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-RC3

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-RC3

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-RC3

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-RC3

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-RC3"

62"++3.8.0-RC3 -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-RC3 """{"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 9.063s.

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-RC3

93OpenCB::Changing crossVersion 3.1.3 -> 3.8.0-RC3 in root/crossScalaVersions

94OpenCB::Changing crossVersion 3.1.3 -> 3.8.0-RC3 in library/crossScalaVersions

95OpenCB::Changing crossVersion 3.1.3 -> 3.8.0-RC3 in apps/crossScalaVersions

96OpenCB::Changing crossVersion 3.1.3 -> 3.8.0-RC3 in debugger/crossScalaVersions

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

98[info] Setting Scala version to 3.8.0-RC3 on 4 projects.

99[info] Switching Scala version on:

100[info] * root (2.12.19, 2.11.12, 2.13.14, 3.8.0-RC3)

101[info] library (2.12.19, 2.11.12, 2.13.14, 3.8.0-RC3)

102[info] debugger (2.12.19, 2.11.12, 2.13.14, 3.8.0-RC3)

103[info] apps (2.12.19, 2.11.12, 2.13.14, 3.8.0-RC3)

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 4, 2025, 3:34:18 PM

129Build config: {"tests":null}

131Starting build...

132Projects: Set(library, apps, debugger)

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

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

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

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

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

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

139[info] compiling 194 Scala sources and 5 Java sources to /build/repo/library/target/scala-3.8.0-RC3/classes ...

156[info] done compiling

157[info] compiling 85 Scala sources to /build/repo/library/target/scala-3.8.0-RC3/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-15499647889299413183.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)

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

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

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

672[info] ...

674loading props from file library/src/test/resources/org/clulab/utils/test.properties

750Using the following properties:

751 p1 = /some/path

752 p2 = /some/path/subdir/123

753 p3 = 123

754loading props from file library/src/test/resources/org/clulab/utils/test.properties

755Using the following properties:

756 p1 = /some/path

757 p2 = /some/path/subdir/123

758 p3 = 123

759[info] TestArgsToProperties:

760Using the following properties:

761 = in inDirectory out outDirectory

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

953Accuracy: 0.965

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

955[info] TestLiblinearClassifier:

956[info] LiblinearClassifier

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

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

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

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

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

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

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] ...

1412Tokenizing text: the of $><1/2 1.3 another test.

1450[info] TestTokenizer:

1451[info] the tokenizer

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

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

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

1455Tokenizing text: first sentence. second sentence.

1456 Sentence #0: first sentence .

1457 Sentence #1: second sentence .

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

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

1460 Sentence #1: Second sentence .

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

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

1463 Sentence #1: Second sentence .

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

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

1466Tokenizing text: Campylobacter spp. are ubiquitous.

1467 Sentence #0: Campylobacter spp. are ubiquitous .

1468Tokenizing text: today is 12/25/2017

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

1470Tokenizing text: today is 12/255/2017

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

1472Tokenizing text: number is -122,333

1473 Sentence #0: number is -122,333

1474Tokenizing text: gap-mediated reaction

1475 Sentence #0: gap-mediated reaction

1476Tokenizing text: 3M is a company

1477 Sentence #0: 3M is a company

1478Tokenizing text: cont'd nat'l program

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

1480Tokenizing text: @user_1 likes #havingfun

1481 Sentence #0: @user_1 likes #havingfun

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

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

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

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

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

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

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

1489 Sentence #0: will not is not had not

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

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

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

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

1494Tokenizing text: IBM is Co. not Ltd.

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

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

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

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

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

1500[info] - should provide fundamental tokenization functionality

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

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

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

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

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

1506[info] - should handle contractions correctly

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

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

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

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

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

1512[info] - should tokenize quotes correctly

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

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

1515[info] - should normalize parentheses correctly

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

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

1518Tokenizing text: ATP :dephospho-CoA triphosphoribosyl transferase

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

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

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

1522Tokenizing text: T=pseudo3 icosahedral viral capsid

1523 Sentence #0: T = pseudo3 icosahedral viral capsid

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

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

1526Tokenizing text: I am :), she said

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

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

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

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[info] - should tokenize question mark correctly

1533 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 ?

1534 Sentence #1: 17 The overall percentage of functional boreholes increased across WBeG , specifically in Jur River and Wau Counties in November .

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

1541Tokenizing 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

1542[info] - should tokenize common emoticons correctly

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

1544Tokenizing 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].

1545[info] - should tokenize emoticons with letters correctly

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 ] .

1551Tokenizing text: Weather is nice in mid-July

1552[info] - should split sentences correctly

1553 Sentence #0: Weather is nice in mid July

1554Tokenizing text: This is ​​a test.

1555[info] - should split some hyphenated words

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[info] TestPrintUtils:

1723[info] PrintUtils

1724[I@7b50b7c8

1725Array(1, 2, 3)

1726List(11, 12, 13)

1727List(11, 12, 13)

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

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

1730List(31, 32, 33)

1731List(31, 32, 33)

1732(a,42,43)

1733(a,42,43)

1734[info] - should print with no arguments

1735<5>

1736<hello>

1737<1-2-3>

1738<11-12-13>

1739<(a,21)-(b,22)-(c,23)>

1740<31-32-33>

1741<(a,42,43)>

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] ...

1997[info] TestLiblinearRegression:

1998[info] LiblinearRegression

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

2000[info] - 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 = 0.02749999999999999

