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Make errors
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
Build failed
Hi Folks,
I am not able to build rdpTools.
I have just followed installation procedure:
- git clone https://github.com/rdpstaff/RDPTools.git
- cd RDPTools
- git submodule init
- git submodule update
- make
Here the build fails, throwing following error:
BUILD FAILED
/home/denir/bin/RDPTools/Clustering/nbproject/build-impl.xml:896: The following error occurred while executing this line:
/home/denir/bin/RDPTools/Clustering/nbproject/build-impl.xml:1470: The following error occurred while executing this line:
/home/denir/bin/RDPTools/AlignmentTools/nbproject/build-impl.xml:896: The following error occurred while executing this line:
/home/denir/bin/RDPTools/AlignmentTools/nbproject/build-impl.xml:1414: The following error occurred while executing this line:
/home/denir/bin/RDPTools/ReadSeq/nbproject/build-impl.xml:920: The following error occurred while executing this line:
/home/denir/bin/RDPTools/ReadSeq/nbproject/build-impl.xml:300: Compile failed; see the compiler error output for details.
Total time: 1 second
Makefile:15: recipe for target 'Clustering/dist/Clustering.jar' failed
make: *** [Clustering/dist/Clustering.jar] Error 1
Any clues?
Deni
How to match RDP Nomenclature and NCBI Nomenclature
Hi
I am using the standalone RDP classifier to annotate our assemblies. But I find that the RDP nomenclature is different from NCBI nomenclature, such as the NCBI genus Anabaena of phylum Cyanobacteria is named GpI according to RDP classification. The inconsistence between two nomenclatural systems makes me confuse and cannot determine the identity apparently. Is there any tool can give the mapping between these two nomenclatures?
Thank you very much.
rdpclassifiertraindata download timeouts and breaks the build
hello,
while trying to build a docker image for RDPTools I have a problem with the donload of the classifier training set that timesout
see:
download-traindata:
[get] Getting: http://rdp.cme.msu.edu/download/rdpclassifiertraindata/data.tgz
[get] To: /local/gensoft2/src/RDPTools/RDPTools-2.0.2/classifier/build/classes/data.tgz
[untar] Expanding: /local/gensoft2/src/RDPTools/RDPTools-2.0.2/classifier/build/classes/data.tgz into /local/gensoft2/src/RDPTools/RDPTools-2.0.2/classifier/build/classes
BUILD FAILED
/local/gensoft2/src/RDPTools/RDPTools-2.0.2/classifier/build.xml:112: Error while expanding /local/gensoft2/src/RDPTools/RDPTools-2.0.2/classifier/build/classes/data.tgz
java.io.EOFException: Unexpected end of ZLIB input stream
at java.util.zip.InflaterInputStream.fill(InflaterInputStream.java:240)
at java.util.zip.InflaterInputStream.read(InflaterInputStream.java:158)
wget of the same url gives:
wget http://rdp.cme.msu.edu/download/rdpclassifiertraindata/data.tgz
--2016-02-25 11:43:38-- http://rdp.cme.msu.edu/download/rdpclassifiertraindata/data.tgz
Resolving rdp.cme.msu.edu... 35.8.164.79
Connecting to rdp.cme.msu.edu|35.8.164.79|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 149530230 (143M) [application/x-gzip]
Saving to: 'data.tgz'
61% [================================> ] 91,435,408 255KB/s in 3m 30s
2016-02-25 11:47:08 (425 KB/s) - Connection closed at byte 91435408. Retrying.
seems to me that the the get method used does not honour timeout nor the retry
best regards
Eric
Unable to clone into TaxonomyTree to build
Hello,
I am trying to install RDPTools for like one week now, and I have a problem when clonning into TaxonomyTree.
After running
git submodule update
I get
...
Cloning into 'SequenceMatch'...
remote: Enumerating objects: 133, done.
remote: Total 133 (delta 0), reused 0 (delta 0), pack-reused 133
Receiving objects: 100% (133/133), 108.01 KiB | 0 bytes/s, done.
Resolving deltas: 100% (31/31), done.
Checking connectivity... done.
Submodule path 'SequenceMatch': checked out 'd9e902f7a38b2889d9c295b1c6d32af890b0f6e6'
Cloning into 'TaxonomyTree'...
fatal: unable to connect to github.com:
github.com[0: 140.82.118.3]: errno=Connection timed out
fatal: clone of 'git://github.com/rdpstaff/TaxonomyTree' into submodule path 'TaxonomyTree' failed
I am using ant 1.9.6 and java 8 jdk, I can't install java 7 jdk because I'am using Ubuntu 18.04 and java 7 is no longer available for Ubuntu 16.04 and higher.
Any ideas on how to solve this problem are much appreciated.
Thank you
make fail: problem with ant -f Clustering/build.xml jar
I'm trying to install RDPTools on a linux system (RHEL 7.3). When I run:
sudo git submodule init
sudo git submodule update
sudo make
I get an error:
ant -f Clustering/build.xml jar
make: ant: Command not found
make: *** [Clustering/dist/Clustering.jar] Error 127
Despite the "ant: Command not found" my system does recognize ant (and it's in the path); ant just seems to want a good build.xml file.
$ ant
Buildfile: build.xml does not exist!
Build failed
When I run ant using the command in the initial error output, I get a long output, below, which includes this error:
$ ant -f Clustering/build.xml jar
[...]
BUILD FAILED
/usr/local/src/RDPTools/Clustering/build.xml:104: impossible to ivy retrieve: java.lang.RuntimeException: problem during retrieve of edu.cme.rdp#clustering: java.io.FileNotFoundException: /usr/local/src/RDPTools/Clustering/lib/jaxb-impl-2.2.7.jar (No such file or directory)
[...]
Full output:
$ ant -f Clustering/build.xml jar
Buildfile: /usr/local/src/RDPTools/Clustering/build.xml
download-ivy:
[mkdir] Created dir: /home/gadarjat/.ant/lib
[get] Getting: http://repo2.maven.org/maven2/org/apache/ivy/ivy/2.1.0-rc2/ivy-2.1.0-rc2.jar
[get] To: /home/gadarjat/.ant/lib/ivy.jar
init-ivy:
resolve:
[ivy:retrieve] :: Ivy 2.1.0-rc2 - 20090704004254 :: http://ant.apache.org/ivy/ ::
[ivy:retrieve] :: loading settings :: url = jar:file:/home/gadarjat/.ant/lib/ivy.jar!/org/apache/ivy/core/settings/ivysettings.xml
[ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#clustering;[email protected]
[ivy:retrieve] confs: [default]
[ivy:retrieve] found com.sun.xml.bind#jaxb-impl;2.2.7 in public
[ivy:retrieve] found com.sun.xml.bind#jaxb-core;2.2.7 in public
[ivy:retrieve] found javax.xml.bind#jaxb-api;2.2.7 in public
[ivy:retrieve] found com.sun.istack#istack-commons-runtime;2.16 in public
[ivy:retrieve] found com.sun.xml.fastinfoset#FastInfoset;1.2.12 in public
[ivy:retrieve] found javax.xml.bind#jsr173_api;1.0 in public
[ivy:retrieve] found commons-cli#commons-cli;1.2 in public
[ivy:retrieve] found junit#junit;4.8.2 in public
[ivy:retrieve] found commons-codec#commons-codec;1.8 in public
[ivy:retrieve] found commons-io#commons-io;2.4 in public
[ivy:retrieve] downloading http://repo1.maven.org/maven2/com/sun/xml/bind/jaxb-impl/2.2.7/jaxb-impl-2.2.7-javadoc.jar ...
[ivy:retrieve] .............................................................................................................................................................................................................................................................. (1449kB)
[ivy:retrieve] .. (0kB)
[ivy:retrieve] [SUCCESSFUL ] com.sun.xml.bind#jaxb-impl;2.2.7!jaxb-impl.jar(javadoc) (142ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/com/sun/xml/bind/jaxb-impl/2.2.7/jaxb-impl-2.2.7.jar ...
[ivy:retrieve] .................................................................................................................................................. (898kB)
[ivy:retrieve] .. (0kB)
[ivy:retrieve] [SUCCESSFUL ] com.sun.xml.bind#jaxb-impl;2.2.7!jaxb-impl.jar (58ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/com/sun/xml/bind/jaxb-impl/2.2.7/jaxb-impl-2.2.7-sources.jar ...
[ivy:retrieve] ......................................................................................................................................................................... (1109kB)
[ivy:retrieve] .. (0kB)
[ivy:retrieve] [SUCCESSFUL ] com.sun.xml.bind#jaxb-impl;2.2.7!jaxb-impl.jar(source) (77ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/commons-cli/commons-cli/1.2/commons-cli-1.2.jar ...
[ivy:retrieve] .. (40kB)
[ivy:retrieve] .. (0kB)
[ivy:retrieve] [SUCCESSFUL ] commons-cli#commons-cli;1.2!commons-cli.jar (19ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/commons-cli/commons-cli/1.2/commons-cli-1.2-sources.jar ...
[ivy:retrieve] .... (47kB)
[ivy:retrieve] .. (0kB)
[ivy:retrieve] [SUCCESSFUL ] commons-cli#commons-cli;1.2!commons-cli.jar(source) (19ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/commons-cli/commons-cli/1.2/commons-cli-1.2-javadoc.jar ...
[ivy:retrieve] ............................ (209kB)
[ivy:retrieve] .. (0kB)
[ivy:retrieve] [SUCCESSFUL ] commons-cli#commons-cli;1.2!commons-cli.jar(javadoc) (25ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/junit/junit/4.8.2/junit-4.8.2-sources.jar ...
[ivy:retrieve] ...................... (143kB)
[ivy:retrieve] .. (0kB)
[ivy:retrieve] [SUCCESSFUL ] junit#junit;4.8.2!junit.jar(source) (22ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/junit/junit/4.8.2/junit-4.8.2-javadoc.jar ...
[ivy:retrieve] ........................................................... (387kB)
[ivy:retrieve] .. (0kB)
[ivy:retrieve] [SUCCESSFUL ] junit#junit;4.8.2!junit.jar(javadoc) (29ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/junit/junit/4.8.2/junit-4.8.2.jar ...
[ivy:retrieve] ............................... (231kB)
[ivy:retrieve] .. (0kB)
[ivy:retrieve] [SUCCESSFUL ] junit#junit;4.8.2!junit.jar (24ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/commons-codec/commons-codec/1.8/commons-codec-1.8-sources.jar ...
[ivy:retrieve] .......................................... (271kB)
[ivy:retrieve] .. (0kB)
[ivy:retrieve] [SUCCESSFUL ] commons-codec#commons-codec;1.8!commons-codec.jar(source) (25ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/commons-codec/commons-codec/1.8/commons-codec-1.8-javadoc.jar ...
[ivy:retrieve] ...................................................... (389kB)
[ivy:retrieve] .. (0kB)
[ivy:retrieve] [SUCCESSFUL ] commons-codec#commons-codec;1.8!commons-codec.jar(javadoc) (27ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/commons-codec/commons-codec/1.8/commons-codec-1.8.jar ...
[ivy:retrieve] .................................... (257kB)
[ivy:retrieve] .. (0kB)
[ivy:retrieve] [SUCCESSFUL ] commons-codec#commons-codec;1.8!commons-codec.jar (24ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/commons-io/commons-io/2.4/commons-io-2.4-sources.jar ...
[ivy:retrieve] ............................... (240kB)
[ivy:retrieve] .. (0kB)
[ivy:retrieve] [SUCCESSFUL ] commons-io#commons-io;2.4!commons-io.jar(source) (24ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/commons-io/commons-io/2.4/commons-io-2.4.jar ...
[ivy:retrieve] ............................ (180kB)
[ivy:retrieve] .. (0kB)
[ivy:retrieve] [SUCCESSFUL ] commons-io#commons-io;2.4!commons-io.jar (31ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/commons-io/commons-io/2.4/commons-io-2.4-javadoc.jar ...
[ivy:retrieve] ..................................................................................................... (707kB)
[ivy:retrieve] .. (0kB)
[ivy:retrieve] [SUCCESSFUL ] commons-io#commons-io;2.4!commons-io.jar(javadoc) (38ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/com/sun/xml/bind/jaxb-core/2.2.7/jaxb-core-2.2.7.jar ...
