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-RC4

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-RC4

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-RC4

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-RC4

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-RC4"

62"++3.8.0-RC4 -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-RC4 """{"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 8.602s.

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-RC4

93OpenCB::Changing crossVersion 3.1.3 -> 3.8.0-RC4 in root/crossScalaVersions

94OpenCB::Changing crossVersion 3.1.3 -> 3.8.0-RC4 in library/crossScalaVersions

95OpenCB::Changing crossVersion 3.1.3 -> 3.8.0-RC4 in apps/crossScalaVersions

96OpenCB::Changing crossVersion 3.1.3 -> 3.8.0-RC4 in debugger/crossScalaVersions

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

98[info] Setting Scala version to 3.8.0-RC4 on 4 projects.

99[info] Switching Scala version on:

100[info] * root (2.12.19, 2.11.12, 2.13.14, 3.8.0-RC4)

101[info] library (2.12.19, 2.11.12, 2.13.14, 3.8.0-RC4)

102[info] debugger (2.12.19, 2.11.12, 2.13.14, 3.8.0-RC4)

103[info] apps (2.12.19, 2.11.12, 2.13.14, 3.8.0-RC4)

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 Dec 22, 2025, 6:42:15 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-RC4/classes ...

156[info] done compiling

157[info] compiling 85 Scala sources to /build/repo/library/target/scala-3.8.0-RC4/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

177SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".

178SLF4J: Defaulting to no-operation (NOP) logger implementation

179SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.

180[info] TestDueTo:

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-17939070710770303542.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% │██▉ │ 0/10 (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)

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

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

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

660[info] ...

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

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

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

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

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

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

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

669loading props from file library/src/test/resources/org/clulab/utils/test.properties

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

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

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

673[info] ...

675Using the following properties:

701 p1 = /some/path

718 p2 = /some/path/subdir/123

719 p3 = 123

725loading props from file library/src/test/resources/org/clulab/utils/test.properties

727Using the following properties:

728 p1 = /some/path

729 p2 = /some/path/subdir/123

730 p3 = 123

759Using the following properties:

760 = in inDirectory out outDirectory

761[info] TestArgsToProperties:

762[info] properties

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

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

765[info] properties as a map

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

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

768[info] argsToMap

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

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

954Accuracy: 0.965

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

963[info] - should work with RVFDataset

964iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00 CG 2

965iter 2 act 8.879e-04 pre 8.833e-04 delta 8.463e-01 f 1.459e+00 |g| 5.811e-02 CG 1

966iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00 CG 2

967iter 2 act 8.879e-04 pre 8.833e-04 delta 8.463e-01 f 1.459e+00 |g| 5.811e-02 CG 1

968iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00 CG 2

969iter 2 act 8.879e-04 pre 8.833e-04 delta 8.463e-01 f 1.459e+00 |g| 5.811e-02 CG 1

970iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00 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:

1450[info] the tokenizer

1451Tokenizing text: the of $><1/2 1.3 another test.

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 :( .

1500Tokenizing text: This is an example e.g. a phrase.

1501[info] - should provide fundamental tokenization functionality

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

1530[info] - should not tokenize letter emoticons too aggressively

1531Tokenizing 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 .

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 .

1534[info] - should tokenize question mark correctly

1535Tokenizing 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 .

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

17185

17195

1720hello

1721hello

1722[I@224613a4

1723Array(1, 2, 3)

1724List(11, 12, 13)

1725List(11, 12, 13)

1726Map(a -> 21, b -> 22, c -> 23)

1727Map(a -> 21, b -> 22, c -> 23)

1728List(31, 32, 33)

1729List(31, 32, 33)

1730(a,42,43)

1731(a,42,43)

1732<5>

1733<hello>

1734<1-2-3>

1735<11-12-13>

1736<(a,21)-(b,22)-(c,23)>

1737<31-32-33>

1738<(a,42,43)>

1739[info] TestPrintUtils:

1740[info] PrintUtils

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 [info] TestLiblinearRegression:

19986.896e-01 pre 6.896e-01 delta 3.922e-01 f [info] LiblinearRegression

19997.726e-01 |g| 3.749e+00 CG 2

2000[info] - should work with RVFRegDataset

2001iter 1 act 6.896e-01 pre 6.896e-01 delta 3.922e-01 f 7.726e-01 |g| 3.749e+00 CG 2