2052obj = -0.0015125, rho = -0.285

2053nSV = 2, nBSV = 0

2054*

2055optimization finished, #iter = 1

2056nu = 0.055238095238095246

2057obj = -0.02402857142857143, rho = -0.39571428571428574

2058nSV = 2, nBSV = 0

2059*

2060optimization finished, #iter = 1

2061nu = 0.038571428571428576

2062obj = -0.005207142857142858, rho = -0.6171428571428572

2063nSV = 2, nBSV = 0

2064*

2065optimization finished, #iter = 1

2066nu = 0.08285714285714287

2067obj = -0.02402857142857143, rho = -0.39571428571428574

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 = 0.08285714285714287

2117obj = -0.02402857142857143, rho = -0.39571428571428574

2118nSV = 2, nBSV = 0

2119*

2120optimization finished, #iter = 1

2121nu = 0.055238095238095246

2122obj = -0.02402857142857143, rho = -0.39571428571428574

2123nSV = 2, nBSV = 0

2124*

2125optimization finished, #iter = 1

2126nu = 0.02749999999999999

2127obj = -0.0015125, rho = -0.285

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 = 34426

2145nu = 0.31924913178789005

2146obj = -39.88268458990111, rho = -0.7964296782268231

2147nSV = 520, nBSV = 411

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

2149optimization finished, #iter = 28430

2150nu = 0.30815262199459736

2151obj = -40.719955925493636, rho = -0.44791723753429713

2152nSV = 495, nBSV = 391

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

2154optimization finished, #iter = 36007

2155nu = 0.3079159697707264

2156obj = -38.62871638036957, rho = -0.34819024384790387

2157nSV = 497, nBSV = 389

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

2159optimization finished, #iter = 34210

2160nu = 0.3170785216097767

2161obj = -40.24174092973383, rho = -0.4087852038433439

2162nSV = 516, nBSV = 402

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

2164optimization finished, #iter = 33959

2165nu = 0.32334987471530363

2166obj = -41.90193856466128, rho = -0.5322096772970961

2167nSV = 516, nBSV = 415

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

2169z: Laplace distribution e^(-|z|/sigma)/(2sigma),sigma=0.09847700586262648

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

2171optimization finished, #iter = 41834

2172nu = 0.3169820033369704

2173obj = -51.480338813026364, rho = -0.5860073666273288

2174nSV = 633, nBSV = 512

2175*

2176optimization finished, #iter = 340

2177nu = 0.32093441427633357

2178obj = -50.262034683102335, rho = -0.31849689740306747

2179nSV = 473, nBSV = 447

2180*

2181optimization finished, #iter = 414

2182nu = 0.32390432680485753

2183obj = -50.363788336349174, rho = -0.3378389751283927

2184nSV = 486, nBSV = 447

2185*

2186optimization finished, #iter = 420

2187nu = 0.32764531069503766

2188obj = -51.98144146776237, rho = -0.3229291403220915

2189nSV = 492, nBSV = 454

2190*

2191optimization finished, #iter = 455

2192nu = 0.3294411900898125

2193obj = -50.18181219930673, rho = -0.3274466647315037

2194nSV = 488, nBSV = 456

2195*

2196optimization finished, #iter = 424

2197nu = 0.3432851080983848

2198obj = -54.333902320754, rho = -0.34400635567525933

2199nSV = 508, nBSV = 475

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

2201z: Laplace distribution e^(-|z|/sigma)/(2sigma),sigma=0.0957949336093151

2202*

2203optimization finished, #iter = 559

2204nu = 0.32873173531098426

2205obj = -63.35295557273505, rho = -0.34803081450672674

2206nSV = 614, nBSV = 574

2207*

2208optimization finished, #iter = 554

2209nu = 0.31496140254386723

2210obj = -47.47651766858346, rho = -0.07078628792450056

2211nSV = 479, nBSV = 432

2212*

2213optimization finished, #iter = 508

2214nu = 0.3137067911493844

2215obj = -46.31478620814275, rho = -0.14052725101510452

2216nSV = 474, nBSV = 423

2217*

2218optimization finished, #iter = 489

2219nu = 0.3099347994005572

2220obj = -48.6228532302045, rho = -0.05803398147596895

2221nSV = 473, nBSV = 420

2222*

2223optimization finished, #iter = 519

2224nu = 0.314522429625119

2225obj = -48.32947238066246, rho = -0.14988224167817624

2226nSV = 478, nBSV = 429

2227*

2228optimization finished, #iter = 543

2229nu = 0.30905585299589106

2230obj = -47.54386848486968, rho = -0.3100998428078414

2231nSV = 476, nBSV = 420

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

2233z: Laplace distribution e^(-|z|/sigma)/(2sigma),sigma=0.09469480500273796

2234*

2235optimization finished, #iter = 629

2236nu = 0.31050957630127235

2237obj = -58.99742838311287, rho = -0.11795899327038137

2238nSV = 584, nBSV = 528

2239*

2240optimization finished, #iter = 432

2241nu = 0.332808438273609

2242obj = -52.42381892212391, rho = -0.3497131944828267

2243nSV = 500, nBSV = 459

2244*

2245optimization finished, #iter = 375

2246nu = 0.33436782304830515

2247obj = -54.242445367741894, rho = -0.3418245333994896

2248nSV = 495, nBSV = 466

2249*

2250optimization finished, #iter = 427

2251nu = 0.341509943560584

2252obj = -49.74083107598033, rho = -0.3375707533373116

2253nSV = 503, nBSV = 479

2254*

2255optimization finished, #iter = 423

2256nu = 0.32289345975670863

2257obj = -49.42053929560217, rho = -0.3231532727742852

2258nSV = 479, nBSV = 448

2259*

2260optimization finished, #iter = 459

2261nu = 0.33810921423817475

2262obj = -52.473991005318915, rho = -0.31480476176909095

2263nSV = 503, nBSV = 471

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

2265z: Laplace distribution e^(-|z|/sigma)/(2sigma),sigma=0.09630647239081286

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 = 49434

2275epsilon = 0.05959308356006498

2276obj = -105.73603866115391, rho = -0.17625968568225328

2277nSV = 775, nBSV = 659

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

2279optimization finished, #iter = 94938

2280epsilon = 0.05682390443446447

2281obj = -104.60744396557159, rho = -0.30764725392072

2282nSV = 774, nBSV = 656

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

2284optimization finished, #iter = 59177

2285epsilon = 0.05805032067185771

2286obj = -107.66562250602873, rho = -0.2921117939797214

2287nSV = 775, nBSV = 662

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

2289optimization finished, #iter = 65744

2290epsilon = 0.05684192628103968

2291obj = -104.25717105671089, rho = -0.38860454460593125

2292nSV = 777, nBSV = 659

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

2294optimization finished, #iter = 69312

2295epsilon = 0.059388299074605744

2296obj = -106.84451411060228, rho = -0.2963363218347312

2297nSV = 776, nBSV = 659

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

2299z: Laplace distribution e^(-|z|/sigma)/(2sigma),sigma=0.09562114535359112

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

2301optimization finished, #iter = 91034

2302epsilon = 0.05944570893531101

2303obj = -133.67027363116608, rho = -0.22082834234372709

2304nSV = 961, nBSV = 839

2305*

2306optimization finished, #iter = 866

2307epsilon = 0.05740064422852156

2308obj = -118.90272969022493, rho = -0.33878336601401304

2309nSV = 738, nBSV = 698

2310*

2311optimization finished, #iter = 807

2312epsilon = 0.05578807313704015

2313obj = -116.95419793319816, rho = -0.22887512887250516

2314nSV = 736, nBSV = 698

2315*

2316optimization finished, #iter = 834

2317epsilon = 0.055200631653374604

2318obj = -118.31760039203107, rho = -0.2431743136502306

2319nSV = 745, nBSV = 699

2320*

2321optimization finished, #iter = 847

2322epsilon = 0.0554955416040096

2323obj = -116.58419442595923, rho = -0.29361563915748434

2324nSV = 739, nBSV = 695

2325*

2326optimization finished, #iter = 818

2327epsilon = 0.05593818125126099

2328obj = -116.47365700171603, rho = -0.3136543604881914

2329nSV = 736, nBSV = 695

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

2331z: Laplace distribution e^(-|z|/sigma)/(2sigma),sigma=0.09356641117737034

2332.*

2333optimization finished, #iter = 1030

2334epsilon = 0.05639765783061974

2335obj = -145.96471729318776, rho = -0.2866861483069072

2336nSV = 917, nBSV = 874

2337.*

2338optimization finished, #iter = 1153

2339epsilon = 0.05454900309028918

2340obj = -113.89114273981824, rho = -0.15244240575022786

2341nSV = 749, nBSV = 686

2342.*

2343optimization finished, #iter = 1178

2344epsilon = 0.056343781318037064

2345obj = -113.4244494481308, rho = -0.2217979115335844

2346nSV = 750, nBSV = 685

2347.*

2348optimization finished, #iter = 1248

2349epsilon = 0.05426632844178235

2350obj = -112.34380924277323, rho = -0.23385425653676994

2351nSV = 754, nBSV = 683

2352.*

2353optimization finished, #iter = 1267

2354epsilon = 0.055985609071878606

2355obj = -113.50180649830592, rho = -0.16600040800219754

2356nSV = 750, nBSV = 681

2357.*

2358optimization finished, #iter = 1158

2359epsilon = 0.05128963577589525

2360obj = -110.2155994312037, rho = -0.19605266970298557

2361nSV = 752, nBSV = 686

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

2363z: Laplace distribution e^(-|z|/sigma)/(2sigma),sigma=0.09025906595305305

2364.

