Build Logs

1##################################

2Clonning https://github.com/clulab/processors.git into /build/repo using revision v10.0.1

3##################################

4Note: switching to '06a48e758cf7a0fb348b0ebc1c53e0d77c18c4c4'.

6You are in 'detached HEAD' state. You can look around, make experimental

7changes and commit them, and you can discard any commits you make in this

8state without impacting any branches by switching back to a branch.

10If you want to create a new branch to retain commits you create, you may

11do so (now or later) by using -c with the switch command. Example:

13 git switch -c <new-branch-name>

15Or undo this operation with:

17 git switch -

19Turn off this advice by setting config variable advice.detachedHead to false

21----

22Preparing build for 3.8.0

23Scala binary version found: 3.8

24Implicitly using source version 3.8

25Scala binary version found: 3.8

26Implicitly using source version 3.8

27Would try to apply common scalacOption (best-effort, sbt/mill only):

28Append: ,REQUIRE:-source:3.8

29Remove: ,-deprecation,-feature,-Xfatal-warnings,-Werror,MATCH:.*-Wconf.*any:e

30----

31Starting build for 3.8.0

32Execute tests: true

33sbt project found:

34Sbt version 1.7.2 is not supported, minimal supported version is 1.11.5

35Enforcing usage of sbt in version 1.11.5

36No prepare script found for project clulab/processors

37##################################

38Scala version: 3.8.0

39Targets: org.clulab%processors org.clulab%processors-apps org.clulab%processors-debugger

40Project projectConfig: {"tests":null}

41##################################

42Using extra scalacOptions: ,REQUIRE:-source:3.8

43Filtering out scalacOptions: ,-deprecation,-feature,-Xfatal-warnings,-Werror,MATCH:.*-Wconf.*any:e

44[sbt_options] declare -a sbt_options=()

45[process_args] java_version = '17'

46[copyRt] java9_rt = '/root/.sbt/1.0/java9-rt-ext-eclipse_adoptium_17_0_8/rt.jar'

47# Executing command line:

48java

49-Dfile.encoding=UTF-8

50-Xmx10g

51-XX:MaxMetaspaceSize=10g

52-Dcommunitybuild.scala=3.8.0

53-Dcommunitybuild.project.dependencies.add=

54-Xmx7G

55-Xms4G

56-Xss8M

57-Dsbt.script=/root/.sdkman/candidates/sbt/current/bin/sbt

58-Dscala.ext.dirs=/root/.sbt/1.0/java9-rt-ext-eclipse_adoptium_17_0_8

59-jar

60/root/.sdkman/candidates/sbt/1.11.5/bin/sbt-launch.jar

61"setCrossScalaVersions 3.8.0"

62"++3.8.0 -v"

63"mapScalacOptions ",REQUIRE:-source:3.8,-Wconf:msg=can be rewritten automatically under:s" ",-deprecation,-feature,-Xfatal-warnings,-Werror,MATCH:.*-Wconf.*any:e""

64"set every credentials := Nil"

65"excludeLibraryDependency com.github.ghik:zerowaste_{scalaVersion} com.olegpy:better-monadic-for_3 org.polyvariant:better-tostring_{scalaVersion} org.wartremover:wartremover_{scalaVersion}"

66"removeScalacOptionsStartingWith -P:wartremover"

68moduleMappings

69"runBuild 3.8.0 """{"tests":null}""" org.clulab%processors org.clulab%processors-apps org.clulab%processors-debugger"

71[info] welcome to sbt 1.11.5 (Eclipse Adoptium Java 17.0.8)

72[info] loading settings for project repo-build from akka.sbt, plugins.sbt...

73[info] loading project definition from /build/repo/project

79[info] compiling 3 Scala sources to /build/repo/project/target/scala-2.12/sbt-1.0/classes ...

80[info] Non-compiled module 'compiler-bridge_2.12' for Scala 2.12.20. Compiling...

81[info] Compilation completed in 8.81s.

82[info] done compiling

84version in ThisBuild := "10.0.1"

85 ^

86[info] loading settings for project root from build.sbt, compile.sbt, publish.sbt, release.sbt, test.sbt, version.sbt...

87[info] loading settings for project library from assembly.sbt, build.sbt, compile.sbt, publish.sbt, test.sbt...

88[info] loading settings for project apps from assembly.sbt, build.sbt...

89[info] loading settings for project webapp from build.sbt, docker.sbt...

90[info] loading settings for project debugger from build.sbt, publish.sbt...

91[info] set current project to root (in build file:/build/repo/)

92Execute setCrossScalaVersions: 3.8.0

93OpenCB::Changing crossVersion 3.1.3 -> 3.8.0 in root/crossScalaVersions

94OpenCB::Changing crossVersion 3.1.3 -> 3.8.0 in library/crossScalaVersions

95OpenCB::Changing crossVersion 3.1.3 -> 3.8.0 in apps/crossScalaVersions

96OpenCB::Changing crossVersion 3.1.3 -> 3.8.0 in debugger/crossScalaVersions

97[info] set current project to root (in build file:/build/repo/)

98[info] Setting Scala version to 3.8.0 on 4 projects.

99[info] Switching Scala version on:

100[info] * root (2.12.19, 2.11.12, 2.13.14, 3.8.0)

101[info] library (2.12.19, 2.11.12, 2.13.14, 3.8.0)

102[info] debugger (2.12.19, 2.11.12, 2.13.14, 3.8.0)

103[info] apps (2.12.19, 2.11.12, 2.13.14, 3.8.0)

104[info] Excluding projects:

105[info] webapp (2.12.19)

106[info] Reapplying settings...

107[info] set current project to root (in build file:/build/repo/)

108Execute mapScalacOptions: ,REQUIRE:-source:3.8,-Wconf:msg=can be rewritten automatically under:s ,-deprecation,-feature,-Xfatal-warnings,-Werror,MATCH:.*-Wconf.*any:e

109[info] Reapplying settings...

110[info] set current project to root (in build file:/build/repo/)

111[info] Defining Global / credentials, apps / credentials and 3 others.

112[info] The new values will be used by Global / pgpSelectPassphrase, allCredentials and 23 others.

113[info] Run `last` for details.

114[info] Reapplying settings...

115[info] set current project to root (in build file:/build/repo/)

116Execute excludeLibraryDependency: com.github.ghik:zerowaste_{scalaVersion} com.olegpy:better-monadic-for_3 org.polyvariant:better-tostring_{scalaVersion} org.wartremover:wartremover_{scalaVersion}

117[info] Reapplying settings...

118OpenCB::Failed to reapply settings in excludeLibraryDependency: Reference to undefined setting:

120 Global / allExcludeDependencies from Global / allExcludeDependencies (CommunityBuildPlugin.scala:331)

121 Did you mean allExcludeDependencies ?

122 , retry without global scopes

123[info] Reapplying settings...

124[info] set current project to root (in build file:/build/repo/)

125Execute removeScalacOptionsStartingWith: -P:wartremover

126[info] Reapplying settings...

127[info] set current project to root (in build file:/build/repo/)

128[success] Total time: 0 s, completed Jan 13, 2026, 4:30:18 PM

129Build config: {"tests":null}

131Starting build...

132Projects: Set(library, apps, debugger)

133Starting build for ProjectRef(file:/build/repo/,library) (processors)... [0/3]

134OpenCB::Exclude Scala3 specific scalacOption `REQUIRE:-source:3.8` in Scala 2.12.20 module Global

135OpenCB::Exclude Scala3 specific scalacOption `REQUIRE:-source:3.8` in Scala 2.12.19 module Scope(Select(BuildRef(file:/build/repo/)), Select(ConfigKey(compile)), Zero, Zero)

136OpenCB::Filter out '-feature', matches setting pattern '^-?-feature'

137OpenCB::Filter out '-deprecation', matches setting pattern '^-?-deprecation'

138Compile scalacOptions: -unchecked, -explain, -Wconf:msg=can be rewritten automatically under:s, -source:3.8

139[info] compiling 194 Scala sources and 5 Java sources to /build/repo/library/target/scala-3.8.0/classes ...

156[info] done compiling

157[info] compiling 85 Scala sources to /build/repo/library/target/scala-3.8.0/test-classes ...

167[info] done compiling

168[info] TestHashTrie:

169[info] the trie

170[info] - should label the text correctly with BIO labels

171[info] the trie

172[info] - should have 2 entries and contain 5 unique strings

173[info] the trie

174[info] - should sort and find the entries correctly

175[info] the trie

176[info] - should make use of shouldStop

177[info] TestDueTo:

178SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".

179SLF4J: Defaulting to no-operation (NOP) logger implementation

180SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.

181[Tokenizer] Checking /build/repo for intel-librust_tokenizer.so...

182[Tokenizer] Checking /root for intel-librust_tokenizer.so...

183[Tokenizer] Extracting resource intel-librust_tokenizer.so to /tmp/intel-librust_tokenizer-8576920529627034534.so...

184[info] org.clulab.processors.TestDueTo *** ABORTED ***

186[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

187[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

188[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

189[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

190[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

191[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

192[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

193[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

194[info] at org.scalatest.BeforeAndAfterAll.run$(BeforeAndAfterAll.scala:135)

195[info] at org.clulab.processors.CluTest.run(CluTest.scala:9)

196[info] ...

198[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

199[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

200[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

201[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

202[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

203[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

204[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

205[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

206[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

207[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

208[info] ...

248[info] TestDoc58b0:

249[info] org.clulab.processors.docs.TestDoc58b0 *** ABORTED ***

251[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

252[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

253[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

254[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

255[info] at org.clulab.processors.docs.TestDoc58b0.<init>(TestDoc58b0.scala:10)

256[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

257[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)

258[info] at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)

259[info] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)

260[info] at java.base/java.lang.reflect.ReflectAccess.newInstance(ReflectAccess.java:128)

261[info] ...

263[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

264[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

265[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

266[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

267[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

268[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

269[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

270[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

271[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

272[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

273[info] ...

314[info] TestNumericPatterns:

315[info] Any text

316[info] - should contain one match for pattern `[2+2==4]`

317[info] Any text

318[info] - should contain no matches for pattern `[2+2==5]`

319[info] TestArray:

320[info] Array.toSeq

321[info] - should work as expected without import

322[info] - should work as expected with import

323[info] Array.toIndexedSeq

324[info] - should work as expected without import

325[info] - should work as expected with import

326[info] MutableArraySeq.from

327[info] - should work as expected without import

328[info] - should work as expected with import

329[info] ImmutableArraySeq.unsafeWrapArray

330[info] - should work as expected without import

331[info] - should work as expected with import

332[info] processSeq(array)

333[info] - should work as expected without import

334[info] - should work as expected with import

335[info] processSeq(ImmutableArraySeq.unsafeWrapArray)

336[info] - should work as expected without import

337[info] - should work as expected with import

338[info] processIndexedSeq(array)

339[info] - should work as expected without import

340[info] - should work as expected with import

341[info] processIndexedSeq(ImmutableArraySeq.unsafeWrapArray)

342[info] - should work as expected without import

343[info] - should work as expected with import

344[info] :Seq[]

345[info] - should work as expected without import

346[info] - should work as expected with import

347[info] :IndexedSeq[]

348[info] - should work as expected without import

349[info] - should work as expected with import

350[info] foreach

351[info] - should work as expected without import

352[info] - should work as expected with import

353[info] zip

354[info] - should work as expected without import

355[info] - should work as expected with import

356[info] map

357[info] - should work as expected without import

358[info] - should work as expected with import

359[info] TestNumberParser:

360[info] NumberParser

361[info] - should parse digits

362[info] - should fail on invalid input

363[info] - should fail on empty input

364[info] - should convert words to numbers

365[info] - should parses decimal numbers

366[info] - should convert numbers and words to numbers

367[info] - should parse words to numbers

368[info] TestMinHeap:

369[info] MinHeap

370[info] - should order elements properly

371[info] - should keep correct top K

372[info] TestProgressBar:

373[info] ProgressBar

375Progress 0% │██▉ │ 1/10 (0:00:00 / 0:00:00)

376Progress 20% │█████▊ │ 2/10 (0:00:02 / 0:00:08)

377Progress 30% │████████▋ │ 3/10 (0:00:03 / 0:00:07)

378Progress 40% │███████████▌ │ 4/10 (0:00:04 / 0:00:06)

379Progress 50% │██████████████▌ │ 5/10 (0:00:05 / 0:00:05)

380Progress 60% │█████████████████▍ │ 6/10 (0:00:06 / 0:00:04)

381Progress 70% │████████████████████▎ │ 7/10 (0:00:07 / 0:00:03)

382Progress 80% │███████████████████████▏ │ 8/10 (0:00:08 / 0:00:02)

383Progress 90% │██████████████████████████ │ 9/10 (0:00:09 / 0:00:01)

384Progress 100% │█████████████████████████████│ 10/10 (0:00:10 / 0:00:00) [info] - should progress

386Progress 0% │ │ 0/11 (0:00:00 / ?)

387Progress 9% │██▋ │ 1/11 (0:00:01 / 0:00:10)

388Progress 18% │████▌ │ 2/11 (0:00:02 / 0:00:09) at 0

389Progress 27% │██████▊ │ 3/11 (0:00:03 / 0:00:08) at 1

390Progress 36% │█████████ │ 4/11 (0:00:04 / 0:00:07) at 2

391Progress 45% │███████████▎ │ 5/11 (0:00:05 / 0:00:06) at 3

392Progress 54% │█████████████▋ │ 6/11 (0:00:06 / 0:00:05) at 4

393Progress 63% │███████████████▉ │ 7/11 (0:00:07 / 0:00:04) at 5

394Progress 72% │██████████████████▏ │ 8/11 (0:00:08 / 0:00:03) at 6

395Progress 81% │████████████████████▍ │ 9/11 (0:00:09 / 0:00:02) at 7

396Progress 90% │██████████████████████▋ │ 10/11 (0:00:10 / 0:00:01) at 8

397Progress 100% │█████████████████████████│ 11/11 (0:00:11 / 0:00:00) at 9[info] - should show extra messages

398[info] TestCorefChains:

399[info] CorefChains

400[info] - should sort on sentenceIndex

401[info] - should sort on headIndex

402[info] - should sort on size

403[info] - should sort on index

404[info] TestExtractorEngine:

405[info] ExtractorEngine

406[info] - should read utf8 encoded data

407[info] - should read latin1 encoded data

409[info] - should read data incorrectly if using the wrong charset

410[info] TestNamedEntity:

411[info] NamedEntity identification

412[info] - should collect properly test 1

413[info] - should collect properly test 2

414[info] - should collect properly test 3

415[info] - should collect properly test 4

416[info] - should collect properly test 5

417[info] - should collect properly test 6

418[info] - should collect properly test 7

419[info] - should collect properly test 8

420[info] - should collect properly test 9

421[info] - should collect properly test 10

422[info] - should collect properly test 11

423[info] - should collect properly test 12

424[info] - should collect properly test 13

425[info] - should collect properly test 14

426[info] - should collect properly test 15

427[info] - should combine properly test 1

428[info] - should combine properly test 2

429[info] - should combine properly test 3

430[info] - should combine properly test 4

431[info] - should combine properly test 5

432[info] - should combine properly test 6

433[info] - should combine properly test 7

434[info] - should combine properly test 8

435[info] - should combine properly test 9

436[info] - should combine properly test 10

437[info] - should combine properly test 11

438[info] - should combine properly test 12

439[info] - should combine properly test 13

440[info] - should combine properly test 14

441[info] - should combine properly test 15

442[info] - should combine properly test 16

443[info] - should combine properly test 17

444[info] - should combine properly test 18

445[info] - should combine properly test 19

446[info] - should combine properly test 20

447[info] NamedEntity validation

448[info] - should validate the BIO notation test 1

449[info] - should validate the BIO notation test 2

450[info] - should validate the BIO notation test 3

451[info] - should validate the BIO notation test 4

452[info] - should validate the BIO notation test 5

453[info] - should validate the BIO notation test 6

454[info] - should validate the BIO notation test 7

455[info] - should validate the BIO notation test 8

456[info] - should validate the BIO notation test 9

457[info] NamedEntity correction

458[info] - should correct the BIO notation test 1

459[info] - should correct the BIO notation test 2

460[info] - should correct the BIO notation test 3

461[info] - should correct the BIO notation test 4

462[info] - should correct the BIO notation test 5

463[info] - should correct the BIO notation test 6

464[info] - should correct the BIO notation test 7

465[info] - should correct the BIO notation test 8

466[info] - should correct the BIO notation test 9

467[info] TestTimer:

468[info] timer

469[info] - should use the right divisors

470[info] TestDistributionalSimilarityPatterns:

471[info] I saw a leopard climbing a tree.

472[info] - should produce a mention with the label "Feline" for the word "leopard"

473[info] TestSerializer:

474[info] - should serialize/deserialize a Mention correctly

475[info] - should serialize/deserialize a CrossSentenceMention correctly

476[info] TestUniversalEnhancedDependencies:

477[info] org.clulab.processors.TestUniversalEnhancedDependencies *** ABORTED ***

479[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

480[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

481[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

482[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

483[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

484[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

485[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

486[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

487[info] at org.scalatest.BeforeAndAfterAll.run$(BeforeAndAfterAll.scala:135)

488[info] at org.clulab.processors.CluTest.run(CluTest.scala:9)

489[info] ...

491[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

492[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

493[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

494[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

495[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

496[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

497[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

498[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

499[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

500[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

501[info] ...

541[info] CluTest:

542[info] TestJSONSerializer:

543[info] JSONSerializer

544[info] - should serialize/deserialize a Document to/from json correctly

545[info] - should serialize/deserialize a Sentence to/from json correctly

546[info] A Document with an ID

547[info] - should produce json with an "id" field

548[info] A Document without an ID

549[info] - should produce json without an "id" field

550[info] A Document with text

551[info] - should produce json with a "text" field

552[info] A Document without text

553[info] - should produce json without a "text" field

554[info] A Document recovered from JSON

555[info] - should be equivalent to the original

556[info] A Sentence recovered from JSON

557[info] - should be equivalent to the original

558[info] A Document saved and loaded

559[info] - should have JSON equivalent to the original

560[info] TestGraphPatternSD:

561[info] GraphPattern

562[info] - should support multiline patterns

563[info] - should produce one mention at a time for an argument without any quantifier

564[info] - should support optional arguments

565[info] - should support exact quantifiers for arguments

566[info] - should support * for arguments

567[info] - should support + for arguments

568[info] - should support greedy open range quantifiers for arguments

569[info] - should handle multitoken triggers

570[info] - should support 'type: graph'

571[info] - should support 'graph: ' key

572[info] - should ignore 'graph: ' when 'type: dependency'

573[info] TestNumericEntityRecognition:

574[info] org.clulab.numeric.TestNumericEntityRecognition *** ABORTED ***

576[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

577[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

578[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

579[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

580[info] at org.clulab.numeric.TestNumericEntityRecognition$HabitusProcessor.<init>(TestNumericEntityRecognition.scala:44)

581[info] at org.clulab.numeric.TestNumericEntityRecognition.<init>(TestNumericEntityRecognition.scala:50)

582[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

583[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)

584[info] at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)

585[info] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)

586[info] ...

588[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

589[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

590[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

591[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

592[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

593[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

594[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

595[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

596[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

597[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

598[info] ...

640[info] TestMarkdownGeneration:

641[info] MarkdownGeneration

642[info] - should not crash

643[info] - should properly aggregate argument requiredness

644[info] TestCrLf:

645[info] resources

646[info] TestEvalTimeNorm:

647[info] temporal parser

648[info] org.clulab.numeric.TestEvalTimeNorm *** ABORTED ***

650[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

651[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

652[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

653[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

654[info] at org.clulab.numeric.TestEvalTimeNorm.testFun$proxy1$1(TestEvalTimeNorm.scala:12)

655[info] at org.clulab.numeric.TestEvalTimeNorm.$init$$$anonfun$1(TestEvalTimeNorm.scala:10)

656[info] at org.scalatest.Transformer.apply$$anonfun$1(Transformer.scala:22)

657loading props from file library/src/test/resources/org/clulab/utils/test.properties

658[info] at org.scalatest.OutcomeOf.outcomeOf(OutcomeOf.scala:85)

659[info] at org.scalatest.OutcomeOf.outcomeOf$(OutcomeOf.scala:31)

660Using the following properties:

661[info] at org.scalatest.OutcomeOf$.outcomeOf(OutcomeOf.scala:104)

662[info] ...

664[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

665[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

666[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

667[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

668[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

669[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

670 p1 = /some/path

671[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

672 p2 = /some/path/subdir/123

673[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

674 p3 = 123

675[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

676[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

677[info] ...

679loading props from file library/src/test/resources/org/clulab/utils/test.properties

680Using the following properties:

681 p1 = /some/path

682 p2 = /some/path/subdir/123

683 p3 = 123

759[info] TestArgsToProperties:

760[info] properties

761[info] - should contain p1 with value /some/path

762[info] - should contain p2 with the value /some/path/subdir/123

763[info] properties as a map

764[info] - should contain p1 with value /some/path

765[info] - should contain p2 with the value /some/path/subdir/123

766[info] argsToMap

767Using the following properties:

768 = in inDirectory out outDirectory

769[info] - should deal with plain values

770[info] TestInst:

771[info] Inst

772[info] - should not distinguish Done and Done

773[info] - should distinguish Done and Pass

774[info] - should distinguish MatchLookAhead and MatchLookBehind

775[info] - should distinguish SaveStart and SaveEnd

776[info] - should distinguish Done and MatchToken

777[info] - should distinguish between Pass and Pass

778[info] - should distinguish between MatchToken and MatchToken

779[info] - should copy Pass appropriately

780[info] - should copy Split appropriately

781[info] - should copy SaveStart appropriately

782[info] - should copy SaveEnd appropriately

783[info] - should copy MatchToken appropriately

784[info] - should copy MatchMention appropriately

785[info] - should copy MatchSentenceStart appropriately

786[info] - should copy MatchSentenceEnd appropriately

787[info] - should copy MatchLookAhead appropriately

788[info] - should copy MatchLookBehind appropriately

789[info] - should distinguish complicated instances

790[info] CaseClasses

791[info] - should compare as intended

792[info] tuple hashes

793[info] - should be called recursively

794[info] TestGraphPattern:

795[info] graph range {0,n}

797[info] GraphPattern

798[info] - should support multiline patterns

799[info] - should produce one mention at a time for an argument without any quantifier

800[info] - should support optional arguments

801[info] - should support exact quantifiers for arguments

802[info] - should support * for arguments

804[info] - should support + for arguments

806[info] - should support greedy open range quantifiers for arguments

809[info] - should handle multitoken triggers

810[info] - should support 'type: graph'

811[info] - should support 'graph: ' key

812[info] - should ignore 'graph: ' when 'type: dependency'

813[info] - should require a registered graph type wherever 'graph: ' is specified

814[info] - should handle colons in dependencies

815[info] - should handle colons in dependencies without quotes

816[info] TestRandomForestClassifier:

817[info] RFClassifier

818Current utility:

819UTILITY DEBUG:

820Using dataset:

821label:0 features:[0:2.0, 1:1.0]

822label:1 features:[0:2.0, 2:1.0, 3:1.0]

823label:1 features:[0:1.0, 4:1.0]

824Using feature 3 with threshold 0.5

825Contingency table for this feature+threshold is: SMALLER: [0:1.0, 1:1.0], GREATER: [1:1.0]

826Overall utility: 0.2516291673878229

827Parent utility: 0.9182958340544896

828Utility of left child: 1.0

829Utility of right child: 0.0

830CHOSEN NEW BEST!

831Current utility:

832UTILITY DEBUG:

833Using dataset:

834label:0 features:[0:2.0, 1:1.0]

835label:1 features:[0:2.0, 2:1.0, 3:1.0]

836label:1 features:[0:1.0, 4:1.0]

837Using feature 4 with threshold 0.5

838Contingency table for this feature+threshold is: SMALLER: [0:1.0, 1:1.0], GREATER: [1:1.0]

839Overall utility: 0.2516291673878229

840Parent utility: 0.9182958340544896

841Utility of left child: 1.0

842Utility of right child: 0.0

843Current utility:

844UTILITY DEBUG:

845Using dataset:

846label:0 features:[0:2.0, 1:1.0]

847label:1 features:[0:2.0, 2:1.0, 3:1.0]

848label:1 features:[0:1.0, 4:1.0]

849Using feature 0 with threshold 1.5

850Contingency table for this feature+threshold is: SMALLER: [0:0.0, 1:1.0], GREATER: [0:1.0, 1:1.0]

851Overall utility: 0.2516291673878229

852Parent utility: 0.9182958340544896

853Utility of left child: 0.0

854Utility of right child: 1.0

855Current utility:

856UTILITY DEBUG:

857Using dataset:

858label:0 features:[0:2.0, 1:1.0]

859label:1 features:[0:2.0, 2:1.0, 3:1.0]

860label:1 features:[0:1.0, 4:1.0]

861Using feature 1 with threshold 0.5

862Contingency table for this feature+threshold is: SMALLER: [0:0.0, 1:2.0], GREATER: [0:1.0]

863Overall utility: 0.9182958340544896

864Parent utility: 0.9182958340544896

865Utility of left child: 0.0

866Utility of right child: 0.0

867CHOSEN NEW BEST!

868Current utility:

869UTILITY DEBUG:

870Using dataset:

871label:0 features:[0:2.0, 1:1.0]

872label:1 features:[0:2.0, 2:1.0, 3:1.0]

873label:1 features:[0:1.0, 4:1.0]

874Using feature 2 with threshold 0.5

875Contingency table for this feature+threshold is: SMALLER: [0:1.0, 1:1.0], GREATER: [1:1.0]

876Overall utility: 0.2516291673878229

877Parent utility: 0.9182958340544896

878Utility of left child: 1.0

879Utility of right child: 0.0

880BEST OVERALL:

881UTILITY DEBUG:

882Using dataset:

883label:0 features:[0:2.0, 1:1.0]

884label:1 features:[0:2.0, 2:1.0, 3:1.0]

885label:1 features:[0:1.0, 4:1.0]

886Using feature 1 with threshold 0.5

887Contingency table for this feature+threshold is: SMALLER: [0:0.0, 1:2.0], GREATER: [0:1.0]

888Overall utility: 0.9182958340544896

889Parent utility: 0.9182958340544896

890Utility of left child: 0.0

891Utility of right child: 0.0

892Current utility:

893UTILITY DEBUG:

894Using dataset:

895label:1 features:[0:2.0, 2:1.0, 3:1.0]

896label:1 features:[0:1.0, 4:1.0]

897Using feature 2 with threshold 0.5

898Contingency table for this feature+threshold is: SMALLER: [1:1.0], GREATER: [1:1.0]

899Overall utility: 0.0

900Parent utility: 0.0

901Utility of left child: 0.0

902Utility of right child: 0.0

903CHOSEN NEW BEST!

904Current utility:

905UTILITY DEBUG:

906Using dataset:

907label:1 features:[0:2.0, 2:1.0, 3:1.0]

908label:1 features:[0:1.0, 4:1.0]

909Using feature 4 with threshold 0.5

910Contingency table for this feature+threshold is: SMALLER: [1:1.0], GREATER: [1:1.0]

911Overall utility: 0.0

912Parent utility: 0.0

913Utility of left child: 0.0

914Utility of right child: 0.0

915Current utility:

916UTILITY DEBUG:

917Using dataset:

918label:1 features:[0:2.0, 2:1.0, 3:1.0]

919label:1 features:[0:1.0, 4:1.0]

920Using feature 0 with threshold 1.5

921Contingency table for this feature+threshold is: SMALLER: [1:1.0], GREATER: [1:1.0]

922Overall utility: 0.0

923Parent utility: 0.0

924Utility of left child: 0.0

925Utility of right child: 0.0

926Current utility:

927UTILITY DEBUG:

928Using dataset:

929label:1 features:[0:2.0, 2:1.0, 3:1.0]

930label:1 features:[0:1.0, 4:1.0]

931Using feature 3 with threshold 0.5

932Contingency table for this feature+threshold is: SMALLER: [1:1.0], GREATER: [1:1.0]

933Overall utility: 0.0

934Parent utility: 0.0

935Utility of left child: 0.0

936Utility of right child: 0.0

937BEST OVERALL:

938UTILITY DEBUG:

939Using dataset:

940label:1 features:[0:2.0, 2:1.0, 3:1.0]

941label:1 features:[0:1.0, 4:1.0]

942Using feature 2 with threshold 0.5

943Contingency table for this feature+threshold is: SMALLER: [1:1.0], GREATER: [1:1.0]

944Overall utility: 0.0

945Parent utility: 0.0

946Utility of left child: 0.0

947Utility of right child: 0.0

948Class of List(good, horrible): -

949Class of List(bad, horrible): -

950Class of List(good, great): +

951[info] - should work with BVFDataset

952[info] RandomForestClassifier

953Accuracy: 0.965

954[info] - should have an accuracy > .95 on this dataset

955[info] TestLiblinearClassifier:

956[info] LiblinearClassifier

957iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00 CG 2

958iter 2 act 8.879e-04 pre 8.833e-04 delta 8.463e-01 f 1.459e+00 |g| 5.811e-02 CG 1

959iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00 CG 2

960iter 2 act 8.879e-04 pre 8.833e-04 delta 8.463e-01 f 1.459e+00 |g| 5.811e-02 CG 1

961iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00 CG 2

962iter 2 act 8.879e-04 pre 8.833e-04 delta 8.463e-01 f 1.459e+00 |g| 5.811e-02 CG 1

963iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00 CG 2

964iter 2 act 8.879e-04 pre 8.833e-04 delta 8.463e-01 f 1.459e+00 |g| 5.811e-02 CG 1

965iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00 CG 2

966iter 2 act 8.879e-04 pre 8.833e-04 delta 8.463e-01 f 1.459e+00 |g| 5.811e-02 CG 1

967iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00 CG 2

968iter 2 act 8.879e-04 pre 8.833e-04 delta 8.463e-01 f 1.459e+00 |g| 5.811e-02 CG 1

969iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00[info] - should work with RVFDataset

970 CG 2

971iter 2 act 8.879e-04 pre 8.833e-04 delta 8.463e-01 f 1.459e+00 |g| 5.811e-02 CG 1

972iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00 CG 2

973iter 2 act 8.879e-04 pre 8.833e-04 delta 8.463e-01 f 1.459e+00 |g| 5.811e-02 CG 1

974iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00 CG 2

975iter 2 act 8.879e-04 pre 8.833e-04 delta 8.463e-01 f 1.459e+00 |g| 5.811e-02 CG 1

976[info] - should work with BVFDataset

977iter 1 act 4.528e-01 pre 4.444e-01 delta 7.000e-01 f 1.386e+00 |g| 1.323e+00 CG 2

978iter 2 act 8.651e-04 pre 8.605e-04 delta 7.000e-01 f 9.335e-01 |g| 5.750e-02 CG 1

979[info] - should work with a two-label dataset

980[info] LogisticRegressionClassifier

981iter 1 act 7.243e+02 pre 6.698e+02 delta 1.883e+01 f 1.386e+03 |g| 9.617e+01 CG 4

982iter 2 act 3.382e+01 pre 3.043e+01 delta 1.883e+01 f 6.620e+02 |g| 1.841e+01 CG 3

983iter 3 act 2.260e+00 pre 2.083e+00 delta 1.883e+01 f 6.282e+02 |g| 4.186e+00 CG 3

984iter 4 act 6.468e-02 pre 6.350e-02 delta 1.883e+01 f 6.259e+02 |g| 6.366e-01 CG 3

985[info] - should have an accuracy > .97 in this dataset

986[info] LinearSVMClassifier

987iter 1 act 1.779e+03 pre 1.753e+03 delta 1.414e+01 f 2.000e+03 |g| 3.847e+02 CG 5

988iter 2 act 4.189e+01 pre 4.076e+01 delta 1.414e+01 f 2.214e+02 |g| 3.417e+01 CG 6

989iter 3 act 3.859e+00 pre 3.685e+00 delta 1.414e+01 f 1.795e+02 |g| 8.599e+00 CG 7

990iter 4 act 5.435e-01 pre 5.117e-01 delta 1.414e+01 f 1.757e+02 |g| 2.475e+00 CG 6

991[info] - should have an accuracy > .97 in this dataset

992[info] HexaDecoderTest:

993[info] HexaDecoder

994Some(L (0, 3) (1, root)

995 R (0, 1) (1, root)

996 (0, nsubj)

997 (1, root)

998 R (2, 3) (3, dobj)

999 (2, nmod)

1000 (3, dobj)

1001)

1002Dependencies (3):

1003Edge(1,3,dobj)

1004Edge(1,0,nsubj)

1005Edge(3,2,nmod)

1006Roots: 1

1007[info] - should decode a simple tree

1008Terminal tags: tl-nsubj, tl-cop, tl-det, tr-root

1009Nonterm tags: nl-R, nr-R, nr-R, eos

1010Processing terminal tag: tl-nsubj

1011Pushing:

1012(0, nsubj)

1013onto the stack.

1014Processing non-terminal tag: nl-R

1015Pushing:

1016R (0, -1) (-1, dummy)

1017 (0, nsubj)

1018 dummy

1019onto the stack.

1020Processing terminal tag: tl-cop

1021Pushing:

1022(1, cop)

1023onto the stack.

1024Processing non-terminal tag: nr-R

1025Pushing:

1026R (0, -1) (-1, dummy)

1027 (0, nsubj)

1028 R (1, -1) (-1, dummy)

1029 (1, cop)

1030 dummy

1031onto the stack.

1032Processing terminal tag: tl-det

1033Pushing:

1034(2, det)

1035onto the stack.

1036Processing non-terminal tag: nr-R

1037Pushing:

1038R (0, -1) (-1, dummy)

1039 (0, nsubj)

1040 R (1, -1) (-1, dummy)

1041 (1, cop)

1042 R (2, -1) (-1, dummy)

1043 (2, det)

1044 dummy

1045onto the stack.

1046Processing terminal tag: tr-root

1047Pushing:

1048R (0, 3) (3, root)

1049 (0, nsubj)

1050 R (1, 3) (3, root)

1051 (1, cop)

1052 R (2, 3) (3, root)

1053 (2, det)

1054 (3, root)

1055onto the stack.

1056Some(R (0, 3) (3, root)

1057 (0, nsubj)

1058 R (1, 3) (3, root)

1059 (1, cop)

1060 R (2, 3) (3, root)

1061 (2, det)

1062 (3, root)

1063)

1064Dependencies (3):

1065List(Edge(3,0,nsubj), Edge(3,1,cop), Edge(3,2,det))

1066Roots: 3

1067[info] - should decode another simple tree

1068[info] Test:

1069[info] TestEntityConstraints:

1070[info] Uneven parentheses

1071[info] - should be disallowed in entities

1072[info] Even parentheses

1073[info] - should be valid in entities

1074[info] Entities longer than n tokens

1075[info] - should be pruned

1076[info] TestMkCombinedDocument:

1077[info] org.clulab.processors.TestMkCombinedDocument *** ABORTED ***

1079[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

1080[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

1081[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

1082[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

1083[info] at org.clulab.processors.TestMkCombinedDocument.<init>(TestMkCombinedDocument.scala:28)

1084[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

1085[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)

1086[info] at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)

1087[info] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)

1088[info] at java.base/java.lang.reflect.ReflectAccess.newInstance(ReflectAccess.java:128)

1089[info] ...

1091[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

1092[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

1093[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

1094[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

1095[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

1096[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

1097[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

1098[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

1099[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

1100[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

1101[info] ...

1142[info] TestMathUtils:

1143[info] - should work with Seq

1144[info] - should not produce negative mean or variance

1145[info] - should work with Array

1146[info] - should work with any numeric collection

1147[info] - should be reasonably resilient to overflow

1148[info] TestDirectedGraph:

1149[info] DirectedGraph

1150[info] - should process a loop with a source

1151[info] - should process a loop without a source

1152[info] - should add lone roots

1153[info] - should handle disjoint loops

1154[info] - should not use a leading destination as a root

1155[info] - should be empty

1156[info] TestDependencyUtils:

1157[info] Because the substrates of Shp2 are for the most part unknown, we were additionally interested in examining the state of EGFR tyrosine phosphorylation following treatment with EGF in order to determine if the failure of Gab1 to bind p85, and potentially recruit Shp2, would influence levels of EGFR autophosphorylation.

1158[info] - should produce 'substrates' as the head of 'the substrates of Shp2'

1159[info] - should produce 'are' as the head of 'the substrates of Shp2 are'

1160[info] - should produce None for an empty Interval

1161[info] The docking protein Gab1 is the primary mediator of EGF-stimulated activation of the PI-3K/Akt cell survival pathway

1162[info] - should have the same getHeadStrict as roots

1163[info] - should produce only one head for getHeadsStrict

1164[info] - should produce None for an empty Interval

1165[info] - should produce two heads for 'docking protein' using getHeadsLocal

1166[info] - should think 'docking protein' is nested in 'docking protein Gab1'

1167[info] - should think 'the' is nested in 'Gab1'

1168[info] - should not think 'is' is nested in 'Gab1'

1169[info] - should think Interval(3,3) is nested in 'Gab1'

1170[info] - should not think 'pathway' is nested in 'Gab1'

1171[info] .

1172[info] - should produce one head using findHeads

1173[info] - should produce no heads using findHeadsStrict

1174[info] DependencyUtils

1175[info] - should handle cycles in the dependencyGraph correctly

1176[info] - should handle roots with incoming dependencies

1177[info] - should handle invalid dependency trees in findHeads

1178[info] - should only match complete stop tags

1179[info] TestNumericMentions:

1180[info] org.clulab.numeric.TestNumericMentions *** ABORTED ***

1182[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

1183[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

1184[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

1185[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

1186[info] at org.clulab.numeric.TestNumericMentions.<init>(TestNumericMentions.scala:7)

1187[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

1188[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)

1189[info] at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)

1190[info] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)

1191[info] at java.base/java.lang.reflect.ReflectAccess.newInstance(ReflectAccess.java:128)

1192[info] ...

1194[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

1195[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

1196[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

1197[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

1198[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

1199[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

1200[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

1201[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

1202[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

1203[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

1204[info] ...

1245[info] TestArrayView:

1246[info] ArrayView

1247[info] - should work with no offset

1248[info] - should work with an offset

1249[info] - should work when clipped

1250[info] TestDoc5501:

1251[info] org.clulab.processors.docs.TestDoc5501 *** ABORTED ***

1253[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

1254[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

1255[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

1256[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

1257[info] at org.clulab.processors.docs.TestDoc5501.<init>(TestDoc5501.scala:10)

1258[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

1259[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)

1260[info] at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)

1261[info] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)

1262[info] at java.base/java.lang.reflect.ReflectAccess.newInstance(ReflectAccess.java:128)

1263[info] ...

1265[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

1266[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

1267[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

1268[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

1269[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

1270[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

1271[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

1272[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

1273[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

1274[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

1275[info] ...

1316[info] TestLexiconNER:

1317[info] org.clulab.processors.TestLexiconNER *** ABORTED ***

1319[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

1320[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

1321[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

1322[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

1323[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

1324[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

1325[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

1326[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

1327[info] at org.scalatest.BeforeAndAfterAll.run$(BeforeAndAfterAll.scala:135)

1328[info] at org.clulab.processors.CluTest.run(CluTest.scala:9)

1329[info] ...

1331[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

1332[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

1333[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

1334[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

1335[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

1336[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

1337[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

1338[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

1339[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

1340[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

1341[info] ...

1381[info] TestTaxonomy:

1382[info] taxonomy

1383[info] - should inform a rule's labels

1384[info] TestProcessor:

1385[info] org.clulab.processors.TestProcessor *** ABORTED ***

1387[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

1388[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

1389[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

1390[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

1391[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

1392[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

1393[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

1394[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

1395[info] at org.scalatest.BeforeAndAfterAll.run$(BeforeAndAfterAll.scala:135)

1396[info] at org.clulab.processors.CluTest.run(CluTest.scala:9)

1397[info] ...

1399[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

1400[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

1401[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

1402[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

1403[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

1404[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

1405[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

1406[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

1407[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

1408[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

1409[info] ...

1449[info] TestTokenizer:

1450Tokenizing text: the of $><1/2 1.3 another test.

1451[info] the tokenizer

1452 Sentence #0: the of $ > < 1/2 1.3 another test .

1453Tokenizing text: -LRB- -RRB- -LCB- -RCB- -LSB- -RSB-.

1454 Sentence #0: -LRB- -RRB- -LCB- -RCB- -LSB- -RSB- .

1455Tokenizing text: first sentence. second sentence.

1456 Sentence #0: first sentence .

1457 Sentence #1: second sentence .

1458Tokenizing text: Artocarpus lacucha Buch.-Ham. ex D.Don is monkey fruit. Second sentence.

1459 Sentence #0: Artocarpus lacucha Buch. - Ham. ex D.Don is monkey fruit .

1460 Sentence #1: Second sentence .

1461Tokenizing text: Zizania caduciflora Hand.-Mazz. is a grass. Second sentence.

1462 Sentence #0: Zizania caduciflora Hand. - Mazz. is a grass .

1463 Sentence #1: Second sentence .

1464Tokenizing text: Fig. 1 shows the fungus Gaeumannomyces graminis var. tritici (Ggt), a major root disease of wheat.

1465 Sentence #0: Fig. 1 shows the fungus Gaeumannomyces graminis var. tritici ( Ggt ) , a major root disease of wheat .

1466Tokenizing text: Campylobacter spp. are ubiquitous.

1467 Sentence #0: Campylobacter spp. are ubiquitous .

1468Tokenizing text: today is 12/25/2017

1469 Sentence #0: today is 12/25/2017

1470Tokenizing text: today is 12/255/2017

1471 Sentence #0: today is 12/255 / 2017

1472Tokenizing text: number is -122,333

1473 Sentence #0: number is -122,333

1474Tokenizing text: gap-mediated reaction

1475 Sentence #0: gap-mediated reaction

1476Tokenizing text: 3M is a company

1477 Sentence #0: 3M is a company

1478Tokenizing text: cont'd nat'l program

1479 Sentence #0: cont'd nat'l program

1480Tokenizing text: @user_1 likes #havingfun

1481 Sentence #0: @user_1 likes #havingfun

1482Tokenizing text: h1.cpp is a C++ file

1483 Sentence #0: h1.cpp is a C++ file

1484Tokenizing text: http://google.com is Google's home page

1485 Sentence #0: http://google.com is Google 's home page

1486Tokenizing text: so is www.google.com and google.com

1487 Sentence #0: so is www.google.com and google.com

1488Tokenizing text: won't isn't hadn't

1489 Sentence #0: will not is not had not

1490Tokenizing text: me@privacy.net is a valid email, while me#privacy.net is not.

1491 Sentence #0: me@privacy.net is a valid email , while me#privacy.net is not .

1492Tokenizing text: <start-text>some text</end-text>

1493 Sentence #0: <start-text> some text </end-text>

1494Tokenizing text: IBM is Co. not Ltd.

1495 Sentence #0: IBM is Co. not Ltd.

1496Tokenizing text: A.M. Bancorp. A.T.B.

1497 Sentence #0: A.M. Bancorp. A.T.B.

1498Tokenizing text: I'm happy :) not sad :(.

1499 Sentence #0: I am happy :) not sad :( .

1500[info] - should provide fundamental tokenization functionality

1501Tokenizing text: This is an example e.g. a phrase.

1502 Sentence #0: This is an example e.g. a phrase .

1503[info] - should tokenize e.g. correctly

1504Tokenizing text: I'm won't don't cont'd he's he'd.

1505 Sentence #0: I am will not do not cont'd he 's he 'd .

1506[info] - should handle contractions correctly

1507Tokenizing text: "I'm happy", he said.

1508 Sentence #0: `` I am happy '' , he said .

1509[info] - should transform double quotes into Treebank quotes

1510Tokenizing text: "The levels of malnutrition among children continue to be truly alarming," said Mahimbo Mdoe, UNICEF's Representative in South Sudan.

1511 Sentence #0: `` The levels of malnutrition among children continue to be truly alarming , '' said Mahimbo Mdoe , UNICEF 's Representative in South Sudan .

1512[info] - should tokenize quotes correctly

1513Tokenizing text: This is a test (of parentheses).

1514 Sentence #0: This is a test ( of parentheses ) .

1515[info] - should normalize parentheses correctly

1516Tokenizing text: Lecithin :cholesterol and phospholipid :diacylglycerol acyltransferase

1517 Sentence #0: Lecithin : cholesterol and phospholipid : diacylglycerol acyltransferase

1518Tokenizing text: ATP :dephospho-CoA triphosphoribosyl transferase

1519 Sentence #0: ATP : dephospho-CoA triphosphoribosyl transferase

1520Tokenizing text: CDP-Glycerol :Poly (glycerophosphate) glycerophosphotransferase

1521 Sentence #0: CDP-Glycerol : Poly ( glycerophosphate ) glycerophosphotransferase

1522Tokenizing text: T=pseudo3 icosahedral viral capsid

1523 Sentence #0: T = pseudo3 icosahedral viral capsid

1524Tokenizing text: Myristoyl-CoA :protein N-myristoyltransferase,C-terminal

1525 Sentence #0: Myristoyl-CoA : protein N-myristoyltransferase , C-terminal

1526Tokenizing text: I am :), she said

1527 Sentence #0: I am :) , she said

1528Tokenizing text: I am :( today, she said

1529 Sentence #0: I am :( today , she said

1530Tokenizing text: An increase in assessed settlements reported access to functional boreholes in November , which can be attributed to the scaling up of humanitarian activities from the WASH cluster to rehabilitate boreholes in Jur River and Wau Counties?17 The overall percentage of functional boreholes increased across WBeG , specifically in Jur River and Wau Counties in November .