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 = 0.08285714285714287

2052obj = -0.02402857142857143, rho = -0.39571428571428574

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 = 0.038571428571428576

2062obj = -0.005207142857142858, rho = -0.6171428571428572

2063nSV = 2, nBSV = 0

2064*

2065optimization finished, #iter = 1

2066nu = 0.02749999999999999

2067obj = -0.0015125, rho = -0.285

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 = 0.038571428571428576

2085obj = -0.005207142857142858, rho = -0.6171428571428572

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 = 0.02749999999999999

2095obj = -0.0015125, rho = -0.285

2096nSV = 2, nBSV = 0

2097*

2098optimization finished, #iter = 1

2099nu = 0.08285714285714287

2100obj = -0.02402857142857143, rho = -0.39571428571428574

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 = 0.02749999999999999

2117obj = -0.0015125, rho = -0.285

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 = 0.08285714285714287

2127obj = -0.02402857142857143, rho = -0.39571428571428574

2128nSV = 2, nBSV = 0

2129*

2130optimization finished, #iter = 1

2131nu = 0.038571428571428576

2132obj = -0.005207142857142858, rho = -0.6171428571428572

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 = 31641

2145nu = 0.3084668003972934

2146obj = -38.82237081112438, rho = -0.5400445814072947

2147nSV = 508, nBSV = 399

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

2149optimization finished, #iter = 40423

2150nu = 0.328263158433633

2151obj = -42.372764926937165, rho = -0.5039304884525466

2152nSV = 529, nBSV = 422

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

2154optimization finished, #iter = 30107

2155nu = 0.30677305516371245

2156obj = -39.958447995824436, rho = -0.36724531429032303

2157nSV = 499, nBSV = 391

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

2159optimization finished, #iter = 29396

2160nu = 0.3160225054943844

2161obj = -39.556180037783896, rho = -0.5610036627994738

2162nSV = 510, nBSV = 400

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

2164optimization finished, #iter = 42731

2165nu = 0.31405906953053414

2166obj = -41.6543527325516, rho = -0.41257803523077263

2167nSV = 510, nBSV = 402

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

2169z: Laplace distribution e^(-|z|/sigma)/(2sigma),sigma=0.09720086668744882

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

2171optimization finished, #iter = 41834

2172nu = 0.3169820033369704

2173obj = -51.480338813026364, rho = -0.5860073666273288

2174nSV = 633, nBSV = 512

2175*

2176optimization finished, #iter = 411

2177nu = 0.32085054347535824

2178obj = -49.90329723898701, rho = -0.3391030193649359

2179nSV = 479, nBSV = 444

2180*

2181optimization finished, #iter = 460

2182nu = 0.33767398112704433

2183obj = -52.471525468353235, rho = -0.31360075375669283

2184nSV = 501, nBSV = 470

2185*

2186optimization finished, #iter = 420

2187nu = 0.33641319140184855

2188obj = -50.504554595979066, rho = -0.3204751438875021

2189nSV = 501, nBSV = 464

2190*

2191optimization finished, #iter = 397

2192nu = 0.3312932109453277

2193obj = -52.361270076543356, rho = -0.34067405810682033

2194nSV = 490, nBSV = 463

2195*

2196optimization finished, #iter = 401

2197nu = 0.3308922866813711

2198obj = -51.88971174927009, rho = -0.33963576315400684

2199nSV = 494, nBSV = 460

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

2201z: Laplace distribution e^(-|z|/sigma)/(2sigma),sigma=0.0960703952541998

2202*

2203optimization finished, #iter = 559

2204nu = 0.32873173531098426

2205obj = -63.35295557273505, rho = -0.34803081450672674

2206nSV = 614, nBSV = 574

2207*

2208optimization finished, #iter = 518

2209nu = 0.31816945581038114

2210obj = -47.44571541213841, rho = -0.17201229158106623

2211nSV = 482, nBSV = 432

2212*

2213optimization finished, #iter = 510

2214nu = 0.31405881292242316

2215obj = -47.86918290020019, rho = -0.20638205442797955

2216nSV = 475, nBSV = 425

2217*

2218optimization finished, #iter = 466

2219nu = 0.2965720096839707

2220obj = -46.68378043845659, rho = -0.21714883554369271

2221nSV = 447, nBSV = 400

2222*

2223optimization finished, #iter = 550

2224nu = 0.3191311753637975

2225obj = -48.30381118891735, rho = -0.10724303695638131

2226nSV = 485, nBSV = 435

2227*

