Build Logs

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

2Clonning https://github.com/clulab/processors.git into /opencb/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 3.8.3-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 3.8.3-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: 3.8.3-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=3.8.3-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 3.8.3-RC3"

62"++3.8.3-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 3.8.3-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 /opencb/repo/project

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

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

81[info] Compilation completed in 8.435s.

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:/opencb/repo/)

92Execute setCrossScalaVersions: 3.8.3-RC3

93OpenCB::Changing crossVersion 3.1.3 -> 3.8.3-RC3 in root/crossScalaVersions

94OpenCB::Changing crossVersion 3.1.3 -> 3.8.3-RC3 in apps/crossScalaVersions

95OpenCB::Changing crossVersion 3.1.3 -> 3.8.3-RC3 in debugger/crossScalaVersions

96OpenCB::Changing crossVersion 3.1.3 -> 3.8.3-RC3 in library/crossScalaVersions

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

98[info] Setting Scala version to 3.8.3-RC3 on 4 projects.

99[info] Switching Scala version on:

100[info] * root (2.12.19, 2.11.12, 2.13.14, 3.8.3-RC3)

101[info] library (2.12.19, 2.11.12, 2.13.14, 3.8.3-RC3)

102[info] debugger (2.12.19, 2.11.12, 2.13.14, 3.8.3-RC3)

103[info] apps (2.12.19, 2.11.12, 2.13.14, 3.8.3-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:/opencb/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:/opencb/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:/opencb/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:326)

121 Did you mean webapp / allExcludeDependencies ?

122 , retry without global scopes

123[info] Reapplying settings...

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

125Execute removeScalacOptionsStartingWith: -P:wartremover

126[info] Reapplying settings...

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

128[success] Total time: 0 s, completed Mar 21, 2026, 7:53:40 PM

129Build config: {"tests":null}

131Starting build...

132Projects: Set(library, apps, debugger)

133Starting build for ProjectRef(file:/opencb/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:/opencb/repo/)), Select(ConfigKey(compile)), Zero, Zero)

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

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

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 /opencb/repo/library/target/scala-3.8.3-RC3/classes ...

156[info] done compiling

157[info] compiling 85 Scala sources to /opencb/repo/library/target/scala-3.8.3-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

177[info] TestDueTo:

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

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

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

181[Tokenizer] Checking /opencb/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-14203394619418207375.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] ...

736loading 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:

760[info] properties

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

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

763[info] properties as a map

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

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

766[info] argsToMap

767[info] - should deal with plain values

768Using the following properties:

769 = in inDirectory out outDirectory

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

994[info] - should decode a simple tree

995Some(L (0, 3) (1, root)

996 R (0, 1) (1, root)

997 (0, nsubj)

998 (1, root)

999 R (2, 3) (3, dobj)

1000 (2, nmod)

1001 (3, dobj)

1002)

1003Dependencies (3):

1004Edge(1,3,dobj)

1005Edge(1,0,nsubj)

1006Edge(3,2,nmod)

1007Roots: 1

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] ...

1449Tokenizing 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 ) .

1515Tokenizing text: Lecithin :cholesterol and phospholipid :diacylglycerol acyltransferase

1516[info] - should normalize parentheses correctly

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

1518Tokenizing text: ATP :dephospho-CoA triphosphoribosyl transferase

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

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

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

1522Tokenizing text: T=pseudo3 icosahedral viral capsid

1523 Sentence #0: T = pseudo3 icosahedral viral capsid

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

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

1526Tokenizing text: I am :), she said

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

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

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

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

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

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

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

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

1535[info] - should tokenize question mark correctly

1536[info] - should tokenize punctuation correctly

1537 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 .

1538 Sentence #1: 17 The overall percentage of functional boreholes increased across WBeG , specifically in Jur River and Wau Counties in November .

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

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

1541[info] - should tokenize common emoticons correctly

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

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

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 ] .

1551[info] - should split sentences correctly

1552Tokenizing text: Weather is nice in mid-July

1553 Sentence #0: Weather is nice in mid July

1554[info] - should split some hyphenated words

1555Tokenizing text: This is ​​a test.

1556 Sentence #0: This is a test .

1557[info] - should not create empty words

1558[info] TestDoc5da3:

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

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

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

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

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

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

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

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

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

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

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

1571[info] ...

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

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

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

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

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

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

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

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

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

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

1583[info] ...

1624[info] TestLazy:

1625[info] Lazy

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

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

1628[info] TestBioPreProcessor:

1629[info] ScienceUtils

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

1631[info] ScienceUtils

1632[info] - should convert unknown Unicode to spaces

1633[info] ScienceUtils

1634[info] - should convert all Unicode

1635[info] - should remove simple BIB REF

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

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

1638[info] TestVs:

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

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

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

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

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

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

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

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

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

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

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

1651[info] ...

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

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

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

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

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

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

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

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

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

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

1663[info] ...

1703[info] TestPorterStemmer:

1704[info] PorterStemmer

1705[info] - should stem words properly

1706[info] TestCounter:

1707[info] TestCounter

1708[info] - should serialize content correctly in saveTo

1709[info] TestSVMRankingClassifier:

1710[info] SVMRankingClassifier

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

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

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

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

1715[info] TestPerceptronClassifier:

1716[info] PerceptronClassifier

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

1718[info] TestPrintUtils:

1719[info] PrintUtils

17205

17215

1722hello

1723hello

1724[I@3050142a

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] ...

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

1998[info] TestLiblinearRegression:

1999[info] LiblinearRegression

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 = 0.038571428571428576

2052obj = -0.005207142857142858, rho = -0.6171428571428572

2053nSV = 2, nBSV = 0

2054*

2055optimization finished, #iter = 1

2056nu = 0.055238095238095246

2057obj = -0.02402857142857143, rho = -0.39571428571428574

2058nSV = 2, nBSV = 0

2059*

2060optimization finished, #iter = 1

2061nu = 0.08285714285714287

2062obj = -0.02402857142857143, rho = -0.39571428571428574

2063nSV = 2, nBSV = 0

2064*

2065optimization finished, #iter = 1

2066nu = 0.02749999999999999

2067obj = -0.0015125, rho = -0.285

2068nSV = 2, nBSV = 0

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

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

2071*

2072optimization finished, #iter = 1

2073nu = 0.055238095238095246

2074obj = -0.02402857142857143, rho = -0.39571428571428574

2075nSV = 2, nBSV = 0

2076[info] - should work with RVFDataset

2077*

2078optimization finished, #iter = 1

2079nu = 0.055238095238095246

2080obj = -0.02402857142857143, rho = -0.39571428571428574

2081nSV = 2, nBSV = 0

2082*

2083optimization finished, #iter = 1

2084nu = 0.08285714285714287

2085obj = -0.02402857142857143, rho = -0.39571428571428574

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 = 0.038571428571428576

2100obj = -0.005207142857142858, rho = -0.6171428571428572

2101nSV = 2, nBSV = 0

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

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

2104*

2105optimization finished, #iter = 1

2106nu = 0.055238095238095246

2107obj = -0.02402857142857143, rho = -0.39571428571428574

2108nSV = 2, nBSV = 0

2109*

2110optimization finished, #iter = 1

2111nu = 0.055238095238095246

2112obj = -0.02402857142857143, rho = -0.39571428571428574

2113nSV = 2, nBSV = 0

2114*

2115optimization finished, #iter = 1

2116nu = 0.038571428571428576

2117obj = -0.005207142857142858, rho = -0.6171428571428572

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 = 0.08285714285714287

2132obj = -0.02402857142857143, rho = -0.39571428571428574

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 = 28652

2145nu = 0.3274169741216888

2146obj = -41.865417354797216, rho = -0.6849648970874875

2147nSV = 526, nBSV = 413

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

2149optimization finished, #iter = 32701

2150nu = 0.3047934426866372

2151obj = -38.76063362899975, rho = -0.5912166857444758

2152nSV = 497, nBSV = 387

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

2154optimization finished, #iter = 34027

2155nu = 0.3144182788390263

2156obj = -39.94874184172005, rho = -0.4435876229147593

2157nSV = 505, nBSV = 397

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

2159optimization finished, #iter = 35279

2160nu = 0.321816764506396

2161obj = -41.352072868525205, rho = -0.3432317991504908

2162nSV = 513, nBSV = 403

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

2164optimization finished, #iter = 31265

2165nu = 0.306826894764184

2166obj = -40.262126168925576, rho = -0.536731157369377

2167nSV = 499, nBSV = 383

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

2169z: Laplace distribution e^(-|z|/sigma)/(2sigma),sigma=0.09655552479966087

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

2171optimization finished, #iter = 41834

2172nu = 0.3169820033369704

2173obj = -51.480338813026364, rho = -0.5860073666273288

2174nSV = 633, nBSV = 512

2175*

2176optimization finished, #iter = 404

2177nu = 0.3341878540861597

2178obj = -50.953858542775386, rho = -0.32003842779019626

2179nSV = 502, nBSV = 468

2180*

2181optimization finished, #iter = 386

2182nu = 0.3298169121980069

2183obj = -50.760300787651715, rho = -0.3297468173702505

2184nSV = 489, nBSV = 457

2185*

2186optimization finished, #iter = 441

2187nu = 0.32496380620791804

2188obj = -51.00999998015456, rho = -0.3833901321345207

2189nSV = 488, nBSV = 449

2190*

2191optimization finished, #iter = 383

2192nu = 0.330504026345391

2193obj = -51.46859245236389, rho = -0.3528474464932669

2194nSV = 491, nBSV = 460

2195*

2196optimization finished, #iter = 449

2197nu = 0.338370275296045

2198obj = -52.88803979376785, rho = -0.29989422330646764

2199nSV = 503, nBSV = 468

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

2201z: Laplace distribution e^(-|z|/sigma)/(2sigma),sigma=0.09621286378132438

2202*

2203optimization finished, #iter = 559

2204nu = 0.32873173531098426

2205obj = -63.35295557273505, rho = -0.34803081450672674

2206nSV = 614, nBSV = 574

2207*

2208optimization finished, #iter = 530

2209nu = 0.3131443580798628

2210obj = -49.446612386671426, rho = -0.22967213278252377

2211nSV = 476, nBSV = 425

2212*

2213optimization finished, #iter = 493

2214nu = 0.313307675553551

2215obj = -46.40559158734984, rho = -0.2010541691220869

2216nSV = 476, nBSV = 427

2217*

2218optimization finished, #iter = 596

2219nu = 0.324377872668966

2220obj = -49.392463024125924, rho = -0.023783174949275523

2221nSV = 495, nBSV = 436

2222*

2223optimization finished, #iter = 523

2224nu = 0.3239854899284953

2225obj = -49.307654102969764, rho = -0.22192004166641116

2226nSV = 495, nBSV = 442

2227*

2228optimization finished, #iter = 582

2229nu = 0.2979342863241879

2230obj = -43.822175566431824, rho = -0.15183808874398058

2231nSV = 450, nBSV = 400

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

2233z: Laplace distribution e^(-|z|/sigma)/(2sigma),sigma=0.09487198325732477

2234*

2235optimization finished, #iter = 629

2236nu = 0.31050957630127235

2237obj = -58.99742838311287, rho = -0.11795899327038137

2238nSV = 584, nBSV = 528

2239*

2240optimization finished, #iter = 401

2241nu = 0.3357819912224276

2242obj = -53.1937511168297, rho = -0.34472046061947453

2243nSV = 500, nBSV = 467

2244*

2245optimization finished, #iter = 405

2246nu = 0.33931747208511415

2247obj = -52.825749853398854, rho = -0.33210291059557484

2248nSV = 506, nBSV = 472

2249*

2250optimization finished, #iter = 406

2251nu = 0.327758972701011

2252obj = -52.443496661889185, rho = -0.32107380222095155

2253nSV = 488, nBSV = 455

2254*

2255optimization finished, #iter = 397

2256nu = 0.33035180430785

2257obj = -49.46045432027818, rho = -0.3415144844397694

2258nSV = 493, nBSV = 458

2259*

2260optimization finished, #iter = 427

2261nu = 0.32701923805438365

2262obj = -50.508168407055244, rho = -0.339569478938985

2263nSV = 489, nBSV = 448

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

2265z: Laplace distribution e^(-|z|/sigma)/(2sigma),sigma=0.09626159735397428

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 = 55367

2275epsilon = 0.06020010825117281

2276obj = -108.64613603733548, rho = -0.3903627246677034

2277nSV = 774, nBSV = 661

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

2279optimization finished, #iter = 61602

2280epsilon = 0.058376483564791026

2281obj = -105.8156839736418, rho = -0.2817740554795554

2282nSV = 773, nBSV = 660

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

2284optimization finished, #iter = 69545

2285epsilon = 0.05478301144113955

2286obj = -104.34348782762272, rho = -0.23041181599968608

2287nSV = 777, nBSV = 659

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

2289optimization finished, #iter = 62735

2290epsilon = 0.05575715085771249

2291obj = -104.99465734078952, rho = -0.2572110418305412

2292nSV = 775, nBSV = 660

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

2294optimization finished, #iter = 47771

2295epsilon = 0.058137540919910816

2296obj = -106.13293225218942, rho = -0.15942607911638623

2297nSV = 773, nBSV = 660

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

2299z: Laplace distribution e^(-|z|/sigma)/(2sigma),sigma=0.09461475804018699

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

2301optimization finished, #iter = 91034

2302epsilon = 0.05944570893531101

2303obj = -133.67027363116608, rho = -0.22082834234372709

2304nSV = 961, nBSV = 839

2305*

2306optimization finished, #iter = 798

2307epsilon = 0.05906500568303738

2308obj = -118.16609864694784, rho = -0.29422963297194527

2309nSV = 730, nBSV = 698

2310*

2311optimization finished, #iter = 788

2312epsilon = 0.05571443779516484

2313obj = -115.53925278719933, rho = -0.27122007302182904

2314nSV = 738, nBSV = 700

2315*

2316optimization finished, #iter = 828

2317epsilon = 0.055564306059641896

2318obj = -118.84388248635433, rho = -0.2906853646325761

2319nSV = 737, nBSV = 703

2320*

2321optimization finished, #iter = 833

2322epsilon = 0.05667655890683232

2323obj = -117.38243320113321, rho = -0.303462558090125

2324nSV = 736, nBSV = 697

2325*

2326optimization finished, #iter = 869

2327epsilon = 0.05675517583962572

2328obj = -117.69553106296507, rho = -0.3032973495694552

2329nSV = 741, nBSV = 696

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

2331z: Laplace distribution e^(-|z|/sigma)/(2sigma),sigma=0.09214813685458759

2332.*

2333optimization finished, #iter = 1030

2334epsilon = 0.05639765783061974

2335obj = -145.96471729318776, rho = -0.2866861483069072

2336nSV = 917, nBSV = 874

2337.*

2338optimization finished, #iter = 1139

2339epsilon = 0.05400355816586311

2340obj = -111.5605121620185, rho = -0.31390768445100947

2341nSV = 749, nBSV = 689

2342.*

2343optimization finished, #iter = 1142

2344epsilon = 0.05585617310990479

2345obj = -111.17945993493795, rho = -0.16773703221095557

2346nSV = 754, nBSV = 682

2347*

2348optimization finished, #iter = 995

2349epsilon = 0.05432462436170633

2350obj = -113.19560614749845, rho = -0.22072937266826492

2351nSV = 743, nBSV = 687

2352.*

2353optimization finished, #iter = 1158

2354epsilon = 0.05355121059904544

2355obj = -113.91472579361606, rho = -0.15319514533056183

2356nSV = 748, nBSV = 688

2357.*

2358optimization finished, #iter = 1127

2359epsilon = 0.052509468781614

2360obj = -113.61045486075143, rho = -0.15719746988958574

2361nSV = 756, nBSV = 683

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

2363z: Laplace distribution e^(-|z|/sigma)/(2sigma),sigma=0.08986258539292168

2364.

