of this change should
likely be evaluated.

[Melissa Linkert <melissa.linkert@…>]

(In [b0ea1559abf8e52c83099715c1081bd697bf06d5/bioformats.git] on branch develop) Merge pull request #1340 from joshmoore/kryo-2.24

kryo: update to 2.24.0 with shading changes (see #10852)

[Snoopy Crime Cop <snoopycrimecop@…>]

(In [583db74bd0f154b884b1d5e2ebb961ba31162bdc/ome.git] on branch develop) Update develop submodules

Repository: openmicroscopy/openmicroscopy
Already up-to-date.

Repository: openmicroscopy/bioformats
Updating 0819d22..a9cad62
Previously merged:

# PR 1054 qidane 'Additional annotation points throughout the model'
# PR 1350 melissalinkert 'Update version history for 5.0.5 (rebased onto develop)'
# PR 1343 rleigh-dundee 'C++: TIFF pixel data read/write interfaces and skeleton implementation'
# PR 1349 rleigh-dundee 'cmake: Add missing include directories'
# PR 1348 melissalinkert 'PCORAW: fix offsets for files larger than 4 GB'
# PR 1347 melissalinkert 'AIM: fix offset calculation for > 4GB files'
# PR 1323 melissalinkert 'Add bit-level operations to RandomAccess?{Input, Output}Stream'
# PR 1342 joshmoore 'Catch all exceptions on loadMemo'
# PR 1340 joshmoore 'kryo: update to 2.24.0 with shading changes (see #10852)'
# PR 1331 rleigh-dundee 'C++: Add FormatWriter? interface'
# PR 1335 melissalinkert 'ND2: prevent NumberFormatExceptions? when parsing text data (rebased onto develop)'
# PR 1324 melissalinkert 'Deltavision: conditionally ignore stage position values of 0'
# PR 1317 melissalinkert 'Gatan: fix physical dimension parsing when the Z size is missing'

Repository: ome/scripts
Already up-to-date.

Repository: openmicroscopy/ome-documentation
Updating 01a91b2..1cf122e
Previously merged:

# PR 995 mtbc 'add note for omero.jvmcfg.* setters about admin jvmcfg'
# PR 992 ximenesuk 'Add disk usage sections to cli pages.'
# PR 989 sbesson 'Add paragraph about the store recycling while retrieving pixel data'
# PR 986 sbesson 'Document usage of new OMERO_SESSION_DIR envvar for the CLI'
# PR 987 snoopycrimecop 'Update auto-generated properties'
# PR 984 aleksandra-tarkowska 'adding support for django directives'

Generated by OMERO-5.1-latest-submods#204 (​http://ci.openmicroscopy.org/job/OMERO-5.1-latest-submods/204/)