1531[info] - should not tokenize letter emoticons too aggressively

1532 Sentence #0: An increase in assessed settlements reported access to functional boreholes in November , which can be attributed to the scaling up of humanitarian activities from the WASH cluster to rehabilitate boreholes in Jur River and Wau Counties ?

1533 Sentence #1: 17 The overall percentage of functional boreholes increased across WBeG , specifically in Jur River and Wau Counties in November .

1534Tokenizing text: An increase in assessed settlements reported access to functional boreholes in November , which can be attributed to the scaling up of humanitarian activities from the WASH cluster to rehabilitate boreholes in Jur River and Wau Counties.17 The overall percentage of functional boreholes increased across WBeG , specifically in Jur River and Wau Counties in November .

1535[info] - should tokenize question mark correctly

1536 Sentence #0: An increase in assessed settlements reported access to functional boreholes in November , which can be attributed to the scaling up of humanitarian activities from the WASH cluster to rehabilitate boreholes in Jur River and Wau Counties .

1537 Sentence #1: 17 The overall percentage of functional boreholes increased across WBeG , specifically in Jur River and Wau Counties in November .

1538[info] - should tokenize punctuation correctly

1539Tokenizing text: :-) :) :-] :] :-> :> :-} :} :^) =] =) :-)) :-( :( :-< :< :-[ :[ :-|| >:[ :{ :@ >:( :-( :( :-) :) :-* :* ;-) ;) ;-] ;] ;^) :-, :-/ :/ :-. >:\\ >:/ :\\ =/ =\\ :-| :| :$ :-# :# :-& :& >:-) >:) }:-) }:) >;) |;-) <:-| ,:-|

1540 Sentence #0: :-) :) :-] :] :-> :> :-} :} :^) =] =) :-)) :-( :( :-< :< :-[ :[ :-|| >:[ :{ :@ >:( :-( :( :-) :) :-* :* ;-) ;) ;-] ;] ;^) :-, :-/ :/ :-. >:\\ >:/ :\\ =/ =\\ :-| :| :$ :-# :# :-& :& >:-) >:) }:-) }:) >;) |;-) <:-| ,:-|

1541[info] - should tokenize common emoticons correctly

1542Tokenizing text: :-3 :3 8-) 8) :-D :D 8-D 8D x-D xD X-D XD =D =3 :-c :c :o) :c) :-O :O :-o :o :-0 8-0 >:O ;D :-P :P X-P XP x-p xp :x :-p :p :-P :P :-b :b =p >:P :L =L :S ://3 :-X :X O:-) O:) 0:-3 0:3 0:-) 0:) 0;^) >:3 >;3 :-J ,:-l

1543 Sentence #0: :-3 :3 8-) 8) :-D :D 8-D 8D x-D xD X-D XD =D =3 :-c :c :o) :c) :-O :O :-o :o :-0 8-0 >:O ;D :-P :P X-P XP x-p xp :x :-p :p :-P :P :-b :b =p >:P :L =L :S ://3 :-X :X O:-) O:) 0:-3 0:3 0:-) 0:) 0;^) >:3 >;3 :-J ,:-l

1544[info] - should tokenize emoticons with letters correctly

1545Tokenizing text: Rapidly deploying as many as 25,000 troops, over 1,000 armored vehicles and a strategy that included the Russian navy taking control of Poti, Georgia’s main port city, 2 some argued that Russia’s actions resembled a well planned offensive strike.3 According to Russian President Dmitry Medvedev, however, Russia’s actions were necessary to “protect . . . the Russian citizens living in [South Ossetia].

1546 Sentence #0: Rapidly deploying as many as 25,000 troops , over 1,000 armored vehicles and a strategy that included the Russian navy taking control of Poti , Georgia ' s main port city , 2 some argued that Russia ' s actions resembled a well planned offensive strike .

1547 Sentence #1: 3 According to Russian President Dmitry Medvedev , however , Russia ' s actions were necessary to " protect .

1548 Sentence #2: .

1549 Sentence #3: .

1550 Sentence #4: the Russian citizens living in [ South Ossetia ] .

1551[info] - should split sentences correctly

1552Tokenizing text: Weather is nice in mid-July

1553 Sentence #0: Weather is nice in mid July

1554[info] - should split some hyphenated words

1555Tokenizing text: This is ​​a test.

1556 Sentence #0: This is a test .

1557[info] - should not create empty words

1558[info] TestDoc5da3:

1559[info] org.clulab.processors.docs.TestDoc5da3 *** ABORTED ***

1561[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

1562[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

1563[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

1564[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

1565[info] at org.clulab.processors.docs.TestDoc5da3.<init>(TestDoc5da3.scala:10)

1566[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

1567[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)

1568[info] at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)

1569[info] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)

1570[info] at java.base/java.lang.reflect.ReflectAccess.newInstance(ReflectAccess.java:128)

1571[info] ...

1573[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

1574[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

1575[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

1576[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

1577[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

1578[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

1579[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

1580[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

1581[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

1582[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

1583[info] ...

1624[info] TestLazy:

1625[info] Lazy

1626[info] - should not retrieve a Cat from an Animal

1627[info] - should retrieve an Animal from a Cat

1628[info] TestBioPreProcessor:

1629[info] ScienceUtils

1630[info] - should convert (known) Unicode to ASCII

1631[info] ScienceUtils

1632[info] - should convert unknown Unicode to spaces

1633[info] ScienceUtils

1634[info] - should convert all Unicode

1635[info] - should remove simple BIB REF

1636[info] - should remove BIB REF but leave other paren expression

1637[info] - should remove complex BIB REF but leave other paren expressions

1638[info] TestVs:

1639[info] org.clulab.processors.TestVs *** ABORTED ***

1641[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

1642[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

1643[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

1644[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

1645[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

1646[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

1647[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

1648[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

1649[info] at org.scalatest.BeforeAndAfterAll.run$(BeforeAndAfterAll.scala:135)

1650[info] at org.clulab.processors.CluTest.run(CluTest.scala:9)

1651[info] ...

1653[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

1654[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

1655[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

1656[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

1657[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

1658[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

1659[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

1660[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

1661[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

1662[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

1663[info] ...

1703[info] TestPorterStemmer:

1704[info] PorterStemmer

1705[info] - should stem words properly

1706[info] TestCounter:

1707[info] TestCounter

1708[info] - should serialize content correctly in saveTo

1709[info] TestSVMRankingClassifier:

1710[info] SVMRankingClassifier

1711[info] - should perform similarly to the command line svm_rank_classify !!! CANCELED !!!

1712[info] TestSVMRankingClassifier.this.hasExternalBinary was false (TestSVMRankingClassifier.scala:27)

1713[info] - should perform better than 0.50 P@1 on this dataset !!! CANCELED !!!

1714[info] TestSVMRankingClassifier.this.hasExternalBinary was false (TestSVMRankingClassifier.scala:90)

1715[info] TestPerceptronClassifier:

1716[info] PerceptronClassifier

1717[info] - should have an accuracy > .97 on this dataset

1718[info] TestPrintUtils:

1719[info] PrintUtils

17205

17215

1722hello

1723hello

1724[I@33baa054

1725Array(1, 2, 3)

1726List(11, 12, 13)

1727List(11, 12, 13)

1728Map(a -> 21, b -> 22, c -> 23)

1729Map(a -> 21, b -> 22, c -> 23)

1730List(31, 32, 33)

1731List(31, 32, 33)

1732(a,42,43)

1733(a,42,43)

1734<5>

1735<hello>

1736<1-2-3>

1737<11-12-13>

1738<(a,21)-(b,22)-(c,23)>

1739<31-32-33>

1740<(a,42,43)>

1741[info] - should print with no arguments

1742[info] - should print with separators

1743[info] TestContractions:

1744[info] TokenizerStepContractions

1745[info] - should run specifications with Tokenizer

1746[info] - should run short specifications with Tokenizer

1747[info] - should run specifications with TokenizerStepContractions

1748[info] - should run short specifications with TokenizerStepContractions

1749[info] - should run quickly !!! IGNORED !!!

1750[info] TestCustomizableRuleBasedEntityFinder:

1751[info] CustomizableRuleBasedEntityFinder

1752[info] - should expand using specified dependencies

1753[info] - should prune invalid base entities using NER

1754[info] - should trim entity edges as specified

1755[info] - should require N/V only when asked to

1756[info] TestHash:

1757[info] org.clulab.utils.TestHash *** ABORTED ***

1759[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

1760[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

1761[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

1762[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

1763[info] at org.clulab.utils.TestHash.<init>(TestHash.scala:20)

1764[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

1765[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)

1766[info] at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)

1767[info] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)

1768[info] at java.base/java.lang.reflect.ReflectAccess.newInstance(ReflectAccess.java:128)

1769[info] ...

1771[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

1772[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

1773[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

1774[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

1775[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

1776[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

1777[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

1778[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

1779[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

1780[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

1781[info] ...

1822[info] TestTokenPattern:

1823[info] TGFBR2 phosphorylates peri-kappa B and inhibits the ubiquitination of SMAD3.

1824[info] - should contain one match

1825[info] TGFBR2 phosphorylates peri-kappa B and peri-kappa C and inhibits the ubiquitination of SMAD3.

1826[info] - should contain one match

1827[info] TGFBR2 phosphorylates peri-kappa B and peri-kappa C by TGFBR3 and inhibits the ubiquitination of SMAD3.

1828[info] - should contain two matches

1829[info] - should also contain two matches if mentions in state are reversed

1830[info] a b c d e f g h i c

1831[info] - should match with a lazy plus

1832[info] - should match with a greedy plus

1833[info] - should match with a lazy star

1834[info] - should match with a greedy star

1835[info] - should match with positive lookbehind

1836[info] - should match with several lookarounds

1837[info] - should match with negative lookbehind that goes beyond sentence start

1838[info] - should not match with positive lookbehind that goes beyond sentence start

1839[info] - should not match with negative lookbehind

1840[info] - should match with positive lookahead

1841[info] - should not match with negative lookahead

1842[info] - should keep complete match interval when capturing a RelationMention

1843[info] - should keep complete match interval when capturing an EventMention

1844[info] - should match with variable length lookbehind

1845[info] - should match with nested lookbehind

1846[info] - should match with lookahead in lookbehind

1847[info] - should match nested captures

1848[info] JAK3 phosphorylates three HuR residues (Y63, Y68, Y200)

1849[info] - should match Y200 using greedy plus

1850[info] - should match Y63 using lazy plus

1851[info] - should match event with lazy plus

1852[info] - should match event with greedy plus

1853[info] JAK3 complex phosphorylates three HuR residues (Y63, Y68, Y200)

1854[info] - should match event when there are several entity mentions

1855[info] JAK3 binds to MEK and RAS

1856[info] - should match three mentions with argument name 'theme'

1857[info] - should capture three arguments with name 'theme'

1858[info] - should capture text and mentions with same argument name

1859[info] rule

1860[info] - should not compile with unit: "lemma"

1861[info] - should capture text and mentions using unit: "tag"

1862[info] TokenPattern

1863[info] - should handle repetition in lookbehind

1864[info] (?<= ^ [lemma=/(?i)^doctor$/] "Robert") Doback"

1865[info] - should allow for multi-token positive lookbehind assertions at the beginning of a sentence

1866[info] (?<! ^ @Title+) @person:Person

1867[info] - should allow for variable-length negative lookbehind assertion

1868[info] (?<! [tag=/^N/]+) [tag=/^N/] (?! [tag=/^N/]+)

1869[info] - should find only single-noun NPs

1870[info] (?<! (?<= a) mangy) black cat

1871[info] - should not match "black cat" in "a mangy black cat"

1872[info] - should match "black cat" in "the mangy black cat", and "the curious black cat"

1873[info] - should not match "the curious blue cat"

1874[info] (?<! (?<! the) mangy) black cat

1875[info] - should not match "a mangy black cat", "a mangy blue cat", or "the mangy black cat"

1876[info] - should match "black cat" in "the mangy black cat"

1877[info] - should match "black cat" in "a curious black cat"

1878[info] @Binding.theme @trig1:Binding.trigger @Binding.theme @trig2:Binding.trigger

1879[info] - should match "MEK bound Ras binds with Kras"

1880[info] @Binding.theme [mention=Binding.trigger & tag=VBD] @Binding.theme [mention=Binding.trigger & tag=VBZ]

1881[info] - should match "MEK bound Ras binds with Kras"

1882[info] overlapping mentions

1883[info] - should all be considered for matching

1884[info] - should all be considered for matching here too

1885[info] @effect:Crop [!mention="Entity"]{,3}? [lemma=/^suffer/ & tag=/VBN/] from [!mention="Entity"]{0,3}? @cause:Indicator

1886[info] - should match '@effect:Crop [!mention="Entity"]{,3}? [lemma=/^suffer/ & tag=/VBN/] from [!mention="Entity"]{0,3}? @cause:Indicator'

1887[info] JAK3 binds to MEK and RAS

1888[info] - should find a trigger in named mentions

1889[info] TestRuleBasedEntityFinder:

1890[info] Coordinated entities

1891[info] - should be split into separate entities

1892[info] Orphaned adjectives

1893[info] - should not be considered entities

1894[info] expansion

1895[info] - should not consume avoided content

1896[info] TestMention:

1897[info] mention.text

1898[info] - should properly reconstruct the original span

1899[info] Mention.getRootDistOpt

1900[info] - should get None when there are no roots

1901[info] - should get None when the Interval is empty

1902[info] TestJSONSerializer:

1903[info] - should serialize/deserialize a Mention to/from json correctly

1904[info] - should serialize/deserialize a CrossSentenceMention to/from json correctly

1905[info] - should serialize/deserialize a Seq[Mention] to/from json correctly

1906[info] When non-empty, Mention.paths

1907[info] - should be represented in Mention's json

1908[info] serialization.json.MentionOps

1909[info] - should produce an invariant id for a serialized/deserialzed Mention

1910[info] TestSerializer:

1911[info] Serializer

1912[info] - should not close a null resource

1913[info] TestOps:

1914[info] ObjectOps

1915[info] - should convert instances

1916[info] TestAutoClosing:

1917[info] Closing

1918[info] - should be able to produce a simple result

1919[info] - should be able to produce a null result

1920[info] - should be able to produce a None result

1921[info] - should be able to produce a Some result

1931[info] - should work with a plain Source, even in Scala 2.11

1932[info] TestLemmatizer:

1933[info] org.clulab.processors.TestLemmatizer *** ABORTED ***

1935[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

1936[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

1937[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

1938[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

1939[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

1940[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

1941[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

1942[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

1943[info] at org.scalatest.BeforeAndAfterAll.run$(BeforeAndAfterAll.scala:135)

1944[info] at org.clulab.processors.CluTest.run(CluTest.scala:9)

1945[info] ...

1947[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

1948[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

1949[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

1950[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

1951[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

1952[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

1953[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

1954[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

1955[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

1956[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

1957[info] ...

