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"make all" output of mois-fba
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
[info] Loading project definition from /home/rhz/src/scala/mois-fba/project
[info] Set current project to mois-fba (in build file:/home/rhz/src/scala/mois-fba/)
[info] Compiling 2 Scala sources to /home/rhz/src/scala/mois-fba/target/scala-2.11/classes...
[error] /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
[error] import uk.ac.ed.inf.mois.reaction.RateLawReactionNetwork
[error]  ^
[error] /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
[error] import uk.ac.ed.inf.mois.Bounds
[error]  ^
[error] /home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:44: not found: type RateLawReactionNetwork
[error] class LinOptProcess extends RateLawReactionNetwork[Double] {
[error]  ^
[error] /home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:51: not found: type BaseReaction
[error]  extends BaseReaction with Bounds[Double] {
[error]  ^
[error] /home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:51: not found: type Bounds
[error]  extends BaseReaction with Bounds[Double] {
[error]  ^
[error] /home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:64: not found: type Species
[error]  protected implicit class SpeciesSyntax(s: Species) {
[error]  ^
[error] /home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:50: not found: type Species
[error]  class LinearNetwork(val lhs: Multiset[Species], val rhs: Multiset[Species])
[error]  ^
[error] /home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:50: not found: type Species
[error]  class LinearNetwork(val lhs: Multiset[Species], val rhs: Multiset[Species])
[error]  ^
[error] /home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:52: not found: value RateLawReaction
[error]  def at(k: => Double) = RateLawReaction(lhs, rhs, () => k)
[error]  ^
[error] /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
[error]  Note: implicit method rxnToSeq is not applicable here because it comes after the application point and it lacks an explicit result type
[error]  def gte(b: Double) = { n.lowerBound = Some(new n.LowerBound(b)); n }
[error]  ^
[error] /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
[error]  Note: implicit method rxnToSeq is not applicable here because it comes after the application point and it lacks an explicit result type
[error]  def lte(b: Double) = { n.upperBound = Some(new n.UpperBound(b)); n }
[error]  ^
[error] /home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:63: not found: type Species
[error]  private val fixed_species = mutable.ArrayBuffer.empty[Species]
[error]  ^
[error] /home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:68: not found: type ReactionFactory
[error]  object Reaction extends ReactionFactory {
[error]  ^
[error] /home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:69: not found: type Species
[error]  def apply(lhs: Multiset[Species], rhs: Multiset[Species]) = new Reaction(lhs, rhs)
[error]  ^
[error] /home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:69: not found: type Species
[error]  def apply(lhs: Multiset[Species], rhs: Multiset[Species]) = new Reaction(lhs, rhs)
[error]  ^
[error] /home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:79: not found: type Species
[error]  private var obj: Multiset[Species] = null
[error]  ^
[error] /home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:81: not found: type Species
[error]  def minimise(s: Multiset[Species]) {
[error]  ^
[error] /home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:86: not found: type Species
[error]  def maximise(s: Multiset[Species]) {
[error]  ^
[error] /home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:99: not found: value species
[error]  row += species.indexOf(s)
[error]  ^
[error] /home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:103: not found: value species
[error]  val mat = new CompRowMatrix(rxns.size, species.size, nz.toArray)
[error]  ^
[error] /home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:107: not found: value species
[error]  mat.set(i, species.indexOf(s), r.lhs(s))
[error]  ^
[error] /home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:109: not found: value species
[error]  mat.set(i, species.indexOf(s), -r.rhs(s))
[error]  ^
[error] /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
[error]  super.init(t)
[error]  ^
[error] /home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:150: not found: value species
[error]  GLPK.glp_add_cols(lp, species.size)
[error]  ^
[error] /home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:151: not found: value species
[error]  for (i <- 0 until species.size) {
[error]  ^
[error] /home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:152: not found: value species
[error]  val s = species(i)
[error]  ^
[error] /home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:153: not found: value species
[error]  GLPK.glp_set_col_name(lp, i+1, species(i).meta.identifier)
[error]  ^
[error] /home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:158: not found: value species
[error]  GLPK.glp_set_obj_coef(lp, species.indexOf(s)+1, c)
[error]  ^
[error] /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
[error]  if (r.lowerBound.isDefined && r.upperBound.isDefined) {
[error]  ^
[error] /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
[error]  if (r.lowerBound.isDefined && r.upperBound.isDefined) {
[error]  ^
[error] /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
[error]  val lower = r.lowerBound.get.bound
[error]  ^
[error] /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
[error]  val upper = r.upperBound.get.bound
[error]  ^
[error] /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
[error]  } else if (r.lowerBound.isDefined)
[error]  ^
[error] /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
[error]  GLPK.glp_set_row_bnds(lp, i+1, GLP_LO, r.lowerBound.get.bound, 0)
[error]  ^
[error] /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
[error]  else if (r.upperBound.isDefined)
[error]  ^
[error] /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
[error]  GLPK.glp_set_row_bnds(lp, i+1, GLP_UP, 0, r.upperBound.get.bound)
[error]  ^
[error] /home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:206: not found: value species
[error]  while (i < species.size) {
[error]  ^
[error] /home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:207: not found: value species
[error]  val s = species(i)
[error]  ^
[error] /home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:230: not found: value species
[error]  GLPK.glp_set_col_bnds(lp, species.indexOf(s)+1, GLP_FX, s.value, s.value)
[error]  ^
[error] /home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:252: not found: value species
[error]  else println(species(v-rxns.size-1))
[error]  ^
[error] /home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:259: not found: value species
[error]  while (i < species.size) {
[error]  ^
[error] /home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:260: not found: value species
[error]  species(i) := GLPK.glp_get_col_prim(lp, i+1)
[error]  ^
[error] /home/rhz/src/scala/mois-fba/src/main/scala/uk/ac/ed/inf/mois/fba/Linear.scala:285: not found: value species
[error]  while (i < species.size) {
[error]  ^
[error] 43 errors found
[error] (compile:compile) Compilation failed
[error] Total time: 5 s, completed 26-Sep-2014 17:18:28
[error] Not a valid command: no-colors
[error] Not a valid project ID: no-colors
[error] Expected ':' (if selecting a configuration)
[error] Not a valid key: no-colors (similar: compilers)
[error] no-colors
[error]  ^
Makefile:21: recipe for target 'all' failed
make: *** [all] Error 1
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