2366*

2367optimization finished, #iter = 1485

2368epsilon = 0.054878816933817506

2369obj = -140.12235768223275, rho = -0.15015265276473888

2370nSV = 932, nBSV = 860

2371*

2372optimization finished, #iter = 885

2373epsilon = 0.05855462396868866

2374obj = -116.83424606642679, rho = -0.2987345087813784

2375nSV = 738, nBSV = 695

2376*

2377optimization finished, #iter = 792

2378epsilon = 0.05782035658388522

2379obj = -117.70005655861804, rho = -0.2937524645985628

2380nSV = 736, nBSV = 691

2381*

2382optimization finished, #iter = 866

2383epsilon = 0.055876387754978094

2384obj = -117.02683961552181, rho = -0.281852278703776

2385nSV = 738, nBSV = 698

2386*

2387optimization finished, #iter = 937

2388epsilon = 0.05695603220010849

2389obj = -119.42559381540217, rho = -0.2923276639202392

2390nSV = 741, nBSV = 697

2391*

2392optimization finished, #iter = 813

2393epsilon = 0.056640087675864065

2394obj = -118.8297121831166, rho = -0.30449218920197696

2395nSV = 737, nBSV = 697

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

2397z: Laplace distribution e^(-|z|/sigma)/(2sigma),sigma=0.09265943308713301

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

248323

248425

248524

248613

248718

248815

248921

249020

249116

249222

249317

249414

249519

2496[info] TestThreading:

2497[info] TestParentheses:

2499Build timeouts: 1, would retry

2500Retrying build, retry 1/2, force Scala version:false, enable migration:

2501[sbt_options] declare -a sbt_options=()

2502[process_args] java_version = '17'

2503[copyRt] java9_rt = '/root/.sbt/1.0/java9-rt-ext-eclipse_adoptium_17_0_8/rt.jar'

2504# Executing command line:

2505java

2506-Dfile.encoding=UTF-8

2507-Xmx10g

2508-XX:MaxMetaspaceSize=10g

2509-Dcommunitybuild.scala=3.8.0-RC3

2510-Dcommunitybuild.project.dependencies.add=

2511-Xmx7G

2512-Xms4G

2513-Xss8M

2514-Dsbt.script=/root/.sdkman/candidates/sbt/current/bin/sbt

2515-Dscala.ext.dirs=/root/.sbt/1.0/java9-rt-ext-eclipse_adoptium_17_0_8

2516-jar

2517/root/.sdkman/candidates/sbt/1.11.5/bin/sbt-launch.jar

2518"setCrossScalaVersions 3.8.0-RC3"

2519"++3.8.0-RC3 -v"

2520"mapScalacOptions ",REQUIRE:-source:3.8,-Wconf:msg=can be rewritten automatically under:s" ",-deprecation,-feature,-Xfatal-warnings,-Werror,MATCH:.*-Wconf.*any:e""

2521"set every credentials := Nil"

2522"excludeLibraryDependency com.github.ghik:zerowaste_{scalaVersion} com.olegpy:better-monadic-for_3 org.polyvariant:better-tostring_{scalaVersion} org.wartremover:wartremover_{scalaVersion}"

2523"removeScalacOptionsStartingWith -P:wartremover"

2525moduleMappings

2526"runBuild 3.8.0-RC3 """{"tests":null}""" org.clulab%processors org.clulab%processors-apps org.clulab%processors-debugger"

2528[info] welcome to sbt 1.11.5 (Eclipse Adoptium Java 17.0.8)

2529[info] loading settings for project repo-build from akka.sbt, plugins.sbt...

2530[info] loading project definition from /build/repo/project

2531[info] loading settings for project root from build.sbt, compile.sbt, publish.sbt, release.sbt, test.sbt, version.sbt...

2532[info] loading settings for project library from assembly.sbt, build.sbt, compile.sbt, publish.sbt, test.sbt...

2533[info] loading settings for project apps from assembly.sbt, build.sbt...

2534[info] loading settings for project webapp from build.sbt, docker.sbt...

2535[info] loading settings for project debugger from build.sbt, publish.sbt...

2536[info] set current project to root (in build file:/build/repo/)

2537Execute setCrossScalaVersions: 3.8.0-RC3

2538OpenCB::Changing crossVersion 3.1.3 -> 3.8.0-RC3 in root/crossScalaVersions

2539OpenCB::Changing crossVersion 3.1.3 -> 3.8.0-RC3 in library/crossScalaVersions

2540OpenCB::Changing crossVersion 3.1.3 -> 3.8.0-RC3 in apps/crossScalaVersions

2541OpenCB::Changing crossVersion 3.1.3 -> 3.8.0-RC3 in debugger/crossScalaVersions

2542[info] set current project to root (in build file:/build/repo/)

2543[info] Setting Scala version to 3.8.0-RC3 on 4 projects.

2544[info] Switching Scala version on:

2545[info] * root (2.12.19, 2.11.12, 2.13.14, 3.8.0-RC3)

2546[info] library (2.12.19, 2.11.12, 2.13.14, 3.8.0-RC3)

2547[info] debugger (2.12.19, 2.11.12, 2.13.14, 3.8.0-RC3)

2548[info] apps (2.12.19, 2.11.12, 2.13.14, 3.8.0-RC3)

2549[info] Excluding projects:

2550[info] webapp (2.12.19)

2551[info] Reapplying settings...

2552[info] set current project to root (in build file:/build/repo/)

2553Execute mapScalacOptions: ,REQUIRE:-source:3.8,-Wconf:msg=can be rewritten automatically under:s ,-deprecation,-feature,-Xfatal-warnings,-Werror,MATCH:.*-Wconf.*any:e

2554[info] Reapplying settings...

2555[info] set current project to root (in build file:/build/repo/)

2556[info] Defining Global / credentials, apps / credentials and 3 others.

2557[info] The new values will be used by Global / pgpSelectPassphrase, allCredentials and 23 others.

2558[info] Run `last` for details.

2559[info] Reapplying settings...

2560[info] set current project to root (in build file:/build/repo/)

2561Execute excludeLibraryDependency: com.github.ghik:zerowaste_{scalaVersion} com.olegpy:better-monadic-for_3 org.polyvariant:better-tostring_{scalaVersion} org.wartremover:wartremover_{scalaVersion}

2562[info] Reapplying settings...

2563OpenCB::Failed to reapply settings in excludeLibraryDependency: Reference to undefined setting:

2565 Global / allExcludeDependencies from Global / allExcludeDependencies (CommunityBuildPlugin.scala:331)

2566 Did you mean allExcludeDependencies ?

2567 , retry without global scopes

2568[info] Reapplying settings...

2569[info] set current project to root (in build file:/build/repo/)

2570Execute removeScalacOptionsStartingWith: -P:wartremover

2571[info] Reapplying settings...

2572[info] set current project to root (in build file:/build/repo/)

2573[success] Total time: 0 s, completed Dec 4, 2025, 5:23:46 PM

2574Build config: {"tests":null}

2576Starting build...

2577Projects: Set(library, apps, debugger)

2578Starting build for ProjectRef(file:/build/repo/,library) (processors)... [0/3]

2579OpenCB::Exclude Scala3 specific scalacOption `REQUIRE:-source:3.8` in Scala 2.12.20 module Global

2580OpenCB::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)

2581OpenCB::Filter out '-feature', matches setting pattern '^-?-feature'

2582OpenCB::Filter out '-deprecation', matches setting pattern '^-?-deprecation'

2583Compile scalacOptions: -unchecked, -explain, -Wconf:msg=can be rewritten automatically under:s, -source:3.8

2584[info] TestHashTrie:

2585[info] the trie

2586[info] - should label the text correctly with BIO labels

2587[info] the trie

2588[info] - should have 2 entries and contain 5 unique strings

2589[info] the trie

2590[info] - should sort and find the entries correctly

2591[info] the trie

2592[info] - should make use of shouldStop

2593SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".

2594SLF4J: Defaulting to no-operation (NOP) logger implementation

2595SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.

2596[info] TestDueTo:

2597[Tokenizer] Checking /build/repo for intel-librust_tokenizer.so...

2598[Tokenizer] Checking /root for intel-librust_tokenizer.so...

2599[Tokenizer] Extracting resource intel-librust_tokenizer.so to /tmp/intel-librust_tokenizer-17979377711070039211.so...

2600[info] org.clulab.processors.TestDueTo *** ABORTED ***

2602[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

2603[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

2604[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

2605[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

2606[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

2607[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

2608[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

2609[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

2610[info] at org.scalatest.BeforeAndAfterAll.run$(BeforeAndAfterAll.scala:135)

2611[info] at org.clulab.processors.CluTest.run(CluTest.scala:9)

2612[info] ...

2614[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

2615[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

2616[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

2617[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

2618[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

2619[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

2620[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

2621[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

2622[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

2623[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

2624[info] ...

2664[info] TestDoc58b0:

2665[info] org.clulab.processors.docs.TestDoc58b0 *** ABORTED ***

2667[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

2668[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

2669[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

2670[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

2671[info] at org.clulab.processors.docs.TestDoc58b0.<init>(TestDoc58b0.scala:10)

2672[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

2673[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)

2674[info] at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)

2675[info] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)

2676[info] at java.base/java.lang.reflect.ReflectAccess.newInstance(ReflectAccess.java:128)

2677[info] ...

2679[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

2680[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

2681[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

2682[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

2683[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

2684[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

2685[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

2686[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

2687[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

2688[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

2689[info] ...

2730[info] TestNumericPatterns:

2731[info] Any text

2732[info] - should contain one match for pattern `[2+2==4]`

2733[info] Any text

2734[info] - should contain no matches for pattern `[2+2==5]`

2735[info] TestArray:

2736[info] Array.toSeq

2737[info] - should work as expected without import

2738[info] - should work as expected with import

2739[info] Array.toIndexedSeq

2740[info] - should work as expected without import

2741[info] - should work as expected with import

2742[info] MutableArraySeq.from

2743[info] - should work as expected without import

2744[info] - should work as expected with import

2745[info] ImmutableArraySeq.unsafeWrapArray

2746[info] - should work as expected without import

2747[info] - should work as expected with import

2748[info] processSeq(array)

2749[info] - should work as expected without import

2750[info] - should work as expected with import

2751[info] processSeq(ImmutableArraySeq.unsafeWrapArray)

2752[info] - should work as expected without import

2753[info] - should work as expected with import

2754[info] processIndexedSeq(array)

2755[info] - should work as expected without import

2756[info] - should work as expected with import

2757[info] processIndexedSeq(ImmutableArraySeq.unsafeWrapArray)

2758[info] - should work as expected without import

2759[info] - should work as expected with import

2760[info] :Seq[]

2761[info] - should work as expected without import

2762[info] - should work as expected with import

2763[info] :IndexedSeq[]

2764[info] - should work as expected without import

2765[info] - should work as expected with import

2766[info] foreach

2767[info] - should work as expected without import

2768[info] - should work as expected with import

2769[info] zip

2770[info] - should work as expected without import

2771[info] - should work as expected with import

2772[info] map

2773[info] - should work as expected without import

2774[info] - should work as expected with import

2775[info] TestNumberParser:

2776[info] NumberParser

2777[info] - should parse digits

2778[info] - should fail on invalid input

2779[info] - should fail on empty input

2780[info] - should convert words to numbers

2781[info] - should parses decimal numbers

2782[info] - should convert numbers and words to numbers

2783[info] - should parse words to numbers

2784[info] TestMinHeap:

2785[info] MinHeap

2786[info] - should order elements properly

2787[info] - should keep correct top K

2788[info] TestProgressBar:

2789[info] ProgressBar

2791Progress 0% │██▉ │ 0/10 (0:00:00 / 0:00:00)

2792Progress 20% │█████▊ │ 2/10 (0:00:02 / 0:00:08)

2793Progress 30% │████████▋ │ 3/10 (0:00:03 / 0:00:07)

2794Progress 40% │███████████▌ │ 4/10 (0:00:04 / 0:00:06)

2795Progress 50% │██████████████▌ │ 5/10 (0:00:05 / 0:00:05)

2796Progress 60% │█████████████████▍ │ 6/10 (0:00:06 / 0:00:04)

2797Progress 70% │████████████████████▎ │ 7/10 (0:00:07 / 0:00:03)

2798Progress 80% │███████████████████████▏ │ 8/10 (0:00:08 / 0:00:02)

2799Progress 90% │██████████████████████████ │ 9/10 (0:00:09 / 0:00:01)

2800Progress 100% │█████████████████████████████│ 10/10 (0:00:10 / 0:00:00) [info] - should progress

2802Progress 0% │ │ 0/11 (0:00:00 / ?)

2803Progress 9% │██▋ │ 1/11 (0:00:01 / 0:00:10)

2804Progress 18% │████▌ │ 2/11 (0:00:02 / 0:00:09) at 0

2805Progress 27% │██████▊ │ 3/11 (0:00:03 / 0:00:08) at 1

2806Progress 36% │█████████ │ 4/11 (0:00:04 / 0:00:07) at 2

2807Progress 45% │███████████▎ │ 5/11 (0:00:05 / 0:00:06) at 3

2808Progress 54% │█████████████▋ │ 6/11 (0:00:06 / 0:00:05) at 4

2809Progress 63% │███████████████▉ │ 7/11 (0:00:07 / 0:00:04) at 5

2810Progress 72% │██████████████████▏ │ 8/11 (0:00:08 / 0:00:03) at 6

2811Progress 81% │████████████████████▍ │ 9/11 (0:00:09 / 0:00:02) at 7

2812Progress 90% │██████████████████████▋ │ 10/11 (0:00:10 / 0:00:01) at 8

2813Progress 100% │█████████████████████████│ 11/11 (0:00:11 / 0:00:00) at 9[info] - should show extra messages

2814[info] TestCorefChains:

2815[info] CorefChains

2816[info] - should sort on sentenceIndex

2817[info] - should sort on headIndex

2818[info] - should sort on size

2819[info] - should sort on index

2820[info] TestExtractorEngine:

2821[info] ExtractorEngine

2822[info] - should read utf8 encoded data

2823[info] - should read latin1 encoded data

2825[info] - should read data incorrectly if using the wrong charset

2826[info] TestNamedEntity:

2827[info] NamedEntity identification

2828[info] - should collect properly test 1

2829[info] - should collect properly test 2

2830[info] - should collect properly test 3

2831[info] - should collect properly test 4

2832[info] - should collect properly test 5

2833[info] - should collect properly test 6

2834[info] - should collect properly test 7

2835[info] - should collect properly test 8

2836[info] - should collect properly test 9

2837[info] - should collect properly test 10

2838[info] - should collect properly test 11

2839[info] - should collect properly test 12

2840[info] - should collect properly test 13

2841[info] - should collect properly test 14

2842[info] - should collect properly test 15

2843[info] - should combine properly test 1

2844[info] - should combine properly test 2

2845[info] - should combine properly test 3

2846[info] - should combine properly test 4

2847[info] - should combine properly test 5

2848[info] - should combine properly test 6

2849[info] - should combine properly test 7

2850[info] - should combine properly test 8

2851[info] - should combine properly test 9

2852[info] - should combine properly test 10

2853[info] - should combine properly test 11

2854[info] - should combine properly test 12

2855[info] - should combine properly test 13

2856[info] - should combine properly test 14

2857[info] - should combine properly test 15

2858[info] - should combine properly test 16

2859[info] - should combine properly test 17

2860[info] - should combine properly test 18

2861[info] - should combine properly test 19

2862[info] - should combine properly test 20

2863[info] NamedEntity validation

2864[info] - should validate the BIO notation test 1

2865[info] - should validate the BIO notation test 2

2866[info] - should validate the BIO notation test 3

2867[info] - should validate the BIO notation test 4

2868[info] - should validate the BIO notation test 5

2869[info] - should validate the BIO notation test 6

2870[info] - should validate the BIO notation test 7

2871[info] - should validate the BIO notation test 8

2872[info] - should validate the BIO notation test 9

2873[info] NamedEntity correction

2874[info] - should correct the BIO notation test 1

2875[info] - should correct the BIO notation test 2

2876[info] - should correct the BIO notation test 3

2877[info] - should correct the BIO notation test 4

2878[info] - should correct the BIO notation test 5

2879[info] - should correct the BIO notation test 6

2880[info] - should correct the BIO notation test 7

2881[info] - should correct the BIO notation test 8

2882[info] - should correct the BIO notation test 9

2883[info] TestTimer:

2884[info] timer

2885[info] - should use the right divisors

2886[info] TestDistributionalSimilarityPatterns:

2887[info] I saw a leopard climbing a tree.

2888[info] - should produce a mention with the label "Feline" for the word "leopard"

2889[info] TestSerializer:

2890[info] - should serialize/deserialize a Mention correctly

2891[info] - should serialize/deserialize a CrossSentenceMention correctly

2892[info] TestUniversalEnhancedDependencies:

2893[info] org.clulab.processors.TestUniversalEnhancedDependencies *** ABORTED ***

2895[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

2896[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

2897[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

2898[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

2899[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

2900[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

2901[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

2902[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

2903[info] at org.scalatest.BeforeAndAfterAll.run$(BeforeAndAfterAll.scala:135)

2904[info] at org.clulab.processors.CluTest.run(CluTest.scala:9)

2905[info] ...

2907[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

2908[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

2909[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

2910[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

2911[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

2912[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

2913[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

2914[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

2915[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

2916[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

2917[info] ...

2957[info] CluTest:

2958[info] TestJSONSerializer:

2959[info] JSONSerializer

2960[info] - should serialize/deserialize a Document to/from json correctly

2961[info] - should serialize/deserialize a Sentence to/from json correctly

2962[info] A Document with an ID

2963[info] - should produce json with an "id" field

2964[info] A Document without an ID

2965[info] - should produce json without an "id" field

2966[info] A Document with text

2967[info] - should produce json with a "text" field

2968[info] A Document without text

2969[info] - should produce json without a "text" field

2970[info] A Document recovered from JSON

2971[info] - should be equivalent to the original

2972[info] A Sentence recovered from JSON

2973[info] - should be equivalent to the original

2974[info] A Document saved and loaded

2975[info] - should have JSON equivalent to the original

2976[info] TestGraphPatternSD:

2977[info] GraphPattern

2978[info] - should support multiline patterns

2979[info] - should produce one mention at a time for an argument without any quantifier

2980[info] - should support optional arguments

2981[info] - should support exact quantifiers for arguments

2982[info] - should support * for arguments

2983[info] - should support + for arguments

2984[info] - should support greedy open range quantifiers for arguments

2985[info] - should handle multitoken triggers

2986[info] - should support 'type: graph'

2987[info] - should support 'graph: ' key

2988[info] - should ignore 'graph: ' when 'type: dependency'

2989[info] TestNumericEntityRecognition:

2990[info] org.clulab.numeric.TestNumericEntityRecognition *** ABORTED ***

2992[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

2993[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

2994[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

2995[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

2996[info] at org.clulab.numeric.TestNumericEntityRecognition$HabitusProcessor.<init>(TestNumericEntityRecognition.scala:44)

2997[info] at org.clulab.numeric.TestNumericEntityRecognition.<init>(TestNumericEntityRecognition.scala:50)

2998[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

2999[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)

3000[info] at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)

3001[info] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)

3002[info] ...

3004[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

3005[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

3006[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3007[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3008[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3009[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3010[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

3011[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

3012[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

3013[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

3014[info] ...

3056[info] TestMarkdownGeneration:

3057[info] MarkdownGeneration

3058[info] - should not crash

3059[info] - should properly aggregate argument requiredness

3060[info] TestCrLf:

3061[info] resources

3062[info] TestEvalTimeNorm:

3063[info] temporal parser

3064[info] org.clulab.numeric.TestEvalTimeNorm *** ABORTED ***

3066[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3067[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3068[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3069[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3070[info] at org.clulab.numeric.TestEvalTimeNorm.testFun$proxy1$1(TestEvalTimeNorm.scala:12)

3071[info] at org.clulab.numeric.TestEvalTimeNorm.$init$$$anonfun$1(TestEvalTimeNorm.scala:10)

3072[info] at org.scalatest.Transformer.apply$$anonfun$1(Transformer.scala:22)

3073[info] at org.scalatest.OutcomeOf.outcomeOf(OutcomeOf.scala:85)

3074[info] at org.scalatest.OutcomeOf.outcomeOf$(OutcomeOf.scala:31)

3075[info] at org.scalatest.OutcomeOf$.outcomeOf(OutcomeOf.scala:104)

3076[info] ...

3078[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

3079[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

3080[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3081[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3082[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3083[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3084[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

3085[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

3086[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

3087[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

3088[info] ...

3098loading props from file library/src/test/resources/org/clulab/utils/test.properties

3099Using the following properties:

3100 p1 = /some/path

3101 p2 = /some/path/subdir/123

3102 p3 = 123

3103loading props from file library/src/test/resources/org/clulab/utils/test.properties

3104Using the following properties:

3105 p1 = /some/path

3106 p2 = /some/path/subdir/123

3107 p3 = 123

3175[info] TestArgsToProperties:

3176[info] properties

3177[info] - should contain p1 with value /some/path

3178[info] - should contain p2 with the value /some/path/subdir/123

3179[info] properties as a map

3180[info] - should contain p1 with value /some/path

3181[info] - should contain p2 with the value /some/path/subdir/123

3182[info] argsToMap

3183[info] - should deal with plain values

3184Using the following properties:

3185 = in inDirectory out outDirectory

3186[info] TestInst:

3187[info] Inst

3188[info] - should not distinguish Done and Done

3189[info] - should distinguish Done and Pass

3190[info] - should distinguish MatchLookAhead and MatchLookBehind

3191[info] - should distinguish SaveStart and SaveEnd

3192[info] - should distinguish Done and MatchToken

3193[info] - should distinguish between Pass and Pass

3194[info] - should distinguish between MatchToken and MatchToken

3195[info] - should copy Pass appropriately

3196[info] - should copy Split appropriately

3197[info] - should copy SaveStart appropriately

3198[info] - should copy SaveEnd appropriately

3199[info] - should copy MatchToken appropriately

3200[info] - should copy MatchMention appropriately

3201[info] - should copy MatchSentenceStart appropriately

3202[info] - should copy MatchSentenceEnd appropriately

3203[info] - should copy MatchLookAhead appropriately

3204[info] - should copy MatchLookBehind appropriately

3205[info] - should distinguish complicated instances

3206[info] CaseClasses

3207[info] - should compare as intended

3208[info] tuple hashes

3209[info] - should be called recursively

3210[info] TestGraphPattern:

3211[info] graph range {0,n}

3213[info] GraphPattern

3214[info] - should support multiline patterns

3215[info] - should produce one mention at a time for an argument without any quantifier

3216[info] - should support optional arguments

3217[info] - should support exact quantifiers for arguments

3218[info] - should support * for arguments

3220[info] - should support + for arguments

3222[info] - should support greedy open range quantifiers for arguments

3225[info] - should handle multitoken triggers

3226[info] - should support 'type: graph'

3227[info] - should support 'graph: ' key

3228[info] - should ignore 'graph: ' when 'type: dependency'

3229[info] - should require a registered graph type wherever 'graph: ' is specified

3230[info] - should handle colons in dependencies

3231[info] - should handle colons in dependencies without quotes

3232[info] TestRandomForestClassifier:

3233[info] RFClassifier

3234Current utility:

3235UTILITY DEBUG:

3236Using dataset:

3237label:0 features:[0:2.0, 1:1.0]

3238label:1 features:[0:2.0, 2:1.0, 3:1.0]

3239label:1 features:[0:1.0, 4:1.0]

3240Using feature 3 with threshold 0.5

3241Contingency table for this feature+threshold is: SMALLER: [0:1.0, 1:1.0], GREATER: [1:1.0]

3242Overall utility: 0.2516291673878229

3243Parent utility: 0.9182958340544896

3244Utility of left child: 1.0

3245Utility of right child: 0.0

3246CHOSEN NEW BEST!

3247Current utility:

3248UTILITY DEBUG:

3249Using dataset:

3250label:0 features:[0:2.0, 1:1.0]

3251label:1 features:[0:2.0, 2:1.0, 3:1.0]

3252label:1 features:[0:1.0, 4:1.0]

3253Using feature 4 with threshold 0.5

3254Contingency table for this feature+threshold is: SMALLER: [0:1.0, 1:1.0], GREATER: [1:1.0]

3255Overall utility: 0.2516291673878229

3256Parent utility: 0.9182958340544896

3257Utility of left child: 1.0

3258Utility of right child: 0.0

3259Current utility:

3260UTILITY DEBUG:

3261Using dataset:

3262label:0 features:[0:2.0, 1:1.0]

3263label:1 features:[0:2.0, 2:1.0, 3:1.0]

3264label:1 features:[0:1.0, 4:1.0]

3265Using feature 0 with threshold 1.5

3266Contingency table for this feature+threshold is: SMALLER: [0:0.0, 1:1.0], GREATER: [0:1.0, 1:1.0]

3267Overall utility: 0.2516291673878229

3268Parent utility: 0.9182958340544896

3269Utility of left child: 0.0

3270Utility of right child: 1.0

3271Current utility:

3272UTILITY DEBUG:

3273Using dataset:

3274label:0 features:[0:2.0, 1:1.0]

3275label:1 features:[0:2.0, 2:1.0, 3:1.0]

3276label:1 features:[0:1.0, 4:1.0]

3277Using feature 1 with threshold 0.5

3278Contingency table for this feature+threshold is: SMALLER: [0:0.0, 1:2.0], GREATER: [0:1.0]

3279Overall utility: 0.9182958340544896

3280Parent utility: 0.9182958340544896

3281Utility of left child: 0.0

3282Utility of right child: 0.0

3283CHOSEN NEW BEST!

3284Current utility:

3285UTILITY DEBUG:

3286Using dataset:

3287label:0 features:[0:2.0, 1:1.0]

3288label:1 features:[0:2.0, 2:1.0, 3:1.0]

3289label:1 features:[0:1.0, 4:1.0]

3290Using feature 2 with threshold 0.5

3291Contingency table for this feature+threshold is: SMALLER: [0:1.0, 1:1.0], GREATER: [1:1.0]

3292Overall utility: 0.2516291673878229

3293Parent utility: 0.9182958340544896

3294Utility of left child: 1.0

3295Utility of right child: 0.0

3296BEST OVERALL:

3297UTILITY DEBUG:

3298Using dataset:

3299label:0 features:[0:2.0, 1:1.0]

3300label:1 features:[0:2.0, 2:1.0, 3:1.0]

3301label:1 features:[0:1.0, 4:1.0]

3302Using feature 1 with threshold 0.5

3303Contingency table for this feature+threshold is: SMALLER: [0:0.0, 1:2.0], GREATER: [0:1.0]

3304Overall utility: 0.9182958340544896

3305Parent utility: 0.9182958340544896

3306Utility of left child: 0.0

3307Utility of right child: 0.0

3308Current utility:

3309UTILITY DEBUG:

3310Using dataset:

3311label:1 features:[0:2.0, 2:1.0, 3:1.0]

3312label:1 features:[0:1.0, 4:1.0]

3313Using feature 2 with threshold 0.5

3314Contingency table for this feature+threshold is: SMALLER: [1:1.0], GREATER: [1:1.0]

3315Overall utility: 0.0

3316Parent utility: 0.0

3317Utility of left child: 0.0

3318Utility of right child: 0.0

3319CHOSEN NEW BEST!

3320Current utility:

3321UTILITY DEBUG:

3322Using dataset:

3323label:1 features:[0:2.0, 2:1.0, 3:1.0]

3324label:1 features:[0:1.0, 4:1.0]

3325Using feature 4 with threshold 0.5

3326Contingency table for this feature+threshold is: SMALLER: [1:1.0], GREATER: [1:1.0]

3327Overall utility: 0.0

3328Parent utility: 0.0

3329Utility of left child: 0.0

3330Utility of right child: 0.0

3331Current utility:

3332UTILITY DEBUG:

3333Using dataset:

3334label:1 features:[0:2.0, 2:1.0, 3:1.0]

3335label:1 features:[0:1.0, 4:1.0]

3336Using feature 0 with threshold 1.5

3337Contingency table for this feature+threshold is: SMALLER: [1:1.0], GREATER: [1:1.0]

3338Overall utility: 0.0

3339Parent utility: 0.0

3340Utility of left child: 0.0

3341Utility of right child: 0.0

3342Current utility:

3343UTILITY DEBUG:

3344Using dataset:

3345label:1 features:[0:2.0, 2:1.0, 3:1.0]

3346label:1 features:[0:1.0, 4:1.0]

3347Using feature 3 with threshold 0.5

3348Contingency table for this feature+threshold is: SMALLER: [1:1.0], GREATER: [1:1.0]

3349Overall utility: 0.0

3350Parent utility: 0.0

3351Utility of left child: 0.0

3352Utility of right child: 0.0

3353BEST OVERALL:

3354UTILITY DEBUG:

3355Using dataset:

3356label:1 features:[0:2.0, 2:1.0, 3:1.0]

3357label:1 features:[0:1.0, 4:1.0]

3358Using feature 2 with threshold 0.5

3359Contingency table for this feature+threshold is: SMALLER: [1:1.0], GREATER: [1:1.0]

3360Overall utility: 0.0

3361Parent utility: 0.0

3362Utility of left child: 0.0

3363Utility of right child: 0.0

3364Class of List(good, horrible): -

3365Class of List(bad, horrible): -

3366Class of List(good, great): +

3367[info] - should work with BVFDataset

3368[info] RandomForestClassifier

3369Accuracy: 0.965

3370[info] - should have an accuracy > .95 on this dataset

3371[info] TestLiblinearClassifier:

3372[info] LiblinearClassifier

3373iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00 CG 2

3374iter 2 act 8.879e-04 pre 8.833e-04 delta 8.463e-01 f 1.459e+00 |g| 5.811e-02 CG 1

3375iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00 CG 2

3376iter 2 act 8.879e-04 pre 8.833e-04 delta 8.463e-01 f 1.459e+00 |g| 5.811e-02 CG 1

3377iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00 CG 2

3378iter 2 act 8.879e-04 pre 8.833e-04 delta 8.463e-01 f 1.459e+00 |g| 5.811e-02 CG 1

3379[info] - should work with RVFDataset

3380iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00 CG 2

3381iter 2 act 8.879e-04 pre 8.833e-04 delta 8.463e-01 f 1.459e+00 |g| 5.811e-02 CG 1

3382iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00 CG 2

3383iter 2 act 8.879e-04 pre 8.833e-04 delta 8.463e-01 f 1.459e+00 |g| 5.811e-02 CG 1

3384iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00 CG 2

3385iter 2 act 8.879e-04 pre 8.833e-04 delta 8.463e-01 f 1.459e+00 |g| 5.811e-02 CG 1

3386iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00 CG 2

3387iter 2 act 8.879e-04 pre 8.833e-04 delta 8.463e-01 f 1.459e+00 |g| 5.811e-02 CG 1

3388iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00 CG 2

3389iter 2 act 8.879e-04 pre 8.833e-04 delta 8.463e-01 f 1.459e+00 |g| 5.811e-02 CG 1

3390iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00 CG 2

3391iter 2 act 8.879e-04 pre 8.833e-04 delta 8.463e-01 f 1.459e+00 |g| 5.811e-02 CG 1

3392[info] - should work with BVFDataset

3393iter 1 act 4.528e-01 pre 4.444e-01 delta 7.000e-01 f 1.386e+00 |g| 1.323e+00 CG 2

3394iter 2 act 8.651e-04 pre 8.605e-04 delta 7.000e-01 f 9.335e-01 |g| 5.750e-02 CG 1

3395[info] - should work with a two-label dataset

3396[info] LogisticRegressionClassifier

3397iter 1 act 7.243e+02 pre 6.698e+02 delta 1.883e+01 f 1.386e+03 |g| 9.617e+01 CG 4

3398iter 2 act 3.382e+01 pre 3.043e+01 delta 1.883e+01 f 6.620e+02 |g| 1.841e+01 CG 3

3399iter 3 act 2.260e+00 pre 2.083e+00 delta 1.883e+01 f 6.282e+02 |g| 4.186e+00 CG 3

3400iter 4 act 6.468e-02 pre 6.350e-02 delta 1.883e+01 f 6.259e+02 |g| 6.366e-01 CG 3

3401[info] - should have an accuracy > .97 in this dataset

3402[info] LinearSVMClassifier

3403iter 1 act 1.779e+03 pre 1.753e+03 delta 1.414e+01 f 2.000e+03 |g| 3.847e+02 CG 5

3404iter 2 act 4.189e+01 pre 4.076e+01 delta 1.414e+01 f 2.214e+02 |g| 3.417e+01 CG 6

3405iter 3 act 3.859e+00 pre 3.685e+00 delta 1.414e+01 f 1.795e+02 |g| 8.599e+00 CG 7

3406iter 4 act 5.435e-01 pre 5.117e-01 delta 1.414e+01 f 1.757e+02 |g| 2.475e+00 CG 6

3407[info] - should have an accuracy > .97 in this dataset

3408[info] HexaDecoderTest:

3409[info] HexaDecoder

3410Some(L (0, 3) (1, root)

3411 R (0, 1) (1, root)

3412 (0, nsubj)

3413 (1, root)

3414 R (2, 3) (3, dobj)

3415 (2, nmod)

3416 (3, dobj)

3417)

3418Dependencies (3):

3419Edge(1,3,dobj)

3420Edge(1,0,nsubj)

3421Edge(3,2,nmod)

3422Roots: 1

3423[info] - should decode a simple tree

3424Terminal tags: tl-nsubj, tl-cop, tl-det, tr-root

3425Nonterm tags: nl-R, nr-R, nr-R, eos

3426Processing terminal tag: tl-nsubj

3427Pushing:

3428(0, nsubj)

3429onto the stack.