1997iter 1 act 6.896e-01 pre 6.896e-01 delta 3.922e-01 f 7.726e-01 |g| 3.749e+00 CG 2

1998[info] TestLiblinearRegression:

1999iter 1 act 6.896e-01 pre 6.896e-01 delta 3.922e-01 f 7.726e-01 |g| 3.749e+00 CG 2

2000[info] LiblinearRegression

2001[info] - should work with RVFRegDataset

2002iter 1 act 6.896e-01 pre 6.896e-01 delta 3.922e-01 f 7.726e-01 |g| 3.749e+00 CG 2

2003[info] - should work with BVFDataset

2004[info] LinearSVMRegression

2005iter 1 act 1.487e+02 pre 1.455e+02 delta 4.161e-01 f 1.938e+02 |g| 3.343e+03 CG 2

2006[info] - should have a mse < .021 in this dataset

2007[info] LinearSVMRegressionDual

2008.........

2009optimization finished, #iter = 98

2010Objective value = -26.6229

2011nSV = 1729

2012[info] - should have a mse < .021 in this dataset

2013[info] L1LinearSVMRegression

2014......................................*.*

2015optimization finished, #iter = 395

2016Objective value = -132.612

2017nSV = 1775

2018[info] - should have a mse < .02 in this dataset

2019[info] TestPortugueseTokenizerStepContractions:

2020[info] the step contratctions tokenizer component

2021[info] - should expand contractions correctly

2022[info] - should work for do, da, dos, das, dum, duma, duns, and dumas

2023[info] - should work for dele, dela, deles, and delas

2024[info] - should work for deste, desta, destes, destas, desse, dessa, desses, dessas

2025[info] - should work for daquele, daquela, daqueles, daquelas

2026[info] - should work for no, na, nos nas

2027[info] - should work for num, numa, nuns, numas

2028[info] - should work for nele, nela, neles, nelas

2029[info] - should work for neste, nesta, nestes, nestas

2030[info] - should work for nesse, nessa, nesses, nessas

2031[info] - should work for aquele, aquela, aqueles, aquelas

2032[info] - should work for ao, à, aos, às

2033[info] - should work for àquele, àquela, àqueles, àquelas

2034[info] - should work for pelo, pela, pelos, pelas

2035[info] - should work for doutro

2036[info] - should work for noutro

2037[info] - should work for danlgum

2038[info] - should work for nalgum

2039[info] - should work for donde

2040[info] - should work for mesocliticos with 2 parts

2041[info] - should work for mesocliticos with 3 parts

2042[info] TestLibSvmRegression:

2043[info] LibSVMRegression

2044*

2045optimization finished, #iter = 1

2046nu = 0.055238095238095246

2047obj = -0.02402857142857143, rho = -0.39571428571428574

2048nSV = 2, nBSV = 0

2049*

2050optimization finished, #iter = 1

2051nu = 0.02749999999999999

2052obj = -0.0015125, rho = -0.285

2053nSV = 2, nBSV = 0

2054*

2055optimization finished, #iter = 1

2056nu = 0.055238095238095246

2057obj = -0.02402857142857143, rho = -0.39571428571428574

2058nSV = 2, nBSV = 0

2059*

2060optimization finished, #iter = 1

2061nu = 0.08285714285714287

2062obj = -0.02402857142857143, rho = -0.39571428571428574

2063nSV = 2, nBSV = 0

2064*

2065optimization finished, #iter = 1

2066nu = 0.038571428571428576

2067obj = -0.005207142857142858, rho = -0.6171428571428572

2068nSV = 2, nBSV = 0

2069Prob. model for test data: target value = predicted value + z,

2070z: Laplace distribution e^(-|z|/sigma)/(2sigma),sigma=0.3854761904761905

2071*

2072optimization finished, #iter = 1

2073nu = 0.055238095238095246

2074obj = -0.02402857142857143, rho = -0.39571428571428574

2075nSV = 2, nBSV = 0

2076[info] - should work with RVFDataset

2077*

2078optimization finished, #iter = 1

2079nu = 0.055238095238095246

2080obj = -0.02402857142857143, rho = -0.39571428571428574

2081nSV = 2, nBSV = 0

2082*

2083optimization finished, #iter = 1

2084nu = 0.02749999999999999

2085obj = -0.0015125, rho = -0.285

2086nSV = 2, nBSV = 0

2087*

2088optimization finished, #iter = 1

2089nu = 0.055238095238095246

2090obj = -0.02402857142857143, rho = -0.39571428571428574

2091nSV = 2, nBSV = 0

2092*

2093optimization finished, #iter = 1

2094nu = 0.08285714285714287

2095obj = -0.02402857142857143, rho = -0.39571428571428574

2096nSV = 2, nBSV = 0

2097*

2098optimization finished, #iter = 1

2099nu = 0.038571428571428576

2100obj = -0.005207142857142858, rho = -0.6171428571428572

2101nSV = 2, nBSV = 0

2102Prob. model for test data: target value = predicted value + z,

2103z: Laplace distribution e^(-|z|/sigma)/(2sigma),sigma=0.3854761904761905

2104*

2105optimization finished, #iter = 1

2106nu = 0.055238095238095246

2107obj = -0.02402857142857143, rho = -0.39571428571428574

2108nSV = 2, nBSV = 0

2109*

2110optimization finished, #iter = 1

2111nu = 0.055238095238095246

2112obj = -0.02402857142857143, rho = -0.39571428571428574

2113nSV = 2, nBSV = 0

2114*

2115optimization finished, #iter = 1

2116nu = 0.08285714285714287

2117obj = -0.02402857142857143, rho = -0.39571428571428574

2118nSV = 2, nBSV = 0

2119*

2120optimization finished, #iter = 1

2121nu = 0.055238095238095246

2122obj = -0.02402857142857143, rho = -0.39571428571428574

2123nSV = 2, nBSV = 0

2124*

2125optimization finished, #iter = 1

2126nu = 0.038571428571428576

2127obj = -0.005207142857142858, rho = -0.6171428571428572

2128nSV = 2, nBSV = 0

2129*

2130optimization finished, #iter = 1

2131nu = 0.02749999999999999

2132obj = -0.0015125, rho = -0.285

2133nSV = 2, nBSV = 0

2134Prob. model for test data: target value = predicted value + z,

2135z: Laplace distribution e^(-|z|/sigma)/(2sigma),sigma=0.3854761904761905

2136*

2137optimization finished, #iter = 1

2138nu = 0.055238095238095246

2139obj = -0.02402857142857143, rho = -0.39571428571428574

2140nSV = 2, nBSV = 0

2141[info] - should work with BVFDataset

2142[info] LibSvmEpsilonRegression

2143.....................*.*

2144optimization finished, #iter = 21507

2145nu = 0.3151801645190357

2146obj = -41.64506435642411, rho = -0.31348848758954223

2147nSV = 508, nBSV = 405

2148...............................*..*

2149optimization finished, #iter = 33047

2150nu = 0.31119562190554745

2151obj = -38.7749204672866, rho = -0.31229216642531343

2152nSV = 501, nBSV = 397

2153..................................*..........*

2154optimization finished, #iter = 43205

2155nu = 0.30800786769415595

2156obj = -38.070927216791105, rho = -0.7220537841105291

2157nSV = 500, nBSV = 390

2158........................*...*

2159optimization finished, #iter = 27581

2160nu = 0.31872797331693703

2161obj = -41.59418040464569, rho = -0.5314023725671134

2162nSV = 517, nBSV = 412

2163......................................*....*.*

2164optimization finished, #iter = 42521

2165nu = 0.3189950893253246

2166obj = -41.74797909182551, rho = -0.4661158650760102

2167nSV = 518, nBSV = 409

2168Prob. model for test data: target value = predicted value + z,

2169z: Laplace distribution e^(-|z|/sigma)/(2sigma),sigma=0.09744350012986383

2170........................................*..*

2171optimization finished, #iter = 41834

2172nu = 0.3169820033369704

2173obj = -51.480338813026364, rho = -0.5860073666273288

2174nSV = 633, nBSV = 512

2175*

2176optimization finished, #iter = 386

2177nu = 0.33042727967988783

2178obj = -52.54222813034517, rho = -0.3780556207865308

2179nSV = 494, nBSV = 457

2180*

2181optimization finished, #iter = 428

2182nu = 0.31967945782474255

2183obj = -50.86577546825611, rho = -0.29449858408707974

2184nSV = 477, nBSV = 444

2185*

2186optimization finished, #iter = 422

2187nu = 0.32628086802013795

2188obj = -49.25633080992082, rho = -0.3319438552335511

2189nSV = 486, nBSV = 453

2190*

2191optimization finished, #iter = 444

2192nu = 0.337362069295419

2193obj = -51.16367134030541, rho = -0.33483321526624593

2194nSV = 502, nBSV = 470

2195*

2196optimization finished, #iter = 450

2197nu = 0.3445472732123525

2198obj = -53.05328363945473, rho = -0.3283336530067446

2199nSV = 512, nBSV = 474

2200Prob. model for test data: target value = predicted value + z,

2201z: Laplace distribution e^(-|z|/sigma)/(2sigma),sigma=0.09585143136321932

2202*

2203optimization finished, #iter = 559

2204nu = 0.32873173531098426

2205obj = -63.35295557273505, rho = -0.34803081450672674

2206nSV = 614, nBSV = 574

2207*

2208optimization finished, #iter = 510

2209nu = 0.31520034089451765

2210obj = -49.3183524297433, rho = -0.12396836355716297

2211nSV = 479, nBSV = 430

2212*

2213optimization finished, #iter = 514

2214nu = 0.3080466550448445

2215obj = -45.28368055609688, rho = -0.28624544686276965

2216nSV = 472, nBSV = 416

2217*

2218optimization finished, #iter = 554

2219nu = 0.31751602817535085

2220obj = -48.71169961140251, rho = -0.17076431968129713

2221nSV = 484, nBSV = 424

2222*

2223optimization finished, #iter = 503

2224nu = 0.3099580111669417

2225obj = -45.64721984088306, rho = -0.11467075205168367

2226nSV = 471, nBSV = 419

2227*

2228optimization finished, #iter = 533

2229nu = 0.3252844516719198

2230obj = -49.57892014430274, rho = -0.24188892365997328

2231nSV = 496, nBSV = 444

2232Prob. model for test data: target value = predicted value + z,

2233z: Laplace distribution e^(-|z|/sigma)/(2sigma),sigma=0.09433037819914195

2234*

2235optimization finished, #iter = 629

2236nu = 0.31050957630127235

2237obj = -58.99742838311287, rho = -0.11795899327038137

2238nSV = 584, nBSV = 528

2239*

2240optimization finished, #iter = 412

2241nu = 0.3230984108330212

2242obj = -49.40162956690807, rho = -0.3532629931587026

2243nSV = 481, nBSV = 445

2244*

2245optimization finished, #iter = 513

2246nu = 0.3376063218365368

2247obj = -52.53159645094587, rho = -0.333288867129509

2248nSV = 503, nBSV = 465

2249*

2250optimization finished, #iter = 401

2251nu = 0.3470744380180894

2252obj = -53.89517356388733, rho = -0.3487460048947017

2253nSV = 511, nBSV = 486

2254*

2255optimization finished, #iter = 436

2256nu = 0.3333769534181584

2257obj = -51.48164815397145, rho = -0.3512565950432801

2258nSV = 496, nBSV = 463

2259*

2260optimization finished, #iter = 395

2261nu = 0.32442390148090466

2262obj = -51.04034699187783, rho = -0.297654833393037

2263nSV = 478, nBSV = 458

2264Prob. model for test data: target value = predicted value + z,

2265z: Laplace distribution e^(-|z|/sigma)/(2sigma),sigma=0.09608740623580009

2266*

2267optimization finished, #iter = 556

2268nu = 0.3319019009501211

2269obj = -63.680877913871136, rho = -0.3522993089618323

2270nSV = 614, nBSV = 577

2271[info] - should have an MSE < 0.02 on this dataset

2272[info] LibSvmNuRegression

2273...............................................................*......*

2274optimization finished, #iter = 69273

2275epsilon = 0.058121214140648816

2276obj = -104.48368574200089, rho = -0.2983861377353955

2277nSV = 775, nBSV = 666

2278............................................................*.......................*.*

2279optimization finished, #iter = 83739

2280epsilon = 0.05755247272305311

2281obj = -105.54701747789613, rho = -0.3304842431405981

2282nSV = 777, nBSV = 656

2283...................................................*..*

2284optimization finished, #iter = 52963

2285epsilon = 0.06075721456969002

2286obj = -110.73316180717447, rho = -0.2928492827099489

2287nSV = 777, nBSV = 661

2288..................................................*.......*

2289optimization finished, #iter = 56459

2290epsilon = 0.05767555073640973

2291obj = -106.1335639308071, rho = -0.2195995674752625

2292nSV = 776, nBSV = 668

2293.......................................................*......*

2294optimization finished, #iter = 60888

2295epsilon = 0.05524425445100911

2296obj = -103.15429957732933, rho = -0.21381086914444203

2297nSV = 776, nBSV = 666

2298Prob. model for test data: target value = predicted value + z,

2299z: Laplace distribution e^(-|z|/sigma)/(2sigma),sigma=0.09380186501379086

2300...........................................................................*................*

2301optimization finished, #iter = 91034

2302epsilon = 0.05944570893531101

2303obj = -133.67027363116608, rho = -0.22082834234372709

2304nSV = 961, nBSV = 839

2305*

2306optimization finished, #iter = 946

2307epsilon = 0.05537159224997126

2308obj = -114.7196702332354, rho = -0.3369347765000934

2309nSV = 739, nBSV = 696

2310*

2311optimization finished, #iter = 791

2312epsilon = 0.05561295364709232

2313obj = -116.46963911950347, rho = -0.2940683082361236

2314nSV = 738, nBSV = 699

2315*

2316optimization finished, #iter = 813

2317epsilon = 0.057159062599294985

2318obj = -117.86326326367255, rho = -0.2797376847920708

2319nSV = 744, nBSV = 699

2320*

2321optimization finished, #iter = 845

2322epsilon = 0.05628983225255153

2323obj = -117.95318716158421, rho = -0.29869623557728137

2324nSV = 733, nBSV = 695

2325*

2326optimization finished, #iter = 876

2327epsilon = 0.05681540390477613

2328obj = -120.21175406350666, rho = -0.27697706405017036

2329nSV = 743, nBSV = 695

2330Prob. model for test data: target value = predicted value + z,

2331z: Laplace distribution e^(-|z|/sigma)/(2sigma),sigma=0.09350833591669092

2332.*

2333optimization finished, #iter = 1030

2334epsilon = 0.05639765783061974

2335obj = -145.96471729318776, rho = -0.2866861483069072

2336nSV = 917, nBSV = 874

2337.*

2338optimization finished, #iter = 1204

2339epsilon = 0.054112641939082856

2340obj = -115.11848381521723, rho = -0.12626003198594327

2341nSV = 751, nBSV = 690

2342.*

2343optimization finished, #iter = 1219

2344epsilon = 0.05557179019642994

2345obj = -112.85439673129471, rho = -0.2421620140390109

2346nSV = 757, nBSV = 683

2347.*

2348optimization finished, #iter = 1092

2349epsilon = 0.053462587246729164

2350obj = -111.32173925948095, rho = -0.11109256799939987

2351nSV = 755, nBSV = 689

2352.*

2353optimization finished, #iter = 1092

2354epsilon = 0.05512905244342861

2355obj = -112.01347266610706, rho = -0.23188685573950216

2356nSV = 751, nBSV = 686

2357.*

2358optimization finished, #iter = 1206

2359epsilon = 0.053190734655296654

2360obj = -112.07829295266532, rho = -0.19763916253123492

2361nSV = 756, nBSV = 689

2362Prob. model for test data: target value = predicted value + z,

2363z: Laplace distribution e^(-|z|/sigma)/(2sigma),sigma=0.09023741962462928

2364.