[ivy:retrieve] ......................... (216kB)
[ivy:retrieve] .. (0kB)
[ivy:retrieve] [SUCCESSFUL ] com.sun.xml.bind#jaxb-core;2.2.7!jaxb-core.jar (22ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/com/sun/xml/fastinfoset/FastInfoset/1.2.12/FastInfoset-1.2.12.jar ...
[ivy:retrieve] ....................................... (286kB)
[ivy:retrieve] .. (0kB)
[ivy:retrieve] [SUCCESSFUL ] com.sun.xml.fastinfoset#FastInfoset;1.2.12!FastInfoset.jar (24ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/javax/xml/bind/jaxb-api/2.2.7/jaxb-api-2.2.7.jar ...
[ivy:retrieve] ............. (97kB)
[ivy:retrieve] .. (0kB)
[ivy:retrieve] [SUCCESSFUL ] javax.xml.bind#jaxb-api;2.2.7!jaxb-api.jar (20ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/com/sun/istack/istack-commons-runtime/2.16/istack-commons-runtime-2.16.jar ...
[ivy:retrieve] .. (22kB)
[ivy:retrieve] .. (0kB)
[ivy:retrieve] [SUCCESSFUL ] com.sun.istack#istack-commons-runtime;2.16!istack-commons-runtime.jar (19ms)
[ivy:retrieve] downloading http://repo1.maven.org/maven2/javax/xml/bind/jsr173_api/1.0/jsr173_api-1.0.jar ...
[ivy:retrieve] ...... (48kB)
[ivy:retrieve] .. (0kB)
[ivy:retrieve] [SUCCESSFUL ] javax.xml.bind#jsr173_api;1.0!jsr173_api.jar (19ms)
[ivy:retrieve] :: resolution report :: resolve 1488ms :: artifacts dl 699ms
---------------------------------------------------------------------
| | modules || artifacts |
| conf | number| search|dwnlded|evicted|| number|dwnlded|
---------------------------------------------------------------------
| default | 10 | 10 | 10 | 0 || 20 | 20 |
---------------------------------------------------------------------
[ivy:retrieve] :: retrieving :: edu.cme.rdp#clustering
[ivy:retrieve] confs: [default]
BUILD FAILED
/usr/local/src/RDPTools/Clustering/build.xml:104: impossible to ivy retrieve: java.lang.RuntimeException: problem during retrieve of edu.cme.rdp#clustering: java.io.FileNotFoundException: /usr/local/src/RDPTools/Clustering/lib/jaxb-impl-2.2.7.jar (No such file or directory)
at org.apache.ivy.core.retrieve.RetrieveEngine.retrieve(RetrieveEngine.java:206)
at org.apache.ivy.Ivy.retrieve(Ivy.java:540)
at org.apache.ivy.ant.IvyRetrieve.doExecute(IvyRetrieve.java:59)
at org.apache.ivy.ant.IvyTask.execute(IvyTask.java:277)
at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:293)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
at org.apache.tools.ant.Task.perform(Task.java:348)
at org.apache.tools.ant.Target.execute(Target.java:435)
at org.apache.tools.ant.Target.performTasks(Target.java:456)
at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1405)
at org.apache.tools.ant.Project.executeTarget(Project.java:1376)
at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
at org.apache.tools.ant.Project.executeTargets(Project.java:1260)
at org.apache.tools.ant.Main.runBuild(Main.java:857)
at org.apache.tools.ant.Main.startAnt(Main.java:236)
at org.apache.tools.ant.launch.Launcher.run(Launcher.java:287)
at org.apache.tools.ant.launch.Launcher.main(Launcher.java:113)
Caused by: java.io.FileNotFoundException: /usr/local/src/RDPTools/Clustering/lib/jaxb-impl-2.2.7.jar (No such file or directory)
at java.io.FileOutputStream.open0(Native Method)
at java.io.FileOutputStream.open(FileOutputStream.java:270)
at java.io.FileOutputStream.<init>(FileOutputStream.java:213)
at java.io.FileOutputStream.<init>(FileOutputStream.java:162)
at org.apache.ivy.util.FileUtil.copy(FileUtil.java:147)
at org.apache.ivy.util.FileUtil.copy(FileUtil.java:122)
at org.apache.ivy.core.retrieve.RetrieveEngine.retrieve(RetrieveEngine.java:140)
... 20 more
Total time: 3 seconds
Error while expanding /RDPTools/classifier/build/classes/data.tgz
Error while expanding /RDPTools/classifier/build/classes/data.tgz
java.io.EOFException: Unexpected end of ZLIB input stream
at java.util.zip.InflaterInputStream.fill(InflaterInputStream.java:240)
at java.util.zip.InflaterInputStream.read(InflaterInputStream.java:158)
at java.util.zip.GZIPInputStream.read(GZIPInputStream.java:117)
at org.apache.tools.tar.TarBuffer.readBlock(TarBuffer.java:253)
at org.apache.tools.tar.TarBuffer.readRecord(TarBuffer.java:220)
at org.apache.tools.tar.TarInputStream.read(TarInputStream.java:603)
at java.io.FilterInputStream.read(FilterInputStream.java:107)
at org.apache.tools.ant.taskdefs.Expand.extractFile(Expand.java:358)
at org.apache.tools.ant.taskdefs.Untar.expandStream(Untar.java:163)
at org.apache.tools.ant.taskdefs.Untar.expandFile(Untar.java:109)
at org.apache.tools.ant.taskdefs.Expand.execute(Expand.java:148)
at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:293)
at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
at org.apache.tools.ant.Task.perform(Task.java:348)
at org.apache.tools.ant.Target.execute(Target.java:435)
at org.apache.tools.ant.Target.performTasks(Target.java:456)
at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1405)
at org.apache.tools.ant.Project.executeTarget(Project.java:1376)
at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
at org.apache.tools.ant.Project.executeTargets(Project.java:1260)
at org.apache.tools.ant.Main.runBuild(Main.java:857)
at org.apache.tools.ant.Main.startAnt(Main.java:236)
at org.apache.tools.ant.launch.Launcher.run(Launcher.java:287)
at org.apache.tools.ant.launch.Launcher.main(Launcher.java:113)
Total time: 15 seconds
make: *** [classifier/dist/classifier.jar] Error 1
RDP traindata not found
Hi guys
make will fail because of missing data at rdp:
Download-traindata:
[get] Getting: http://rdp.cme.msu.edu/download/rdpclassifiertraindata/data.tgz
[get] To: /home/gisle/RDPTools/classifier/build/classes/data.tgz
[get] Error opening connection java.io.FileNotFoundException: http://rdp.cme.msu.edu/download/rdpclassifiertraindata/data.tgz
[get] Error opening connection java.io.FileNotFoundException: http://rdp.cme.msu.edu/download/rdpclassifiertraindata/data.tgz
[get] Error opening connection java.io.FileNotFoundException: http://rdp.cme.msu.edu/download/rdpclassifiertraindata/data.tgz
[get] Can't get http://rdp.cme.msu.edu/download/rdpclassifiertraindata/data.tgz to /home/gisle/RDPTools/classifier/build/classes/data.tgz
BUILD FAILED
/home/gisle/RDPTools/classifier/build.xml:50: Can't get http://rdp.cme.msu.edu/download/rdpclassifiertraindata/data.tgz to /home/gisle/RDPTools/classifier/build/classes/data.tgz
Total time: 7 seconds
make: *** [classifier/dist/classifier.jar] Error 1
Hope to hear from you soon,
Gisle Vestergaard
Helmholtz Zentrum Mรผnchen
rdp.cme.msu.edu/download/rdpclassifiertraindata/data.tgz not available
I have problems accessing the RDP server. is it still running or has it been moved?
download-traindata:
[get] Getting: http://rdp.cme.msu.edu/download/rdpclassifiertraindata/data.tgz
[get] To: $INSTALLPATH/data.tgz
[get] Error getting http://rdp.cme.msu.edu/download/rdpclassifiertraindata/data.tgz to $INSTALLPATH
BUILD FAILED
$INSTALLPATH/build.xml:50: java.net.ConnectException: Connection timed out (Connection timed out)
edit: server was restarted and it works now
classifier/dist/classifier.jar] Error 1
Dear all
I have a problem in make
BUILD FAILED
/root/RDPTools/classifier/build.xml:50: java.net.SocketException: Resource temporarily unavailable
at java.net.PlainSocketImpl.socketConnect(Native Method)
at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:339)
at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:200)
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:182)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:579)
at java.net.Socket.connect(Socket.java:528)
at sun.net.NetworkClient.doConnect(NetworkClient.java:180)
at sun.net.www.http.HttpClient.openServer(HttpClient.java:432)
at sun.net.www.http.HttpClient.openServer(HttpClient.java:527)
at sun.net.www.http.HttpClient.(HttpClient.java:211)
at sun.net.www.http.HttpClient.New(HttpClient.java:308)
at sun.net.www.http.HttpClient.New(HttpClient.java:326)
at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:997)
at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:933)
at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:851)
at org.apache.tools.ant.taskdefs.Get$GetThread.openConnection(Get.java:736)
at org.apache.tools.ant.taskdefs.Get$GetThread.get(Get.java:652)
at org.apache.tools.ant.taskdefs.Get$GetThread.run(Get.java:642)
Total time: 23 seconds
make: *** [Makefile:24: classifier/dist/classifier.jar] Error 1
Error testing RDPTools on Frogs
When i run:
root@raquel-X555LDB:/home/raquel/FROGS-master/test# bash test.sh /home/raquel/FROGS-master/ 2 4 /tmp/results
Frogs can't found RDPTools jar classes:
Step preprocess tum awu 5 17:42:20 PET 2018
Step clustering tum awu 5 17:43:36 PET 2018
Step remove_chimera tum awu 5 17:44:20 PET 2018
Step filters tum awu 5 17:45:57 PET 2018
Step affiliation_OTU tum awu 5 17:45:58 PET 2018
Exception in thread "main" java.lang.NoClassDefFoundError: edu/msu/cme/rdp/taxatree/interfaces/TreeVisitor
at edu.msu.cme.rdp.classifier.cli.ClassifierMain.main(ClassifierMain.java:67)
Caused by: java.lang.ClassNotFoundException: edu.msu.cme.rdp.taxatree.interfaces.TreeVisitor
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
... 1 more
Exception in thread Thread-1:
Traceback (most recent call last):
File "/usr/lib/python2.7/threading.py", line 801, in __bootstrap_inner
self.run()
File "/usr/lib/python2.7/threading.py", line 754, in run
self.__target(*self.__args, **self.__kwargs)
File "/home/raquel/FROGS-master//app/affiliation_OTU.py", line 192, in process_rdp
rdp_cmd.submit(log_file)
File "/home/raquel/FROGS-master/lib/frogsUtils.py", line 140, in submit
subprocess.check_output( self.get_cmd(), shell=True )
File "/usr/lib/python2.7/subprocess.py", line 574, in check_output
raise CalledProcessError(retcode, cmd, output=output)
CalledProcessError: Command 'taskset -c 0 java -Xmx4g -jar /home/raquel/FROGS-master/libexec/classifier.jar classify -c 0.0 -t /home/raquel/FROGS-master//test/data/db.fasta.properties -o /tmp/results/1533509158.25_11883_1533509158.25_11883_04-filters.fasta_0.rdp /tmp/results/1533509158.25_11883_04-filters.fasta_0' returned non-zero exit status 1
Traceback (most recent call last):
File "/home/raquel/FROGS-master//app/affiliation_OTU.py", line 370, in
Blast(args.reference, args.input_fasta, blast_out_list[0], args.nb_cpus).submit(log_blast_list[0])
File "/home/raquel/FROGS-master/lib/frogsUtils.py", line 135, in submit
FH_log.write( '# ' + self.description + ' (' + os.path.basename(self.program) + ' version : ' + self.get_version() + ')\n' )
File "/home/raquel/FROGS-master//app/affiliation_OTU.py", line 75, in get_version
return Cmd.get_version(self, 'stdout').split()[1].strip()
IndexError: list index out of range
Error in affiliation_OTU
I copied all rdptools jars to libexec.
Help
new version 2.14
Hell RDP team,
I noticed that v2.14 is already on source forge but this GitHub channel which is the source for the bioconda channel has not been updated yet. Can you please update it and then also update the biconda channel?