2366*

2367optimization finished, #iter = 1485

2368epsilon = 0.054878816933817506

2369obj = -140.12235768223275, rho = -0.15015265276473888

2370nSV = 932, nBSV = 860

2371*

2372optimization finished, #iter = 802

2373epsilon = 0.05703803500861179

2374obj = -116.29395131501434, rho = -0.2955280947418256

2375nSV = 736, nBSV = 698

2376*

2377optimization finished, #iter = 846

2378epsilon = 0.056091601357160986

2379obj = -116.82903855730423, rho = -0.2586524756550118

2380nSV = 737, nBSV = 700

2381*

2382optimization finished, #iter = 874

2383epsilon = 0.05602838180484307

2384obj = -117.89743116112582, rho = -0.3105508932825938

2385nSV = 737, nBSV = 701

2386*

2387optimization finished, #iter = 920

2388epsilon = 0.057618767615514085

2389obj = -122.55910628694392, rho = -0.2981872301631441

2390nSV = 737, nBSV = 696

2391*

2392optimization finished, #iter = 914

2393epsilon = 0.05637379250692326

2394obj = -116.08605551542168, rho = -0.3226202727915824

2395nSV = 739, nBSV = 697

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

2397z: Laplace distribution e^(-|z|/sigma)/(2sigma),sigma=0.09282857065056142

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

2405Build timeouts: 1, would retry

2406Retrying build, retry 1/2, force Scala version:false, enable migration:

2407[sbt_options] declare -a sbt_options=()

2408[process_args] java_version = '17'

2409[copyRt] java9_rt = '/root/.sbt/1.0/java9-rt-ext-eclipse_adoptium_17_0_8/rt.jar'

2410# Executing command line:

2411java

2412-Dfile.encoding=UTF-8

2413-Xmx10g

2414-XX:MaxMetaspaceSize=10g

2415-Dcommunitybuild.scala=3.8.3-RC3

2416-Dcommunitybuild.project.dependencies.add=

2417-Xmx7G

2418-Xms4G

2419-Xss8M

2420-Dsbt.script=/root/.sdkman/candidates/sbt/current/bin/sbt

2421-Dscala.ext.dirs=/root/.sbt/1.0/java9-rt-ext-eclipse_adoptium_17_0_8

2422-jar

2423/root/.sdkman/candidates/sbt/1.11.5/bin/sbt-launch.jar

2424"setCrossScalaVersions 3.8.3-RC3"

2425"++3.8.3-RC3 -v"

2426"mapScalacOptions ",REQUIRE:-source:3.8,-Wconf:msg=can be rewritten automatically under:s" ",-deprecation,-feature,-Xfatal-warnings,-Werror,MATCH:.*-Wconf.*any:e""

2427"set every credentials := Nil"

2428"excludeLibraryDependency com.github.ghik:zerowaste_{scalaVersion} com.olegpy:better-monadic-for_3 org.polyvariant:better-tostring_{scalaVersion} org.wartremover:wartremover_{scalaVersion}"

2429"removeScalacOptionsStartingWith -P:wartremover"

2431moduleMappings

2432"runBuild 3.8.3-RC3 """{"tests":null}""" org.clulab%processors org.clulab%processors-apps org.clulab%processors-debugger"

2434[info] welcome to sbt 1.11.5 (Eclipse Adoptium Java 17.0.8)

2435[info] loading settings for project repo-build from akka.sbt, plugins.sbt...

2436[info] loading project definition from /opencb/repo/project

2437[info] loading settings for project root from build.sbt, compile.sbt, publish.sbt, release.sbt, test.sbt, version.sbt...

2438[info] loading settings for project library from assembly.sbt, build.sbt, compile.sbt, publish.sbt, test.sbt...

2439[info] loading settings for project apps from assembly.sbt, build.sbt...

2440[info] loading settings for project webapp from build.sbt, docker.sbt...

2441[info] loading settings for project debugger from build.sbt, publish.sbt...

2442[info] set current project to root (in build file:/opencb/repo/)

2443Execute setCrossScalaVersions: 3.8.3-RC3

2444OpenCB::Changing crossVersion 3.1.3 -> 3.8.3-RC3 in root/crossScalaVersions

2445OpenCB::Changing crossVersion 3.1.3 -> 3.8.3-RC3 in apps/crossScalaVersions

2446OpenCB::Changing crossVersion 3.1.3 -> 3.8.3-RC3 in debugger/crossScalaVersions

2447OpenCB::Changing crossVersion 3.1.3 -> 3.8.3-RC3 in library/crossScalaVersions

2448[info] set current project to root (in build file:/opencb/repo/)

2449[info] Setting Scala version to 3.8.3-RC3 on 4 projects.

2450[info] Switching Scala version on:

2451[info] * root (2.12.19, 2.11.12, 2.13.14, 3.8.3-RC3)

2452[info] library (2.12.19, 2.11.12, 2.13.14, 3.8.3-RC3)

2453[info] debugger (2.12.19, 2.11.12, 2.13.14, 3.8.3-RC3)

2454[info] apps (2.12.19, 2.11.12, 2.13.14, 3.8.3-RC3)

2455[info] Excluding projects:

2456[info] webapp (2.12.19)

2457[info] Reapplying settings...

2458[info] set current project to root (in build file:/opencb/repo/)

2459Execute mapScalacOptions: ,REQUIRE:-source:3.8,-Wconf:msg=can be rewritten automatically under:s ,-deprecation,-feature,-Xfatal-warnings,-Werror,MATCH:.*-Wconf.*any:e

2460[info] Reapplying settings...

2461[info] set current project to root (in build file:/opencb/repo/)

2462[info] Defining Global / credentials, apps / credentials and 3 others.

2463[info] The new values will be used by Global / pgpSelectPassphrase, allCredentials and 23 others.

2464[info] Run `last` for details.

2465[info] Reapplying settings...

2466[info] set current project to root (in build file:/opencb/repo/)

2467Execute excludeLibraryDependency: com.github.ghik:zerowaste_{scalaVersion} com.olegpy:better-monadic-for_3 org.polyvariant:better-tostring_{scalaVersion} org.wartremover:wartremover_{scalaVersion}

2468[info] Reapplying settings...

2469OpenCB::Failed to reapply settings in excludeLibraryDependency: Reference to undefined setting:

2471 Global / allExcludeDependencies from Global / allExcludeDependencies (CommunityBuildPlugin.scala:326)

2472 Did you mean webapp / allExcludeDependencies ?

2473 , retry without global scopes

2474[info] Reapplying settings...

2475[info] set current project to root (in build file:/opencb/repo/)

2476Execute removeScalacOptionsStartingWith: -P:wartremover

2477[info] Reapplying settings...

2478[info] set current project to root (in build file:/opencb/repo/)

2479[success] Total time: 0 s, completed Mar 21, 2026, 9:43:10 PM

2480Build config: {"tests":null}

2482Starting build...

2483Projects: Set(library, apps, debugger)

2484Starting build for ProjectRef(file:/opencb/repo/,library) (processors)... [0/3]

2485OpenCB::Exclude Scala3 specific scalacOption `REQUIRE:-source:3.8` in Scala 2.12.20 module Global

2486OpenCB::Exclude Scala3 specific scalacOption `REQUIRE:-source:3.8` in Scala 2.12.19 module Scope(Select(BuildRef(file:/opencb/repo/)), Select(ConfigKey(compile)), Zero, Zero)

2487OpenCB::Filter out '-feature', matches setting pattern '^-?\Q-feature\E'

2488OpenCB::Filter out '-deprecation', matches setting pattern '^-?\Q-deprecation\E'

2489Compile scalacOptions: -unchecked, -explain, -Wconf:msg=can be rewritten automatically under:s, -source:3.8

2490[info] TestHashTrie:

2491[info] the trie

2492[info] - should label the text correctly with BIO labels

2493[info] the trie

2494[info] - should have 2 entries and contain 5 unique strings

2495[info] the trie

2496[info] - should sort and find the entries correctly

2497[info] the trie

2498[info] - should make use of shouldStop

2499SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".

2500SLF4J: Defaulting to no-operation (NOP) logger implementation

2501SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.

2502[info] TestDueTo:

2503[Tokenizer] Checking /opencb/repo for intel-librust_tokenizer.so...

2504[Tokenizer] Checking /root for intel-librust_tokenizer.so...

2505[Tokenizer] Extracting resource intel-librust_tokenizer.so to /tmp/intel-librust_tokenizer-7933643213806615713.so...

2506[info] org.clulab.processors.TestDueTo *** ABORTED ***

2508[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

2509[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

2510[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

2511[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

2512[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

2513[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

2514[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

2515[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

2516[info] at org.scalatest.BeforeAndAfterAll.run$(BeforeAndAfterAll.scala:135)

2517[info] at org.clulab.processors.CluTest.run(CluTest.scala:9)

2518[info] ...

2520[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

2521[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

2522[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

2523[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

2524[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

2525[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

2526[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

2527[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

2528[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

2529[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

2530[info] ...

2570[info] TestDoc58b0:

2571[info] org.clulab.processors.docs.TestDoc58b0 *** ABORTED ***

2573[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

2574[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

2575[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

2576[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

2577[info] at org.clulab.processors.docs.TestDoc58b0.<init>(TestDoc58b0.scala:10)

2578[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

2579[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)

2580[info] at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)

2581[info] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)

2582[info] at java.base/java.lang.reflect.ReflectAccess.newInstance(ReflectAccess.java:128)

2583[info] ...