3430Processing non-terminal tag: nl-R

3431Pushing:

3432R (0, -1) (-1, dummy)

3433 (0, nsubj)

3434 dummy

3435onto the stack.

3436[info] - should decode another simple tree

3437Processing terminal tag: tl-cop

3438Pushing:

3439(1, cop)

3440onto the stack.

3441Processing non-terminal tag: nr-R

3442Pushing:

3443R (0, -1) (-1, dummy)

3444 (0, nsubj)

3445 R (1, -1) (-1, dummy)

3446 (1, cop)

3447 dummy

3448onto the stack.

3449Processing terminal tag: tl-det

3450Pushing:

3451(2, det)

3452onto the stack.

3453Processing non-terminal tag: nr-R

3454Pushing:

3455R (0, -1) (-1, dummy)

3456 (0, nsubj)

3457 R (1, -1) (-1, dummy)

3458 (1, cop)

3459 R (2, -1) (-1, dummy)

3460 (2, det)

3461 dummy

3462onto the stack.

3463Processing terminal tag: tr-root

3464Pushing:

3465R (0, 3) (3, root)

3466 (0, nsubj)

3467 R (1, 3) (3, root)

3468 (1, cop)

3469 R (2, 3) (3, root)

3470 (2, det)

3471 (3, root)

3472onto the stack.

3473Some(R (0, 3) (3, root)

3474 (0, nsubj)

3475 R (1, 3) (3, root)

3476 (1, cop)

3477 R (2, 3) (3, root)

3478 (2, det)

3479 (3, root)

3480)

3481Dependencies (3):

3482List(Edge(3,0,nsubj), Edge(3,1,cop), Edge(3,2,det))

3483Roots: 3

3484[info] Test:

3485[info] TestEntityConstraints:

3486[info] Uneven parentheses

3487[info] - should be disallowed in entities

3488[info] Even parentheses

3489[info] - should be valid in entities

3490[info] Entities longer than n tokens

3491[info] - should be pruned

3492[info] TestMkCombinedDocument:

3493[info] org.clulab.processors.TestMkCombinedDocument *** ABORTED ***

3495[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3496[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3497[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3498[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3499[info] at org.clulab.processors.TestMkCombinedDocument.<init>(TestMkCombinedDocument.scala:28)

3500[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

3501[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)

3502[info] at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)

3503[info] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)

3504[info] at java.base/java.lang.reflect.ReflectAccess.newInstance(ReflectAccess.java:128)

3505[info] ...

3507[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

3508[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

3509[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3510[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3511[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3512[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3513[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

3514[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

3515[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

3516[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

3517[info] ...

3558[info] TestMathUtils:

3559[info] - should work with Seq

3560[info] - should not produce negative mean or variance

3561[info] - should work with Array

3562[info] - should work with any numeric collection

3563[info] - should be reasonably resilient to overflow

3564[info] TestDirectedGraph:

3565[info] DirectedGraph

3566[info] - should process a loop with a source

3567[info] - should process a loop without a source

3568[info] - should add lone roots

3569[info] - should handle disjoint loops

3570[info] - should not use a leading destination as a root

3571[info] - should be empty

3572[info] TestDependencyUtils:

3573[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.

3574[info] - should produce 'substrates' as the head of 'the substrates of Shp2'

3575[info] - should produce 'are' as the head of 'the substrates of Shp2 are'

3576[info] - should produce None for an empty Interval

3577[info] The docking protein Gab1 is the primary mediator of EGF-stimulated activation of the PI-3K/Akt cell survival pathway

3578[info] - should have the same getHeadStrict as roots

3579[info] - should produce only one head for getHeadsStrict

3580[info] - should produce None for an empty Interval

3581[info] - should produce two heads for 'docking protein' using getHeadsLocal

3582[info] - should think 'docking protein' is nested in 'docking protein Gab1'

3583[info] - should think 'the' is nested in 'Gab1'

3584[info] - should not think 'is' is nested in 'Gab1'

3585[info] - should think Interval(3,3) is nested in 'Gab1'

3586[info] - should not think 'pathway' is nested in 'Gab1'

3587[info] .

3588[info] - should produce one head using findHeads

3589[info] - should produce no heads using findHeadsStrict

3590[info] DependencyUtils

3591[info] - should handle cycles in the dependencyGraph correctly

3592[info] - should handle roots with incoming dependencies

3593[info] - should handle invalid dependency trees in findHeads

3594[info] - should only match complete stop tags

3595[info] TestNumericMentions:

3596[info] org.clulab.numeric.TestNumericMentions *** ABORTED ***

3598[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3599[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3600[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3601[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3602[info] at org.clulab.numeric.TestNumericMentions.<init>(TestNumericMentions.scala:7)

3603[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

3604[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)

3605[info] at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)

3606[info] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)

3607[info] at java.base/java.lang.reflect.ReflectAccess.newInstance(ReflectAccess.java:128)

3608[info] ...

3610[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

3611[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

3612[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3613[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3614[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3615[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3616[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

3617[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

3618[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

3619[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

3620[info] ...

3661[info] TestArrayView:

3662[info] ArrayView

3663[info] - should work with no offset

3664[info] - should work with an offset

3665[info] - should work when clipped

3666[info] TestDoc5501:

3667[info] org.clulab.processors.docs.TestDoc5501 *** ABORTED ***

3669[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3670[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3671[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3672[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3673[info] at org.clulab.processors.docs.TestDoc5501.<init>(TestDoc5501.scala:10)

3674[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

3675[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)

3676[info] at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)

3677[info] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)

3678[info] at java.base/java.lang.reflect.ReflectAccess.newInstance(ReflectAccess.java:128)

3679[info] ...

3681[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

3682[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

3683[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3684[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3685[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3686[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3687[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

3688[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

3689[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

3690[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

3691[info] ...

3732[info] TestLexiconNER:

3733[info] org.clulab.processors.TestLexiconNER *** ABORTED ***

3735[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3736[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3737[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3738[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3739[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

3740[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

3741[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

3742[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

3743[info] at org.scalatest.BeforeAndAfterAll.run$(BeforeAndAfterAll.scala:135)

3744[info] at org.clulab.processors.CluTest.run(CluTest.scala:9)

3745[info] ...

3747[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

3748[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

3749[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3750[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3751[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3752[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3753[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

3754[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

3755[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

3756[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

3757[info] ...

3797[info] TestTaxonomy:

3798[info] taxonomy

3799[info] - should inform a rule's labels

3800[info] TestProcessor:

3801[info] org.clulab.processors.TestProcessor *** ABORTED ***

3803[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3804[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3805[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3806[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3807[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

3808[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

3809[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

3810[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

3811[info] at org.scalatest.BeforeAndAfterAll.run$(BeforeAndAfterAll.scala:135)

3812[info] at org.clulab.processors.CluTest.run(CluTest.scala:9)

3813[info] ...

3815[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

3816[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

3817[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3818[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3819[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3820[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3821[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

3822[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

3823[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

3824[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

3825[info] ...

3865Tokenizing text: the of $><1/2 1.3 another test.