Thanks,
Jianshu
Installation failed on Mac M1
Dear RDPstaffers,
I am trying to install RDPTools on Mac M1, I install the package following the instructions online, I tries jdk6\7\8๏ผant 1.9.16, but I keep getting the following error:
ant -f Clustering/build.xml jar
Buildfile: /usr/local/RDPTools/Clustering/build.xml
download-ivy:
[get] Getting: http://insecure.repo1.maven.org/maven2/org/apache/ivy/ivy/2.1.0-rc2/ivy-2.1.0-rc2.jar
[get] To: /var/root/.ant/lib/ivy.jar
[get] Not modified - so not downloaded
init-ivy:
resolve:
[ivy:retrieve] :: Ivy 2.1.0-rc2 - 20090704004254 :: http://ant.apache.org/ivy/ ::
[ivy:retrieve] :: loading settings :: file = /usr/local/RDPTools/Clustering/ivysettings.xml
[ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#clustering;[email protected]
[ivy:retrieve] confs: [default]
[ivy:retrieve] found com.sun.xml.bind#jaxb-impl;2.2.7 in public
[ivy:retrieve] found com.sun.xml.bind#jaxb-core;2.2.7 in public
[ivy:retrieve] found javax.xml.bind#jaxb-api;2.2.7 in public
[ivy:retrieve] found com.sun.istack#istack-commons-runtime;2.16 in public
[ivy:retrieve] found com.sun.xml.fastinfoset#FastInfoset;1.2.12 in public
[ivy:retrieve] found javax.xml.bind#jsr173_api;1.0 in public
[ivy:retrieve] found commons-cli#commons-cli;1.2 in public
[ivy:retrieve] found junit#junit;4.8.2 in public
[ivy:retrieve] found commons-codec#commons-codec;1.8 in public
[ivy:retrieve] found junit#junit;4.11 in public
[ivy:retrieve] found org.hamcrest#hamcrest-core;1.3 in public
[ivy:retrieve] found commons-io#commons-io;2.4 in public
[ivy:retrieve] :: resolution report :: resolve 467ms :: artifacts dl 29ms
[ivy:retrieve] :: evicted modules:
[ivy:retrieve] junit#junit;3.8.1 by [junit#junit;4.8.2] in [default]
[ivy:retrieve] junit#junit;4.8.2 by [junit#junit;4.11] in [default]
[ivy:retrieve] junit#junit;4.10 by [junit#junit;4.11] in [default]
---------------------------------------------------------------------
| | modules || artifacts |
| conf | number| search|dwnlded|evicted|| number|dwnlded|
---------------------------------------------------------------------
| default | 14 | 0 | 0 | 3 || 21 | 0 |
---------------------------------------------------------------------
[ivy:retrieve] :: retrieving :: edu.cme.rdp#clustering
[ivy:retrieve] confs: [default]
[ivy:retrieve] 0 artifacts copied, 21 already retrieved (0kB/10ms)
-pre-init:
-init-private:
-init-user:
-init-project:
-init-macrodef-property:
-do-init:
-post-init:
-init-check:
-init-ap-cmdline-properties:
-init-macrodef-javac-with-processors:
-init-macrodef-javac-without-processors:
-init-macrodef-javac:
-init-macrodef-test-impl:
-init-macrodef-junit-init:
-init-macrodef-junit-single:
-init-test-properties:
-init-macrodef-junit-batch:
-init-macrodef-junit:
-init-macrodef-junit-impl:
-init-macrodef-testng:
-init-macrodef-testng-impl:
-init-macrodef-test:
-init-macrodef-junit-debug:
-init-macrodef-junit-debug-batch:
-init-macrodef-junit-debug-impl:
-init-macrodef-test-debug-junit:
-init-macrodef-testng-debug:
-init-macrodef-testng-debug-impl:
-init-macrodef-test-debug-testng:
-init-macrodef-test-debug:
-init-debug-args:
-init-macrodef-nbjpda:
-init-macrodef-debug:
-init-macrodef-java:
-init-presetdef-jar:
-init-ap-cmdline-supported:
-init-ap-cmdline:
init:
-deps-jar-init:
[delete] Deleting: /usr/local/RDPTools/Clustering/build/built-jar.properties
deps-jar:
-warn-already-built-jar:
[propertyfile] Updating property file: /usr/local/RDPTools/Clustering/build/built-jar.properties
-check-call-dep:
-maybe-call-dep:
download-ivy:
[get] Getting: http://insecure.repo1.maven.org/maven2/org/apache/ivy/ivy/2.1.0-rc2/ivy-2.1.0-rc2.jar
[get] To: /var/root/.ant/lib/ivy.jar
[get] Not modified - so not downloaded
init-ivy:
resolve:
[ivy:retrieve] :: loading settings :: file = /usr/local/RDPTools/AlignmentTools/ivysettings.xml
[ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#AlignmentTools;[email protected]
[ivy:retrieve] confs: [default]
[ivy:retrieve] found commons-lang#commons-lang;2.6 in public
[ivy:retrieve] found junit#junit;3.8.1 in public
[ivy:retrieve] found commons-cli#commons-cli;1.2 in public
[ivy:retrieve] :: resolution report :: resolve 105ms :: artifacts dl 7ms
---------------------------------------------------------------------
| | modules || artifacts |
| conf | number| search|dwnlded|evicted|| number|dwnlded|
---------------------------------------------------------------------
| default | 3 | 0 | 0 | 0 || 7 | 0 |
---------------------------------------------------------------------
[ivy:retrieve] :: retrieving :: edu.cme.rdp#AlignmentTools
[ivy:retrieve] confs: [default]
[ivy:retrieve] 0 artifacts copied, 7 already retrieved (0kB/2ms)
-pre-init:
-init-private:
-init-user:
-init-project:
-init-macrodef-property:
-do-init:
-post-init:
-init-check:
-init-ap-cmdline-properties:
-init-macrodef-javac-with-processors:
-init-macrodef-javac-without-processors:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:javac
-init-macrodef-javac:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:depend
-init-macrodef-test-impl:
-init-macrodef-junit-init:
-init-macrodef-junit-single:
-init-test-properties:
-init-macrodef-junit-batch:
-init-macrodef-junit:
-init-macrodef-junit-impl:
-init-macrodef-testng:
-init-macrodef-testng-impl:
-init-macrodef-test:
-init-macrodef-junit-debug:
-init-macrodef-junit-debug-batch:
-init-macrodef-junit-debug-impl:
-init-macrodef-test-debug-junit:
-init-macrodef-testng-debug:
-init-macrodef-testng-debug-impl:
-init-macrodef-test-debug-testng:
-init-macrodef-test-debug:
-init-debug-args:
-init-macrodef-nbjpda:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/1:nbjpdastart
-init-macrodef-debug:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:debug
-init-macrodef-java:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/1:java
-init-presetdef-jar:
-init-ap-cmdline-supported:
-init-ap-cmdline:
init:
-deps-jar-init:
deps-jar:
-warn-already-built-jar:
[propertyfile] Updating property file: /usr/local/RDPTools/Clustering/build/built-jar.properties
-check-call-dep:
-maybe-call-dep:
download-ivy:
[get] Getting: http://insecure.repo1.maven.org/maven2/org/apache/ivy/ivy/2.1.0-rc2/ivy-2.1.0-rc2.jar
[get] To: /var/root/.ant/lib/ivy.jar
[get] Not modified - so not downloaded
init-ivy:
resolve:
[ivy:retrieve] :: loading settings :: file = /usr/local/RDPTools/ReadSeq/ivysettings.xml
[ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#ReadSeq;[email protected]
[ivy:retrieve] confs: [default]
[ivy:retrieve] found commons-lang#commons-lang;2.6 in public
[ivy:retrieve] found junit#junit;3.8.1 in public
[ivy:retrieve] found commons-cli#commons-cli;1.2 in public
[ivy:retrieve] found commons-io#commons-io;2.4 in public
[ivy:retrieve] found junit#junit;4.10 in public
[ivy:retrieve] found org.hamcrest#hamcrest-core;1.1 in public
[ivy:retrieve] :: resolution report :: resolve 214ms :: artifacts dl 11ms
[ivy:retrieve] :: evicted modules:
[ivy:retrieve] junit#junit;3.8.1 by [junit#junit;4.10] in [default]
---------------------------------------------------------------------
| | modules || artifacts |
| conf | number| search|dwnlded|evicted|| number|dwnlded|
---------------------------------------------------------------------
| default | 6 | 0 | 0 | 1 || 11 | 0 |
---------------------------------------------------------------------
[ivy:retrieve] :: retrieving :: edu.cme.rdp#ReadSeq
[ivy:retrieve] confs: [default]
[ivy:retrieve] 0 artifacts copied, 11 already retrieved (0kB/26ms)
-pre-init:
-init-private:
-init-user:
-init-project:
-init-macrodef-property:
-do-init:
-post-init:
-init-check:
-init-ap-cmdline-properties:
-init-macrodef-javac-with-processors:
-init-macrodef-javac-without-processors:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:javac
-init-macrodef-javac:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:depend
-init-macrodef-test-impl:
-init-macrodef-junit-init:
-init-macrodef-junit-single:
-init-test-properties:
-init-macrodef-junit-batch:
-init-macrodef-junit:
-init-macrodef-junit-impl:
-init-macrodef-testng:
-init-macrodef-testng-impl:
-init-macrodef-test:
-init-macrodef-junit-debug:
-init-macrodef-junit-debug-batch:
-init-macrodef-junit-debug-impl:
-init-macrodef-test-debug-junit:
-init-macrodef-testng-debug:
-init-macrodef-testng-debug-impl:
-init-macrodef-test-debug-testng:
-init-macrodef-test-debug:
-init-debug-args:
-init-macrodef-nbjpda:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/1:nbjpdastart
-init-macrodef-debug:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:debug
-init-macrodef-java:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/1:java
-init-presetdef-jar:
-init-ap-cmdline-supported:
-init-ap-cmdline:
init:
-deps-jar-init:
deps-jar:
-warn-already-built-jar:
[propertyfile] Updating property file: /usr/local/RDPTools/Clustering/build/built-jar.properties
-check-automatic-build:
-clean-after-automatic-build:
-verify-automatic-build:
-pre-pre-compile:
-pre-compile:
-copy-persistence-xml:
-compile-depend:
-do-compile:
[javac] Compiling 73 source files to /usr/local/RDPTools/ReadSeq/build/classes
[javac] warning: [options] bootstrap class path not set in conjunction with -source 5
[javac] error: Source option 5 is no longer supported. Use 7 or later.
[javac] error: Target option 5 is no longer supported. Use 7 or later.
BUILD FAILED
/usr/local/RDPTools/Clustering/nbproject/build-impl.xml:896: The following error occurred while executing this line:
/usr/local/RDPTools/Clustering/nbproject/build-impl.xml:1470: The following error occurred while executing this line:
/usr/local/RDPTools/AlignmentTools/nbproject/build-impl.xml:896: The following error occurred while executing this line:
/usr/local/RDPTools/AlignmentTools/nbproject/build-impl.xml:1414: The following error occurred while executing this line:
/usr/local/RDPTools/ReadSeq/nbproject/build-impl.xml:920: The following error occurred while executing this line:
/usr/local/RDPTools/ReadSeq/nbproject/build-impl.xml:300: Compile failed; see the compiler error output for details.
Total time: 4 seconds
make: *** [Clustering/dist/Clustering.jar] Error 1
Any idea on how to go about it?
Thanks.
Does not compile (javac problem ubuntu)
Hello,
i run on ubuntu 16.04 LTS and openjdk 9-internal.
RDPtool compilation fails with this error:
-do-compile:
[javac] Compiling 73 source files to /home/mulot/repo/RDPTools/ReadSeq/build/classes
[javac] warning: [options] bootstrap class path not set in conjunction with -source 1.5
[javac] error: Source option 1.5 is no longer supported. Use 1.6 or later.
[javac] error: Target option 1.5 is no longer supported. Use 1.6 or later.
BUILD FAILED
/home/mulot/repo/RDPTools/Clustering/nbproject/build-impl.xml:896: The following error occurred while executing this line:
/home/mulot/repo/RDPTools/Clustering/nbproject/build-impl.xml:1470: The following error occurred while executing this line:
/home/mulot/repo/RDPTools/AlignmentTools/nbproject/build-impl.xml:896: The following error occurred while executing this line:
/home/mulot/repo/RDPTools/AlignmentTools/nbproject/build-impl.xml:1414: The following error occurred while executing this line:
/home/mulot/repo/RDPTools/ReadSeq/nbproject/build-impl.xml:920: The following error occurred while executing this line:
/home/mulot/repo/RDPTools/ReadSeq/nbproject/build-impl.xml:300: Compile failed; see the compiler error output for details.
