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  1. compile-module:
  2. [echo] Compiling classes for CDK's fingerprint module from src/main...
  3. [echo] Datafiles defined: true
  4. [echo] Extra files defined: ${module.extrafiles.present}
  5. [echo] CDK dependencies defined: true
  6. [echo] Library dependencies defined: true
  7. [echo] Developer Library dependencies defined: ${module.devellibdepends.present}
  8. [echo] Autogenerated files specified: ${module.autogenerated.present}
  9. [mkdir] Created dir: /Users/jonathan/Work/cdk/build/src/fingerprint
  10. [mkdir] Created dir: /Users/jonathan/Work/cdk/build/fingerprint
  11. [copy] Copying 9 files to /Users/jonathan/Work/cdk/build/src/fingerprint
  12. [copy] Copying 1 file to /Users/jonathan/Work/cdk/build
  13. [javac] Compiling 9 source files to /Users/jonathan/Work/cdk/build/fingerprint
  14. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/EStateFingerprinter.java:27: package org.openscience.cdk.annotations does not exist
  15. [javac] import org.openscience.cdk.annotations.TestClass;
  16. [javac] ^
  17. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/EStateFingerprinter.java:28: package org.openscience.cdk.annotations does not exist
  18. [javac] import org.openscience.cdk.annotations.TestMethod;
  19. [javac] ^
  20. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/EStateFingerprinter.java:29: package org.openscience.cdk.config.fragments does not exist
  21. [javac] import org.openscience.cdk.config.fragments.EStateFragments;
  22. [javac] ^
  23. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/EStateFingerprinter.java:30: package org.openscience.cdk.exception does not exist
  24. [javac] import org.openscience.cdk.exception.CDKException;
  25. [javac] ^
  26. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/EStateFingerprinter.java:31: package org.openscience.cdk.interfaces does not exist
  27. [javac] import org.openscience.cdk.interfaces.IAtomContainer;
  28. [javac] ^
  29. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/EStateFingerprinter.java:32: package org.openscience.cdk.smiles.smarts does not exist
  30. [javac] import org.openscience.cdk.smiles.smarts.SMARTSQueryTool;
  31. [javac] ^
  32. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/EStateFingerprinter.java:62: cannot find symbol
  33. [javac] symbol: class IFingerprinter
  34. [javac] public class EStateFingerprinter implements IFingerprinter {
  35. [javac] ^
  36. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/EStateFingerprinter.java:61: cannot find symbol
  37. [javac] symbol: class TestClass
  38. [javac] @TestClass("org.openscience.cdk.fingerprint.EStateFingerprinterTest")
  39. [javac] ^
  40. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/EStateFingerprinter.java:74: cannot find symbol
  41. [javac] symbol : class IAtomContainer
  42. [javac] location: class org.openscience.cdk.fingerprint.EStateFingerprinter
  43. [javac] public BitSet getFingerprint(IAtomContainer atomContainer)
  44. [javac] ^
  45. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/EStateFingerprinter.java:75: cannot find symbol
  46. [javac] symbol : class CDKException
  47. [javac] location: class org.openscience.cdk.fingerprint.EStateFingerprinter
  48. [javac] throws CDKException {
  49. [javac] ^
  50. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/ExtendedFingerprinter.java:27: package org.openscience.cdk.annotations does not exist
  51. [javac] import org.openscience.cdk.annotations.TestClass;
  52. [javac] ^
  53. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/ExtendedFingerprinter.java:28: package org.openscience.cdk.annotations does not exist
  54. [javac] import org.openscience.cdk.annotations.TestMethod;
  55. [javac] ^
  56. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/ExtendedFingerprinter.java:29: package org.openscience.cdk.exception does not exist
  57. [javac] import org.openscience.cdk.exception.CDKException;
  58. [javac] ^
  59. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/ExtendedFingerprinter.java:30: package org.openscience.cdk.interfaces does not exist
  60. [javac] import org.openscience.cdk.interfaces.IAtomContainer;
  61. [javac] ^
  62. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/ExtendedFingerprinter.java:31: package org.openscience.cdk.interfaces does not exist
  63. [javac] import org.openscience.cdk.interfaces.IRingSet;
  64. [javac] ^
  65. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/ExtendedFingerprinter.java:32: package org.openscience.cdk.ringsearch does not exist
  66. [javac] import org.openscience.cdk.ringsearch.RingPartitioner;
  67. [javac] ^
  68. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/ExtendedFingerprinter.java:33: package org.openscience.cdk.ringsearch does not exist
  69. [javac] import org.openscience.cdk.ringsearch.SSSRFinder;
  70. [javac] ^
  71. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/ExtendedFingerprinter.java:34: package org.openscience.cdk.tools.manipulator does not exist
  72. [javac] import org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator;
  73. [javac] ^
  74. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/ExtendedFingerprinter.java:54: cannot find symbol
  75. [javac] symbol: class IFingerprinter
  76. [javac] public class ExtendedFingerprinter implements IFingerprinter {
  77. [javac] ^
  78. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/ExtendedFingerprinter.java:53: cannot find symbol
  79. [javac] symbol: class TestClass
  80. [javac] @TestClass("org.openscience.cdk.fingerprint.ExtendedFingerprinterTest")
  81. [javac] ^
  82. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/ExtendedFingerprinter.java:58: cannot find symbol
  83. [javac] symbol : class Fingerprinter
  84. [javac] location: class org.openscience.cdk.fingerprint.ExtendedFingerprinter
  85. [javac] private Fingerprinter fingerprinter = null;
  86. [javac] ^
  87. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/ExtendedFingerprinter.java:97: cannot find symbol
  88. [javac] symbol : class IAtomContainer
  89. [javac] location: class org.openscience.cdk.fingerprint.ExtendedFingerprinter
  90. [javac] public BitSet getFingerprint(IAtomContainer container)
  91. [javac] ^
  92. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/ExtendedFingerprinter.java:98: cannot find symbol
  93. [javac] symbol : class CDKException
  94. [javac] location: class org.openscience.cdk.fingerprint.ExtendedFingerprinter
  95. [javac] throws CDKException {
  96. [javac] ^
  97. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/ExtendedFingerprinter.java:122: cannot find symbol
  98. [javac] symbol : class IAtomContainer
  99. [javac] location: class org.openscience.cdk.fingerprint.ExtendedFingerprinter
  100. [javac] public BitSet getFingerprint(IAtomContainer atomContainer,
  101. [javac] ^
  102. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/ExtendedFingerprinter.java:123: cannot find symbol
  103. [javac] symbol : class IRingSet
  104. [javac] location: class org.openscience.cdk.fingerprint.ExtendedFingerprinter
  105. [javac] IRingSet ringSet,
  106. [javac] ^
  107. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/ExtendedFingerprinter.java:124: cannot find symbol
  108. [javac] symbol : class IRingSet
  109. [javac] location: class org.openscience.cdk.fingerprint.ExtendedFingerprinter
  110. [javac] List<IRingSet> rslist) throws CDKException {
  111. [javac] ^
  112. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/ExtendedFingerprinter.java:124: cannot find symbol
  113. [javac] symbol : class CDKException
  114. [javac] location: class org.openscience.cdk.fingerprint.ExtendedFingerprinter
  115. [javac] List<IRingSet> rslist) throws CDKException {
  116. [javac] ^
  117. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/KlekotaRothFingerprinter.java:11: package org.openscience.cdk.annotations does not exist
  118. [javac] import org.openscience.cdk.annotations.TestClass;
  119. [javac] ^
  120. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/SubstructureFingerprinter.java:30: package org.openscience.cdk.annotations does not exist
  121. [javac] import org.openscience.cdk.annotations.TestClass;
  122. [javac] ^
  123. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/SubstructureFingerprinter.java:31: package org.openscience.cdk.annotations does not exist
  124. [javac] import org.openscience.cdk.annotations.TestMethod;
  125. [javac] ^
  126. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/SubstructureFingerprinter.java:32: package org.openscience.cdk.exception does not exist
  127. [javac] import org.openscience.cdk.exception.CDKException;
  128. [javac] ^
  129. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/SubstructureFingerprinter.java:33: package org.openscience.cdk.interfaces does not exist
  130. [javac] import org.openscience.cdk.interfaces.IAtomContainer;
  131. [javac] ^
  132. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/SubstructureFingerprinter.java:34: package org.openscience.cdk.smiles.smarts does not exist
  133. [javac] import org.openscience.cdk.smiles.smarts.SMARTSQueryTool;
  134. [javac] ^
  135. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/SubstructureFingerprinter.java:373: cannot find symbol
  136. [javac] symbol: class IFingerprinter
  137. [javac] public class SubstructureFingerprinter implements IFingerprinter {
  138. [javac] ^
  139. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/SubstructureFingerprinter.java:372: cannot find symbol
  140. [javac] symbol: class TestClass
  141. [javac] @TestClass("org.openscience.cdk.fingerprint.SubstructureFingerprinterTest")
  142. [javac] ^
  143. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/KlekotaRothFingerprinter.java:23: cannot find symbol
  144. [javac] symbol: class TestClass
  145. [javac] @TestClass("org.openscience.cdk.fingerprint.KlekotaRothFingerprinterTest")
  146. [javac] ^
  147. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/SubstructureFingerprinter.java:404: cannot find symbol
  148. [javac] symbol : class IAtomContainer
  149. [javac] location: class org.openscience.cdk.fingerprint.SubstructureFingerprinter
  150. [javac] public BitSet getFingerprint(IAtomContainer atomContainer)
  151. [javac] ^
  152. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/SubstructureFingerprinter.java:405: cannot find symbol
  153. [javac] symbol : class CDKException
  154. [javac] location: class org.openscience.cdk.fingerprint.SubstructureFingerprinter
  155. [javac] throws CDKException {
  156. [javac] ^
  157. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/MACCSFingerprinter.java:36: cannot find symbol
  158. [javac] symbol : class CDKConstants
  159. [javac] location: package org.openscience.cdk
  160. [javac] import org.openscience.cdk.CDKConstants;
  161. [javac] ^
  162. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/MACCSFingerprinter.java:37: package org.openscience.cdk.annotations does not exist
  163. [javac] import org.openscience.cdk.annotations.TestClass;
  164. [javac] ^
  165. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/MACCSFingerprinter.java:38: package org.openscience.cdk.annotations does not exist
  166. [javac] import org.openscience.cdk.annotations.TestMethod;
  167. [javac] ^
  168. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/MACCSFingerprinter.java:39: package org.openscience.cdk.exception does not exist
  169. [javac] import org.openscience.cdk.exception.CDKException;
  170. [javac] ^
  171. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/MACCSFingerprinter.java:40: package org.openscience.cdk.graph does not exist
  172. [javac] import org.openscience.cdk.graph.ConnectivityChecker;
  173. [javac] ^
  174. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/MACCSFingerprinter.java:41: package org.openscience.cdk.interfaces does not exist
  175. [javac] import org.openscience.cdk.interfaces.IAtomContainer;
  176. [javac] ^
  177. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/MACCSFingerprinter.java:42: package org.openscience.cdk.interfaces does not exist
  178. [javac] import org.openscience.cdk.interfaces.IBond;
  179. [javac] ^
  180. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/MACCSFingerprinter.java:43: package org.openscience.cdk.interfaces does not exist
  181. [javac] import org.openscience.cdk.interfaces.IMoleculeSet;
  182. [javac] ^
  183. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/MACCSFingerprinter.java:44: package org.openscience.cdk.interfaces does not exist
  184. [javac] import org.openscience.cdk.interfaces.IRingSet;
  185. [javac] ^
  186. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/MACCSFingerprinter.java:45: package org.openscience.cdk.ringsearch does not exist
  187. [javac] import org.openscience.cdk.ringsearch.AllRingsFinder;
  188. [javac] ^
  189. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/MACCSFingerprinter.java:46: package org.openscience.cdk.smiles.smarts does not exist
  190. [javac] import org.openscience.cdk.smiles.smarts.SMARTSQueryTool;
  191. [javac] ^
  192. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/MACCSFingerprinter.java:47: package org.openscience.cdk.tools does not exist
  193. [javac] import org.openscience.cdk.tools.ILoggingTool;
  194. [javac] ^
  195. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/MACCSFingerprinter.java:48: package org.openscience.cdk.tools does not exist
  196. [javac] import org.openscience.cdk.tools.LoggingToolFactory;
  197. [javac] ^
  198. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/MACCSFingerprinter.java:73: cannot find symbol
  199. [javac] symbol: class IFingerprinter
  200. [javac] public class MACCSFingerprinter implements IFingerprinter {
  201. [javac] ^
  202. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/MACCSFingerprinter.java:72: cannot find symbol
  203. [javac] symbol: class TestClass
  204. [javac] @TestClass("org.openscience.cdk.fingerprint.MACCSFingerprinterTest")
  205. [javac] ^
  206. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/MACCSFingerprinter.java:74: cannot find symbol
  207. [javac] symbol : class ILoggingTool
  208. [javac] location: class org.openscience.cdk.fingerprint.MACCSFingerprinter
  209. [javac] private static ILoggingTool logger =
  210. [javac] ^
  211. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/MACCSFingerprinter.java:93: cannot find symbol
  212. [javac] symbol : class IAtomContainer
  213. [javac] location: class org.openscience.cdk.fingerprint.MACCSFingerprinter
  214. [javac] public BitSet getFingerprint(IAtomContainer atomContainer)
  215. [javac] ^
  216. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/MACCSFingerprinter.java:94: cannot find symbol
  217. [javac] symbol : class CDKException
  218. [javac] location: class org.openscience.cdk.fingerprint.MACCSFingerprinter
  219. [javac] throws CDKException {
  220. [javac] ^
  221. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/MACCSFingerprinter.java:158: cannot find symbol
  222. [javac] symbol : class CDKException
  223. [javac] location: class org.openscience.cdk.fingerprint.MACCSFingerprinter
  224. [javac] private MaccsKey[] readKeyDef() throws IOException, CDKException {
  225. [javac] ^
  226. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/PubchemFingerprinter.java:27: cannot find symbol
  227. [javac] symbol : class CDKConstants
  228. [javac] location: package org.openscience.cdk
  229. [javac] import org.openscience.cdk.CDKConstants;
  230. [javac] ^
  231. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/PubchemFingerprinter.java:28: package org.openscience.cdk.annotations does not exist
  232. [javac] import org.openscience.cdk.annotations.TestClass;
  233. [javac] ^
  234. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/PubchemFingerprinter.java:29: package org.openscience.cdk.annotations does not exist
  235. [javac] import org.openscience.cdk.annotations.TestMethod;
  236. [javac] ^
  237. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/PubchemFingerprinter.java:30: package org.openscience.cdk.exception does not exist
  238. [javac] import org.openscience.cdk.exception.CDKException;
  239. [javac] ^
  240. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/PubchemFingerprinter.java:31: package org.openscience.cdk.interfaces does not exist
  241. [javac] import org.openscience.cdk.interfaces.IAtom;
  242. [javac] ^
  243. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/PubchemFingerprinter.java:32: package org.openscience.cdk.interfaces does not exist
  244. [javac] import org.openscience.cdk.interfaces.IAtomContainer;
  245. [javac] ^
  246. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/PubchemFingerprinter.java:33: package org.openscience.cdk.interfaces does not exist
  247. [javac] import org.openscience.cdk.interfaces.IBond;
  248. [javac] ^
  249. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/PubchemFingerprinter.java:34: package org.openscience.cdk.interfaces does not exist
  250. [javac] import org.openscience.cdk.interfaces.IRingSet;
  251. [javac] ^
  252. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/PubchemFingerprinter.java:35: package org.openscience.cdk.ringsearch does not exist
  253. [javac] import org.openscience.cdk.ringsearch.SSSRFinder;
  254. [javac] ^
  255. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/PubchemFingerprinter.java:36: package org.openscience.cdk.smiles.smarts does not exist
  256. [javac] import org.openscience.cdk.smiles.smarts.SMARTSQueryTool;
  257. [javac] ^
  258. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/PubchemFingerprinter.java:37: package org.openscience.cdk.tools.periodictable does not exist
  259. [javac] import org.openscience.cdk.tools.periodictable.PeriodicTable;
  260. [javac] ^
  261. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/PubchemFingerprinter.java:86: cannot find symbol
  262. [javac] symbol: class IFingerprinter
  263. [javac] public class PubchemFingerprinter implements IFingerprinter {
  264. [javac] ^
  265. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/PubchemFingerprinter.java:85: cannot find symbol
  266. [javac] symbol: class TestClass
  267. [javac] @TestClass("org.openscience.cdk.fingerprint.PubchemFingerprinterTest")
  268. [javac] ^
  269. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/PubchemFingerprinter.java:93: cannot find symbol
  270. [javac] symbol : class SMARTSQueryTool
  271. [javac] location: class org.openscience.cdk.fingerprint.PubchemFingerprinter
  272. [javac] private static SMARTSQueryTool sqt;
  273. [javac] ^
  274. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/PubchemFingerprinter.java:120: cannot find symbol
  275. [javac] symbol : class IAtomContainer
  276. [javac] location: class org.openscience.cdk.fingerprint.PubchemFingerprinter
  277. [javac] public BitSet getFingerprint(IAtomContainer atomContainer)
  278. [javac] ^
  279. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/PubchemFingerprinter.java:121: cannot find symbol
  280. [javac] symbol : class CDKException
  281. [javac] location: class org.openscience.cdk.fingerprint.PubchemFingerprinter
  282. [javac] throws CDKException {
  283. [javac] ^
  284. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/PubchemFingerprinter.java:319: cannot find symbol
  285. [javac] symbol : class IAtomContainer
  286. [javac] location: class org.openscience.cdk.fingerprint.PubchemFingerprinter
  287. [javac] static private void _generateFp(byte[] fp, IAtomContainer mol)
  288. [javac] ^
  289. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/PubchemFingerprinter.java:320: cannot find symbol
  290. [javac] symbol : class CDKException
  291. [javac] location: class org.openscience.cdk.fingerprint.PubchemFingerprinter
  292. [javac] throws CDKException {
  293. [javac] ^
  294. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/PubchemFingerprinter.java:326: cannot find symbol
  295. [javac] symbol : class IAtomContainer
  296. [javac] location: class org.openscience.cdk.fingerprint.PubchemFingerprinter
  297. [javac] private void generateFp(IAtomContainer mol) throws CDKException {
  298. [javac] ^
  299. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/PubchemFingerprinter.java:326: cannot find symbol
  300. [javac] symbol : class CDKException
  301. [javac] location: class org.openscience.cdk.fingerprint.PubchemFingerprinter
  302. [javac] private void generateFp(IAtomContainer mol) throws CDKException {
  303. [javac] ^
  304. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/PubchemFingerprinter.java:522: cannot find symbol
  305. [javac] symbol : class IAtomContainer
  306. [javac] location: class org.openscience.cdk.fingerprint.PubchemFingerprinter
  307. [javac] private static void countElements(byte[] fp, IAtomContainer mol) {
  308. [javac] ^
  309. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/PubchemFingerprinter.java:767: cannot find symbol
  310. [javac] symbol : class IAtomContainer
  311. [javac] location: class org.openscience.cdk.fingerprint.PubchemFingerprinter
  312. [javac] private static void countRings(byte[] fp, IAtomContainer mol) {
  313. [javac] ^
  314. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/PubchemFingerprinter.java:1089: cannot find symbol
  315. [javac] symbol : class IAtomContainer
  316. [javac] location: class org.openscience.cdk.fingerprint.PubchemFingerprinter
  317. [javac] private static void countSubstructures(byte[] fp, IAtomContainer mol) throws CDKException {
  318. [javac] ^
  319. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/PubchemFingerprinter.java:1089: cannot find symbol
  320. [javac] symbol : class CDKException
  321. [javac] location: class org.openscience.cdk.fingerprint.PubchemFingerprinter
  322. [javac] private static void countSubstructures(byte[] fp, IAtomContainer mol) throws CDKException {
  323. [javac] ^
  324. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/PubchemFingerprinter.java:143: cannot find symbol
  325. [javac] symbol : class IAtomContainer
  326. [javac] location: class org.openscience.cdk.fingerprint.PubchemFingerprinter.CountElements
  327. [javac] public CountElements(IAtomContainer m) {
  328. [javac] ^
  329. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/PubchemFingerprinter.java:159: cannot find symbol
  330. [javac] symbol : class IRingSet
  331. [javac] location: class org.openscience.cdk.fingerprint.PubchemFingerprinter.CountRings
  332. [javac] IRingSet ringSet;
  333. [javac] ^
  334. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/PubchemFingerprinter.java:161: cannot find symbol
  335. [javac] symbol : class IAtomContainer
  336. [javac] location: class org.openscience.cdk.fingerprint.PubchemFingerprinter.CountRings
  337. [javac] public CountRings(IAtomContainer m) {
  338. [javac] ^
  339. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/PubchemFingerprinter.java:175: cannot find symbol
  340. [javac] symbol : class IAtomContainer
  341. [javac] location: class org.openscience.cdk.fingerprint.PubchemFingerprinter.CountRings
  342. [javac] private boolean isCarbonOnlyRing(IAtomContainer ring) {
  343. [javac] ^
  344. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/PubchemFingerprinter.java:182: cannot find symbol
  345. [javac] symbol : class IAtomContainer
  346. [javac] location: class org.openscience.cdk.fingerprint.PubchemFingerprinter.CountRings
  347. [javac] private boolean isRingSaturated(IAtomContainer ring) {
  348. [javac] ^
  349. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/PubchemFingerprinter.java:189: cannot find symbol
  350. [javac] symbol : class IAtomContainer
  351. [javac] location: class org.openscience.cdk.fingerprint.PubchemFingerprinter.CountRings
  352. [javac] private boolean isRingUnsaturated(IAtomContainer ring) {
  353. [javac] ^
  354. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/PubchemFingerprinter.java:193: cannot find symbol
  355. [javac] symbol : class IAtomContainer
  356. [javac] location: class org.openscience.cdk.fingerprint.PubchemFingerprinter.CountRings
  357. [javac] private int countNitrogenInRing(IAtomContainer ring) {
  358. [javac] ^
  359. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/PubchemFingerprinter.java:201: cannot find symbol
  360. [javac] symbol : class IAtomContainer
  361. [javac] location: class org.openscience.cdk.fingerprint.PubchemFingerprinter.CountRings
  362. [javac] private int countHeteroInRing(IAtomContainer ring) {
  363. [javac] ^
  364. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/PubchemFingerprinter.java:211: cannot find symbol
  365. [javac] symbol : class IAtomContainer
  366. [javac] location: class org.openscience.cdk.fingerprint.PubchemFingerprinter.CountRings
  367. [javac] private boolean isAromaticRing(IAtomContainer ring) {
  368. [javac] ^
  369. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/PubchemFingerprinter.java:304: cannot find symbol
  370. [javac] symbol : class IAtomContainer
  371. [javac] location: class org.openscience.cdk.fingerprint.PubchemFingerprinter.CountSubstructures
  372. [javac] private IAtomContainer mol;
  373. [javac] ^
  374. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/PubchemFingerprinter.java:306: cannot find symbol
  375. [javac] symbol : class IAtomContainer
  376. [javac] location: class org.openscience.cdk.fingerprint.PubchemFingerprinter.CountSubstructures
  377. [javac] public CountSubstructures(IAtomContainer m) {
  378. [javac] ^
  379. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/PubchemFingerprinter.java:310: cannot find symbol
  380. [javac] symbol : class CDKException
  381. [javac] location: class org.openscience.cdk.fingerprint.PubchemFingerprinter.CountSubstructures
  382. [javac] public int countSubstructure(String smarts) throws CDKException {
  383. [javac] ^
  384. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/StandardSubstructureSets.java:3: package org.openscience.cdk.annotations does not exist
  385. [javac] import org.openscience.cdk.annotations.TestClass;
  386. [javac] ^
  387. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/StandardSubstructureSets.java:4: package org.openscience.cdk.annotations does not exist
  388. [javac] import org.openscience.cdk.annotations.TestMethod;
  389. [javac] ^
  390. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/fingerprint/StandardSubstructureSets.java:20: cannot find symbol
  391. [javac] symbol: class TestClass
  392. [javac] @TestClass("org.openscience.cdk.fingerprint.StandardSubstructureSetsTest")
  393. [javac] ^
  394. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/similarity/DistanceMoment.java:3: package org.openscience.cdk.annotations does not exist
  395. [javac] import org.openscience.cdk.annotations.TestClass;
  396. [javac] ^
  397. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/similarity/DistanceMoment.java:4: package org.openscience.cdk.annotations does not exist
  398. [javac] import org.openscience.cdk.annotations.TestMethod;
  399. [javac] ^
  400. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/similarity/DistanceMoment.java:5: package org.openscience.cdk.exception does not exist
  401. [javac] import org.openscience.cdk.exception.CDKException;
  402. [javac] ^
  403. [javac] /Users/jonathan/Work/cdk/build/src/fingerprint/org/openscience/cdk/similarity/DistanceMoment.java:6: package org.openscience.cdk.interfaces does not exist
  404. [javac] import org.openscience.cdk.interfaces.IAtom;
  405. [javac] ^
  406. [javac] 100 errors
  407.  
  408.  
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