2228optimization finished, #iter = 541

2229nu = 0.32283205280335203

2230obj = -48.06678145124886, rho = -0.18531485159726774

2231nSV = 490, nBSV = 441

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

2233z: Laplace distribution e^(-|z|/sigma)/(2sigma),sigma=0.09503357886734466

2234*

2235optimization finished, #iter = 629

2236nu = 0.31050957630127235

2237obj = -58.99742838311287, rho = -0.11795899327038137

2238nSV = 584, nBSV = 528

2239*

2240optimization finished, #iter = 380

2241nu = 0.32224065741938507

2242obj = -49.85389145252693, rho = -0.3453265709402925

2243nSV = 478, nBSV = 445

2244*

2245optimization finished, #iter = 434

2246nu = 0.3339727020135994

2247obj = -52.15023210119807, rho = -0.3583565010331022

2248nSV = 497, nBSV = 463

2249*

2250optimization finished, #iter = 437

2251nu = 0.3308612695491384

2252obj = -51.649300644933234, rho = -0.3482358400610062

2253nSV = 491, nBSV = 460

2254*

2255optimization finished, #iter = 455

2256nu = 0.33538114148441484

2257obj = -50.381167932697196, rho = -0.30902605126302085

2258nSV = 497, nBSV = 465

2259*

2260optimization finished, #iter = 404

2261nu = 0.3473214998957084

2262obj = -54.288207208350734, rho = -0.31596888773749726

2263nSV = 514, nBSV = 482

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

2265z: Laplace distribution e^(-|z|/sigma)/(2sigma),sigma=0.09627906615331938

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 = 75983

2275epsilon = 0.057232546043656754

2276obj = -106.38239186307267, rho = -0.14937030315241884

2277nSV = 786, nBSV = 662

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

2279optimization finished, #iter = 66274

2280epsilon = 0.05844892635920117

2281obj = -105.33516465280061, rho = -0.30530681916652463

2282nSV = 775, nBSV = 659

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

2284optimization finished, #iter = 91101

2285epsilon = 0.058379302307679404

2286obj = -106.0964686516382, rho = -0.310447711167764

2287nSV = 779, nBSV = 659

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

2289optimization finished, #iter = 70448

2290epsilon = 0.05700193608110976

2291obj = -107.11121755934556, rho = -0.17055518880906684

2292nSV = 780, nBSV = 663

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

2294optimization finished, #iter = 82115

2295epsilon = 0.057287122960048495

2296obj = -105.26162034247216, rho = -0.2906828210473967

2297nSV = 776, nBSV = 660

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

2299z: Laplace distribution e^(-|z|/sigma)/(2sigma),sigma=0.09400162162200067

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

2301optimization finished, #iter = 91034

2302epsilon = 0.05944570893531101

2303obj = -133.67027363116608, rho = -0.22082834234372709

2304nSV = 961, nBSV = 839

2305*

2306optimization finished, #iter = 854

2307epsilon = 0.055168399339848156

2308obj = -116.66902167813923, rho = -0.2885046884697008

2309nSV = 740, nBSV = 698

2310*

2311optimization finished, #iter = 860

2312epsilon = 0.058090709357346976

2313obj = -118.92464130223027, rho = -0.3095506186258876

2314nSV = 739, nBSV = 694

2315*

2316optimization finished, #iter = 956

2317epsilon = 0.05718098581378711

2318obj = -118.6142702655779, rho = -0.3105511828453335

2319nSV = 743, nBSV = 699

2320*

2321optimization finished, #iter = 858

2322epsilon = 0.05459748257668505

2323obj = -116.35467453248387, rho = -0.26548928685669976

2324nSV = 736, nBSV = 698

2325*

2326optimization finished, #iter = 904

2327epsilon = 0.05839975962841171

2328obj = -116.89476751585848, rho = -0.3121243182957069

2329nSV = 737, nBSV = 696

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

2331z: Laplace distribution e^(-|z|/sigma)/(2sigma),sigma=0.09304415323622653

2332.*

2333optimization finished, #iter = 1030

2334epsilon = 0.05639765783061974

2335obj = -145.96471729318776, rho = -0.2866861483069072

2336nSV = 917, nBSV = 874

2337.*

2338optimization finished, #iter = 1285

2339epsilon = 0.05456412365679502

2340obj = -114.0875023641833, rho = -0.14491270765148148

2341nSV = 755, nBSV = 677

2342.*

2343optimization finished, #iter = 1256

2344epsilon = 0.0541416169480768

2345obj = -110.52116846719449, rho = -0.15764280469049535

2346nSV = 752, nBSV = 682

2347.*

2348optimization finished, #iter = 1353

2349epsilon = 0.05433144921523966