I got stuck on this for hal a day and couldn't find any workaround. Maybe you have an idea ?
Cheers,
Matthieu
make: *** [Clustering/dist/Clustering.jar] Error 1
Dear All,
I am trying to download the RDP tools, and am facing the following error:
(base) tanshiming@S620100019205:~/tools/RDPTools$ make
ant -f Clustering/build.xml jar
Buildfile: /home/tanshiming/tools/RDPTools/Clustering/build.xml
download-ivy:
[get] Getting: http://repo2.maven.org/maven2/org/apache/ivy/ivy/2.1.0-rc2/ivy-2.1.0-rc2.jar
[get] To: /home/tanshiming/.ant/lib/ivy.jar
[get] Not modified - so not downloaded
init-ivy:
resolve:
[ivy:retrieve] :: Ivy 2.1.0-rc2 - 20090704004254 :: http://ant.apache.org/ivy/ ::
[ivy:retrieve] :: loading settings :: url = jar:file:/home/tanshiming/.ant/lib/ivy.jar!/org/apache/ivy/core/settings/ivysettings.xml
[ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#clustering;working@S620100019205
[ivy:retrieve] confs: [default]
[ivy:retrieve] found com.sun.xml.bind#jaxb-impl;2.2.7 in public
[ivy:retrieve] found com.sun.xml.bind#jaxb-core;2.2.7 in public
[ivy:retrieve] found javax.xml.bind#jaxb-api;2.2.7 in public
[ivy:retrieve] found com.sun.istack#istack-commons-runtime;2.16 in public
[ivy:retrieve] found com.sun.xml.fastinfoset#FastInfoset;1.2.12 in public
[ivy:retrieve] found javax.xml.bind#jsr173_api;1.0 in public
[ivy:retrieve] found commons-cli#commons-cli;1.2 in public
[ivy:retrieve] found junit#junit;4.8.2 in public
[ivy:retrieve] found commons-codec#commons-codec;1.8 in public
[ivy:retrieve] found commons-io#commons-io;2.4 in public
[ivy:retrieve] :: resolution report :: resolve 197ms :: artifacts dl 13ms
---------------------------------------------------------------------
| | modules || artifacts |
| conf | number| search|dwnlded|evicted|| number|dwnlded|
---------------------------------------------------------------------
| default | 10 | 0 | 0 | 0 || 20 | 0 |
---------------------------------------------------------------------
[ivy:retrieve] :: retrieving :: edu.cme.rdp#clustering
[ivy:retrieve] confs: [default]
[ivy:retrieve] 0 artifacts copied, 20 already retrieved (0kB/5ms)
-pre-init:
-init-private:
-init-user:
-init-project:
-init-macrodef-property:
-do-init:
-post-init:
-init-check:
-init-ap-cmdline-properties:
-init-macrodef-javac-with-processors:
-init-macrodef-javac-without-processors:
-init-macrodef-javac:
-init-macrodef-test-impl:
-init-macrodef-junit-init:
-init-macrodef-junit-single:
-init-test-properties:
-init-macrodef-junit-batch:
-init-macrodef-junit:
-init-macrodef-junit-impl:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:test-impl
-init-macrodef-testng:
-init-macrodef-testng-impl:
-init-macrodef-test:
-init-macrodef-junit-debug:
-init-macrodef-junit-debug-batch:
-init-macrodef-junit-debug-impl:
-init-macrodef-test-debug-junit:
-init-macrodef-testng-debug:
-init-macrodef-testng-debug-impl:
-init-macrodef-test-debug-testng:
-init-macrodef-test-debug:
-init-debug-args:
-init-macrodef-nbjpda:
-init-macrodef-debug:
-init-macrodef-java:
-init-presetdef-jar:
-init-ap-cmdline-supported:
-init-ap-cmdline:
init:
-deps-jar-init:
[delete] Deleting: /home/tanshiming/tools/RDPTools/Clustering/build/built-jar.properties
deps-jar:
-warn-already-built-jar:
[propertyfile] Updating property file: /home/tanshiming/tools/RDPTools/Clustering/build/built-jar.properties
-check-call-dep:
-maybe-call-dep:
download-ivy:
[get] Getting: http://repo2.maven.org/maven2/org/apache/ivy/ivy/2.1.0-rc2/ivy-2.1.0-rc2.jar
[get] To: /home/tanshiming/.ant/lib/ivy.jar
[get] Not modified - so not downloaded
init-ivy:
resolve:
[ivy:retrieve] :: loading settings :: url = jar:file:/home/tanshiming/.ant/lib/ivy.jar!/org/apache/ivy/core/settings/ivysettings.xml
[ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#AlignmentTools;working@S620100019205
[ivy:retrieve] confs: [default]
[ivy:retrieve] found commons-lang#commons-lang;2.6 in public
[ivy:retrieve] found commons-cli#commons-cli;1.2 in public
[ivy:retrieve] :: resolution report :: resolve 21ms :: artifacts dl 2ms
---------------------------------------------------------------------
| | modules || artifacts |
| conf | number| search|dwnlded|evicted|| number|dwnlded|
---------------------------------------------------------------------
| default | 2 | 0 | 0 | 0 || 6 | 0 |
---------------------------------------------------------------------
[ivy:retrieve] :: retrieving :: edu.cme.rdp#AlignmentTools
[ivy:retrieve] confs: [default]
[ivy:retrieve] 0 artifacts copied, 6 already retrieved (0kB/1ms)
-pre-init:
-init-private:
-init-user:
-init-project:
-init-macrodef-property:
-do-init:
-post-init:
-init-check:
-init-ap-cmdline-properties:
-init-macrodef-javac-with-processors:
-init-macrodef-javac-without-processors:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:javac
-init-macrodef-javac:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:depend
-init-macrodef-test-impl:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:test-impl
-init-macrodef-junit-init:
-init-macrodef-junit-single:
-init-test-properties:
-init-macrodef-junit-batch:
-init-macrodef-junit:
-init-macrodef-junit-impl:
-init-macrodef-testng:
-init-macrodef-testng-impl:
-init-macrodef-test:
-init-macrodef-junit-debug:
-init-macrodef-junit-debug-batch:
-init-macrodef-junit-debug-impl:
-init-macrodef-test-debug-junit:
-init-macrodef-testng-debug:
-init-macrodef-testng-debug-impl:
-init-macrodef-test-debug-testng:
-init-macrodef-test-debug:
-init-debug-args:
-init-macrodef-nbjpda:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/1:nbjpdastart
-init-macrodef-debug:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:debug
-init-macrodef-java:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/1:java
-init-presetdef-jar:
-init-ap-cmdline-supported:
-init-ap-cmdline:
init:
-deps-jar-init:
deps-jar:
-warn-already-built-jar:
[propertyfile] Updating property file: /home/tanshiming/tools/RDPTools/Clustering/build/built-jar.properties
-check-call-dep:
-maybe-call-dep:
download-ivy:
[get] Getting: http://repo2.maven.org/maven2/org/apache/ivy/ivy/2.1.0-rc2/ivy-2.1.0-rc2.jar
[get] To: /home/tanshiming/.ant/lib/ivy.jar
[get] Not modified - so not downloaded
init-ivy:
resolve:
[ivy:retrieve] :: loading settings :: url = jar:file:/home/tanshiming/.ant/lib/ivy.jar!/org/apache/ivy/core/settings/ivysettings.xml
[ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#ReadSeq;working@S620100019205
[ivy:retrieve] confs: [default]
[ivy:retrieve] found commons-lang#commons-lang;2.6 in public
[ivy:retrieve] found commons-cli#commons-cli;1.2 in public
[ivy:retrieve] found commons-io#commons-io;2.4 in public
[ivy:retrieve] :: resolution report :: resolve 21ms :: artifacts dl 3ms
---------------------------------------------------------------------
| | modules || artifacts |
| conf | number| search|dwnlded|evicted|| number|dwnlded|
---------------------------------------------------------------------
| default | 3 | 0 | 0 | 0 || 9 | 0 |
---------------------------------------------------------------------
[ivy:retrieve] :: retrieving :: edu.cme.rdp#ReadSeq
[ivy:retrieve] confs: [default]
[ivy:retrieve] 0 artifacts copied, 9 already retrieved (0kB/1ms)
-pre-init:
-init-private:
-init-user:
-init-project:
-init-macrodef-property:
-do-init:
-post-init:
-init-check:
-init-ap-cmdline-properties:
-init-macrodef-javac-with-processors:
-init-macrodef-javac-without-processors:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:javac
-init-macrodef-javac:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:depend
-init-macrodef-test-impl:
-init-macrodef-junit-init:
-init-macrodef-junit-single:
-init-test-properties:
-init-macrodef-junit-batch:
-init-macrodef-junit:
-init-macrodef-junit-impl:
-init-macrodef-testng:
-init-macrodef-testng-impl:
-init-macrodef-test:
-init-macrodef-junit-debug:
-init-macrodef-junit-debug-batch:
-init-macrodef-junit-debug-impl:
-init-macrodef-test-debug-junit:
-init-macrodef-testng-debug:
-init-macrodef-testng-debug-impl:
-init-macrodef-test-debug-testng:
-init-macrodef-test-debug:
-init-debug-args:
-init-macrodef-nbjpda:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/1:nbjpdastart
-init-macrodef-debug:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:debug
-init-macrodef-java:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/1:java
-init-presetdef-jar:
-init-ap-cmdline-supported:
-init-ap-cmdline:
init:
-deps-jar-init:
deps-jar:
-warn-already-built-jar:
[propertyfile] Updating property file: /home/tanshiming/tools/RDPTools/Clustering/build/built-jar.properties
-check-automatic-build:
-clean-after-automatic-build:
-verify-automatic-build:
-pre-pre-compile:
-pre-compile:
-copy-persistence-xml:
-compile-depend:
-do-compile:
[javac] Compiling 73 source files to /home/tanshiming/tools/RDPTools/ReadSeq/build/classes
[javac] warning: [options] bootstrap class path not set in conjunction with -source 5
[javac] error: Source option 5 is no longer supported. Use 7 or later.
[javac] error: Target option 5 is no longer supported. Use 7 or later.
BUILD FAILED
/home/tanshiming/tools/RDPTools/Clustering/nbproject/build-impl.xml:896: The following error occurred while executing this line:
/home/tanshiming/tools/RDPTools/Clustering/nbproject/build-impl.xml:1470: The following error occurred while executing this line:
/home/tanshiming/tools/RDPTools/AlignmentTools/nbproject/build-impl.xml:896: The following error occurred while executing this line:
/home/tanshiming/tools/RDPTools/AlignmentTools/nbproject/build-impl.xml:1414: The following error occurred while executing this line:
/home/tanshiming/tools/RDPTools/ReadSeq/nbproject/build-impl.xml:920: The following error occurred while executing this line:
/home/tanshiming/tools/RDPTools/ReadSeq/nbproject/build-impl.xml:300: Compile failed; see the compiler error output for details.
Total time: 2 seconds
Makefile:15: recipe for target 'Clustering/dist/Clustering.jar' failed
make: *** [Clustering/dist/Clustering.jar] Error 1
```
Will appreciate any advice I can get.
Thank You!
installation problem
Hello,
I want to install RDPTools on my computer,
I had to resolve several errors when I launch the make command:
I had to use a java jdk version at 8 instead of 11
I had to modify the url http://repo2.maven by https://repo1.maven.
Unfortunately I am stuck with this error :
RDPTools/Clustering/build.xml:122: Warning: Could not find resource file "/RDPTools/Clustering/lib/jaxb-api-2.2.7.jar" to copy.
Indeed, I have only in my "lib" dir these files :
"RDPTools/Clustering/lib/commons-cli-1.2.jar
RDPTools/Clustering/lib/commons-codec-1.8.jar
RDPTools/Clustering/lib/commons-io-2.4.jar
RDPTools/Clustering/lib/jaxb-impl-2.2.7.jar
RDPTools/Clustering/lib/junit-4.8.2.jar"
Can you help me please?
Sincerely,
Jรฉrรฉmy Tournayre
Error when running 'git submodule update'
I'm attempting to install RDP Tools using the following commands.
git clone https://github.com/rdpstaff/RDPTools.git
cd RDPTools/
git submodule init
git submodule update
The last commend runs, but then fails at this step:
Cloning into TaxonomyTree...
github.com[0: 192.30.252.128]: errno=Connection refused
fatal: unable to connect a socket (Connection refused)
Clone of 'git://github.com/rdpstaff/TaxonomyTree' into submodule path 'TaxonomyTree' failed
Any suggestions?
Thank you developing this software. I look forward to using it.
make issues
Dear rdp-tools,
I have problem with (2015_june_02 downloaded) rdp-tools "make", this break fairly instantly. See what I did below:
$ git clone https://github.com/rdpstaff/RDPTools.git
$ cd RDPTools
$ git submodule init
$ git submodule update
$ make
ant -f Clustering/build.xml jar
make: execvp: ant: Permission denied
make: *** [Clustering/dist/Clustering.jar] Error 127
I am sorry if this is a daft squestion, but I am lost as to how to proceed. I dont have admin rights, so no sudo.. This is all the error produces. Any thoughts?
Kind regards,
Peter Thorpe
which version?
Hello Team,
Thanks for maintaining this tool, and repository.
I downloaded the directory, followed instructions as on readme and install, typed "make", which resulted in successful build. I get couple of .jar files, including with the classifier jar.
My query:
Which version of RDP is it?
java -Xmx1g -jar classifier.jar -v
or running without any flag doesn't spit version of classifier present.
Kindly help.
Server errors with jdk8 & ant1.9
Hi,
I ran into this problem while I tried most of the jdk versions and ant 1.10 and ant1.9 several times.
With my Mac, it says
[ivy:retrieve] :::: ERRORS
[ivy:retrieve] SERVER ERROR: HTTPS Required url=http://repo1.maven.org/maven2/junit/junit/4.8.2/junit-4.8.2-sources.jar
[ivy:retrieve] SERVER ERROR: HTTPS Required url=http://repo1.maven.org/maven2/junit/junit/4.8.2/junit-4.8.2-javadoc.jar
[ivy:retrieve] SERVER ERROR: HTTPS Required url=http://repo1.maven.org/maven2/junit/junit/4.8.2/junit-4.8.2.jar
[ivy:retrieve]
[ivy:retrieve] :: USE VERBOSE OR DEBUG MESSAGE LEVEL FOR MORE DETAILS
BUILD FAILED
/Users/minsikkim/RDPTools/Clustering/nbproject/build-impl.xml:910: The following error occurred while executing this line:
/Users/minsikkim/RDPTools/Clustering/nbproject/build-impl.xml:1470: The following error occurred while executing this line:
/Users/minsikkim/RDPTools/SeqFilters/nbproject/build-impl.xml:896: The following error occurred while executing this line:
/Users/minsikkim/RDPTools/SeqFilters/nbproject/build-impl.xml:1428: The following error occurred while executing this line:
/Users/minsikkim/RDPTools/ProbeMatch/build.xml:104: impossible to resolve dependencies:
resolve failed - see output for details
Total time: 3 seconds
make: *** [Clustering/dist/Clustering.jar] Error 1
I am using jdk8
(base) minsikkim@Minsiks-MacBook-Pro RDPTools % java -version
openjdk version "1.8.0_382"
OpenJDK Runtime Environment (Zulu 8.72.0.17-CA-macosx) (build 1.8.0_382-b05)
OpenJDK 64-Bit Server VM (Zulu 8.72.0.17-CA-macosx) (build 25.382-b05, mixed mode)
And I am using ant1.9
(base) minsikkim@Minsiks-MacBook-Pro RDPTools % ant -version
Apache Ant(TM) version 1.9.16 compiled on July 10 2021
Maybe it's because of my firewall settings? Or, does it due to the version issue (2.14 release)? Please let me know how can I resolve this.
++ I tried them with my linux server but I ran into another problem, showing
download-traindata:
[get] Getting: http://rdp.cme.msu.edu/download/rdpclassifiertraindata/data.tgz
[get] To: /home/bagel/RDPTools/classifier/build/classes/data.tgz
[get] Error getting http://rdp.cme.msu.edu/download/rdpclassifiertraindata/data.tgz to /home/bagel/RDPTools/classifier/build/classes/data.tgz
BUILD FAILED
/home/bagel/RDPTools/classifier/build.xml:50: java.net.NoRouteToHostException: No route to host (Host unreachable)
at java.net.PlainSocketImpl.socketConnect(Native Method)
Currently all my firewalls are off so it shouldn't be a firewall issue.
Thanks in advance,
git clone recursive
In documentation, the following command is enough. Don't need to use submodule update.
git clone --recursive
Do not create output files on error
I used the wrong path to my database for RDPTools classify, and got the corresponding error:
Command Error: Unable to process file format UNKNOWN
However, empty output files still have been created.
I use Snakemake pipeline system, and if the output of the pipeline step is created, it thinks that everything is all right.
I would suggest either return error code to the system or at least do not create output files in such case, so the pipeline could understand that this step was broken.
make command issue
Hello! I see that a number of users have had issues with the make step, but since there have been edits more recently than those threads I wanted to ask about the errors I am getting:ant -f Clustering/build.xml jar
Buildfile: /RDPTools/Clustering/build.xml
download-ivy:
[get] Getting: http://insecure.repo1.maven.org/maven2/org/apache/ivy/ivy/2.1.0-rc2/ivy-2.1.0-rc2.jar
[get] To: /root/.ant/lib/ivy.jar
[get] Not modified - so not downloaded
init-ivy:
resolve:
[ivy:retrieve] :: Ivy 2.1.0-rc2 - 20090704004254 :: http://ant.apache.org/ivy/ ::
[ivy:retrieve] :: loading settings :: file = /RDPTools/Clustering/ivysettings.xml
[ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#clustering;working@metro-pes3307
[ivy:retrieve] confs: [default]
[ivy:retrieve] found com.sun.xml.bind#jaxb-impl;2.2.7 in maven
[ivy:retrieve] found com.sun.xml.bind#jaxb-core;2.2.7 in maven
[ivy:retrieve] found javax.xml.bind#jaxb-api;2.2.7 in maven
[ivy:retrieve] found com.sun.istack#istack-commons-runtime;2.16 in maven
[ivy:retrieve] found com.sun.xml.fastinfoset#FastInfoset;1.2.12 in maven
[ivy:retrieve] found javax.xml.bind#jsr173_api;1.0 in maven
[ivy:retrieve] found commons-cli#commons-cli;1.2 in maven
[ivy:retrieve] found junit#junit;4.8.2 in maven
[ivy:retrieve] found commons-codec#commons-codec;1.8 in maven
[ivy:retrieve] found commons-io#commons-io;2.4 in maven
[ivy:retrieve] :: resolution report :: resolve 150ms :: artifacts dl 7ms
---------------------------------------------------------------------
| | modules || artifacts |
| conf | number| search|dwnlded|evicted|| number|dwnlded|
---------------------------------------------------------------------
| default | 10 | 0 | 0 | 0 || 10 | 0 |
---------------------------------------------------------------------
[ivy:retrieve] :: retrieving :: edu.cme.rdp#clustering
[ivy:retrieve] confs: [default]
[ivy:retrieve] 0 artifacts copied, 10 already retrieved (0kB/5ms)
-pre-init:
-init-private:
-init-user:
-init-project:
-init-macrodef-property:
-do-init:
-post-init:
-init-check:
-init-ap-cmdline-properties:
-init-macrodef-javac-with-processors:
-init-macrodef-javac-without-processors:
-init-macrodef-javac:
-init-macrodef-test-impl:
-init-macrodef-junit-init:
-init-macrodef-junit-single:
-init-test-properties:
-init-macrodef-junit-batch:
-init-macrodef-junit:
-init-macrodef-junit-impl:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:test-impl
-init-macrodef-testng:
-init-macrodef-testng-impl:
-init-macrodef-test:
-init-macrodef-junit-debug:
-init-macrodef-junit-debug-batch:
-init-macrodef-junit-debug-impl:
-init-macrodef-test-debug-junit:
-init-macrodef-testng-debug:
-init-macrodef-testng-debug-impl:
-init-macrodef-test-debug-testng:
-init-macrodef-test-debug:
-init-debug-args:
-init-macrodef-nbjpda:
-init-macrodef-debug:
-init-macrodef-java:
-init-presetdef-jar:
-init-ap-cmdline-supported:
-init-ap-cmdline:
init:
-deps-jar-init:
[delete] Deleting: /RDPTools/Clustering/build/built-jar.properties
deps-jar:
-warn-already-built-jar:
[propertyfile] Updating property file: /RDPTools/Clustering/build/built-jar.properties
-check-call-dep:
-maybe-call-dep:
download-ivy:
[get] Getting: http://insecure.repo1.maven.org/maven2/org/apache/ivy/ivy/2.1.0-rc2/ivy-2.1.0-rc2.jar
[get] To: /root/.ant/lib/ivy.jar
[get] Not modified - so not downloaded
init-ivy:
resolve:
[ivy:retrieve] :: loading settings :: file = /RDPTools/AlignmentTools/ivysettings.xml
[ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#AlignmentTools;working@metro-pes3307
[ivy:retrieve] confs: [default]
[ivy:retrieve] found commons-lang#commons-lang;2.6 in maven
[ivy:retrieve] found commons-cli#commons-cli;1.2 in maven
[ivy:retrieve] :: resolution report :: resolve 21ms :: artifacts dl 1ms
---------------------------------------------------------------------
| | modules || artifacts |
| conf | number| search|dwnlded|evicted|| number|dwnlded|
---------------------------------------------------------------------
| default | 2 | 0 | 0 | 0 || 2 | 0 |
---------------------------------------------------------------------
[ivy:retrieve] :: retrieving :: edu.cme.rdp#AlignmentTools
[ivy:retrieve] confs: [default]
[ivy:retrieve] 0 artifacts copied, 2 already retrieved (0kB/2ms)
-pre-init:
-init-private:
-init-user:
-init-project:
-init-macrodef-property:
-do-init:
-post-init:
-init-check:
-init-ap-cmdline-properties:
-init-macrodef-javac-with-processors:
-init-macrodef-javac-without-processors:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:javac
-init-macrodef-javac:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:depend
-init-macrodef-test-impl:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:test-impl
-init-macrodef-junit-init:
-init-macrodef-junit-single:
-init-test-properties:
-init-macrodef-junit-batch:
-init-macrodef-junit:
-init-macrodef-junit-impl:
-init-macrodef-testng:
-init-macrodef-testng-impl:
-init-macrodef-test:
-init-macrodef-junit-debug:
-init-macrodef-junit-debug-batch:
-init-macrodef-junit-debug-impl:
-init-macrodef-test-debug-junit:
-init-macrodef-testng-debug:
-init-macrodef-testng-debug-impl:
-init-macrodef-test-debug-testng:
-init-macrodef-test-debug:
-init-debug-args:
-init-macrodef-nbjpda:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/1:nbjpdastart
-init-macrodef-debug:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:debug
-init-macrodef-java:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/1:java
-init-presetdef-jar:
-init-ap-cmdline-supported:
-init-ap-cmdline:
init:
-deps-jar-init:
deps-jar:
-warn-already-built-jar:
[propertyfile] Updating property file: /RDPTools/Clustering/build/built-jar.properties
-check-call-dep:
-maybe-call-dep:
download-ivy:
[get] Getting: http://insecure.repo1.maven.org/maven2/org/apache/ivy/ivy/2.1.0-rc2/ivy-2.1.0-rc2.jar
[get] To: /root/.ant/lib/ivy.jar
[get] Not modified - so not downloaded
init-ivy:
resolve:
[ivy:retrieve] :: loading settings :: file = /RDPTools/ReadSeq/ivysettings.xml
[ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#ReadSeq;working@metro-pes3307
[ivy:retrieve] confs: [default]
[ivy:retrieve] found commons-lang#commons-lang;2.6 in maven
[ivy:retrieve] found commons-cli#commons-cli;1.2 in maven
[ivy:retrieve] found commons-io#commons-io;2.4 in maven
[ivy:retrieve] :: resolution report :: resolve 26ms :: artifacts dl 2ms
---------------------------------------------------------------------
| | modules || artifacts |
| conf | number| search|dwnlded|evicted|| number|dwnlded|
---------------------------------------------------------------------
| default | 3 | 0 | 0 | 0 || 3 | 0 |
---------------------------------------------------------------------
[ivy:retrieve] :: retrieving :: edu.cme.rdp#ReadSeq
[ivy:retrieve] confs: [default]
[ivy:retrieve] 0 artifacts copied, 3 already retrieved (0kB/2ms)
-pre-init:
-init-private:
-init-user:
-init-project:
-init-macrodef-property:
-do-init:
-post-init:
-init-check:
-init-ap-cmdline-properties:
-init-macrodef-javac-with-processors:
-init-macrodef-javac-without-processors:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:javac
-init-macrodef-javac:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:depend
-init-macrodef-test-impl:
-init-macrodef-junit-init:
-init-macrodef-junit-single:
-init-test-properties:
-init-macrodef-junit-batch:
-init-macrodef-junit:
-init-macrodef-junit-impl:
-init-macrodef-testng:
-init-macrodef-testng-impl:
-init-macrodef-test:
-init-macrodef-junit-debug:
-init-macrodef-junit-debug-batch:
-init-macrodef-junit-debug-impl:
-init-macrodef-test-debug-junit:
-init-macrodef-testng-debug:
-init-macrodef-testng-debug-impl:
-init-macrodef-test-debug-testng:
-init-macrodef-test-debug:
-init-debug-args:
-init-macrodef-nbjpda:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/1:nbjpdastart
-init-macrodef-debug:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:debug
-init-macrodef-java:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/1:java
-init-presetdef-jar:
-init-ap-cmdline-supported:
-init-ap-cmdline:
init:
-deps-jar-init:
deps-jar:
-warn-already-built-jar:
[propertyfile] Updating property file: /RDPTools/Clustering/build/built-jar.properties
-check-automatic-build:
-clean-after-automatic-build:
-verify-automatic-build:
-pre-pre-compile:
-pre-compile:
-copy-persistence-xml:
-compile-depend:
-do-compile:
[javac] Compiling 73 source files to /RDPTools/ReadSeq/build/classes
[javac] warning: [options] bootstrap class path not set in conjunction with -source 5
[javac] error: Source option 5 is no longer supported. Use 6 or later.
[javac] error: Target option 1.5 is no longer supported. Use 1.6 or later.
BUILD FAILED
/RDPTools/Clustering/nbproject/build-impl.xml:896: The following error occurred while executing this line:
/RDPTools/Clustering/nbproject/build-impl.xml:1470: The following error occurred while executing this line:
/RDPTools/AlignmentTools/nbproject/build-impl.xml:896: The following error occurred while executing this line:
/RDPTools/AlignmentTools/nbproject/build-impl.xml:1414: The following error occurred while executing this line:
/RDPTools/ReadSeq/nbproject/build-impl.xml:920: The following error occurred while executing this line:
/RDPTools/ReadSeq/nbproject/build-impl.xml:300: Compile failed; see the compiler error output for details.
Total time: 1 second
Makefile:15: recipe for target 'Clustering/dist/Clustering.jar' failed
make: *** [Clustering/dist/Clustering.jar] Error 1
Here is additional relevant version information:
(Java)
openjdk version "11.0.9.1" 2020-11-04
OpenJDK Runtime Environment (build 11.0.9.1+1-Ubuntu-0ubuntu1.18.04)
OpenJDK 64-Bit Server VM (build 11.0.9.1+1-Ubuntu-0ubuntu1.18.04, mixed mode, sharing)
(ant)
Apache Ant(TM) version 1.10.5 compiled on March 28 2019
Thank you!
rdp train
I try to train using this command from tutorial:
java -Xmx1g -jar /path/to/classifier.jar train -o mytrained -s samplefiles/new_trainset.fasta -t samplefiles/new_trainset_db_taxid.txt -c gene_copynumber.txt
cp samplefiles/rRNAClassifier.properties mytrained/
However, I get an error that "-s" in not an option. I try to run it on a cluster that does not have ant. Could that explain this error?
Is there anything else that could go wrong and explain that kind of error?!
Thank you!
Training data for classifier
It looks like the RDP server is getting hammer right now and I can't download the training data to run things locally. If possible, could someone please make a copy of xxx/rdpclassifiertrainingdata/data.tgz available through Dropbox or similar service? Thanks!
dependency on commons/io/
Good afternoon,
I've just deployed the RDP Tools as directed. I'm having trouble using them.
This command works fine.
java -Xmx1g -jar /Users/bris469/anaconda/envs/_test/bin/classifier.jar
USAGE: ClassifierMain <subcommand> <subcommand args ...>
default command is classify
classify - classify one or multiple samples
crossvalidate - cross validate accuracy testing
...
This command fails:
(root)WE2292:recipes bris469$ java -Xmx1g -jar /Users/bris469/anaconda/envs/_test/bin/classifier.jar classify -c 0.5 -o usga_classified.txt -h soil_hier.txt /Users/bris469/anaconda/conda-bld/work/classifier/samplefiles/USGA_2_4_B_trimmed.fasta
Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/commons/io/output/NullWriter
at edu.msu.cme.rdp.classifier.cli.ClassifierMain.main(ClassifierMain.java:65)
Caused by: java.lang.ClassNotFoundException: org.apache.commons.io.output.NullWriter
at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
... 1 more
(The path to the .fasta file is correct.)
Build Failed
Hi I am trying to install RDPTools, and I keep getting the same error "Build Failed". I install the package using the instructions online
git clone https://github.com/rdpstaff/RDPTools.git
git submodule init
git submodule update
make
ant -f Clustering/build.xml jar
Buildfile: /Users/pasteur/RDPTools/Clustering/build.xml
download-ivy:
[get] Getting: http://repo2.maven.org/maven2/org/apache/ivy/ivy/2.1.0-rc2/ivy-2.1.0-rc2.jar
[get] To: /Users/pasteur/.ant/lib/ivy.jar
[get] Not modified - so not downloaded
init-ivy:
resolve:
[ivy:retrieve] :: Ivy 2.1.0-rc2 - 20090704004254 :: http://ant.apache.org/ivy/ ::
[ivy:retrieve] :: loading settings :: url = jar:file:/Users/pasteur/.ant/lib/ivy.jar!/org/apache/ivy/core/settings/ivysettings.xml
[ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#clustering;[email protected]
[ivy:retrieve] confs: [default]
[ivy:retrieve] found com.sun.xml.bind#jaxb-impl;2.2.7 in public
[ivy:retrieve] found com.sun.xml.bind#jaxb-core;2.2.7 in public
[ivy:retrieve] found javax.xml.bind#jaxb-api;2.2.7 in public
[ivy:retrieve] found com.sun.istack#istack-commons-runtime;2.16 in public
[ivy:retrieve] found com.sun.xml.fastinfoset#FastInfoset;1.2.12 in public
[ivy:retrieve] found javax.xml.bind#jsr173_api;1.0 in public
[ivy:retrieve] found commons-cli#commons-cli;1.2 in public
[ivy:retrieve] found junit#junit;4.8.2 in public
[ivy:retrieve] found commons-codec#commons-codec;1.8 in public
[ivy:retrieve] found commons-io#commons-io;2.4 in public
[ivy:retrieve] :: resolution report :: resolve 199ms :: artifacts dl 10ms
---------------------------------------------------------------------
| | modules || artifacts |
| conf | number| search|dwnlded|evicted|| number|dwnlded|
---------------------------------------------------------------------
| default | 10 | 0 | 0 | 0 || 20 | 0 |
---------------------------------------------------------------------
[ivy:retrieve] :: retrieving :: edu.cme.rdp#clustering
[ivy:retrieve] confs: [default]
[ivy:retrieve] 0 artifacts copied, 20 already retrieved (0kB/6ms)
-pre-init:
-init-private:
-init-user:
-init-project:
-init-macrodef-property:
-do-init:
-post-init:
-init-check:
-init-ap-cmdline-properties:
-init-macrodef-javac-with-processors:
-init-macrodef-javac-without-processors:
-init-macrodef-javac:
-init-macrodef-test-impl:
-init-macrodef-junit-init:
-init-macrodef-junit-single:
-init-test-properties:
-init-macrodef-junit-batch:
-init-macrodef-junit:
-init-macrodef-junit-impl:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:test-impl
-init-macrodef-testng:
-init-macrodef-testng-impl:
-init-macrodef-test:
-init-macrodef-junit-debug:
-init-macrodef-junit-debug-batch:
-init-macrodef-junit-debug-impl:
-init-macrodef-test-debug-junit:
-init-macrodef-testng-debug:
-init-macrodef-testng-debug-impl:
-init-macrodef-test-debug-testng:
-init-macrodef-test-debug:
-init-debug-args:
-init-macrodef-nbjpda:
-init-macrodef-debug:
-init-macrodef-java:
-init-presetdef-jar:
-init-ap-cmdline-supported:
-init-ap-cmdline:
init:
-deps-jar-init:
[delete] Deleting: /Users/pasteur/RDPTools/Clustering/build/built-jar.properties
deps-jar:
BUILD FAILED
/Users/pasteur/RDPTools/Clustering/nbproject/build-impl.xml:890: Can not change modification date of read-only file /Users/pasteur/RDPTools/Clustering/build/built-jar.properties
Total time: 1 second
make: *** [Clustering/dist/Clustering.jar] Error 1
I'm a very new user of the terminal so as much detail for any suggestions to fix this issue would be greatly appreciated....
Thanks!