2585[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

2586[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

2587[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

2588[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

2589[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

2590[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

2591[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

2592[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

2593[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

2594[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

2595[info] ...

2636[info] TestNumericPatterns:

2637[info] Any text

2638[info] - should contain one match for pattern `[2+2==4]`

2639[info] Any text

2640[info] - should contain no matches for pattern `[2+2==5]`

2641[info] TestArray:

2642[info] Array.toSeq

2643[info] - should work as expected without import

2644[info] - should work as expected with import

2645[info] Array.toIndexedSeq

2646[info] - should work as expected without import

2647[info] - should work as expected with import

2648[info] MutableArraySeq.from

2649[info] - should work as expected without import

2650[info] - should work as expected with import

2651[info] ImmutableArraySeq.unsafeWrapArray

2652[info] - should work as expected without import

2653[info] - should work as expected with import

2654[info] processSeq(array)

2655[info] - should work as expected without import

2656[info] - should work as expected with import

2657[info] processSeq(ImmutableArraySeq.unsafeWrapArray)

2658[info] - should work as expected without import

2659[info] - should work as expected with import

2660[info] processIndexedSeq(array)

2661[info] - should work as expected without import

2662[info] - should work as expected with import

2663[info] processIndexedSeq(ImmutableArraySeq.unsafeWrapArray)

2664[info] - should work as expected without import

2665[info] - should work as expected with import

2666[info] :Seq[]

2667[info] - should work as expected without import

2668[info] - should work as expected with import

2669[info] :IndexedSeq[]

2670[info] - should work as expected without import

2671[info] - should work as expected with import

2672[info] foreach

2673[info] - should work as expected without import

2674[info] - should work as expected with import

2675[info] zip

2676[info] - should work as expected without import

2677[info] - should work as expected with import

2678[info] map

2679[info] - should work as expected without import

2680[info] - should work as expected with import

2681[info] TestNumberParser:

2682[info] NumberParser

2683[info] - should parse digits

2684[info] - should fail on invalid input

2685[info] - should fail on empty input

2686[info] - should convert words to numbers

2687[info] - should parses decimal numbers

2688[info] - should convert numbers and words to numbers

2689[info] - should parse words to numbers

2690[info] TestMinHeap:

2691[info] MinHeap

2692[info] - should order elements properly

2693[info] - should keep correct top K

2694[info] TestProgressBar:

2695[info] ProgressBar

2697Progress 0% │██▉ │ 1/10 (0:00:00 / 0:00:00)

2698Progress 20% │█████▊ │ 2/10 (0:00:02 / 0:00:08)

2699Progress 30% │████████▋ │ 3/10 (0:00:03 / 0:00:07)

2700Progress 40% │███████████▌ │ 4/10 (0:00:04 / 0:00:06)

2701Progress 50% │██████████████▌ │ 5/10 (0:00:05 / 0:00:05)

2702Progress 60% │█████████████████▍ │ 6/10 (0:00:06 / 0:00:04)

2703Progress 70% │████████████████████▎ │ 7/10 (0:00:07 / 0:00:03)

2704Progress 80% │███████████████████████▏ │ 8/10 (0:00:08 / 0:00:02)

2705Progress 90% │██████████████████████████ │ 9/10 (0:00:09 / 0:00:01)

2706Progress 100% │█████████████████████████████│ 10/10 (0:00:10 / 0:00:00) [info] - should progress

2708Progress 0% │ │ 0/11 (0:00:00 / ?)

2709Progress 9% │██▋ │ 1/11 (0:00:01 / 0:00:10)

2710Progress 18% │████▌ │ 2/11 (0:00:02 / 0:00:09) at 0

2711Progress 27% │██████▊ │ 3/11 (0:00:03 / 0:00:08) at 1

2712Progress 36% │█████████ │ 4/11 (0:00:04 / 0:00:07) at 2

2713Progress 45% │███████████▎ │ 5/11 (0:00:05 / 0:00:06) at 3

2714Progress 54% │█████████████▋ │ 6/11 (0:00:06 / 0:00:05) at 4

2715Progress 63% │███████████████▉ │ 7/11 (0:00:07 / 0:00:04) at 5

2716Progress 72% │██████████████████▏ │ 8/11 (0:00:08 / 0:00:03) at 6

2717Progress 81% │████████████████████▍ │ 9/11 (0:00:09 / 0:00:02) at 7

2718Progress 90% │██████████████████████▋ │ 10/11 (0:00:10 / 0:00:01) at 8

2719Progress 100% │█████████████████████████│ 11/11 (0:00:11 / 0:00:00) at 9[info] - should show extra messages

2720[info] TestCorefChains:

2721[info] CorefChains

2722[info] - should sort on sentenceIndex

2723[info] - should sort on headIndex

2724[info] - should sort on size

2725[info] - should sort on index

2726[info] TestExtractorEngine:

2727[info] ExtractorEngine

2728[info] - should read utf8 encoded data

2729[info] - should read latin1 encoded data

2731[info] - should read data incorrectly if using the wrong charset

2732[info] TestNamedEntity:

2733[info] NamedEntity identification

2734[info] - should collect properly test 1

2735[info] - should collect properly test 2

2736[info] - should collect properly test 3

2737[info] - should collect properly test 4

2738[info] - should collect properly test 5

2739[info] - should collect properly test 6

2740[info] - should collect properly test 7

2741[info] - should collect properly test 8

2742[info] - should collect properly test 9

2743[info] - should collect properly test 10

2744[info] - should collect properly test 11

2745[info] - should collect properly test 12

2746[info] - should collect properly test 13

2747[info] - should collect properly test 14

2748[info] - should collect properly test 15

2749[info] - should combine properly test 1

2750[info] - should combine properly test 2

2751[info] - should combine properly test 3

2752[info] - should combine properly test 4

2753[info] - should combine properly test 5

2754[info] - should combine properly test 6

2755[info] - should combine properly test 7

2756[info] - should combine properly test 8

2757[info] - should combine properly test 9

2758[info] - should combine properly test 10

2759[info] - should combine properly test 11

2760[info] - should combine properly test 12

2761[info] - should combine properly test 13

2762[info] - should combine properly test 14

2763[info] - should combine properly test 15

2764[info] - should combine properly test 16

2765[info] - should combine properly test 17

2766[info] - should combine properly test 18

2767[info] - should combine properly test 19

2768[info] - should combine properly test 20

2769[info] NamedEntity validation

2770[info] - should validate the BIO notation test 1

2771[info] - should validate the BIO notation test 2

2772[info] - should validate the BIO notation test 3

2773[info] - should validate the BIO notation test 4

2774[info] - should validate the BIO notation test 5

2775[info] - should validate the BIO notation test 6

2776[info] - should validate the BIO notation test 7

2777[info] - should validate the BIO notation test 8

2778[info] - should validate the BIO notation test 9

2779[info] NamedEntity correction

2780[info] - should correct the BIO notation test 1

2781[info] - should correct the BIO notation test 2

2782[info] - should correct the BIO notation test 3

2783[info] - should correct the BIO notation test 4

2784[info] - should correct the BIO notation test 5

2785[info] - should correct the BIO notation test 6

2786[info] - should correct the BIO notation test 7

2787[info] - should correct the BIO notation test 8

2788[info] - should correct the BIO notation test 9

2789[info] TestTimer:

2790[info] timer

2791[info] - should use the right divisors

2792[info] TestDistributionalSimilarityPatterns:

2793[info] I saw a leopard climbing a tree.

2794[info] - should produce a mention with the label "Feline" for the word "leopard"

2795[info] TestSerializer:

2796[info] - should serialize/deserialize a Mention correctly

2797[info] - should serialize/deserialize a CrossSentenceMention correctly

2798[info] TestUniversalEnhancedDependencies:

2799[info] org.clulab.processors.TestUniversalEnhancedDependencies *** ABORTED ***

2801[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

2802[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

2803[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

2804[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

2805[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

2806[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

2807[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

2808[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

2809[info] at org.scalatest.BeforeAndAfterAll.run$(BeforeAndAfterAll.scala:135)

2810[info] at org.clulab.processors.CluTest.run(CluTest.scala:9)

2811[info] ...

2813[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

2814[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

2815[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

2816[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

2817[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

2818[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

2819[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

2820[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

2821[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

2822[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

2823[info] ...

