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September 26, 2014 16:42
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"make all" output of mois-fba
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| mkdir -p lib | |
| cp /home/rhz/src/scala/mois-fba/tmp/lib/libglpk.so /home/rhz/src/scala/mois-fba/tmp/lib/jni/libglpk_java.so /home/rhz/src/scala/mois-fba/tmp/share/java/glpk-java.jar lib | |
| sbt -batch -no-colors compile | |
| [0m[[0minfo[0m] [0mLoading project definition from /home/rhz/src/scala/mois-fba/project[0m | |
| [0m[[0minfo[0m] [0mSet current project to mois-fba (in build file:/home/rhz/src/scala/mois-fba/)[0m | |
| [0m[[0minfo[0m] [0mCompiling 2 Scala sources to /home/rhz/src/scala/mois-fba/target/scala-2.11/classes...[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:36: object RateLawReactionNetwork is not a member of package uk.ac.ed.inf.mois.reaction[0m | |
| [0m[[31merror[0m] [0mimport uk.ac.ed.inf.mois.reaction.RateLawReactionNetwork[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:38: object Bounds is not a member of package uk.ac.ed.inf.mois[0m | |
| [0m[[31merror[0m] [0mimport uk.ac.ed.inf.mois.Bounds[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:44: not found: type RateLawReactionNetwork[0m | |
| [0m[[31merror[0m] [0mclass LinOptProcess extends RateLawReactionNetwork[Double] {[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:51: not found: type BaseReaction[0m | |
| [0m[[31merror[0m] [0m extends BaseReaction with Bounds[Double] {[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:51: not found: type Bounds[0m | |
| [0m[[31merror[0m] [0m extends BaseReaction with Bounds[Double] {[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:64: not found: type Species[0m | |
| [0m[[31merror[0m] [0m protected implicit class SpeciesSyntax(s: Species) {[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:50: not found: type Species[0m | |
| [0m[[31merror[0m] [0m class LinearNetwork(val lhs: Multiset[Species], val rhs: Multiset[Species])[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:50: not found: type Species[0m | |
| [0m[[31merror[0m] [0m class LinearNetwork(val lhs: Multiset[Species], val rhs: Multiset[Species])[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:52: not found: value RateLawReaction[0m | |
| [0m[[31merror[0m] [0m def at(k: => Double) = RateLawReaction(lhs, rhs, () => k)[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:57: value lowerBound is not a member of LinOptProcess.this.LinearNetwork[0m | |
| [0m[[31merror[0m] [0m Note: implicit method rxnToSeq is not applicable here because it comes after the application point and it lacks an explicit result type[0m | |
| [0m[[31merror[0m] [0m def gte(b: Double) = { n.lowerBound = Some(new n.LowerBound(b)); n }[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:58: value upperBound is not a member of LinOptProcess.this.LinearNetwork[0m | |
| [0m[[31merror[0m] [0m Note: implicit method rxnToSeq is not applicable here because it comes after the application point and it lacks an explicit result type[0m | |
| [0m[[31merror[0m] [0m def lte(b: Double) = { n.upperBound = Some(new n.UpperBound(b)); n }[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:63: not found: type Species[0m | |
| [0m[[31merror[0m] [0m private val fixed_species = mutable.ArrayBuffer.empty[Species][0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:68: not found: type ReactionFactory[0m | |
| [0m[[31merror[0m] [0m object Reaction extends ReactionFactory {[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:69: not found: type Species[0m | |
| [0m[[31merror[0m] [0m def apply(lhs: Multiset[Species], rhs: Multiset[Species]) = new Reaction(lhs, rhs)[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:69: not found: type Species[0m | |
| [0m[[31merror[0m] [0m def apply(lhs: Multiset[Species], rhs: Multiset[Species]) = new Reaction(lhs, rhs)[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:79: not found: type Species[0m | |
| [0m[[31merror[0m] [0m private var obj: Multiset[Species] = null[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:81: not found: type Species[0m | |
| [0m[[31merror[0m] [0m def minimise(s: Multiset[Species]) {[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:86: not found: type Species[0m | |
| [0m[[31merror[0m] [0m def maximise(s: Multiset[Species]) {[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:99: not found: value species[0m | |
| [0m[[31merror[0m] [0m row += species.indexOf(s)[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:103: not found: value species[0m | |
| [0m[[31merror[0m] [0m val mat = new CompRowMatrix(rxns.size, species.size, nz.toArray)[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:107: not found: value species[0m | |
| [0m[[31merror[0m] [0m mat.set(i, species.indexOf(s), r.lhs(s))[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:109: not found: value species[0m | |
| [0m[[31merror[0m] [0m mat.set(i, species.indexOf(s), -r.rhs(s))[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:136: value init is not a member of AnyRef[0m | |
| [0m[[31merror[0m] [0m super.init(t)[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:150: not found: value species[0m | |
| [0m[[31merror[0m] [0m GLPK.glp_add_cols(lp, species.size)[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:151: not found: value species[0m | |
| [0m[[31merror[0m] [0m for (i <- 0 until species.size) {[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:152: not found: value species[0m | |
| [0m[[31merror[0m] [0m val s = species(i)[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:153: not found: value species[0m | |
| [0m[[31merror[0m] [0m GLPK.glp_set_col_name(lp, i+1, species(i).meta.identifier)[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:158: not found: value species[0m | |
| [0m[[31merror[0m] [0m GLPK.glp_set_obj_coef(lp, species.indexOf(s)+1, c)[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:190: value lowerBound is not a member of LinOptProcess.this.LinearNetwork[0m | |
| [0m[[31merror[0m] [0m if (r.lowerBound.isDefined && r.upperBound.isDefined) {[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:190: value upperBound is not a member of LinOptProcess.this.LinearNetwork[0m | |
| [0m[[31merror[0m] [0m if (r.lowerBound.isDefined && r.upperBound.isDefined) {[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:191: value lowerBound is not a member of LinOptProcess.this.LinearNetwork[0m | |
| [0m[[31merror[0m] [0m val lower = r.lowerBound.get.bound[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:192: value upperBound is not a member of LinOptProcess.this.LinearNetwork[0m | |
| [0m[[31merror[0m] [0m val upper = r.upperBound.get.bound[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:197: value lowerBound is not a member of LinOptProcess.this.LinearNetwork[0m | |
| [0m[[31merror[0m] [0m } else if (r.lowerBound.isDefined)[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:198: value lowerBound is not a member of LinOptProcess.this.LinearNetwork[0m | |
| [0m[[31merror[0m] [0m GLPK.glp_set_row_bnds(lp, i+1, GLP_LO, r.lowerBound.get.bound, 0)[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:199: value upperBound is not a member of LinOptProcess.this.LinearNetwork[0m | |
| [0m[[31merror[0m] [0m else if (r.upperBound.isDefined)[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:200: value upperBound is not a member of LinOptProcess.this.LinearNetwork[0m | |
| [0m[[31merror[0m] [0m GLPK.glp_set_row_bnds(lp, i+1, GLP_UP, 0, r.upperBound.get.bound)[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:206: not found: value species[0m | |
| [0m[[31merror[0m] [0m while (i < species.size) {[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:207: not found: value species[0m | |
| [0m[[31merror[0m] [0m val s = species(i)[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:230: not found: value species[0m | |
| [0m[[31merror[0m] [0m GLPK.glp_set_col_bnds(lp, species.indexOf(s)+1, GLP_FX, s.value, s.value)[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:252: not found: value species[0m | |
| [0m[[31merror[0m] [0m else println(species(v-rxns.size-1))[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:259: not found: value species[0m | |
| [0m[[31merror[0m] [0m while (i < species.size) {[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:260: not found: value species[0m | |
| [0m[[31merror[0m] [0m species(i) := GLPK.glp_get_col_prim(lp, i+1)[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m/home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:285: not found: value species[0m | |
| [0m[[31merror[0m] [0m while (i < species.size) {[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| [0m[[31merror[0m] [0m43 errors found[0m | |
| [0m[[31merror[0m] [0m(compile:[31mcompile[0m) Compilation failed[0m | |
| [0m[[31merror[0m] [0mTotal time: 5 s, completed 26-Sep-2014 17:18:28[0m | |
| [0m[[31merror[0m] [0mNot a valid command: no-colors[0m | |
| [0m[[31merror[0m] [0mNot a valid project ID: no-colors[0m | |
| [0m[[31merror[0m] [0mExpected ':' (if selecting a configuration)[0m | |
| [0m[[31merror[0m] [0mNot a valid key: no-colors (similar: compilers)[0m | |
| [0m[[31merror[0m] [0mno-colors[0m | |
| [0m[[31merror[0m] [0m ^[0m | |
| Makefile:21: recipe for target 'all' failed | |
| make: *** [all] Error 1 |
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