2366*

2367optimization finished, #iter = 1485

2368epsilon = 0.054878816933817506

2369obj = -140.12235768223275, rho = -0.15015265276473888

2370nSV = 932, nBSV = 860

2371*

2372optimization finished, #iter = 918

2373epsilon = 0.05553607877361451

2374obj = -117.39327040052729, rho = -0.27811005847714826

2375nSV = 746, nBSV = 697

2376*

2377optimization finished, #iter = 827

2378epsilon = 0.05720744300878983

2379obj = -117.68514739112416, rho = -0.3102552762782267

2380nSV = 733, nBSV = 699

2381*

2382optimization finished, #iter = 891

2383epsilon = 0.05731388780742905

2384obj = -118.74583775060773, rho = -0.2833973559653993

2385nSV = 740, nBSV = 697

2386*

2387optimization finished, #iter = 918

2388epsilon = 0.05929436304460581

2389obj = -119.77192858145722, rho = -0.35731453351986553

2390nSV = 738, nBSV = 698

2391*

2392optimization finished, #iter = 895

2393epsilon = 0.05527846206564059

2394obj = -115.731067619323, rho = -0.2746457642557659

2395nSV = 738, nBSV = 698

2396Prob. model for test data: target value = predicted value + z,

2397z: Laplace distribution e^(-|z|/sigma)/(2sigma),sigma=0.09360390313739304

2398.*

2399optimization finished, #iter = 1042

2400epsilon = 0.05719178622043486

2401obj = -146.5347079142647, rho = -0.29168490020941773

2402nSV = 915, nBSV = 871

2403[info] - should have an MSE < 0.02 on this dataset

2404[info] TestHolidays:

2405[info] org.clulab.processors.TestHolidays *** ABORTED ***

2407[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

2408[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

2409[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

2410[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

2411[info] at org.clulab.processors.TestHolidays.<init>(TestHolidays.scala:7)

2412[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

2413[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)

2414[info] at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)

2415[info] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)

2416[info] at java.base/java.lang.reflect.ReflectAccess.newInstance(ReflectAccess.java:128)

2417[info] ...

2419[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

2420[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

2421[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

2422[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

2423[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

2424[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

2425[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

2426[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

2427[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

2428[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

2429[info] ...

24700

24711

24722

24733

24744

24755

24766

24777

24788

24799

248010

248111

248212

248319

248420

248521

248625

248723

248818

248915

249013

249116

249224

249322

249414

249517

2496[info] TestThreading:

2497[info] TestParentheses:

2498[info] org.clulab.processors.TestParentheses *** ABORTED ***

2500[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

2501[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

2502[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

2503[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

2504[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

2505[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

2506[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

2507[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

2508[info] at org.scalatest.BeforeAndAfterAll.run$(BeforeAndAfterAll.scala:135)

2509[info] at org.clulab.processors.CluTest.run(CluTest.scala:9)

2510[info] ...

2512[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

2513[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

2514[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

2515[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

2516[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

2517[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

2518[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

2519[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

2520[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

2521[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

2522[info] ...

2562[info] TestPerceptronRankingClassifier:

2563[info] PerceptronRankingClassifier

2564Perceptron weights:

2565 #0: 22 => -1.2892671209448843E9

2566 #1: 44 => 4.726782728316344E8

2567 #2: 23 => 4.591825083758359E9

2568 #3: 45 => -3.399696267655947E8

2569 #4: 24 => 7.683354716260107E8

2570 #5: 46 => -8.49130698E8

2571 #6: 25 => 2.7755820538537896E8

2572 #7: 26 => 2017927.613506265

2573 #8: 27 => 3.937444756727777E8

2574 #9: 28 => -9.436274501760541E7

2575 #10: 29 => -5.326717769791919E8

2576 #11: 30 => 9.279237057671071E8

2577 #12: 31 => -6.108735261587594E8

2578 #13: 10 => 0.0

2579 #14: 32 => -9.950077032703422E7

2580 #15: 11 => 8.917401063355787E8

2581 #16: 33 => 1.5318597889291413E9

2582 #17: 12 => 2.708201999566436E8

2583 #18: 34 => 7.925716853238677E8

2584 #19: 13 => 7.391607422465034E8

2585 #20: 35 => -6.287288234236592E8

2586 #21: 14 => -1.3171261221207082E9

2587 #22: 36 => -6.499682004340925E8

2588 #23: 15 => -1.108571838978513E9

2589 #24: 37 => 1.7369026668502468E8

2590 #25: 16 => 9.071112303728031E8

2591 #26: 38 => -1.4473519955688438E9

2592 #27: 17 => 2.1612716039186582E8

2593 #28: 39 => 9.555031128809661E8

2594 #29: 18 => -7.531737499617782E8

2595 #30: 19 => -2.9842672995313966E8

2596 #31: 1 => 2.5239802997358683E7

2597 #32: 2 => -5.888007940321406E8

2598 #33: 3 => 1.1210587483454521E8

2599 #34: 4 => 9.018601848585874E7

2600 #35: 5 => -2.161115401954981E9

2601 #36: 6 => 0.0

2602 #37: 7 => 0.0

2603 #38: 8 => 0.0

2604 #39: 9 => 0.0

2605 #40: 40 => 1.344519684961319E9

2606 #41: 41 => -4.5687204677466244E8

2607 #42: 20 => 6.985973927905868E8

2608 #43: 42 => -3.6548329163228285E8

2609 #44: 21 => 9.089668680377305E8

2610 #45: 43 => -4.50975215475874E8

2611[info] - should have a P@1 > .50 on this dataset

2612[info] TestVariables:

2613[info] variables

2614[info] - should allow for whitespace

2615[info] - should be applied to imports

2616[info] - should resolve variables in order of precedence

2617success-1

2618[info] - should support nested resolution

2619[info] - should disallow recursive definitions

2620[info] - should allow vars in lists

2621[info] - should allow vars in imported lists

2622[info] TestCharacterOffsets:

2624Build timeouts: 1, would retry

2625Retrying build, retry 1/2, force Scala version:false, enable migration:

2626[sbt_options] declare -a sbt_options=()

2627[process_args] java_version = '17'

2628[copyRt] java9_rt = '/root/.sbt/1.0/java9-rt-ext-eclipse_adoptium_17_0_8/rt.jar'

2629# Executing command line:

2630java

2631-Dfile.encoding=UTF-8

2632-Xmx10g

2633-XX:MaxMetaspaceSize=10g

2634-Dcommunitybuild.scala=3.8.0

2635-Dcommunitybuild.project.dependencies.add=

2636-Xmx7G

2637-Xms4G

2638-Xss8M

2639-Dsbt.script=/root/.sdkman/candidates/sbt/current/bin/sbt

2640-Dscala.ext.dirs=/root/.sbt/1.0/java9-rt-ext-eclipse_adoptium_17_0_8

2641-jar

2642/root/.sdkman/candidates/sbt/1.11.5/bin/sbt-launch.jar

2643"setCrossScalaVersions 3.8.0"

2644"++3.8.0 -v"

2645"mapScalacOptions ",REQUIRE:-source:3.8,-Wconf:msg=can be rewritten automatically under:s" ",-deprecation,-feature,-Xfatal-warnings,-Werror,MATCH:.*-Wconf.*any:e""

2646"set every credentials := Nil"

2647"excludeLibraryDependency com.github.ghik:zerowaste_{scalaVersion} com.olegpy:better-monadic-for_3 org.polyvariant:better-tostring_{scalaVersion} org.wartremover:wartremover_{scalaVersion}"

2648"removeScalacOptionsStartingWith -P:wartremover"

2650moduleMappings

2651"runBuild 3.8.0 """{"tests":null}""" org.clulab%processors org.clulab%processors-apps org.clulab%processors-debugger"

2653[info] welcome to sbt 1.11.5 (Eclipse Adoptium Java 17.0.8)

2654[info] loading settings for project repo-build from akka.sbt, plugins.sbt...

2655[info] loading project definition from /build/repo/project

2656[info] loading settings for project root from build.sbt, compile.sbt, publish.sbt, release.sbt, test.sbt, version.sbt...

2657[info] loading settings for project library from assembly.sbt, build.sbt, compile.sbt, publish.sbt, test.sbt...

2658[info] loading settings for project apps from assembly.sbt, build.sbt...

2659[info] loading settings for project webapp from build.sbt, docker.sbt...

2660[info] loading settings for project debugger from build.sbt, publish.sbt...

2661[info] set current project to root (in build file:/build/repo/)

2662Execute setCrossScalaVersions: 3.8.0

2663OpenCB::Changing crossVersion 3.1.3 -> 3.8.0 in root/crossScalaVersions

2664OpenCB::Changing crossVersion 3.1.3 -> 3.8.0 in library/crossScalaVersions

2665OpenCB::Changing crossVersion 3.1.3 -> 3.8.0 in apps/crossScalaVersions

2666OpenCB::Changing crossVersion 3.1.3 -> 3.8.0 in debugger/crossScalaVersions

2667[info] set current project to root (in build file:/build/repo/)

2668[info] Setting Scala version to 3.8.0 on 4 projects.

2669[info] Switching Scala version on:

2670[info] * root (2.12.19, 2.11.12, 2.13.14, 3.8.0)

2671[info] library (2.12.19, 2.11.12, 2.13.14, 3.8.0)

2672[info] debugger (2.12.19, 2.11.12, 2.13.14, 3.8.0)

2673[info] apps (2.12.19, 2.11.12, 2.13.14, 3.8.0)

2674[info] Excluding projects:

2675[info] webapp (2.12.19)

2676[info] Reapplying settings...

2677[info] set current project to root (in build file:/build/repo/)

2678Execute mapScalacOptions: ,REQUIRE:-source:3.8,-Wconf:msg=can be rewritten automatically under:s ,-deprecation,-feature,-Xfatal-warnings,-Werror,MATCH:.*-Wconf.*any:e

2679[info] Reapplying settings...

2680[info] set current project to root (in build file:/build/repo/)

2681[info] Defining Global / credentials, apps / credentials and 3 others.

2682[info] The new values will be used by Global / pgpSelectPassphrase, allCredentials and 23 others.

2683[info] Run `last` for details.

2684[info] Reapplying settings...

2685[info] set current project to root (in build file:/build/repo/)

2686Execute excludeLibraryDependency: com.github.ghik:zerowaste_{scalaVersion} com.olegpy:better-monadic-for_3 org.polyvariant:better-tostring_{scalaVersion} org.wartremover:wartremover_{scalaVersion}

2687[info] Reapplying settings...

2688OpenCB::Failed to reapply settings in excludeLibraryDependency: Reference to undefined setting:

2690 Global / allExcludeDependencies from Global / allExcludeDependencies (CommunityBuildPlugin.scala:331)

2691 Did you mean allExcludeDependencies ?

2692 , retry without global scopes

2693[info] Reapplying settings...

2694[info] set current project to root (in build file:/build/repo/)

2695Execute removeScalacOptionsStartingWith: -P:wartremover

2696[info] Reapplying settings...

2697[info] set current project to root (in build file:/build/repo/)

2698[success] Total time: 0 s, completed Jan 13, 2026, 6:19:47 PM

2699Build config: {"tests":null}

2701Starting build...

2702Projects: Set(library, apps, debugger)

2703Starting build for ProjectRef(file:/build/repo/,library) (processors)... [0/3]

2704OpenCB::Exclude Scala3 specific scalacOption `REQUIRE:-source:3.8` in Scala 2.12.20 module Global

2705OpenCB::Exclude Scala3 specific scalacOption `REQUIRE:-source:3.8` in Scala 2.12.19 module Scope(Select(BuildRef(file:/build/repo/)), Select(ConfigKey(compile)), Zero, Zero)

2706OpenCB::Filter out '-feature', matches setting pattern '^-?-feature'

2707OpenCB::Filter out '-deprecation', matches setting pattern '^-?-deprecation'

2708Compile scalacOptions: -unchecked, -explain, -Wconf:msg=can be rewritten automatically under:s, -source:3.8

2709[info] TestHashTrie:

2710[info] the trie

2711[info] - should label the text correctly with BIO labels

2712[info] the trie

2713[info] - should have 2 entries and contain 5 unique strings

2714[info] the trie

2715[info] - should sort and find the entries correctly

2716[info] the trie

2717[info] - should make use of shouldStop

2718SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".

2719SLF4J: Defaulting to no-operation (NOP) logger implementation

2720SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.

2721[info] TestDueTo:

2722[Tokenizer] Checking /build/repo for intel-librust_tokenizer.so...

2723[Tokenizer] Checking /root for intel-librust_tokenizer.so...

2724[Tokenizer] Extracting resource intel-librust_tokenizer.so to /tmp/intel-librust_tokenizer-10225912728486908384.so...

2725[info] org.clulab.processors.TestDueTo *** ABORTED ***

2727[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

2728[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

2729[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

2730[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

2731[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

2732[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

2733[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

2734[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

2735[info] at org.scalatest.BeforeAndAfterAll.run$(BeforeAndAfterAll.scala:135)

2736[info] at org.clulab.processors.CluTest.run(CluTest.scala:9)

2737[info] ...

2739[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

2740[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

2741[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

2742[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

2743[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

2744[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

2745[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

2746[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

2747[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

2748[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

2749[info] ...

2789[info] TestDoc58b0:

2790[info] org.clulab.processors.docs.TestDoc58b0 *** ABORTED ***

2792[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

2793[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

2794[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

2795[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

2796[info] at org.clulab.processors.docs.TestDoc58b0.<init>(TestDoc58b0.scala:10)

2797[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

2798[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)

2799[info] at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)

2800[info] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)

2801[info] at java.base/java.lang.reflect.ReflectAccess.newInstance(ReflectAccess.java:128)

2802[info] ...

2804[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

2805[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

2806[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

2807[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

2808[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

2809[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

2810[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

2811[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

2812[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

2813[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

2814[info] ...

2855[info] TestNumericPatterns:

2856[info] Any text

2857[info] - should contain one match for pattern `[2+2==4]`

2858[info] Any text

2859[info] - should contain no matches for pattern `[2+2==5]`

2860[info] TestArray:

2861[info] Array.toSeq

2862[info] - should work as expected without import

2863[info] - should work as expected with import

2864[info] Array.toIndexedSeq

2865[info] - should work as expected without import

2866[info] - should work as expected with import

2867[info] MutableArraySeq.from

2868[info] - should work as expected without import

2869[info] - should work as expected with import

2870[info] ImmutableArraySeq.unsafeWrapArray

2871[info] - should work as expected without import

2872[info] - should work as expected with import

2873[info] processSeq(array)

2874[info] - should work as expected without import

2875[info] - should work as expected with import

2876[info] processSeq(ImmutableArraySeq.unsafeWrapArray)

2877[info] - should work as expected without import

2878[info] - should work as expected with import

2879[info] processIndexedSeq(array)

2880[info] - should work as expected without import

2881[info] - should work as expected with import

2882[info] processIndexedSeq(ImmutableArraySeq.unsafeWrapArray)

2883[info] - should work as expected without import

2884[info] - should work as expected with import

2885[info] :Seq[]

2886[info] - should work as expected without import

2887[info] - should work as expected with import

2888[info] :IndexedSeq[]

2889[info] - should work as expected without import

2890[info] - should work as expected with import

2891[info] foreach

2892[info] - should work as expected without import

2893[info] - should work as expected with import

2894[info] zip

2895[info] - should work as expected without import

2896[info] - should work as expected with import

2897[info] map

2898[info] - should work as expected without import

2899[info] - should work as expected with import

2900[info] TestNumberParser:

2901[info] NumberParser

2902[info] - should parse digits

2903[info] - should fail on invalid input

2904[info] - should fail on empty input

2905[info] - should convert words to numbers

2906[info] - should parses decimal numbers

2907[info] - should convert numbers and words to numbers

2908[info] - should parse words to numbers

2909[info] TestMinHeap:

2910[info] MinHeap

2911[info] - should order elements properly

2912[info] - should keep correct top K

2913[info] TestProgressBar:

2914[info] ProgressBar

2916Progress 0% │██▉ │ 0/10 (0:00:00 / 0:00:00)

2917Progress 20% │█████▊ │ 2/10 (0:00:02 / 0:00:08)

2918Progress 30% │████████▋ │ 3/10 (0:00:03 / 0:00:07)

2919Progress 40% │███████████▌ │ 4/10 (0:00:04 / 0:00:06)

2920Progress 50% │██████████████▌ │ 5/10 (0:00:05 / 0:00:05)

2921Progress 60% │█████████████████▍ │ 6/10 (0:00:06 / 0:00:04)

2922Progress 70% │████████████████████▎ │ 7/10 (0:00:07 / 0:00:03)

2923Progress 80% │███████████████████████▏ │ 8/10 (0:00:08 / 0:00:02)

2924Progress 90% │██████████████████████████ │ 9/10 (0:00:09 / 0:00:01)

2925Progress 100% │█████████████████████████████│ 10/10 (0:00:10 / 0:00:00) [info] - should progress

2927Progress 0% │ │ 0/11 (0:00:00 / ?)

2928Progress 9% │██▋ │ 1/11 (0:00:01 / 0:00:10)

2929Progress 18% │████▌ │ 2/11 (0:00:02 / 0:00:09) at 0

2930Progress 27% │██████▊ │ 3/11 (0:00:03 / 0:00:08) at 1

2931Progress 36% │█████████ │ 4/11 (0:00:04 / 0:00:07) at 2

2932Progress 45% │███████████▎ │ 5/11 (0:00:05 / 0:00:06) at 3

2933Progress 54% │█████████████▋ │ 6/11 (0:00:06 / 0:00:05) at 4

2934Progress 63% │███████████████▉ │ 7/11 (0:00:07 / 0:00:04) at 5

2935Progress 72% │██████████████████▏ │ 8/11 (0:00:08 / 0:00:03) at 6

2936Progress 81% │████████████████████▍ │ 9/11 (0:00:09 / 0:00:02) at 7

2937Progress 90% │██████████████████████▋ │ 10/11 (0:00:10 / 0:00:01) at 8

2938Progress 100% │█████████████████████████│ 11/11 (0:00:11 / 0:00:00) at 9[info] - should show extra messages

2939[info] TestCorefChains:

2940[info] CorefChains

2941[info] - should sort on sentenceIndex

2942[info] - should sort on headIndex

2943[info] - should sort on size

2944[info] - should sort on index

2945[info] TestExtractorEngine:

2946[info] ExtractorEngine

2947[info] - should read utf8 encoded data

2948[info] - should read latin1 encoded data

2950[info] - should read data incorrectly if using the wrong charset

2951[info] TestNamedEntity:

2952[info] NamedEntity identification

2953[info] - should collect properly test 1

2954[info] - should collect properly test 2

2955[info] - should collect properly test 3

2956[info] - should collect properly test 4

2957[info] - should collect properly test 5

2958[info] - should collect properly test 6

2959[info] - should collect properly test 7

2960[info] - should collect properly test 8

2961[info] - should collect properly test 9

2962[info] - should collect properly test 10

2963[info] - should collect properly test 11

2964[info] - should collect properly test 12

2965[info] - should collect properly test 13

2966[info] - should collect properly test 14

2967[info] - should collect properly test 15

2968[info] - should combine properly test 1

2969[info] - should combine properly test 2

2970[info] - should combine properly test 3

2971[info] - should combine properly test 4

2972[info] - should combine properly test 5

2973[info] - should combine properly test 6

2974[info] - should combine properly test 7

2975[info] - should combine properly test 8

2976[info] - should combine properly test 9

2977[info] - should combine properly test 10

2978[info] - should combine properly test 11

2979[info] - should combine properly test 12

2980[info] - should combine properly test 13

2981[info] - should combine properly test 14

2982[info] - should combine properly test 15

2983[info] - should combine properly test 16

2984[info] - should combine properly test 17

2985[info] - should combine properly test 18

2986[info] - should combine properly test 19

2987[info] - should combine properly test 20

2988[info] NamedEntity validation

2989[info] - should validate the BIO notation test 1

2990[info] - should validate the BIO notation test 2

2991[info] - should validate the BIO notation test 3

2992[info] - should validate the BIO notation test 4

2993[info] - should validate the BIO notation test 5

2994[info] - should validate the BIO notation test 6

2995[info] - should validate the BIO notation test 7

2996[info] - should validate the BIO notation test 8

2997[info] - should validate the BIO notation test 9

2998[info] NamedEntity correction

2999[info] - should correct the BIO notation test 1

3000[info] - should correct the BIO notation test 2

3001[info] - should correct the BIO notation test 3

3002[info] - should correct the BIO notation test 4

3003[info] - should correct the BIO notation test 5

3004[info] - should correct the BIO notation test 6

3005[info] - should correct the BIO notation test 7

3006[info] - should correct the BIO notation test 8

3007[info] - should correct the BIO notation test 9

3008[info] TestTimer:

3009[info] timer

3010[info] - should use the right divisors

3011[info] TestDistributionalSimilarityPatterns:

3012[info] I saw a leopard climbing a tree.

3013[info] - should produce a mention with the label "Feline" for the word "leopard"

3014[info] TestSerializer:

3015[info] - should serialize/deserialize a Mention correctly

3016[info] - should serialize/deserialize a CrossSentenceMention correctly

3017[info] TestUniversalEnhancedDependencies:

3018[info] org.clulab.processors.TestUniversalEnhancedDependencies *** ABORTED ***

3020[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3021[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3022[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3023[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3024[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

3025[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

3026[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

3027[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

3028[info] at org.scalatest.BeforeAndAfterAll.run$(BeforeAndAfterAll.scala:135)

3029[info] at org.clulab.processors.CluTest.run(CluTest.scala:9)

3030[info] ...

3032[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

3033[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

3034[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3035[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3036[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3037[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3038[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

3039[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

3040[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

3041[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

3042[info] ...

3082[info] CluTest:

3083[info] TestJSONSerializer:

3084[info] JSONSerializer

3085[info] - should serialize/deserialize a Document to/from json correctly

3086[info] - should serialize/deserialize a Sentence to/from json correctly

3087[info] A Document with an ID

3088[info] - should produce json with an "id" field

3089[info] A Document without an ID

3090[info] - should produce json without an "id" field

3091[info] A Document with text

3092[info] - should produce json with a "text" field

3093[info] A Document without text

3094[info] - should produce json without a "text" field

3095[info] A Document recovered from JSON

3096[info] - should be equivalent to the original

3097[info] A Sentence recovered from JSON

3098[info] - should be equivalent to the original

3099[info] A Document saved and loaded

3100[info] - should have JSON equivalent to the original

3101[info] TestGraphPatternSD:

3102[info] GraphPattern

3103[info] - should support multiline patterns

3104[info] - should produce one mention at a time for an argument without any quantifier

3105[info] - should support optional arguments

3106[info] - should support exact quantifiers for arguments

3107[info] - should support * for arguments

3108[info] - should support + for arguments

3109[info] - should support greedy open range quantifiers for arguments

3110[info] - should handle multitoken triggers

3111[info] - should support 'type: graph'

3112[info] - should support 'graph: ' key

3113[info] - should ignore 'graph: ' when 'type: dependency'

3114[info] TestNumericEntityRecognition:

3115[info] org.clulab.numeric.TestNumericEntityRecognition *** ABORTED ***

3117[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3118[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3119[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3120[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3121[info] at org.clulab.numeric.TestNumericEntityRecognition$HabitusProcessor.<init>(TestNumericEntityRecognition.scala:44)

3122[info] at org.clulab.numeric.TestNumericEntityRecognition.<init>(TestNumericEntityRecognition.scala:50)

3123[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

3124[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)

3125[info] at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)

3126[info] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)

3127[info] ...

3129[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

3130[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

3131[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3132[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3133[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3134[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3135[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

3136[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

3137[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

3138[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

3139[info] ...

3181[info] TestMarkdownGeneration:

3182[info] MarkdownGeneration

3183[info] - should not crash

3184[info] - should properly aggregate argument requiredness

3185[info] TestCrLf:

3186[info] resources

3187[info] TestEvalTimeNorm:

3188[info] temporal parser

3189[info] org.clulab.numeric.TestEvalTimeNorm *** ABORTED ***

3191[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3192[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3193[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3194[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3195[info] at org.clulab.numeric.TestEvalTimeNorm.testFun$proxy1$1(TestEvalTimeNorm.scala:12)

3196[info] at org.clulab.numeric.TestEvalTimeNorm.$init$$$anonfun$1(TestEvalTimeNorm.scala:10)

3197[info] at org.scalatest.Transformer.apply$$anonfun$1(Transformer.scala:22)

3198[info] at org.scalatest.OutcomeOf.outcomeOf(OutcomeOf.scala:85)

3199[info] at org.scalatest.OutcomeOf.outcomeOf$(OutcomeOf.scala:31)

3200[info] at org.scalatest.OutcomeOf$.outcomeOf(OutcomeOf.scala:104)

3201[info] ...

3203loading props from file library/src/test/resources/org/clulab/utils/test.properties

3204[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

3205[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

3206[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3207[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3208[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3209[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3210[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

3211[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

3212[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

3213[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

3214[info] ...

3239Using the following properties:

3288 p1 = /some/path

3293 p2 = /some/path/subdir/123

3294 p3 = 123

3295loading props from file library/src/test/resources/org/clulab/utils/test.properties

3296Using the following properties:

3297 p1 = /some/path

3298 p2 = /some/path/subdir/123

3299 p3 = 123

3300[info] TestArgsToProperties:

3301[info] properties

3302[info] - should contain p1 with value /some/path

3303[info] - should contain p2 with the value /some/path/subdir/123

3304[info] properties as a map

3305[info] - should contain p1 with value /some/path

3306[info] - should contain p2 with the value /some/path/subdir/123

3307[info] argsToMap

3308Using the following properties:

3309 = in inDirectory out outDirectory

3310[info] - should deal with plain values

3311[info] TestInst:

3312[info] Inst

3313[info] - should not distinguish Done and Done

3314[info] - should distinguish Done and Pass

3315[info] - should distinguish MatchLookAhead and MatchLookBehind

3316[info] - should distinguish SaveStart and SaveEnd

3317[info] - should distinguish Done and MatchToken

3318[info] - should distinguish between Pass and Pass

3319[info] - should distinguish between MatchToken and MatchToken

3320[info] - should copy Pass appropriately

3321[info] - should copy Split appropriately

3322[info] - should copy SaveStart appropriately

3323[info] - should copy SaveEnd appropriately

3324[info] - should copy MatchToken appropriately

3325[info] - should copy MatchMention appropriately

3326[info] - should copy MatchSentenceStart appropriately

3327[info] - should copy MatchSentenceEnd appropriately

3328[info] - should copy MatchLookAhead appropriately

3329[info] - should copy MatchLookBehind appropriately

3330[info] - should distinguish complicated instances

3331[info] CaseClasses

3332[info] - should compare as intended

3333[info] tuple hashes

3334[info] - should be called recursively

3335[info] TestGraphPattern:

3336[info] graph range {0,n}

3338[info] GraphPattern

3339[info] - should support multiline patterns

3340[info] - should produce one mention at a time for an argument without any quantifier

3341[info] - should support optional arguments

3342[info] - should support exact quantifiers for arguments

3343[info] - should support * for arguments

3345[info] - should support + for arguments

3347[info] - should support greedy open range quantifiers for arguments

3350[info] - should handle multitoken triggers

3351[info] - should support 'type: graph'

3352[info] - should support 'graph: ' key

3353[info] - should ignore 'graph: ' when 'type: dependency'

3354[info] - should require a registered graph type wherever 'graph: ' is specified

3355[info] - should handle colons in dependencies

3356[info] - should handle colons in dependencies without quotes

3357[info] TestRandomForestClassifier:

3358[info] RFClassifier

3359Current utility:

3360UTILITY DEBUG:

3361Using dataset:

3362label:0 features:[0:2.0, 1:1.0]

3363label:1 features:[0:2.0, 2:1.0, 3:1.0]

3364label:1 features:[0:1.0, 4:1.0]

3365Using feature 3 with threshold 0.5

3366Contingency table for this feature+threshold is: SMALLER: [0:1.0, 1:1.0], GREATER: [1:1.0]

3367Overall utility: 0.2516291673878229

3368Parent utility: 0.9182958340544896

3369Utility of left child: 1.0

3370Utility of right child: 0.0

3371CHOSEN NEW BEST!

3372Current utility:

3373UTILITY DEBUG:

3374Using dataset:

3375label:0 features:[0:2.0, 1:1.0]

3376label:1 features:[0:2.0, 2:1.0, 3:1.0]

3377label:1 features:[0:1.0, 4:1.0]

3378Using feature 4 with threshold 0.5

3379Contingency table for this feature+threshold is: SMALLER: [0:1.0, 1:1.0], GREATER: [1:1.0]

3380Overall utility: 0.2516291673878229

3381Parent utility: 0.9182958340544896

3382Utility of left child: 1.0

3383Utility of right child: 0.0

3384Current utility:

3385UTILITY DEBUG:

3386Using dataset:

3387label:0 features:[0:2.0, 1:1.0]

3388label:1 features:[0:2.0, 2:1.0, 3:1.0]

3389label:1 features:[0:1.0, 4:1.0]

3390Using feature 0 with threshold 1.5

3391Contingency table for this feature+threshold is: SMALLER: [0:0.0, 1:1.0], GREATER: [0:1.0, 1:1.0]

3392Overall utility: 0.2516291673878229

3393Parent utility: 0.9182958340544896

3394Utility of left child: 0.0

3395Utility of right child: 1.0

3396Current utility:

3397UTILITY DEBUG:

3398Using dataset:

3399label:0 features:[0:2.0, 1:1.0]

3400label:1 features:[0:2.0, 2:1.0, 3:1.0]

3401label:1 features:[0:1.0, 4:1.0]

3402Using feature 1 with threshold 0.5

3403Contingency table for this feature+threshold is: SMALLER: [0:0.0, 1:2.0], GREATER: [0:1.0]

3404Overall utility: 0.9182958340544896

3405Parent utility: 0.9182958340544896

3406Utility of left child: 0.0

3407Utility of right child: 0.0

3408CHOSEN NEW BEST!

3409Current utility:

3410UTILITY DEBUG:

3411Using dataset:

3412label:0 features:[0:2.0, 1:1.0]

3413label:1 features:[0:2.0, 2:1.0, 3:1.0]

3414label:1 features:[0:1.0, 4:1.0]

3415Using feature 2 with threshold 0.5

3416Contingency table for this feature+threshold is: SMALLER: [0:1.0, 1:1.0], GREATER: [1:1.0]

3417Overall utility: 0.2516291673878229

3418Parent utility: 0.9182958340544896

3419Utility of left child: 1.0

3420Utility of right child: 0.0

3421BEST OVERALL:

3422UTILITY DEBUG:

3423Using dataset:

3424label:0 features:[0:2.0, 1:1.0]

3425label:1 features:[0:2.0, 2:1.0, 3:1.0]

3426label:1 features:[0:1.0, 4:1.0]

3427Using feature 1 with threshold 0.5

3428Contingency table for this feature+threshold is: SMALLER: [0:0.0, 1:2.0], GREATER: [0:1.0]

3429Overall utility: 0.9182958340544896

3430Parent utility: 0.9182958340544896

3431Utility of left child: 0.0

3432Utility of right child: 0.0

3433Current utility:

3434UTILITY DEBUG:

3435Using dataset:

3436label:1 features:[0:2.0, 2:1.0, 3:1.0]

3437label:1 features:[0:1.0, 4:1.0]

3438Using feature 2 with threshold 0.5

3439Contingency table for this feature+threshold is: SMALLER: [1:1.0], GREATER: [1:1.0]

3440Overall utility: 0.0

3441Parent utility: 0.0

3442Utility of left child: 0.0

3443Utility of right child: 0.0

3444CHOSEN NEW BEST!

3445Current utility:

3446UTILITY DEBUG:

3447Using dataset:

3448label:1 features:[0:2.0, 2:1.0, 3:1.0]

3449label:1 features:[0:1.0, 4:1.0]

3450Using feature 4 with threshold 0.5

3451Contingency table for this feature+threshold is: SMALLER: [1:1.0], GREATER: [1:1.0]

3452Overall utility: 0.0

3453Parent utility: 0.0

3454Utility of left child: 0.0

3455Utility of right child: 0.0

3456Current utility:

3457UTILITY DEBUG:

3458Using dataset:

3459label:1 features:[0:2.0, 2:1.0, 3:1.0]

3460label:1 features:[0:1.0, 4:1.0]

3461Using feature 0 with threshold 1.5

3462Contingency table for this feature+threshold is: SMALLER: [1:1.0], GREATER: [1:1.0]

3463Overall utility: 0.0

3464Parent utility: 0.0

3465Utility of left child: 0.0

3466Utility of right child: 0.0

3467Current utility:

3468UTILITY DEBUG:

3469Using dataset:

3470label:1 features:[0:2.0, 2:1.0, 3:1.0]

3471label:1 features:[0:1.0, 4:1.0]

3472Using feature 3 with threshold 0.5

3473Contingency table for this feature+threshold is: SMALLER: [1:1.0], GREATER: [1:1.0]

3474Overall utility: 0.0

3475Parent utility: 0.0

3476Utility of left child: 0.0

3477Utility of right child: 0.0

3478BEST OVERALL:

3479UTILITY DEBUG:

3480Using dataset:

3481label:1 features:[0:2.0, 2:1.0, 3:1.0]

3482label:1 features:[0:1.0, 4:1.0]

3483Using feature 2 with threshold 0.5

3484Contingency table for this feature+threshold is: SMALLER: [1:1.0], GREATER: [1:1.0]

3485Overall utility: 0.0

3486Parent utility: 0.0

3487Utility of left child: 0.0

3488Utility of right child: 0.0

3489Class of List(good, horrible): -

3490Class of List(bad, horrible): -

3491Class of List(good, great): +

3492[info] - should work with BVFDataset

3493[info] RandomForestClassifier

3494Accuracy: 0.965

3495[info] - should have an accuracy > .95 on this dataset

3496[info] TestLiblinearClassifier:

3497[info] LiblinearClassifier

3498iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00 CG 2

3499iter 2 act 8.879e-04 pre 8.833e-04 delta 8.463e-01 f 1.459e+00 |g| 5.811e-02 CG 1

3500iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00 CG 2

3501iter 2 act 8.879e-04 pre 8.833e-04 delta 8.463e-01 f 1.459e+00 |g| 5.811e-02 CG 1

3502iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00 CG 2

3503iter 2 act 8.879e-04 pre 8.833e-04 delta 8.463e-01 f 1.459e+00 |g| 5.811e-02 CG 1

3504[info] - should work with RVFDataset

3505iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00 CG 2

3506iter 2 act 8.879e-04 pre 8.833e-04 delta 8.463e-01 f 1.459e+00 |g| 5.811e-02 CG 1

3507iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00 CG 2

3508iter 2 act 8.879e-04 pre 8.833e-04 delta 8.463e-01 f 1.459e+00 |g| 5.811e-02 CG 1

3509iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00 CG 2

3510iter 2 act 8.879e-04 pre 8.833e-04 delta 8.463e-01 f 1.459e+00 |g| 5.811e-02 CG 1

3511iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00 CG 2

3512iter 2 act 8.879e-04 pre 8.833e-04 delta 8.463e-01 f 1.459e+00 |g| 5.811e-02 CG 1

3513iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00 CG 2

3514iter 2 act 8.879e-04 pre 8.833e-04 delta 8.463e-01 f 1.459e+00 |g| 5.811e-02 CG 1

3515iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00 CG 2

3516iter 2 act 8.879e-04 pre 8.833e-04 delta 8.463e-01 f 1.459e+00 |g| 5.811e-02 CG 1

3517[info] - should work with BVFDataset

3518iter 1 act 4.528e-01 pre 4.444e-01 delta 7.000e-01 f 1.386e+00 |g| 1.323e+00 CG 2

3519iter 2 act 8.651e-04 pre 8.605e-04 delta 7.000e-01 f 9.335e-01 |g| 5.750e-02 CG 1

3520[info] - should work with a two-label dataset

3521[info] LogisticRegressionClassifier

3522iter 1 act 7.243e+02 pre 6.698e+02 delta 1.883e+01 f 1.386e+03 |g| 9.617e+01 CG 4

3523iter 2 act 3.382e+01 pre 3.043e+01 delta 1.883e+01 f 6.620e+02 |g| 1.841e+01 CG 3

3524iter 3 act 2.260e+00 pre 2.083e+00 delta 1.883e+01 f 6.282e+02 |g| 4.186e+00 CG 3

3525iter 4 act 6.468e-02 pre 6.350e-02 delta 1.883e+01 f 6.259e+02 |g| 6.366e-01 CG 3

3526[info] - should have an accuracy > .97 in this dataset

3527[info] LinearSVMClassifier

3528iter 1 act 1.779e+03 pre 1.753e+03 delta 1.414e+01 f 2.000e+03 |g| 3.847e+02 CG 5

3529iter 2 act 4.189e+01 pre 4.076e+01 delta 1.414e+01 f 2.214e+02 |g| 3.417e+01 CG 6

3530iter 3 act 3.859e+00 pre 3.685e+00 delta 1.414e+01 f 1.795e+02 |g| 8.599e+00 CG 7

3531iter 4 act 5.435e-01 pre 5.117e-01 delta 1.414e+01 f 1.757e+02 |g| 2.475e+00 CG 6

3532[info] - should have an accuracy > .97 in this dataset

3533[info] HexaDecoderTest:

3534[info] HexaDecoder

3535Some(L (0, 3) (1, root)

3536 R (0, 1) (1, root)

3537 (0, nsubj)

3538 (1, root)

3539 R (2, 3) (3, dobj)

3540 (2, nmod)

3541 (3, dobj)

3542)

3543Dependencies (3):

3544Edge(1,3,dobj)

3545Edge(1,0,nsubj)

3546Edge(3,2,nmod)

3547Roots: 1

3548[info] - should decode a simple tree

3549Terminal tags: tl-nsubj, tl-cop, tl-det, tr-root

3550Nonterm tags: nl-R, nr-R, nr-R, eos

3551Processing terminal tag: tl-nsubj

3552Pushing:

3553(0, nsubj)

3554onto the stack.

3555Processing non-terminal tag: nl-R

3556Pushing:

3557R (0, -1) (-1, dummy)

3558 (0, nsubj)

3559 dummy

3560onto the stack.

3561Processing terminal tag: tl-cop

3562Pushing:

3563(1, cop)

3564onto the stack.

3565Processing non-terminal tag: nr-R

3566Pushing:

3567R (0, -1) (-1, dummy)

3568 (0, nsubj)

3569 R (1, -1) (-1, dummy)

3570 (1, cop)

3571 dummy

3572onto the stack.

3573Processing terminal tag: tl-det

3574Pushing:

3575(2, det)

3576onto the stack.

3577Processing non-terminal tag: nr-R

3578Pushing:

3579R (0, -1) (-1, dummy)

3580 (0, nsubj)

3581 R (1, -1) (-1, dummy)

3582 (1, cop)

3583 R (2, -1) (-1, dummy)

3584 (2, det)

3585 dummy

3586onto the stack.

3587Processing terminal tag: tr-root

3588Pushing:

3589R (0, 3) (3, root)

3590 (0, nsubj)

3591 R (1, 3) (3, root)

3592 (1, cop)

3593 R (2, 3) (3, root)

3594 (2, det)

3595 (3, root)

3596onto the stack.

3597Some(R (0, 3) (3, root)

3598 (0, nsubj)

3599 R (1, 3) (3, root)

3600 (1, cop)

3601 R (2, 3) (3, root)

3602 (2, det)

3603 (3, root)

3604)

3605Dependencies (3):

3606List(Edge(3,0,nsubj), Edge(3,1,cop), Edge(3,2,det))

3607Roots: 3

3608[info] - should decode another simple tree

3609[info] Test:

3610[info] TestEntityConstraints:

3611[info] Uneven parentheses

3612[info] - should be disallowed in entities

3613[info] Even parentheses

3614[info] - should be valid in entities

3615[info] Entities longer than n tokens

3616[info] - should be pruned

3617[info] TestMkCombinedDocument:

3618[info] org.clulab.processors.TestMkCombinedDocument *** ABORTED ***

3620[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3621[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3622[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3623[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3624[info] at org.clulab.processors.TestMkCombinedDocument.<init>(TestMkCombinedDocument.scala:28)

3625[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

3626[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)

3627[info] at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)

3628[info] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)

3629[info] at java.base/java.lang.reflect.ReflectAccess.newInstance(ReflectAccess.java:128)

3630[info] ...

3632[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

3633[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

3634[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3635[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3636[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3637[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3638[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

3639[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

3640[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

3641[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

3642[info] ...

3683[info] TestMathUtils:

3684[info] - should work with Seq

3685[info] - should not produce negative mean or variance

3686[info] - should work with Array

3687[info] - should work with any numeric collection

3688[info] - should be reasonably resilient to overflow

3689[info] TestDirectedGraph:

3690[info] DirectedGraph

3691[info] - should process a loop with a source

3692[info] - should process a loop without a source

3693[info] - should add lone roots

3694[info] - should handle disjoint loops

3695[info] - should not use a leading destination as a root

3696[info] - should be empty

3697[info] TestDependencyUtils:

3698[info] Because the substrates of Shp2 are for the most part unknown, we were additionally interested in examining the state of EGFR tyrosine phosphorylation following treatment with EGF in order to determine if the failure of Gab1 to bind p85, and potentially recruit Shp2, would influence levels of EGFR autophosphorylation.

3699[info] - should produce 'substrates' as the head of 'the substrates of Shp2'

3700[info] - should produce 'are' as the head of 'the substrates of Shp2 are'

3701[info] - should produce None for an empty Interval

3702[info] The docking protein Gab1 is the primary mediator of EGF-stimulated activation of the PI-3K/Akt cell survival pathway

3703[info] - should have the same getHeadStrict as roots

3704[info] - should produce only one head for getHeadsStrict

3705[info] - should produce None for an empty Interval

3706[info] - should produce two heads for 'docking protein' using getHeadsLocal

3707[info] - should think 'docking protein' is nested in 'docking protein Gab1'

3708[info] - should think 'the' is nested in 'Gab1'

3709[info] - should not think 'is' is nested in 'Gab1'

3710[info] - should think Interval(3,3) is nested in 'Gab1'

3711[info] - should not think 'pathway' is nested in 'Gab1'

3712[info] .

3713[info] - should produce one head using findHeads

3714[info] - should produce no heads using findHeadsStrict

3715[info] DependencyUtils

3716[info] - should handle cycles in the dependencyGraph correctly

3717[info] - should handle roots with incoming dependencies

3718[info] - should handle invalid dependency trees in findHeads

3719[info] - should only match complete stop tags

3720[info] TestNumericMentions:

3721[info] org.clulab.numeric.TestNumericMentions *** ABORTED ***

3723[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3724[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3725[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3726[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3727[info] at org.clulab.numeric.TestNumericMentions.<init>(TestNumericMentions.scala:7)

3728[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

3729[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)

3730[info] at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)

3731[info] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)

3732[info] at java.base/java.lang.reflect.ReflectAccess.newInstance(ReflectAccess.java:128)

3733[info] ...

3735[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

3736[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

3737[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3738[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3739[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3740[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3741[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

3742[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

3743[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

3744[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

3745[info] ...

3786[info] TestArrayView:

3787[info] ArrayView

3788[info] - should work with no offset

3789[info] - should work with an offset

3790[info] - should work when clipped

3791[info] TestDoc5501:

3792[info] org.clulab.processors.docs.TestDoc5501 *** ABORTED ***

3794[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3795[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3796[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3797[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3798[info] at org.clulab.processors.docs.TestDoc5501.<init>(TestDoc5501.scala:10)

3799[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

3800[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)

3801[info] at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)

3802[info] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)

3803[info] at java.base/java.lang.reflect.ReflectAccess.newInstance(ReflectAccess.java:128)

3804[info] ...

3806[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

3807[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

3808[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3809[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3810[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3811[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3812[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

3813[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

3814[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

3815[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

3816[info] ...

3857[info] TestLexiconNER:

3858[info] org.clulab.processors.TestLexiconNER *** ABORTED ***

3860[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3861[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3862[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3863[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3864[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

3865[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

3866[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

3867[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

3868[info] at org.scalatest.BeforeAndAfterAll.run$(BeforeAndAfterAll.scala:135)

3869[info] at org.clulab.processors.CluTest.run(CluTest.scala:9)

3870[info] ...

3872[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

3873[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

3874[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3875[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3876[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3877[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3878[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

3879[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

3880[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

3881[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

3882[info] ...

3922[info] TestTaxonomy:

3923[info] taxonomy

3924[info] - should inform a rule's labels

3925[info] TestProcessor:

3926[info] org.clulab.processors.TestProcessor *** ABORTED ***

3928[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3929[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3930[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3931[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3932[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

3933[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

3934[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

3935[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

3936[info] at org.scalatest.BeforeAndAfterAll.run$(BeforeAndAfterAll.scala:135)

3937[info] at org.clulab.processors.CluTest.run(CluTest.scala:9)

3938[info] ...

3940[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

3941[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

3942[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3943[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3944[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3945[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3946[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

3947[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

3948[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

3949[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

3950[info] ...

3990[info] TestTokenizer:

3991[info] the tokenizer