3866[info] TestTokenizer:

3867[info] the tokenizer

3868 Sentence #0: the of $ > < 1/2 1.3 another test .

3869Tokenizing text: -LRB- -RRB- -LCB- -RCB- -LSB- -RSB-.

3870 Sentence #0: -LRB- -RRB- -LCB- -RCB- -LSB- -RSB- .

3871Tokenizing text: first sentence. second sentence.

3872 Sentence #0: first sentence .

3873 Sentence #1: second sentence .

3874Tokenizing text: Artocarpus lacucha Buch.-Ham. ex D.Don is monkey fruit. Second sentence.

3875 Sentence #0: Artocarpus lacucha Buch. - Ham. ex D.Don is monkey fruit .

3876 Sentence #1: Second sentence .

3877Tokenizing text: Zizania caduciflora Hand.-Mazz. is a grass. Second sentence.

3878 Sentence #0: Zizania caduciflora Hand. - Mazz. is a grass .

3879 Sentence #1: Second sentence .

3880Tokenizing text: Fig. 1 shows the fungus Gaeumannomyces graminis var. tritici (Ggt), a major root disease of wheat.

3881 Sentence #0: Fig. 1 shows the fungus Gaeumannomyces graminis var. tritici ( Ggt ) , a major root disease of wheat .

3882Tokenizing text: Campylobacter spp. are ubiquitous.

3883 Sentence #0: Campylobacter spp. are ubiquitous .

3884Tokenizing text: today is 12/25/2017

3885 Sentence #0: today is 12/25/2017

3886Tokenizing text: today is 12/255/2017

3887 Sentence #0: today is 12/255 / 2017

3888Tokenizing text: number is -122,333

3889 Sentence #0: number is -122,333

3890Tokenizing text: gap-mediated reaction

3891 Sentence #0: gap-mediated reaction

3892Tokenizing text: 3M is a company

3893 Sentence #0: 3M is a company

3894Tokenizing text: cont'd nat'l program

3895 Sentence #0: cont'd nat'l program

3896Tokenizing text: @user_1 likes #havingfun

3897 Sentence #0: @user_1 likes #havingfun

3898Tokenizing text: h1.cpp is a C++ file

3899 Sentence #0: h1.cpp is a C++ file

3900Tokenizing text: http://google.com is Google's home page

3901 Sentence #0: http://google.com is Google 's home page

3902Tokenizing text: so is www.google.com and google.com

3903 Sentence #0: so is www.google.com and google.com

3904Tokenizing text: won't isn't hadn't

3905 Sentence #0: will not is not had not

3906Tokenizing text: me@privacy.net is a valid email, while me#privacy.net is not.

3907 Sentence #0: me@privacy.net is a valid email , while me#privacy.net is not .

3908Tokenizing text: <start-text>some text</end-text>

3909 Sentence #0: <start-text> some text </end-text>

3910Tokenizing text: IBM is Co. not Ltd.

3911 Sentence #0: IBM is Co. not Ltd.

3912Tokenizing text: A.M. Bancorp. A.T.B.

3913 Sentence #0: A.M. Bancorp. A.T.B.

3914Tokenizing text: I'm happy :) not sad :(.

3915 Sentence #0: I am happy :) not sad :( .

3916[info] - should provide fundamental tokenization functionality

3917Tokenizing text: This is an example e.g. a phrase.

3918 Sentence #0: This is an example e.g. a phrase .

3919[info] - should tokenize e.g. correctly

3920Tokenizing text: I'm won't don't cont'd he's he'd.

3921 Sentence #0: I am will not do not cont'd he 's he 'd .

3922[info] - should handle contractions correctly

3923Tokenizing text: "I'm happy", he said.

3924[info] - should transform double quotes into Treebank quotes

3925 Sentence #0: `` I am happy '' , he said .

3926Tokenizing text: "The levels of malnutrition among children continue to be truly alarming," said Mahimbo Mdoe, UNICEF's Representative in South Sudan.

3927 Sentence #0: `` The levels of malnutrition among children continue to be truly alarming , '' said Mahimbo Mdoe , UNICEF 's Representative in South Sudan .

3928[info] - should tokenize quotes correctly

3929Tokenizing text: This is a test (of parentheses).

3930 Sentence #0: This is a test ( of parentheses ) .

3931[info] - should normalize parentheses correctly

3932Tokenizing text: Lecithin :cholesterol and phospholipid :diacylglycerol acyltransferase

3933 Sentence #0: Lecithin : cholesterol and phospholipid : diacylglycerol acyltransferase

3934Tokenizing text: ATP :dephospho-CoA triphosphoribosyl transferase

3935 Sentence #0: ATP : dephospho-CoA triphosphoribosyl transferase

3936Tokenizing text: CDP-Glycerol :Poly (glycerophosphate) glycerophosphotransferase

3937 Sentence #0: CDP-Glycerol : Poly ( glycerophosphate ) glycerophosphotransferase

3938Tokenizing text: T=pseudo3 icosahedral viral capsid

3939 Sentence #0: T = pseudo3 icosahedral viral capsid

3940Tokenizing text: Myristoyl-CoA :protein N-myristoyltransferase,C-terminal

3941 Sentence #0: Myristoyl-CoA : protein N-myristoyltransferase , C-terminal

3942Tokenizing text: I am :), she said

3943 Sentence #0: I am :) , she said

3944Tokenizing text: I am :( today, she said

3945 Sentence #0: I am :( today , she said

3946Tokenizing 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 .

3947[info] - should not tokenize letter emoticons too aggressively

3948 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 ?

3949 Sentence #1: 17 The overall percentage of functional boreholes increased across WBeG , specifically in Jur River and Wau Counties in November .

3950[info] - should tokenize question mark correctly

3951Tokenizing 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 .

3952 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 .

3953 Sentence #1: 17 The overall percentage of functional boreholes increased across WBeG , specifically in Jur River and Wau Counties in November .

3954[info] - should tokenize punctuation correctly

3955Tokenizing text: :-) :) :-] :] :-> :> :-} :} :^) =] =) :-)) :-( :( :-< :< :-[ :[ :-|| >:[ :{ :@ >:( :-( :( :-) :) :-* :* ;-) ;) ;-] ;] ;^) :-, :-/ :/ :-. >:\\ >:/ :\\ =/ =\\ :-| :| :$ :-# :# :-& :& >:-) >:) }:-) }:) >;) |;-) <:-| ,:-|

3956 Sentence #0: :-) :) :-] :] :-> :> :-} :} :^) =] =) :-)) :-( :( :-< :< :-[ :[ :-|| >:[ :{ :@ >:( :-( :( :-) :) :-* :* ;-) ;) ;-] ;] ;^) :-, :-/ :/ :-. >:\\ >:/ :\\ =/ =\\ :-| :| :$ :-# :# :-& :& >:-) >:) }:-) }:) >;) |;-) <:-| ,:-|

3957Tokenizing 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

3958[info] - should tokenize common emoticons correctly

3959 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

3960[info] - should tokenize emoticons with letters correctly

3961Tokenizing 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].

3962 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 .

3963 Sentence #1: 3 According to Russian President Dmitry Medvedev , however , Russia ' s actions were necessary to " protect .

3964 Sentence #2: .

3965 Sentence #3: .

3966 Sentence #4: the Russian citizens living in [ South Ossetia ] .

3967[info] - should split sentences correctly

3968Tokenizing text: Weather is nice in mid-July

3969 Sentence #0: Weather is nice in mid July

3970Tokenizing text: This is ​​a test.

3971[info] - should split some hyphenated words

3972 Sentence #0: This is a test .

3973[info] - should not create empty words

3974[info] TestDoc5da3:

3975[info] org.clulab.processors.docs.TestDoc5da3 *** ABORTED ***

3977[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3978[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3979[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3980[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3981[info] at org.clulab.processors.docs.TestDoc5da3.<init>(TestDoc5da3.scala:10)

3982[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

3983[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)

3984[info] at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)

3985[info] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)

3986[info] at java.base/java.lang.reflect.ReflectAccess.newInstance(ReflectAccess.java:128)

3987[info] ...

3989[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

3990[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

3991[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)