2863[info] CluTest:

2864[info] TestJSONSerializer:

2865[info] JSONSerializer

2866[info] - should serialize/deserialize a Document to/from json correctly

2867[info] - should serialize/deserialize a Sentence to/from json correctly

2868[info] A Document with an ID

2869[info] - should produce json with an "id" field

2870[info] A Document without an ID

2871[info] - should produce json without an "id" field

2872[info] A Document with text

2873[info] - should produce json with a "text" field

2874[info] A Document without text

2875[info] - should produce json without a "text" field

2876[info] A Document recovered from JSON

2877[info] - should be equivalent to the original

2878[info] A Sentence recovered from JSON

2879[info] - should be equivalent to the original

2880[info] A Document saved and loaded

2881[info] - should have JSON equivalent to the original

2882[info] TestGraphPatternSD:

2883[info] GraphPattern

2884[info] - should support multiline patterns

2885[info] - should produce one mention at a time for an argument without any quantifier

2886[info] - should support optional arguments

2887[info] - should support exact quantifiers for arguments

2888[info] - should support * for arguments

2889[info] - should support + for arguments

2890[info] - should support greedy open range quantifiers for arguments

2891[info] - should handle multitoken triggers

2892[info] - should support 'type: graph'

2893[info] - should support 'graph: ' key

2894[info] - should ignore 'graph: ' when 'type: dependency'

2895[info] TestNumericEntityRecognition:

2896[info] org.clulab.numeric.TestNumericEntityRecognition *** ABORTED ***

2898[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

2899[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

2900[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

2901[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

2902[info] at org.clulab.numeric.TestNumericEntityRecognition$HabitusProcessor.<init>(TestNumericEntityRecognition.scala:44)

2903[info] at org.clulab.numeric.TestNumericEntityRecognition.<init>(TestNumericEntityRecognition.scala:50)

2904[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

2905[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)

2906[info] at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)

2907[info] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)

2908[info] ...

2910[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

2911[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

2912[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

2913[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

2914[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

2915[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

2916[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

2917[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

2918[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

2919[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

2920[info] ...

2962[info] TestMarkdownGeneration:

2963[info] MarkdownGeneration

2964[info] - should not crash

2965[info] - should properly aggregate argument requiredness

2966[info] TestCrLf:

2967[info] resources

2968[info] TestEvalTimeNorm:

2969[info] temporal parser

2970[info] org.clulab.numeric.TestEvalTimeNorm *** ABORTED ***

2972[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

2973[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

2974[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

2975[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

2976[info] at org.clulab.numeric.TestEvalTimeNorm.testFun$proxy1$1(TestEvalTimeNorm.scala:12)

2977[info] at org.clulab.numeric.TestEvalTimeNorm.$init$$$anonfun$1(TestEvalTimeNorm.scala:10)

2978[info] at org.scalatest.Transformer.apply$$anonfun$1(Transformer.scala:22)

2979[info] at org.scalatest.OutcomeOf.outcomeOf(OutcomeOf.scala:85)

2980[info] at org.scalatest.OutcomeOf.outcomeOf$(OutcomeOf.scala:31)

2981[info] at org.scalatest.OutcomeOf$.outcomeOf(OutcomeOf.scala:104)

2982[info] ...

2984[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

2985[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

2986[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

2987[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

2988[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

2989[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

2990[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

2991[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

2992[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

2993[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

2994[info] ...

2996loading props from file library/src/test/resources/org/clulab/utils/test.properties

3072Using the following properties:

3073 p1 = /some/path

3074 p2 = /some/path/subdir/123

3075 p3 = 123

3076loading props from file library/src/test/resources/org/clulab/utils/test.properties

3077Using the following properties:

3078 p1 = /some/path

3079 p2 = /some/path/subdir/123

3080 p3 = 123

3081[info] TestArgsToProperties:

3082[info] properties

3083[info] - should contain p1 with value /some/path

3084Using the following properties:

3085[info] - should contain p2 with the value /some/path/subdir/123

3086[info] properties as a map

3087[info] - should contain p1 with value /some/path

3088[info] - should contain p2 with the value /some/path/subdir/123

3089[info] argsToMap

3090 = in inDirectory out outDirectory

3091[info] - should deal with plain values

3092[info] TestInst:

3093[info] Inst

3094[info] - should not distinguish Done and Done

3095[info] - should distinguish Done and Pass

3096[info] - should distinguish MatchLookAhead and MatchLookBehind

3097[info] - should distinguish SaveStart and SaveEnd

3098[info] - should distinguish Done and MatchToken

3099[info] - should distinguish between Pass and Pass

3100[info] - should distinguish between MatchToken and MatchToken

3101[info] - should copy Pass appropriately

3102[info] - should copy Split appropriately

3103[info] - should copy SaveStart appropriately

3104[info] - should copy SaveEnd appropriately

3105[info] - should copy MatchToken appropriately

3106[info] - should copy MatchMention appropriately

3107[info] - should copy MatchSentenceStart appropriately

3108[info] - should copy MatchSentenceEnd appropriately

3109[info] - should copy MatchLookAhead appropriately

3110[info] - should copy MatchLookBehind appropriately

3111[info] - should distinguish complicated instances

3112[info] CaseClasses

3113[info] - should compare as intended

3114[info] tuple hashes

3115[info] - should be called recursively

3116[info] TestGraphPattern:

3117[info] graph range {0,n}

3119[info] GraphPattern

3120[info] - should support multiline patterns

3121[info] - should produce one mention at a time for an argument without any quantifier

3122[info] - should support optional arguments

3123[info] - should support exact quantifiers for arguments

3124[info] - should support * for arguments

3126[info] - should support + for arguments

3128[info] - should support greedy open range quantifiers for arguments

3131[info] - should handle multitoken triggers

3132[info] - should support 'type: graph'

3133[info] - should support 'graph: ' key

3134[info] - should ignore 'graph: ' when 'type: dependency'

3135[info] - should require a registered graph type wherever 'graph: ' is specified

3136[info] - should handle colons in dependencies

3137[info] - should handle colons in dependencies without quotes

3138[info] TestRandomForestClassifier:

3139[info] RFClassifier

3140Current utility:

3141UTILITY DEBUG:

3142Using dataset:

3143label:0 features:[0:2.0, 1:1.0]

3144label:1 features:[0:2.0, 2:1.0, 3:1.0]

3145label:1 features:[0:1.0, 4:1.0]

3146Using feature 3 with threshold 0.5

3147Contingency table for this feature+threshold is: SMALLER: [0:1.0, 1:1.0], GREATER: [1:1.0]

3148Overall utility: 0.2516291673878229

3149Parent utility: 0.9182958340544896

3150Utility of left child: 1.0

3151Utility of right child: 0.0

3152CHOSEN NEW BEST!

3153Current utility:

3154UTILITY DEBUG:

3155Using dataset:

3156label:0 features:[0:2.0, 1:1.0]

3157label:1 features:[0:2.0, 2:1.0, 3:1.0]

3158label:1 features:[0:1.0, 4:1.0]

3159Using feature 4 with threshold 0.5

3160Contingency table for this feature+threshold is: SMALLER: [0:1.0, 1:1.0], GREATER: [1:1.0]

3161Overall utility: 0.2516291673878229

3162Parent utility: 0.9182958340544896

3163Utility of left child: 1.0

3164Utility of right child: 0.0

3165Current utility:

3166UTILITY DEBUG:

3167Using dataset:

3168label:0 features:[0:2.0, 1:1.0]

3169label:1 features:[0:2.0, 2:1.0, 3:1.0]

3170label:1 features:[0:1.0, 4:1.0]

3171Using feature 0 with threshold 1.5

3172Contingency table for this feature+threshold is: SMALLER: [0:0.0, 1:1.0], GREATER: [0:1.0, 1:1.0]

3173Overall utility: 0.2516291673878229

3174Parent utility: 0.9182958340544896

3175Utility of left child: 0.0

3176Utility of right child: 1.0

3177Current utility:

3178UTILITY DEBUG:

3179Using dataset:

3180label:0 features:[0:2.0, 1:1.0]

3181label:1 features:[0:2.0, 2:1.0, 3:1.0]

3182label:1 features:[0:1.0, 4:1.0]

3183Using feature 1 with threshold 0.5

3184Contingency table for this feature+threshold is: SMALLER: [0:0.0, 1:2.0], GREATER: [0:1.0]

3185Overall utility: 0.9182958340544896

3186Parent utility: 0.9182958340544896

3187Utility of left child: 0.0

3188Utility of right child: 0.0

3189CHOSEN NEW BEST!

3190Current utility:

3191UTILITY DEBUG:

3192Using dataset:

3193label:0 features:[0:2.0, 1:1.0]

3194label:1 features:[0:2.0, 2:1.0, 3:1.0]

3195label:1 features:[0:1.0, 4:1.0]

3196Using feature 2 with threshold 0.5

3197Contingency table for this feature+threshold is: SMALLER: [0:1.0, 1:1.0], GREATER: [1:1.0]

3198Overall utility: 0.2516291673878229

3199Parent utility: 0.9182958340544896

3200Utility of left child: 1.0

3201Utility of right child: 0.0

3202BEST OVERALL:

3203UTILITY DEBUG:

3204Using dataset:

3205label:0 features:[0:2.0, 1:1.0]

3206label:1 features:[0:2.0, 2:1.0, 3:1.0]

3207label:1 features:[0:1.0, 4:1.0]

3208Using feature 1 with threshold 0.5

3209Contingency table for this feature+threshold is: SMALLER: [0:0.0, 1:2.0], GREATER: [0:1.0]

3210Overall utility: 0.9182958340544896

3211Parent utility: 0.9182958340544896

3212Utility of left child: 0.0

3213Utility of right child: 0.0

3214Current utility:

3215UTILITY DEBUG:

3216Using dataset:

3217label:1 features:[0:2.0, 2:1.0, 3:1.0]

3218label:1 features:[0:1.0, 4:1.0]

3219Using feature 2 with threshold 0.5

3220Contingency table for this feature+threshold is: SMALLER: [1:1.0], GREATER: [1:1.0]

3221Overall utility: 0.0

3222Parent utility: 0.0

3223Utility of left child: 0.0

3224Utility of right child: 0.0

3225CHOSEN NEW BEST!

3226Current utility:

3227UTILITY DEBUG:

3228Using dataset:

3229label:1 features:[0:2.0, 2:1.0, 3:1.0]

3230label:1 features:[0:1.0, 4:1.0]

3231Using feature 4 with threshold 0.5

3232Contingency table for this feature+threshold is: SMALLER: [1:1.0], GREATER: [1:1.0]

3233Overall utility: 0.0

3234Parent utility: 0.0

3235Utility of left child: 0.0

3236Utility of right child: 0.0

3237Current utility:

3238UTILITY DEBUG:

3239Using dataset:

3240label:1 features:[0:2.0, 2:1.0, 3:1.0]

3241label:1 features:[0:1.0, 4:1.0]

3242Using feature 0 with threshold 1.5

3243Contingency table for this feature+threshold is: SMALLER: [1:1.0], GREATER: [1:1.0]

3244Overall utility: 0.0

3245Parent utility: 0.0

3246Utility of left child: 0.0

3247Utility of right child: 0.0

3248Current utility:

3249UTILITY DEBUG:

3250Using dataset:

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

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

3253Using feature 3 with threshold 0.5

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

3255Overall utility: 0.0

3256Parent utility: 0.0

3257Utility of left child: 0.0

3258Utility of right child: 0.0

3259BEST OVERALL:

3260UTILITY DEBUG:

3261Using dataset:

3262label:1 features:[0:2.0, 2:1.0, 3:1.0]

3263label:1 features:[0:1.0, 4:1.0]

3264Using feature 2 with threshold 0.5

3265Contingency table for this feature+threshold is: SMALLER: [1:1.0], GREATER: [1:1.0]

3266Overall utility: 0.0

3267Parent utility: 0.0

3268Utility of left child: 0.0

3269Utility of right child: 0.0

3270Class of List(good, horrible): -

3271Class of List(bad, horrible): -

3272Class of List(good, great): +

3273[info] - should work with BVFDataset

3274[info] RandomForestClassifier

3275Accuracy: 0.965

3276[info] - should have an accuracy > .95 on this dataset

3277[info] TestLiblinearClassifier:

3278[info] LiblinearClassifier

3279iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00 CG 2

3280iter 2 act 8.879e-04 pre 8.833e-04 delta 8.463e-01 f 1.459e+00 |g| 5.811e-02 CG 1

3281iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00 CG 2

3282iter 2 act 8.879e-04 pre 8.833e-04 delta 8.463e-01 f 1.459e+00 |g| 5.811e-02 CG 1

3283iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00 CG 2

3284iter 2 act 8.879e-04 pre 8.833e-04 delta 8.463e-01 f 1.459e+00 |g| 5.811e-02 CG 1

3285iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00 CG 2

3286iter 2 act 8.879e-04 pre 8.833e-04 delta [info] - should work with RVFDataset

32878.463e-01 f 1.459e+00 |g| 5.811e-02 CG 1

3288iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00 CG 2

3289iter 2 act 8.879e-04 pre 8.833e-04 delta 8.463e-01 f 1.459e+00 |g| 5.811e-02 CG 1

3290iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00 CG 2

3291iter 2 act 8.879e-04 pre 8.833e-04 delta 8.463e-01 f 1.459e+00 |g| 5.811e-02 CG 1

3292iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00 CG 2

3293iter 2 act 8.879e-04 pre 8.833e-04 delta 8.463e-01 f 1.459e+00 |g| 5.811e-02 CG 1

3294iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00 CG 2

3295iter 2 act 8.879e-04 pre 8.833e-04 delta 8.463e-01 f 1.459e+00 |g| 5.811e-02 CG 1

3296iter 1 act 6.205e-01 pre 6.111e-01 delta 8.463e-01 f 2.079e+00 |g| 1.500e+00 CG 2

3297iter 2 act 8.879e-04 pre 8.833e-04 delta 8.463e-01 f 1.459e+00 |g| 5.811e-02 CG 1

3298[info] - should work with BVFDataset

3299iter 1 act 4.528e-01 pre 4.444e-01 delta 7.000e-01 f 1.386e+00 |g| 1.323e+00 CG 2

3300iter 2 act 8.651e-04 pre 8.605e-04 delta 7.000e-01 f 9.335e-01 |g| 5.750e-02 CG 1

3301[info] - should work with a two-label dataset

3302[info] LogisticRegressionClassifier

3303iter 1 act 7.243e+02 pre 6.698e+02 delta 1.883e+01 f 1.386e+03 |g| 9.617e+01 CG 4

3304iter 2 act 3.382e+01 pre 3.043e+01 delta 1.883e+01 f 6.620e+02 |g| 1.841e+01 CG 3

3305iter 3 act 2.260e+00 pre 2.083e+00 delta 1.883e+01 f 6.282e+02 |g| 4.186e+00 CG 3

3306iter 4 act 6.468e-02 pre 6.350e-02 delta 1.883e+01 f 6.259e+02 |g| 6.366e-01 CG 3

3307[info] - should have an accuracy > .97 in this dataset

3308[info] LinearSVMClassifier

3309iter 1 act 1.779e+03 pre 1.753e+03 delta 1.414e+01 f 2.000e+03 |g| 3.847e+02 CG 5

3310iter 2 act 4.189e+01 pre 4.076e+01 delta 1.414e+01 f 2.214e+02 |g| 3.417e+01 CG 6

3311iter 3 act 3.859e+00 pre 3.685e+00 delta 1.414e+01 f 1.795e+02 |g| 8.599e+00 CG 7

3312iter 4 act 5.435e-01 pre 5.117e-01 delta 1.414e+01 f 1.757e+02 |g| 2.475e+00 CG 6

3313[info] - should have an accuracy > .97 in this dataset

3314[info] HexaDecoderTest:

3315[info] HexaDecoder

3316Some(L (0, 3) (1, root)

3317 R (0, 1) (1, root)

3318 (0, nsubj)

3319 (1, root)

3320 R (2, 3) (3, dobj)

3321 (2, nmod)

3322 (3, dobj)

3323)

3324Dependencies (3):

3325Edge(1,3,dobj)

3326Edge(1,0,nsubj)

3327Edge(3,2,nmod)

3328Roots: 1

3329[info] - should decode a simple tree

3330Terminal tags: tl-nsubj, tl-cop, tl-det, tr-root

3331Nonterm tags: nl-R, nr-R, nr-R, eos

3332Processing terminal tag: tl-nsubj

3333Pushing:

3334(0, nsubj)

3335onto the stack.

3336Processing non-terminal tag: nl-R

3337Pushing:

3338R (0, -1) (-1, dummy)

3339 (0, nsubj)

3340 dummy

3341onto the stack.

3342Processing terminal tag: tl-cop

3343Pushing:

3344(1, cop)

3345onto the stack.

3346Processing non-terminal tag: nr-R

3347Pushing:

3348R (0, -1) (-1, dummy)

3349 (0, nsubj)

3350 R (1, -1) (-1, dummy)

3351 (1, cop)

3352 dummy

3353onto the stack.

3354Processing terminal tag: tl-det

3355Pushing:

3356(2, det)

3357onto the stack.

3358Processing non-terminal tag: nr-R

3359Pushing:

3360R (0, -1) (-1, dummy)

3361 (0, nsubj)

3362 R (1, -1) (-1, dummy)

3363 (1, cop)

3364 R (2, -1) (-1, dummy)

3365 (2, det)

3366 dummy

3367onto the stack.

3368Processing terminal tag: tr-root

3369Pushing:

3370R (0, 3) (3, root)

3371 (0, nsubj)

3372 R (1, 3) (3, root)

3373 (1, cop)

3374 R (2, 3) (3, root)

3375 (2, det)

3376 (3, root)

3377onto the stack.

3378Some(R (0, 3) (3, root)

3379 (0, nsubj)

3380 R (1, 3) (3, root)

3381 (1, cop)

3382 R (2, 3) (3, root)

3383 (2, det)

3384 (3, root)

3385)

3386Dependencies (3):

3387List(Edge(3,0,nsubj), Edge(3,1,cop), Edge(3,2,det))

3388Roots: 3

3389[info] - should decode another simple tree

3390[info] Test:

3391[info] TestEntityConstraints:

3392[info] Uneven parentheses

3393[info] - should be disallowed in entities

3394[info] Even parentheses

3395[info] - should be valid in entities

3396[info] Entities longer than n tokens

3397[info] - should be pruned

3398[info] TestMkCombinedDocument:

3399[info] org.clulab.processors.TestMkCombinedDocument *** ABORTED ***

3401[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3402[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3403[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3404[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3405[info] at org.clulab.processors.TestMkCombinedDocument.<init>(TestMkCombinedDocument.scala:28)

3406[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

3407[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)

3408[info] at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)

3409[info] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)

3410[info] at java.base/java.lang.reflect.ReflectAccess.newInstance(ReflectAccess.java:128)

3411[info] ...

3413[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

3414[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

3415[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3416[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3417[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3418[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3419[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

3420[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

3421[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

3422[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

3423[info] ...

3464[info] TestMathUtils:

3465[info] - should work with Seq

3466[info] - should not produce negative mean or variance

3467[info] - should work with Array

3468[info] - should work with any numeric collection

3469[info] - should be reasonably resilient to overflow

3470[info] TestDirectedGraph:

3471[info] DirectedGraph

3472[info] - should process a loop with a source

3473[info] - should process a loop without a source

3474[info] - should add lone roots

3475[info] - should handle disjoint loops

3476[info] - should not use a leading destination as a root

3477[info] - should be empty

3478[info] TestDependencyUtils:

3479[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.

3480[info] - should produce 'substrates' as the head of 'the substrates of Shp2'

3481[info] - should produce 'are' as the head of 'the substrates of Shp2 are'

3482[info] - should produce None for an empty Interval

3483[info] The docking protein Gab1 is the primary mediator of EGF-stimulated activation of the PI-3K/Akt cell survival pathway

3484[info] - should have the same getHeadStrict as roots

3485[info] - should produce only one head for getHeadsStrict

3486[info] - should produce None for an empty Interval

3487[info] - should produce two heads for 'docking protein' using getHeadsLocal

3488[info] - should think 'docking protein' is nested in 'docking protein Gab1'

3489[info] - should think 'the' is nested in 'Gab1'

3490[info] - should not think 'is' is nested in 'Gab1'

3491[info] - should think Interval(3,3) is nested in 'Gab1'

3492[info] - should not think 'pathway' is nested in 'Gab1'

3493[info] .

3494[info] - should produce one head using findHeads

3495[info] - should produce no heads using findHeadsStrict

3496[info] DependencyUtils

3497[info] - should handle cycles in the dependencyGraph correctly

3498[info] - should handle roots with incoming dependencies

3499[info] - should handle invalid dependency trees in findHeads

3500[info] - should only match complete stop tags

3501[info] TestNumericMentions:

3502[info] org.clulab.numeric.TestNumericMentions *** ABORTED ***

3504[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3505[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3506[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3507[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3508[info] at org.clulab.numeric.TestNumericMentions.<init>(TestNumericMentions.scala:7)

3509[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

3510[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)

3511[info] at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)

3512[info] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)

3513[info] at java.base/java.lang.reflect.ReflectAccess.newInstance(ReflectAccess.java:128)

3514[info] ...

3516[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

3517[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

3518[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3519[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3520[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3521[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3522[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

3523[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

3524[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

3525[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

3526[info] ...

3567[info] TestArrayView:

3568[info] ArrayView

3569[info] - should work with no offset

3570[info] - should work with an offset

3571[info] - should work when clipped

3572[info] TestDoc5501:

3573[info] org.clulab.processors.docs.TestDoc5501 *** ABORTED ***

3575[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3576[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3577[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3578[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3579[info] at org.clulab.processors.docs.TestDoc5501.<init>(TestDoc5501.scala:10)

3580[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

3581[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)

3582[info] at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)

3583[info] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)

3584[info] at java.base/java.lang.reflect.ReflectAccess.newInstance(ReflectAccess.java:128)

3585[info] ...

3587[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

3588[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

3589[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3590[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3591[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3592[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3593[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

3594[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

3595[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

3596[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

3597[info] ...

3638[info] TestLexiconNER:

3639[info] org.clulab.processors.TestLexiconNER *** ABORTED ***

3641[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3642[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3643[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3644[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3645[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

3646[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

3647[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

3648[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

3649[info] at org.scalatest.BeforeAndAfterAll.run$(BeforeAndAfterAll.scala:135)

3650[info] at org.clulab.processors.CluTest.run(CluTest.scala:9)

3651[info] ...

3653[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

3654[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

3655[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3656[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3657[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3658[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3659[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

3660[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

3661[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

3662[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

3663[info] ...

3703[info] TestTaxonomy:

3704[info] taxonomy

3705[info] - should inform a rule's labels

3706[info] TestProcessor:

3707[info] org.clulab.processors.TestProcessor *** ABORTED ***

3709[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3710[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3711[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3712[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3713[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

3714[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

3715[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

3716[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

3717[info] at org.scalatest.BeforeAndAfterAll.run$(BeforeAndAfterAll.scala:135)

3718[info] at org.clulab.processors.CluTest.run(CluTest.scala:9)

3719[info] ...

3721[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

3722[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

3723[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3724[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3725[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3726[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3727[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

3728[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

3729[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

3730[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

3731[info] ...

3771Tokenizing text: the of $><1/2 1.3 another test.

3772[info] TestTokenizer:

3773[info] the tokenizer

3774 Sentence #0: the of $ > < 1/2 1.3 another test .

3775Tokenizing text: -LRB- -RRB- -LCB- -RCB- -LSB- -RSB-.

3776 Sentence #0: -LRB- -RRB- -LCB- -RCB- -LSB- -RSB- .

3777Tokenizing text: first sentence. second sentence.

3778 Sentence #0: first sentence .

3779 Sentence #1: second sentence .

3780Tokenizing text: Artocarpus lacucha Buch.-Ham. ex D.Don is monkey fruit. Second sentence.

3781 Sentence #0: Artocarpus lacucha Buch. - Ham. ex D.Don is monkey fruit .

3782 Sentence #1: Second sentence .

3783Tokenizing text: Zizania caduciflora Hand.-Mazz. is a grass. Second sentence.

3784 Sentence #0: Zizania caduciflora Hand. - Mazz. is a grass .

3785 Sentence #1: Second sentence .

3786Tokenizing text: Fig. 1 shows the fungus Gaeumannomyces graminis var. tritici (Ggt), a major root disease of wheat.

3787 Sentence #0: Fig. 1 shows the fungus Gaeumannomyces graminis var. tritici ( Ggt ) , a major root disease of wheat .

3788Tokenizing text: Campylobacter spp. are ubiquitous.