2350obj = -111.95365827366315, rho = -0.18652015688602386

2351nSV = 757, nBSV = 682

2352.*

2353optimization finished, #iter = 1251

2354epsilon = 0.05356556181087241

2355obj = -113.0596360095607, rho = -0.2311955680704506

2356nSV = 750, nBSV = 683

2357.*

2358optimization finished, #iter = 1238

2359epsilon = 0.05465883821408117

2360obj = -113.26189007415582, rho = -0.19765018324596628

2361nSV = 749, nBSV = 683

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

2363z: Laplace distribution e^(-|z|/sigma)/(2sigma),sigma=0.09062087490751512

2364.

2366*

2367optimization finished, #iter = 1485

2368epsilon = 0.054878816933817506

2369obj = -140.12235768223275, rho = -0.15015265276473888

2370nSV = 932, nBSV = 860

2371*

2372optimization finished, #iter = 898

2373epsilon = 0.05516971630812481

2374obj = -115.81830215025639, rho = -0.29328861142711293

2375nSV = 737, nBSV = 697

2376*

2377optimization finished, #iter = 823

2378epsilon = 0.0567033600632231

2379obj = -116.14506764291067, rho = -0.2870209798335944

2380nSV = 735, nBSV = 698

2381*

2382optimization finished, #iter = 877

2383epsilon = 0.05580049393829414

2384obj = -116.20631575251097, rho = -0.3011902823996766

2385nSV = 743, nBSV = 697

2386*

2387optimization finished, #iter = 826

2388epsilon = 0.05829708016120429

2389obj = -121.5027199412523, rho = -0.29807482747805775

2390nSV = 738, nBSV = 703

2391*

2392optimization finished, #iter = 912

2393epsilon = 0.05838928024481947

2394obj = -120.14454336861837, rho = -0.28924707662510313

2395nSV = 737, nBSV = 697

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

2397z: Laplace distribution e^(-|z|/sigma)/(2sigma),sigma=0.09290843436312891

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

248425

248524

248623

248717

248818

248921

249015

249114

249220

249313

249416

249522

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-RC4

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-RC4"

2644"++3.8.0-RC4 -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-RC4 """{"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-RC4

2663OpenCB::Changing crossVersion 3.1.3 -> 3.8.0-RC4 in root/crossScalaVersions

2664OpenCB::Changing crossVersion 3.1.3 -> 3.8.0-RC4 in library/crossScalaVersions

2665OpenCB::Changing crossVersion 3.1.3 -> 3.8.0-RC4 in apps/crossScalaVersions

2666OpenCB::Changing crossVersion 3.1.3 -> 3.8.0-RC4 in debugger/crossScalaVersions

2667[info] set current project to root (in build file:/build/repo/)

2668[info] Setting Scala version to 3.8.0-RC4 on 4 projects.

2669[info] Switching Scala version on:

2670[info] * root (2.12.19, 2.11.12, 2.13.14, 3.8.0-RC4)

2671[info] library (2.12.19, 2.11.12, 2.13.14, 3.8.0-RC4)

2672[info] debugger (2.12.19, 2.11.12, 2.13.14, 3.8.0-RC4)

2673[info] apps (2.12.19, 2.11.12, 2.13.14, 3.8.0-RC4)

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 Dec 22, 2025, 8:31:45 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-10784434597797894737.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] ...

3203[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

3204[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

3205[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3206[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3207[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3208[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3209[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

3210[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

3211[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

3212[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

3213[info] ...

3290loading props from file library/src/test/resources/org/clulab/utils/test.properties

3291Using the following properties:

3292 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:

3301Using the following properties:

3302 = in inDirectory out outDirectory

3303[info] properties

3304[info] - should contain p1 with value /some/path

3305[info] - should contain p2 with the value /some/path/subdir/123

3306[info] properties as a map

3307[info] - should contain p1 with value /some/path

3308[info] - should contain p2 with the value /some/path/subdir/123

3309[info] argsToMap

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] ...

3953Tokenizing text: the of $><1/2 1.3 another test.

3991[info] TestTokenizer: