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rdpstaff / RDPTools

Collection of commonly used RDP Tools for easy building
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Make errors #3

Closed mstevens-bcs closed 7 years ago

mstevens-bcs commented 9 years ago

Running make against the current source goes part way, then dies with:

[snip] -compile-depend:

-do-compile: [javac] Compiling 55 source files to /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/build/classes [javac] warning: [options] bootstrap class path not set in conjunction with -source 1.5 [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/alignment/hmm/tools/Viterbi.java:19: error: package edu.msu.cme.rdp.alignment.hmm.scoring does not exist [javac] import edu.msu.cme.rdp.alignment.hmm.scoring.ViterbiScorer; [javac] ^ [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/alignment/hmm/tools/Viterbi.java:20: error: package edu.msu.cme.rdp.alignment.hmm.scoring does not exist [javac] import edu.msu.cme.rdp.alignment.hmm.scoring.HMMScorer; [javac] ^ [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/alignment/hmm/tools/Viterbi.java:21: error: cannot find symbol [javac] import edu.msu.cme.rdp.alignment.hmm.HMMER3bParser; [javac] ^ [javac] symbol: class HMMER3bParser [javac] location: package edu.msu.cme.rdp.alignment.hmm [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/alignment/hmm/tools/Viterbi.java:24: error: cannot find symbol [javac] import edu.msu.cme.rdp.alignment.hmm.ProfileHMM; [javac] ^ [javac] symbol: class ProfileHMM [javac] location: package edu.msu.cme.rdp.alignment.hmm [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/alignment/hmm/tools/Viterbi.java:25: error: cannot find symbol [javac] import edu.msu.cme.rdp.alignment.hmm.XSC; [javac] ^ [javac] symbol: class XSC [javac] location: package edu.msu.cme.rdp.alignment.hmm [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/alignment/hmm/tools/Viterbi.java:26: error: cannot find symbol [javac] import edu.msu.cme.rdp.alignment.hmm.XSTATES; [javac] ^ [javac] symbol: class XSTATES [javac] location: package edu.msu.cme.rdp.alignment.hmm [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/alignment/hmm/tools/Viterbi.java:29: error: cannot find symbol [javac] import static edu.msu.cme.rdp.alignment.hmm.TSC.; [javac] ^ [javac] symbol: class TSC [javac] location: package edu.msu.cme.rdp.alignment.hmm [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/alignment/hmm/tools/Viterbi.java:30: error: cannot find symbol [javac] import static edu.msu.cme.rdp.alignment.hmm.XSTATES.; [javac] ^ [javac] symbol: class XSTATES [javac] location: package edu.msu.cme.rdp.alignment.hmm [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/alignment/hmm/tools/Viterbi.java:42: error: cannot find symbol [javac] public static double viterbi(Sequence seq, ProfileHMM hmm) { [javac] ^ [javac] symbol: class ProfileHMM [javac] location: class Viterbi [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/cli/BasicSearch.java:19: error: cannot find symbol [javac] import edu.msu.cme.rdp.alignment.hmm.HMMER3bParser; [javac] ^ [javac] symbol: class HMMER3bParser [javac] location: package edu.msu.cme.rdp.alignment.hmm [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/cli/BasicSearch.java:20: error: cannot find symbol [javac] import edu.msu.cme.rdp.alignment.hmm.ProfileHMM; [javac] ^ [javac] symbol: class ProfileHMM [javac] location: package edu.msu.cme.rdp.alignment.hmm [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/cli/BasicSearch.java:50: error: cannot find symbol [javac] private final ProfileHMM forHMM, revHMM; [javac] ^ [javac] symbol: class ProfileHMM [javac] location: class BasicSearch [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/HMMGraphSearch.java:19: error: cannot find symbol [javac] import edu.msu.cme.rdp.alignment.hmm.ProfileHMM; [javac] ^ [javac] symbol: class ProfileHMM [javac] location: package edu.msu.cme.rdp.alignment.hmm [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/HMMGraphSearch.java:20: error: cannot find symbol [javac] import edu.msu.cme.rdp.alignment.hmm.TSC; [javac] ^ [javac] symbol: class TSC [javac] location: package edu.msu.cme.rdp.alignment.hmm [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/HMMGraphSearch.java:21: error: package edu.msu.cme.rdp.alignment.hmm.scoring does not exist [javac] import edu.msu.cme.rdp.alignment.hmm.scoring.ForwardScorer; [javac] ^ [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/HMMGraphSearch.java:22: error: package edu.msu.cme.rdp.alignment.hmm.scoring does not exist [javac] import edu.msu.cme.rdp.alignment.hmm.scoring.HMMScorer; [javac] ^ [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/cli/BasicSearch.java:55: error: cannot find symbol [javac] public BasicSearch(final int maxPaths, final ProfileHMM forHMM, final ProfileHMM revHMM, final BloomFilter bloom) { [javac] ^ [javac] symbol: class ProfileHMM [javac] location: class BasicSearch [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/cli/BasicSearch.java:55: error: cannot find symbol [javac] public BasicSearch(final int maxPaths, final ProfileHMM forHMM, final ProfileHMM revHMM, final BloomFilter bloom) { [javac] ^ [javac] symbol: class ProfileHMM [javac] location: class BasicSearch [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/heuristic/weight/HeuristicWeight.java:20: error: cannot find symbol [javac] import edu.msu.cme.rdp.alignment.hmm.ProfileHMM; [javac] ^ [javac] symbol: class ProfileHMM [javac] location: package edu.msu.cme.rdp.alignment.hmm [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/SearchTarget.java:21: error: cannot find symbol [javac] import edu.msu.cme.rdp.alignment.hmm.ProfileHMM; [javac] ^ [javac] symbol: class ProfileHMM [javac] location: package edu.msu.cme.rdp.alignment.hmm [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/HMMGraphSearch.java:179: error: cannot find symbol [javac] private List kpathsSearch(ProfileHMM hmm, int startingState, String framedWord, CodonWalker walker, boolean forward) throws InterruptedException { [javac] ^ [javac] symbol: class ProfileHMM [javac] location: class HMMGraphSearch [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/HMMGraphSearch.java:189: error: cannot find symbol [javac] private List kpathsSearchGraph(ProfileHMM hmm, int startingState, String framedWord, CodonWalker walker, boolean forward) throws InterruptedException { [javac] ^ [javac] symbol: class ProfileHMM [javac] location: class HMMGraphSearch [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/HMMGraphSearch.java:301: error: cannot find symbol [javac] private AStarNode astarSearch(final ProfileHMM hmm, [javac] ^ [javac] symbol: class ProfileHMM [javac] location: class HMMGraphSearch [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/HMMGraphSearch.java:342: error: cannot find symbol [javac] private float scoreStart(ProfileHMM hmm, String startingKmer, int startingState) { [javac] ^ [javac] symbol: class ProfileHMM [javac] location: class HMMGraphSearch [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/HMMGraphSearch.java:353: error: cannot find symbol [javac] private float realScoreStart(ProfileHMM hmm, String startingKmer, int startingState) { [javac] ^ [javac] symbol: class ProfileHMM [javac] location: class HMMGraphSearch [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/HMMGraphSearch.java:386: error: cannot find symbol [javac] private AStarNode astarSearch(final ProfileHMM hmm, [javac] ^ [javac] symbol: class ProfileHMM [javac] location: class HMMGraphSearch [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/heuristic/weight/HeuristicWeight.java:33: error: cannot find symbol [javac] protected ProfileHMM hmm; [javac] ^ [javac] symbol: class ProfileHMM [javac] location: class HeuristicWeight [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/heuristic/weight/HeuristicWeight.java:56: error: cannot find symbol [javac] public HeuristicWeight(double epsilon, ProfileHMM hmm) { [javac] ^ [javac] symbol: class ProfileHMM [javac] location: class HeuristicWeight [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/heuristic/weight/HeuristicWeight.java:67: error: cannot find symbol [javac] public void setHMM(ProfileHMM hmm) { [javac] ^ [javac] symbol: class ProfileHMM [javac] location: class HeuristicWeight [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/SearchTarget.java:34: error: cannot find symbol [javac] private ProfileHMM forwardHmm; [javac] ^ [javac] symbol: class ProfileHMM [javac] location: class SearchTarget [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/SearchTarget.java:35: error: cannot find symbol [javac] private ProfileHMM reverseHmm; [javac] ^ [javac] symbol: class ProfileHMM [javac] location: class SearchTarget [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/SearchTarget.java:40: error: cannot find symbol [javac] public SearchTarget(String geneName, String querySeqid, String refSeqid, String kmer, int frame, int startState, ProfileHMM forwardHmm, ProfileHMM reverseHmm, BloomFilter filter) { [javac] ^ [javac] symbol: class ProfileHMM [javac] location: class SearchTarget [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/SearchTarget.java:40: error: cannot find symbol [javac] public SearchTarget(String geneName, String querySeqid, String refSeqid, String kmer, int frame, int startState, ProfileHMM forwardHmm, ProfileHMM reverseHmm, BloomFilter filter) { [javac] ^ [javac] symbol: class ProfileHMM [javac] location: class SearchTarget [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/SearchTarget.java:69: error: cannot find symbol [javac] public ProfileHMM getForwardHmm() { [javac] ^ [javac] symbol: class ProfileHMM [javac] location: class SearchTarget [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/SearchTarget.java:73: error: cannot find symbol [javac] public ProfileHMM getReverseHmm() { [javac] ^ [javac] symbol: class ProfileHMM [javac] location: class SearchTarget [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/cli/TimeLimitedSearch.java:19: error: cannot find symbol [javac] import edu.msu.cme.rdp.alignment.hmm.HMMER3bParser; [javac] ^ [javac] symbol: class HMMER3bParser [javac] location: package edu.msu.cme.rdp.alignment.hmm [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/cli/TimeLimitedSearch.java:20: error: cannot find symbol [javac] import edu.msu.cme.rdp.alignment.hmm.ProfileHMM; [javac] ^ [javac] symbol: class ProfileHMM [javac] location: package edu.msu.cme.rdp.alignment.hmm [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/readcorrection/NodeEnumerator.java:21: error: package edu.msu.cme.rdp.alignment.pairwise does not exist [javac] import edu.msu.cme.rdp.alignment.pairwise.ScoringMatrix; [javac] ^ [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/readcorrection/NodeEnumerator.java:33: error: cannot find symbol [javac] private static final ScoringMatrix sm = ScoringMatrix.getDefaultNuclMatrix(); [javac] ^ [javac] symbol: class ScoringMatrix [javac] location: class NodeEnumerator [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/sandbox/AlignAllLengths.java:19: error: cannot find symbol [javac] import edu.msu.cme.rdp.alignment.hmm.HMMER3bParser; [javac] ^ [javac] symbol: class HMMER3bParser [javac] location: package edu.msu.cme.rdp.alignment.hmm [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/sandbox/AlignAllLengths.java:20: error: cannot find symbol [javac] import edu.msu.cme.rdp.alignment.hmm.ProfileHMM; [javac] ^ [javac] symbol: class ProfileHMM [javac] location: package edu.msu.cme.rdp.alignment.hmm [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/sandbox/AlignAllLengths.java:21: error: package edu.msu.cme.rdp.alignment.hmm.scoring does not exist [javac] import edu.msu.cme.rdp.alignment.hmm.scoring.HMMScorer; [javac] ^ [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/sandbox/AlignAllLengths.java:22: error: package edu.msu.cme.rdp.alignment.hmm.scoring does not exist [javac] import edu.msu.cme.rdp.alignment.hmm.scoring.ViterbiScorer; [javac] ^ [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/sandbox/AlignAllLengthsManualViterbi.java:19: error: cannot find symbol [javac] import edu.msu.cme.rdp.alignment.hmm.HMMER3bParser; [javac] ^ [javac] symbol: class HMMER3bParser [javac] location: package edu.msu.cme.rdp.alignment.hmm [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/sandbox/AlignAllLengthsManualViterbi.java:20: error: cannot find symbol [javac] import edu.msu.cme.rdp.alignment.hmm.ProfileHMM; [javac] ^ [javac] symbol: class ProfileHMM [javac] location: package edu.msu.cme.rdp.alignment.hmm [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/sandbox/AlignAllLengthsManualViterbi.java:21: error: cannot find symbol [javac] import edu.msu.cme.rdp.alignment.hmm.TSC; [javac] ^ [javac] symbol: class TSC [javac] location: package edu.msu.cme.rdp.alignment.hmm [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/sandbox/AlignAllLengthsManualViterbi.java:22: error: package edu.msu.cme.rdp.alignment.hmm.scoring does not exist [javac] import edu.msu.cme.rdp.alignment.hmm.scoring.HMMScorer; [javac] ^ [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/sandbox/AlignAllLengthsManualViterbi.java:23: error: package edu.msu.cme.rdp.alignment.hmm.scoring does not exist [javac] import edu.msu.cme.rdp.alignment.hmm.scoring.ViterbiScorer; [javac] ^ [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/sandbox/ExploreRenderCombinedGraph.java:21: error: cannot find symbol [javac] import edu.msu.cme.rdp.alignment.hmm.HMMER3bParser; [javac] ^ [javac] symbol: class HMMER3bParser [javac] location: package edu.msu.cme.rdp.alignment.hmm [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/sandbox/ExploreRenderCombinedGraph.java:22: error: cannot find symbol [javac] import edu.msu.cme.rdp.alignment.hmm.ProfileHMM; [javac] ^ [javac] symbol: class ProfileHMM [javac] location: package edu.msu.cme.rdp.alignment.hmm [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/sandbox/ExploreRenderCombinedGraph.java:23: error: cannot find symbol [javac] import edu.msu.cme.rdp.alignment.hmm.TSC; [javac] ^ [javac] symbol: class TSC [javac] location: package edu.msu.cme.rdp.alignment.hmm [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/sandbox/ExploreRenderCombinedGraph.java:24: error: package edu.msu.cme.rdp.alignment.hmm.scoring does not exist [javac] import edu.msu.cme.rdp.alignment.hmm.scoring.HMMScorer; [javac] ^ [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/sandbox/ExploreRenderCombinedGraph.java:53: error: cannot find symbol [javac] private final ProfileHMM forHmm; [javac] ^ [javac] symbol: class ProfileHMM [javac] location: class ExploreRenderCombinedGraph [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/sandbox/ExploreRenderCombinedGraph.java:54: error: cannot find symbol [javac] private final ProfileHMM revHmm; [javac] ^ [javac] symbol: class ProfileHMM [javac] location: class ExploreRenderCombinedGraph [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/sandbox/ExploreRenderCombinedGraph.java:60: error: cannot find symbol [javac] public ExploreRenderCombinedGraph(BloomFilter bloom, ProfileHMM forHmm, ProfileHMM revHmm, int radius, boolean allowGaps) { [javac] ^ [javac] symbol: class ProfileHMM [javac] location: class ExploreRenderCombinedGraph [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/sandbox/ExploreRenderCombinedGraph.java:60: error: cannot find symbol [javac] public ExploreRenderCombinedGraph(BloomFilter bloom, ProfileHMM forHmm, ProfileHMM revHmm, int radius, boolean allowGaps) { [javac] ^ [javac] symbol: class ProfileHMM [javac] location: class ExploreRenderCombinedGraph [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/NodeEnumerator.java:20: error: cannot find symbol [javac] import edu.msu.cme.rdp.alignment.hmm.MostProbableHCostHMM; [javac] ^ [javac] symbol: class MostProbableHCostHMM [javac] location: package edu.msu.cme.rdp.alignment.hmm [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/NodeEnumerator.java:21: error: cannot find symbol [javac] import edu.msu.cme.rdp.alignment.hmm.ProfileHMM; [javac] ^ [javac] symbol: class ProfileHMM [javac] location: package edu.msu.cme.rdp.alignment.hmm [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/NodeEnumerator.java:23: error: cannot find symbol [javac] import static edu.msu.cme.rdp.alignment.hmm.TSC.; [javac] ^ [javac] symbol: class TSC [javac] location: package edu.msu.cme.rdp.alignment.hmm [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/sandbox/ExploreRenderCombinedGraph.java:90: error: cannot find symbol [javac] private void walk(CodonWalker walker, AStarNode start, PrintStream out, NodeEnumerator enumerator, ProfileHMM hmm) { [javac] ^ [javac] symbol: class ProfileHMM [javac] location: class ExploreRenderCombinedGraph [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/sandbox/ExploreRenderCombinedGraph.java:213: error: cannot find symbol [javac] private AStarNode getStartNode(String startingKmer, int startingState, ProfileHMM hmm, CodonWalker walker) { [javac] ^ [javac] symbol: class ProfileHMM [javac] location: class ExploreRenderCombinedGraph [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/sandbox/ExploreRenderCombinedGraph.java:241: error: cannot find symbol [javac] private float scoreStart(ProfileHMM hmm, String startingKmer, int startingState) { [javac] ^ [javac] symbol: class ProfileHMM [javac] location: class ExploreRenderCombinedGraph [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/sandbox/ExploreRenderCombinedGraph.java:255: error: cannot find symbol [javac] private float realScoreStart(ProfileHMM hmm, String startingKmer, int startingState) { [javac] ^ [javac] symbol: class ProfileHMM [javac] location: class ExploreRenderCombinedGraph [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/NodeEnumerator.java:48: error: cannot find symbol [javac] private final ProfileHMM hmm; [javac] ^ [javac] symbol: class ProfileHMM [javac] location: class NodeEnumerator [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/NodeEnumerator.java:50: error: cannot find symbol [javac] private final MostProbableHCostHMM hcost; [javac] ^ [javac] symbol: class MostProbableHCostHMM [javac] location: class NodeEnumerator [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/NodeEnumerator.java:53: error: cannot find symbol [javac] public NodeEnumerator(ProfileHMM hmm, HeuristicWeight hweight) { [javac] ^ [javac] symbol: class ProfileHMM [javac] location: class NodeEnumerator [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/SearchMethod.java:19: error: cannot find symbol [javac] import edu.msu.cme.rdp.alignment.hmm.ProfileHMM; [javac] ^ [javac] symbol: class ProfileHMM [javac] location: package edu.msu.cme.rdp.alignment.hmm [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/SearchMethod.java:20: error: package edu.msu.cme.rdp.alignment.hmm.scoring does not exist [javac] import edu.msu.cme.rdp.alignment.hmm.scoring.ForwardScorer; [javac] ^ [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/SearchMethod.java:21: error: package edu.msu.cme.rdp.alignment.hmm.scoring does not exist [javac] import edu.msu.cme.rdp.alignment.hmm.scoring.HMMScorer; [javac] ^ [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/SearchMethod.java:106: error: cannot find symbol [javac] protected abstract List searchInternal(ProfileHMM hmm, int startingState, String framedKmer, boolean isProt, CodonWalker walker, boolean forward); [javac] ^ [javac] symbol: class ProfileHMM [javac] location: class SearchMethod [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/TestHCostHMM.java:19: error: cannot find symbol [javac] import edu.msu.cme.rdp.alignment.hmm.ProfileHMM; [javac] ^ [javac] symbol: class ProfileHMM [javac] location: package edu.msu.cme.rdp.alignment.hmm [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/TestHCostHMM.java:20: error: cannot find symbol [javac] import static edu.msu.cme.rdp.alignment.hmm.TSC.; [javac] ^ [javac] symbol: class TSC [javac] location: package edu.msu.cme.rdp.alignment.hmm [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/TestHCostHMM.java:28: error: cannot find symbol [javac] private ProfileHMM hmm; [javac] ^ [javac] symbol: class ProfileHMM [javac] location: class TestHCostHMM [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/TestHCostHMM.java:32: error: cannot find symbol [javac] public TestHCostHMM(ProfileHMM hmm) { [javac] ^ [javac] symbol: class ProfileHMM [javac] location: class TestHCostHMM [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/heuristic/weight/DynamicHeuristicWeight.java:20: error: cannot find symbol [javac] import edu.msu.cme.rdp.alignment.hmm.ProfileHMM; [javac] ^ [javac] symbol: class ProfileHMM [javac] location: package edu.msu.cme.rdp.alignment.hmm [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/heuristic/weight/DynamicHeuristicWeight.java:33: error: cannot find symbol [javac] public DynamicHeuristicWeight(double epsilon, ProfileHMM hmm) { [javac] ^ [javac] symbol: class ProfileHMM [javac] location: class DynamicHeuristicWeight [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/heuristic/weight/RevisedDynamicHeuristicWeight.java:20: error: cannot find symbol [javac] import edu.msu.cme.rdp.alignment.hmm.ProfileHMM; [javac] ^ [javac] symbol: class ProfileHMM [javac] location: package edu.msu.cme.rdp.alignment.hmm [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/heuristic/weight/RevisedDynamicHeuristicWeight.java:37: error: cannot find symbol [javac] public RevisedDynamicHeuristicWeight(double epsilon, ProfileHMM hmm) { [javac] ^ [javac] symbol: class ProfileHMM [javac] location: class RevisedDynamicHeuristicWeight [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/heuristic/weight/StaticHeuristicWeight.java:20: error: cannot find symbol [javac] import edu.msu.cme.rdp.alignment.hmm.ProfileHMM; [javac] ^ [javac] symbol: class ProfileHMM [javac] location: package edu.msu.cme.rdp.alignment.hmm [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/search/heuristic/weight/StaticHeuristicWeight.java:33: error: cannot find symbol [javac] public StaticHeuristicWeight(double epsilon, ProfileHMM hmm) { [javac] ^ [javac] symbol: class ProfileHMM [javac] location: class StaticHeuristicWeight [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/utils/ContigMerger.java:19: error: cannot find symbol [javac] import edu.msu.cme.rdp.alignment.hmm.HMMER3bParser; [javac] ^ [javac] symbol: class HMMER3bParser [javac] location: package edu.msu.cme.rdp.alignment.hmm [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/utils/ContigMerger.java:20: error: cannot find symbol [javac] import edu.msu.cme.rdp.alignment.hmm.ProfileHMM; [javac] ^ [javac] symbol: class ProfileHMM [javac] location: package edu.msu.cme.rdp.alignment.hmm [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/utils/ContigMerger.java:21: error: package edu.msu.cme.rdp.alignment.hmm.scoring does not exist [javac] import edu.msu.cme.rdp.alignment.hmm.scoring.ForwardScorer; [javac] ^ [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/utils/ContigMerger.java:65: error: cannot find symbol [javac] private static List mergeAllContigs(Map<String, Sequence> leftContigs, Map<String, Sequence> rightContigs, String kmer, ProfileHMM hmm) { [javac] ^ [javac] symbol: class ProfileHMM [javac] location: class ContigMerger [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/utils/ContigMerger.java:97: error: cannot find symbol [javac] private static List mergeContigs(Map<String, Sequence> leftContigs, Map<String, Sequence> rightContigs, String kmer, ProfileHMM hmm) { [javac] ^ [javac] symbol: class ProfileHMM [javac] location: class ContigMerger [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/utils/HMMKmerFilter.java:19: error: package edu.msu.cme.rdp.alignment.hmm.jni does not exist [javac] import edu.msu.cme.rdp.alignment.hmm.jni.HMMER3; [javac] ^ [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/utils/HMMKmerFilter.java:20: error: package edu.msu.cme.rdp.alignment.hmm.jni does not exist [javac] import edu.msu.cme.rdp.alignment.hmm.jni.HMMER3Hit; [javac] ^ [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/visual/GraphSearch.java:19: error: cannot find symbol [javac] import edu.msu.cme.rdp.alignment.hmm.HMMER3bParser; [javac] ^ [javac] symbol: class HMMER3bParser [javac] location: package edu.msu.cme.rdp.alignment.hmm [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/graph/visual/GraphSearch.java:20: error: cannot find symbol [javac] import edu.msu.cme.rdp.alignment.hmm.ProfileHMM; [javac] ^ [javac] symbol: class ProfileHMM [javac] location: package edu.msu.cme.rdp.alignment.hmm [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/alignment/hmm/tools/Viterbi.java:47: error: cannot find symbol [javac] double[][] xmx = new double[bases.length + 1][XSTATES.values().length]; [javac] ^ [javac] symbol: variable XSTATES [javac] location: class Viterbi [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/alignment/hmm/tools/Viterbi.java:49: error: cannot find symbol [javac] xmx[0][N.ordinal()] = 0; [javac] ^ [javac] symbol: variable N [javac] location: class Viterbi [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/alignment/hmm/tools/Viterbi.java:50: error: cannot find symbol [javac] xmx[0][B.ordinal()] = hmm.xsc(N, XSC.MOVE); [javac] ^ [javac] symbol: variable B [javac] location: class Viterbi [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/alignment/hmm/tools/Viterbi.java:50: error: cannot find symbol [javac] xmx[0][B.ordinal()] = hmm.xsc(N, XSC.MOVE); [javac] ^ [javac] symbol: variable N [javac] location: class Viterbi [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/alignment/hmm/tools/Viterbi.java:50: error: cannot find symbol [javac] xmx[0][B.ordinal()] = hmm.xsc(N, XSC.MOVE); [javac] ^ [javac] symbol: variable XSC [javac] location: class Viterbi [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/alignment/hmm/tools/Viterbi.java:51: error: package XSTATES does not exist [javac] xmx[0][XSTATES.E.ordinal()] = xmx[0][C.ordinal()] = xmx[0][J.ordinal()] = Double.NEGATIVE_INFINITY; [javac] ^ [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/alignment/hmm/tools/Viterbi.java:51: error: cannot find symbol [javac] xmx[0][XSTATES.E.ordinal()] = xmx[0][C.ordinal()] = xmx[0][J.ordinal()] = Double.NEGATIVE_INFINITY; [javac] ^ [javac] symbol: variable C [javac] location: class Viterbi [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/alignment/hmm/tools/Viterbi.java:51: error: cannot find symbol [javac] xmx[0][XSTATES.E.ordinal()] = xmx[0][C.ordinal()] = xmx[0][J.ordinal()] = Double.NEGATIVE_INFINITY; [javac] ^ [javac] symbol: variable J [javac] location: class Viterbi [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/alignment/hmm/tools/Viterbi.java:66: error: package XSTATES does not exist [javac] xmx[i][XSTATES.E.ordinal()] = Double.NEGATIVE_INFINITY; [javac] ^ [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/alignment/hmm/tools/Viterbi.java:69: error: cannot find symbol [javac] sc = max(matrix[M][i - 1][k - 1] + hmm.tsc(k - 1, MM), [javac] ^ [javac] symbol: variable MM [javac] location: class Viterbi [javac] /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/src/edu/msu/cme/rdp/alignment/hmm/tools/Viterbi.java:70: error: cannot find symbol [javac] matrix[I][i - 1][k - 1] + hmm.tsc(k - 1, IM)); [javac] ^ [javac] symbol: variable IM [javac] location: class Viterbi [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 100 errors [javac] 1 warning

BUILD FAILED /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/nbproject/build-impl.xml:948: The following error occurred while executing this line: /gpfs1/blxgrid/tools/bioinfo/app/RDPTools/Xander-HMMgs/nbproject/build-impl.xml:300: Compile failed; see the compiler error output for details.

Total time: 7 seconds make: *\ [Xander-HMMgs/dist/hmmgs.jar] Error 1

wangqion commented 9 years ago

Xander depends on a few packages included in RDPTools. Did you clone the RDPTools following the instruction from README?