3789 Sentence #0: Campylobacter spp. are ubiquitous .

3790Tokenizing text: today is 12/25/2017

3791 Sentence #0: today is 12/25/2017

3792Tokenizing text: today is 12/255/2017

3793 Sentence #0: today is 12/255 / 2017

3794Tokenizing text: number is -122,333

3795 Sentence #0: number is -122,333

3796Tokenizing text: gap-mediated reaction

3797 Sentence #0: gap-mediated reaction

3798Tokenizing text: 3M is a company

3799 Sentence #0: 3M is a company

3800Tokenizing text: cont'd nat'l program

3801 Sentence #0: cont'd nat'l program

3802Tokenizing text: @user_1 likes #havingfun

3803 Sentence #0: @user_1 likes #havingfun

3804Tokenizing text: h1.cpp is a C++ file

3805 Sentence #0: h1.cpp is a C++ file

3806Tokenizing text: http://google.com is Google's home page

3807 Sentence #0: http://google.com is Google 's home page

3808Tokenizing text: so is www.google.com and google.com

3809 Sentence #0: so is www.google.com and google.com

3810Tokenizing text: won't isn't hadn't

3811 Sentence #0: will not is not had not

3812Tokenizing text: me@privacy.net is a valid email, while me#privacy.net is not.

3813 Sentence #0: me@privacy.net is a valid email , while me#privacy.net is not .

3814Tokenizing text: <start-text>some text</end-text>

3815 Sentence #0: <start-text> some text </end-text>

3816Tokenizing text: IBM is Co. not Ltd.

3817 Sentence #0: IBM is Co. not Ltd.

3818Tokenizing text: A.M. Bancorp. A.T.B.

3819 Sentence #0: A.M. Bancorp. A.T.B.

3820Tokenizing text: I'm happy :) not sad :(.

3821 Sentence #0: I am happy :) not sad :( .

3822Tokenizing text: This is an example e.g. a phrase.

3823[info] - should provide fundamental tokenization functionality

3824 Sentence #0: This is an example e.g. a phrase .

3825[info] - should tokenize e.g. correctly

3826Tokenizing text: I'm won't don't cont'd he's he'd.

3827 Sentence #0: I am will not do not cont'd he 's he 'd .

3828[info] - should handle contractions correctly

3829Tokenizing text: "I'm happy", he said.

3830 Sentence #0: `` I am happy '' , he said .

3831[info] - should transform double quotes into Treebank quotes

3832Tokenizing text: "The levels of malnutrition among children continue to be truly alarming," said Mahimbo Mdoe, UNICEF's Representative in South Sudan.

3833 Sentence #0: `` The levels of malnutrition among children continue to be truly alarming , '' said Mahimbo Mdoe , UNICEF 's Representative in South Sudan .

3834[info] - should tokenize quotes correctly

3835Tokenizing text: This is a test (of parentheses).

3836 Sentence #0: This is a test ( of parentheses ) .

3837[info] - should normalize parentheses correctly

3838Tokenizing text: Lecithin :cholesterol and phospholipid :diacylglycerol acyltransferase

3839 Sentence #0: Lecithin : cholesterol and phospholipid : diacylglycerol acyltransferase

3840Tokenizing text: ATP :dephospho-CoA triphosphoribosyl transferase

3841 Sentence #0: ATP : dephospho-CoA triphosphoribosyl transferase

3842Tokenizing text: CDP-Glycerol :Poly (glycerophosphate) glycerophosphotransferase

3843 Sentence #0: CDP-Glycerol : Poly ( glycerophosphate ) glycerophosphotransferase

3844Tokenizing text: T=pseudo3 icosahedral viral capsid

3845 Sentence #0: T = pseudo3 icosahedral viral capsid

3846Tokenizing text: Myristoyl-CoA :protein N-myristoyltransferase,C-terminal

3847 Sentence #0: Myristoyl-CoA : protein N-myristoyltransferase , C-terminal

3848Tokenizing text: I am :), she said

3849 Sentence #0: I am :) , she said

3850Tokenizing text: I am :( today, she said

3851 Sentence #0: I am :( today , she said

3852[info] - should not tokenize letter emoticons too aggressively

3853Tokenizing 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 .

3854 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 ?

3855 Sentence #1: 17 The overall percentage of functional boreholes increased across WBeG , specifically in Jur River and Wau Counties in November .

3856[info] - should tokenize question mark correctly

3857Tokenizing 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 .

3858 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 .

3859 Sentence #1: 17 The overall percentage of functional boreholes increased across WBeG , specifically in Jur River and Wau Counties in November .

3860[info] - should tokenize punctuation correctly

3861Tokenizing text: :-) :) :-] :] :-> :> :-} :} :^) =] =) :-)) :-( :( :-< :< :-[ :[ :-|| >:[ :{ :@ >:( :-( :( :-) :) :-* :* ;-) ;) ;-] ;] ;^) :-, :-/ :/ :-. >:\\ >:/ :\\ =/ =\\ :-| :| :$ :-# :# :-& :& >:-) >:) }:-) }:) >;) |;-) <:-| ,:-|

3862 Sentence #0: :-) :) :-] :] :-> :> :-} :} :^) =] =) :-)) :-( :( :-< :< :-[ :[ :-|| >:[ :{ :@ >:( :-( :( :-) :) :-* :* ;-) ;) ;-] ;] ;^) :-, :-/ :/ :-. >:\\ >:/ :\\ =/ =\\ :-| :| :$ :-# :# :-& :& >:-) >:) }:-) }:) >;) |;-) <:-| ,:-|

3863Tokenizing 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

3864[info] - should tokenize common emoticons correctly

3865 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

3866Tokenizing 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].

3867[info] - should tokenize emoticons with letters correctly

3868 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 .

3869 Sentence #1: 3 According to Russian President Dmitry Medvedev , however , Russia ' s actions were necessary to " protect .

3870 Sentence #2: .

3871 Sentence #3: .

3872 Sentence #4: the Russian citizens living in [ South Ossetia ] .

3873[info] - should split sentences correctly

3874Tokenizing text: Weather is nice in mid-July

3875 Sentence #0: Weather is nice in mid July

3876[info] - should split some hyphenated words

3877Tokenizing text: This is ​​a test.

3878 Sentence #0: This is a test .

3879[info] - should not create empty words

3880[info] TestDoc5da3:

3881[info] org.clulab.processors.docs.TestDoc5da3 *** ABORTED ***

3883[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3884[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3885[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3886[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3887[info] at org.clulab.processors.docs.TestDoc5da3.<init>(TestDoc5da3.scala:10)

3888[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

3889[info] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)

3890[info] at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)

3891[info] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)

3892[info] at java.base/java.lang.reflect.ReflectAccess.newInstance(ReflectAccess.java:128)

3893[info] ...

3895[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

3896[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

3897[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3898[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3899[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3900[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3901[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

3902[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

3903[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

3904[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

3905[info] ...

3946[info] TestLazy:

3947[info] Lazy

3948[info] - should not retrieve a Cat from an Animal

3949[info] - should retrieve an Animal from a Cat

3950[info] TestBioPreProcessor:

3951[info] ScienceUtils

3952[info] - should convert (known) Unicode to ASCII

3953[info] ScienceUtils

3954[info] - should convert unknown Unicode to spaces

3955[info] ScienceUtils

3956[info] - should convert all Unicode

3957[info] - should remove simple BIB REF

3958[info] - should remove BIB REF but leave other paren expression

3959[info] - should remove complex BIB REF but leave other paren expressions

3960[info] TestVs:

3961[info] org.clulab.processors.TestVs *** ABORTED ***

3963[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:45)

3964[info] at org.clulab.scala_transformers.encoder.TokenClassifierFactory.newTokenClassifier(TokenClassifierFactory.scala:62)

3965[info] at org.clulab.scala_transformers.encoder.TokenClassifier$.fromResources(TokenClassifier.scala:173)

3966[info] at org.clulab.processors.clu.BalaurProcessor.<init>(BalaurProcessor.scala:46)

3967[info] at org.clulab.processors.CluTest.newProcessor(CluTest.scala:32)

3968[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

3969[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

3970[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

3971[info] at org.scalatest.BeforeAndAfterAll.run$(BeforeAndAfterAll.scala:135)

3972[info] at org.clulab.processors.CluTest.run(CluTest.scala:9)

3973[info] ...

3975[info] at org.clulab.scala_transformers.common.LibraryLoader$.load(LibraryLoader.scala:108)

3976[info] at org.clulab.scala_transformers.tokenizer.jni.ScalaJniTokenizer$.<clinit>(ScalaJniTokenizer.scala:100)

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.CluTest.newProcessor(CluTest.scala:32)

3982[info] at org.clulab.processors.CluTest.beforeAll(CluTest.scala:14)

3983[info] at org.scalatest.BeforeAndAfterAll.liftedTree1$1(BeforeAndAfterAll.scala:212)

3984[info] at org.scalatest.BeforeAndAfterAll.run(BeforeAndAfterAll.scala:217)

3985[info] ...