SERVER ERROR - need to change maven repo URL
Hi,
I have been trying to install RDPTools on Ubuntu 18.06. I have run into the following error when I run make
$ make
ant -f Clustering/build.xml jar
Buildfile: /home/yonathan/RDPTools/Clustering/build.xml
download-ivy:
[get] Getting: https://repo.maven.apache.org/maven2/org/apache/ivy/ivy/2.1.0-rc2/ivy-2.1.0-rc2.jar
[get] To: /home/yonathan/.ant/lib/ivy.jar
[get] Not modified - so not downloaded
init-ivy:
resolve:
[ivy:retrieve] :: Ivy 2.1.0-rc2 - 20090704004254 :: http://ant.apache.org/ivy/ ::
[ivy:retrieve] :: loading settings :: url = jar:file:/home/yonathan/.ant/lib/ivy.jar!/org/apache/ivy/core/settings/ivysettings.xml
[ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#clustering;working@yonathan-Aspire-E5-574
[ivy:retrieve] confs: [default]
[ivy:retrieve] :: resolution report :: resolve 783ms :: artifacts dl 0ms
---------------------------------------------------------------------
| | modules || artifacts |
| conf | number| search|dwnlded|evicted|| number|dwnlded|
---------------------------------------------------------------------
| default | 5 | 0 | 0 | 0 || 0 | 0 |
---------------------------------------------------------------------
[ivy:retrieve]
[ivy:retrieve] :: problems summary ::
[ivy:retrieve] :::: WARNINGS
[ivy:retrieve] module not found: com.sun.xml.bind#jaxb-impl;2.2.7
[ivy:retrieve] ==== local: tried
[ivy:retrieve] /home/yonathan/.ant/local/com.sun.xml.bind/jaxb-impl/2.2.7/ivys/ivy.xml
[ivy:retrieve] -- artifact com.sun.xml.bind#jaxb-impl;2.2.7!jaxb-impl.jar:
[ivy:retrieve] /home/yonathan/.ant/local/com.sun.xml.bind/jaxb-impl/2.2.7/jars/jaxb-impl.jar
[ivy:retrieve] ==== shared: tried
[ivy:retrieve] /home/yonathan/.ant/shared/com.sun.xml.bind/jaxb-impl/2.2.7/ivys/ivy.xml
[ivy:retrieve] -- artifact com.sun.xml.bind#jaxb-impl;2.2.7!jaxb-impl.jar:
[ivy:retrieve] /home/yonathan/.ant/shared/com.sun.xml.bind/jaxb-impl/2.2.7/jars/jaxb-impl.jar
[ivy:retrieve] ==== public: tried
[ivy:retrieve] http://repo1.maven.org/maven2/com/sun/xml/bind/jaxb-impl/2.2.7/jaxb-impl-2.2.7.pom
[ivy:retrieve] -- artifact com.sun.xml.bind#jaxb-impl;2.2.7!jaxb-impl.jar:
[ivy:retrieve] http://repo1.maven.org/maven2/com/sun/xml/bind/jaxb-impl/2.2.7/jaxb-impl-2.2.7.jar
[ivy:retrieve] module not found: commons-cli#commons-cli;1.2
[ivy:retrieve] ==== local: tried
[ivy:retrieve] /home/yonathan/.ant/local/commons-cli/commons-cli/1.2/ivys/ivy.xml
[ivy:retrieve] -- artifact commons-cli#commons-cli;1.2!commons-cli.jar:
[ivy:retrieve] /home/yonathan/.ant/local/commons-cli/commons-cli/1.2/jars/commons-cli.jar
[ivy:retrieve] ==== shared: tried
[ivy:retrieve] /home/yonathan/.ant/shared/commons-cli/commons-cli/1.2/ivys/ivy.xml
[ivy:retrieve] -- artifact commons-cli#commons-cli;1.2!commons-cli.jar:
[ivy:retrieve] /home/yonathan/.ant/shared/commons-cli/commons-cli/1.2/jars/commons-cli.jar
[ivy:retrieve] ==== public: tried
[ivy:retrieve] http://repo1.maven.org/maven2/commons-cli/commons-cli/1.2/commons-cli-1.2.pom
[ivy:retrieve] -- artifact commons-cli#commons-cli;1.2!commons-cli.jar:
[ivy:retrieve] http://repo1.maven.org/maven2/commons-cli/commons-cli/1.2/commons-cli-1.2.jar
[ivy:retrieve] module not found: junit#junit;4.8.2
[ivy:retrieve] ==== local: tried
[ivy:retrieve] /home/yonathan/.ant/local/junit/junit/4.8.2/ivys/ivy.xml
[ivy:retrieve] -- artifact junit#junit;4.8.2!junit.jar:
[ivy:retrieve] /home/yonathan/.ant/local/junit/junit/4.8.2/jars/junit.jar
[ivy:retrieve] ==== shared: tried
[ivy:retrieve] /home/yonathan/.ant/shared/junit/junit/4.8.2/ivys/ivy.xml
[ivy:retrieve] -- artifact junit#junit;4.8.2!junit.jar:
[ivy:retrieve] /home/yonathan/.ant/shared/junit/junit/4.8.2/jars/junit.jar
[ivy:retrieve] ==== public: tried
[ivy:retrieve] http://repo1.maven.org/maven2/junit/junit/4.8.2/junit-4.8.2.pom
[ivy:retrieve] -- artifact junit#junit;4.8.2!junit.jar:
[ivy:retrieve] http://repo1.maven.org/maven2/junit/junit/4.8.2/junit-4.8.2.jar
[ivy:retrieve] module not found: commons-codec#commons-codec;1.8
[ivy:retrieve] ==== local: tried
[ivy:retrieve] /home/yonathan/.ant/local/commons-codec/commons-codec/1.8/ivys/ivy.xml
[ivy:retrieve] -- artifact commons-codec#commons-codec;1.8!commons-codec.jar:
[ivy:retrieve] /home/yonathan/.ant/local/commons-codec/commons-codec/1.8/jars/commons-codec.jar
[ivy:retrieve] ==== shared: tried
[ivy:retrieve] /home/yonathan/.ant/shared/commons-codec/commons-codec/1.8/ivys/ivy.xml
[ivy:retrieve] -- artifact commons-codec#commons-codec;1.8!commons-codec.jar:
[ivy:retrieve] /home/yonathan/.ant/shared/commons-codec/commons-codec/1.8/jars/commons-codec.jar
[ivy:retrieve] ==== public: tried
[ivy:retrieve] http://repo1.maven.org/maven2/commons-codec/commons-codec/1.8/commons-codec-1.8.pom
[ivy:retrieve] -- artifact commons-codec#commons-codec;1.8!commons-codec.jar:
[ivy:retrieve] http://repo1.maven.org/maven2/commons-codec/commons-codec/1.8/commons-codec-1.8.jar
[ivy:retrieve] module not found: commons-io#commons-io;2.4
[ivy:retrieve] ==== local: tried
[ivy:retrieve] /home/yonathan/.ant/local/commons-io/commons-io/2.4/ivys/ivy.xml
[ivy:retrieve] -- artifact commons-io#commons-io;2.4!commons-io.jar:
[ivy:retrieve] /home/yonathan/.ant/local/commons-io/commons-io/2.4/jars/commons-io.jar
[ivy:retrieve] ==== shared: tried
[ivy:retrieve] /home/yonathan/.ant/shared/commons-io/commons-io/2.4/ivys/ivy.xml
[ivy:retrieve] -- artifact commons-io#commons-io;2.4!commons-io.jar:
[ivy:retrieve] /home/yonathan/.ant/shared/commons-io/commons-io/2.4/jars/commons-io.jar
[ivy:retrieve] ==== public: tried
[ivy:retrieve] http://repo1.maven.org/maven2/commons-io/commons-io/2.4/commons-io-2.4.pom
[ivy:retrieve] -- artifact commons-io#commons-io;2.4!commons-io.jar:
[ivy:retrieve] http://repo1.maven.org/maven2/commons-io/commons-io/2.4/commons-io-2.4.jar
[ivy:retrieve] ::::::::::::::::::::::::::::::::::::::::::::::
[ivy:retrieve] :: UNRESOLVED DEPENDENCIES ::
[ivy:retrieve] ::::::::::::::::::::::::::::::::::::::::::::::
[ivy:retrieve] :: com.sun.xml.bind#jaxb-impl;2.2.7: not found
[ivy:retrieve] :: commons-cli#commons-cli;1.2: not found
[ivy:retrieve] :: junit#junit;4.8.2: not found
[ivy:retrieve] :: commons-codec#commons-codec;1.8: not found
[ivy:retrieve] :: commons-io#commons-io;2.4: not found
[ivy:retrieve] ::::::::::::::::::::::::::::::::::::::::::::::
[ivy:retrieve] :::: ERRORS
[ivy:retrieve] SERVER ERROR: HTTPS Required url=http://repo1.maven.org/maven2/com/sun/xml/bind/jaxb-impl/2.2.7/jaxb-impl-2.2.7.pom
[ivy:retrieve] SERVER ERROR: HTTPS Required url=http://repo1.maven.org/maven2/com/sun/xml/bind/jaxb-impl/2.2.7/jaxb-impl-2.2.7.jar
[ivy:retrieve] SERVER ERROR: HTTPS Required url=http://repo1.maven.org/maven2/commons-cli/commons-cli/1.2/commons-cli-1.2.pom
[ivy:retrieve] SERVER ERROR: HTTPS Required url=http://repo1.maven.org/maven2/commons-cli/commons-cli/1.2/commons-cli-1.2.jar
[ivy:retrieve] SERVER ERROR: HTTPS Required url=http://repo1.maven.org/maven2/junit/junit/4.8.2/junit-4.8.2.pom
[ivy:retrieve] SERVER ERROR: HTTPS Required url=http://repo1.maven.org/maven2/junit/junit/4.8.2/junit-4.8.2.jar
[ivy:retrieve] SERVER ERROR: HTTPS Required url=http://repo1.maven.org/maven2/commons-codec/commons-codec/1.8/commons-codec-1.8.pom
[ivy:retrieve] SERVER ERROR: HTTPS Required url=http://repo1.maven.org/maven2/commons-codec/commons-codec/1.8/commons-codec-1.8.jar
[ivy:retrieve] SERVER ERROR: HTTPS Required url=http://repo1.maven.org/maven2/commons-io/commons-io/2.4/commons-io-2.4.pom
[ivy:retrieve] SERVER ERROR: HTTPS Required url=http://repo1.maven.org/maven2/commons-io/commons-io/2.4/commons-io-2.4.jar
[ivy:retrieve]
[ivy:retrieve] :: USE VERBOSE OR DEBUG MESSAGE LEVEL FOR MORE DETAILS
BUILD FAILED
/home/yonathan/RDPTools/Clustering/build.xml:104: impossible to resolve dependencies:
resolve failed - see output for details
Total time: 2 seconds
Makefile:15: recipe for target 'Clustering/dist/Clustering.jar' failed
make: *** [Clustering/dist/Clustering.jar] Error 1
I am fairly certain I know what the problem is, but I can't figure out how to fix it. The URLs for the Maven repository are no longer valid, but can be fixed by simply changing http to https.
My problem: I can't find the file which specifies the URL for the Ivy:retrieve function. I am not very familiar with Java, and don't have an intuitive grasp on where I should be looking. Any help with this issue would be very much appreciated.
Many thanks,
Y.
Installation problem: the 'make' command
Hi.
I'm trying to install the tool. I successfully do the first 3 steps:
(1) cloning the repository,
(2) $ git submodule init
(3) $ git submodule update
However, running the next step: the 'make' command results in the following error message:
mkdir lib
ant -f Clustering/build.xml jar
make: ant: Command not found
Makefile:15: recipe for target 'Clustering/dist/Clustering.jar' failed
make: *** [Clustering/dist/Clustering.jar] Error 127
I have tried many many times, including removing and repeating the steps, but no success. Any idea on how to go about it? Thanks.
Trouble building RDPTools due to Java version
Hi All,
I am trying to build RDPTools on OS 10.14.2 with ant 1.10.5, javac 11.0.1.
The critical piece of make output seems to be:
-do-compile:
[mkdir] Created dir: ../RDPTools/ReadSeq/build/empty
[javac] Compiling 73 source files to ../RDPTools/ReadSeq/build/classes
[javac] warning: [options] bootstrap class path not set in conjunction with -source 5
[javac] error: Source option 5 is no longer supported. Use 6 or later.
[javac] error: Target option 1.5 is no longer supported. Use 1.6 or later.
BUILD FAILED
Any ideas? I tried simply editing build.properties for 1.6 but this did not seem to work...
It also seems that if I do upgrade the target and source to 1.6 instead then the lack of the javax.xml.bind packages in java 11 is a killer.
Best,
Adam
RDP training using custom trainset
So I am trying to use the "train" subcommand of classifier.jar to create a new DB out of custom data. The problem is that the taxonomy data that I have is in qiime format. I want to convert the qiime format to RDP format, but I can't find any good documentation on the rdp taxonomy format. I can certainly write some code to do it, but I need to know the details of the format. So, I have my qiime formatted file which has lines that look like this:
AcrMAj74N231 k_Animalia; p_Nematoda; c_Chromadorea; o_Rhabditida; f_Cephalobidae; g_Acrobeles; s_maeneeneus
And RDP needs lines that look like this (I got this from https://sourceforge.net/projects/rdp-classifier/):
7*Acidimicrobiaceae*6*7*family
The only thing I've found is that the lines are in this format:
taxid*taxon name*parent taxid*depth*rank
However, there are some problems with the sample files that I have.... for example the taxids are not correct for the taxon... e.g. the taxid for Acidimicrobiaceae is 84994, not 7. And then, I have no idea what "depth" means... how do I calculate that?
Any help would be highly appreciated. Thanks!
- Nik.
Make Error: Cannot download http://rdp.cme.msu.edu/download/rdpclassifiertraindata/data.tgz
After following the readme download/installation instructions, the make command hangs up at
download-traindata:
[get] Getting: http://rdp.cme.msu.edu/download/rdpclassifiertraindata/data.tgz [get] To: /home/path/to/RDPTools/classifier/build/classes/data.tgz
trying
wget http://rdp.cme.msu.edu/download/rdpclassifiertraindata/data.tgz
hangs up as well.
Thank you for your patience!
make problem
$ make
ant -f Clustering/build.xml jar
make: ant: Command not found
Makefile:15: recipe for target 'Clustering/dist/Clustering.jar' failed
make: *** [Clustering/dist/Clustering.jar] Error 127
Install RDPTools-make erro
I'm also seeing this error on Linux .....
(base) [zihuiliu@bogon RDPTools]$ make
ant -f classifier/build.xml jar
Buildfile: /home/zihuiliu/software/RDPTools/classifier/build.xml
download-ivy:
[get] Getting: http://repo2.maven.org/maven2/org/apache/ivy/ivy/2.1.0-rc2/ivy-2.1.0-rc2.jar
[get] To: /home/zihuiliu/.ant/lib/ivy.jar
[get] Not modified - so not downloaded
init-ivy:
resolve:
[ivy:retrieve] :: Ivy 2.1.0-rc2 - 20090704004254 :: http://ant.apache.org/ivy/ ::
[ivy:retrieve] :: loading settings :: url = jar:file:/home/zihuiliu/.ant/lib/ivy.jar!/org/apache/ivy/core/settings/ivysettings.xml
[ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#classifier;working@localhost
[ivy:retrieve] confs: [default]
[ivy:retrieve] found commons-cli#commons-cli;1.2 in public
[ivy:retrieve] found commons-io#commons-io;2.4 in public
[ivy:retrieve] found junit#junit;4.8.2 in public
[ivy:retrieve] found jfree#jfreechart;1.0.13 in public
[ivy:retrieve] found jfree#jcommon;1.0.16 in public
[ivy:retrieve] :: resolution report :: resolve 87ms :: artifacts dl 8ms
| | modules || artifacts |
| conf | number| search|dwnlded|evicted|| number|dwnlded|
| default | 5 | 0 | 0 | 0 || 13 | 0 |
[ivy:retrieve] :: retrieving :: edu.cme.rdp#classifier
[ivy:retrieve] confs: [default]
[ivy:retrieve] 0 artifacts copied, 13 already retrieved (0kB/4ms)
-pre-init:
-init-private:
-init-user:
-init-project:
-init-macrodef-property:
-do-init:
-post-init:
-init-check:
-init-ap-cmdline-properties:
-init-macrodef-javac-with-processors:
-init-macrodef-javac-without-processors:
-init-macrodef-javac:
-init-macrodef-test-impl:
-init-macrodef-junit-init:
-init-macrodef-junit-single:
-init-test-properties:
-init-macrodef-junit-batch:
-init-macrodef-junit:
-init-macrodef-junit-impl:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:test-impl
-init-macrodef-testng:
-init-macrodef-testng-impl:
-init-macrodef-test:
-init-macrodef-junit-debug:
-init-macrodef-junit-debug-batch:
-init-macrodef-junit-debug-impl:
-init-macrodef-test-debug-junit:
-init-macrodef-testng-debug:
-init-macrodef-testng-debug-impl:
-init-macrodef-test-debug-testng:
-init-macrodef-test-debug:
-init-debug-args:
-init-macrodef-nbjpda:
-init-macrodef-debug:
-init-macrodef-java:
-init-presetdef-jar:
-init-ap-cmdline-supported:
-init-ap-cmdline:
init:
-deps-jar-init:
[delete] Deleting: /home/zihuiliu/software/RDPTools/classifier/build/built-jar.properties
deps-jar:
-warn-already-built-jar:
[propertyfile] Updating property file: /home/zihuiliu/software/RDPTools/classifier/build/built-jar.properties
-check-call-dep:
-maybe-call-dep:
download-ivy:
[get] Getting: http://repo2.maven.org/maven2/org/apache/ivy/ivy/2.1.0-rc2/ivy-2.1.0-rc2.jar
[get] To: /home/zihuiliu/.ant/lib/ivy.jar
[get] Not modified - so not downloaded
init-ivy:
resolve:
[ivy:retrieve] :: loading settings :: url = jar:file:/home/zihuiliu/.ant/lib/ivy.jar!/org/apache/ivy/core/settings/ivysettings.xml
[ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#AlignmentTools;working@localhost
[ivy:retrieve] confs: [default]
[ivy:retrieve] found commons-lang#commons-lang;2.6 in public
[ivy:retrieve] found commons-cli#commons-cli;1.2 in public
[ivy:retrieve] :: resolution report :: resolve 16ms :: artifacts dl 2ms
| | modules || artifacts |
| conf | number| search|dwnlded|evicted|| number|dwnlded|
| default | 2 | 0 | 0 | 0 || 6 | 0 |
[ivy:retrieve] :: retrieving :: edu.cme.rdp#AlignmentTools
[ivy:retrieve] confs: [default]
[ivy:retrieve] 0 artifacts copied, 6 already retrieved (0kB/1ms)
-pre-init:
-init-private:
-init-user:
-init-project:
-init-macrodef-property:
-do-init:
-post-init:
-init-check:
-init-ap-cmdline-properties:
-init-macrodef-javac-with-processors:
-init-macrodef-javac-without-processors:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:javac
-init-macrodef-javac:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:depend
-init-macrodef-test-impl:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:test-impl
-init-macrodef-junit-init:
-init-macrodef-junit-single:
-init-test-properties:
-init-macrodef-junit-batch:
-init-macrodef-junit:
-init-macrodef-junit-impl:
-init-macrodef-testng:
-init-macrodef-testng-impl:
-init-macrodef-test:
-init-macrodef-junit-debug:
-init-macrodef-junit-debug-batch:
-init-macrodef-junit-debug-impl:
-init-macrodef-test-debug-junit:
-init-macrodef-testng-debug:
-init-macrodef-testng-debug-impl:
-init-macrodef-test-debug-testng:
-init-macrodef-test-debug:
-init-debug-args:
-init-macrodef-nbjpda:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/1:nbjpdastart
-init-macrodef-debug:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:debug
-init-macrodef-java:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/1:java
-init-presetdef-jar:
-init-ap-cmdline-supported:
-init-ap-cmdline:
init:
-deps-jar-init:
deps-jar:
-warn-already-built-jar:
[propertyfile] Updating property file: /home/zihuiliu/software/RDPTools/classifier/build/built-jar.properties
-check-call-dep:
-maybe-call-dep:
download-ivy:
[get] Getting: http://repo2.maven.org/maven2/org/apache/ivy/ivy/2.1.0-rc2/ivy-2.1.0-rc2.jar
[get] To: /home/zihuiliu/.ant/lib/ivy.jar
[get] Not modified - so not downloaded
init-ivy:
resolve:
[ivy:retrieve] :: loading settings :: url = jar:file:/home/zihuiliu/.ant/lib/ivy.jar!/org/apache/ivy/core/settings/ivysettings.xml
[ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#ReadSeq;working@localhost
[ivy:retrieve] confs: [default]
[ivy:retrieve] found commons-lang#commons-lang;2.6 in public
[ivy:retrieve] found commons-cli#commons-cli;1.2 in public
[ivy:retrieve] found commons-io#commons-io;2.4 in public
[ivy:retrieve] :: resolution report :: resolve 19ms :: artifacts dl 3ms
| | modules || artifacts |
| conf | number| search|dwnlded|evicted|| number|dwnlded|
| default | 3 | 0 | 0 | 0 || 9 | 0 |
[ivy:retrieve] :: retrieving :: edu.cme.rdp#ReadSeq
[ivy:retrieve] confs: [default]
[ivy:retrieve] 0 artifacts copied, 9 already retrieved (0kB/1ms)
-pre-init:
-init-private:
-init-user:
-init-project:
-init-macrodef-property:
-do-init:
-post-init:
-init-check:
-init-ap-cmdline-properties:
-init-macrodef-javac-with-processors:
-init-macrodef-javac-without-processors:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:javac
-init-macrodef-javac:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:depend
-init-macrodef-test-impl:
-init-macrodef-junit-init:
-init-macrodef-junit-single:
-init-test-properties:
-init-macrodef-junit-batch:
-init-macrodef-junit:
-init-macrodef-junit-impl:
-init-macrodef-testng:
-init-macrodef-testng-impl:
-init-macrodef-test:
-init-macrodef-junit-debug:
-init-macrodef-junit-debug-batch:
-init-macrodef-junit-debug-impl:
-init-macrodef-test-debug-junit:
-init-macrodef-testng-debug:
-init-macrodef-testng-debug-impl:
-init-macrodef-test-debug-testng:
-init-macrodef-test-debug:
-init-debug-args:
-init-macrodef-nbjpda:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/1:nbjpdastart
-init-macrodef-debug:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:debug
-init-macrodef-java:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/1:java
-init-presetdef-jar:
-init-ap-cmdline-supported:
-init-ap-cmdline:
init:
-deps-jar-init:
deps-jar:
-warn-already-built-jar:
[propertyfile] Updating property file: /home/zihuiliu/software/RDPTools/classifier/build/built-jar.properties
-check-automatic-build:
-clean-after-automatic-build:
-verify-automatic-build:
-pre-pre-compile:
-pre-compile:
-copy-persistence-xml:
-compile-depend:
-do-compile:
-post-compile:
compile:
-pre-jar:
-post-jar:
jar:
[echo] To run this application from the command line without Ant, try:
[echo] java -jar "/home/zihuiliu/software/RDPTools/ReadSeq/dist/ReadSeq.jar"
-check-automatic-build:
-clean-after-automatic-build:
-verify-automatic-build:
-pre-pre-compile:
-pre-compile:
-copy-persistence-xml:
-compile-depend:
-do-compile:
-post-compile:
compile:
-pre-jar:
-post-jar:
jar:
[echo] To run this application from the command line without Ant, try:
[echo] java -jar "/home/zihuiliu/software/RDPTools/AlignmentTools/dist/AlignmentTools.jar"
-check-call-dep:
-maybe-call-dep:
-check-call-dep:
-maybe-call-dep:
download-ivy:
[get] Getting: http://repo2.maven.org/maven2/org/apache/ivy/ivy/2.1.0-rc2/ivy-2.1.0-rc2.jar
[get] To: /home/zihuiliu/.ant/lib/ivy.jar
[get] Not modified - so not downloaded
init-ivy:
resolve:
[ivy:retrieve] :: loading settings :: url = jar:file:/home/zihuiliu/.ant/lib/ivy.jar!/org/apache/ivy/core/settings/ivysettings.xml
[ivy:retrieve] :: resolving dependencies :: edu.cme.rdp#RDPTaxonomyTree;working@localhost
[ivy:retrieve] confs: [default]
[ivy:retrieve] found junit#junit;4.8.2 in public
[ivy:retrieve] :: resolution report :: resolve 7ms :: artifacts dl 1ms
| | modules || artifacts |
| conf | number| search|dwnlded|evicted|| number|dwnlded|
| default | 1 | 0 | 0 | 0 || 3 | 0 |
[ivy:retrieve] :: retrieving :: edu.cme.rdp#RDPTaxonomyTree
[ivy:retrieve] confs: [default]
[ivy:retrieve] 0 artifacts copied, 3 already retrieved (0kB/0ms)
-pre-init:
-init-private:
-init-user:
-init-project:
-init-macrodef-property:
-do-init:
-post-init:
-init-check:
-init-ap-cmdline-properties:
-init-macrodef-javac-with-processors:
-init-macrodef-javac-without-processors:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:javac
-init-macrodef-javac:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:depend
-init-macrodef-test-impl:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:test-impl
-init-macrodef-junit-init:
-init-macrodef-junit-single:
-init-test-properties:
-init-macrodef-junit-batch:
-init-macrodef-junit:
-init-macrodef-junit-impl:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:test-impl
-init-macrodef-testng:
-init-macrodef-testng-impl:
-init-macrodef-test:
-init-macrodef-junit-debug:
-init-macrodef-junit-debug-batch:
-init-macrodef-junit-debug-impl:
-init-macrodef-test-debug-junit:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:test-debug
-init-macrodef-testng-debug:
-init-macrodef-testng-debug-impl:
-init-macrodef-test-debug-testng:
-init-macrodef-test-debug:
-init-debug-args:
-init-macrodef-nbjpda:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/1:nbjpdastart
-init-macrodef-debug:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/3:debug
-init-macrodef-java:
Trying to override old definition of task http://www.netbeans.org/ns/j2se-project/1:java
-init-presetdef-jar:
-init-ap-cmdline-supported:
-init-ap-cmdline:
init:
-deps-jar-init:
deps-jar:
-warn-already-built-jar:
[propertyfile] Updating property file: /home/zihuiliu/software/RDPTools/classifier/build/built-jar.properties
-check-call-dep:
-maybe-call-dep:
-check-automatic-build:
-clean-after-automatic-build:
-verify-automatic-build:
-pre-pre-compile:
-pre-compile:
-copy-persistence-xml:
-compile-depend:
-do-compile:
-post-compile:
compile:
-pre-jar:
-post-jar:
jar:
[echo] To run this application from the command line without Ant, try:
[echo] java -jar "/home/zihuiliu/software/RDPTools/TaxonomyTree/dist/TaxonomyTree.jar"
-check-automatic-build:
-clean-after-automatic-build:
-verify-automatic-build:
-pre-pre-compile:
-pre-compile:
-copy-persistence-xml:
-compile-depend:
-do-compile:
-post-compile:
compile:
-pre-jar:
-post-jar:
download-traindata:
[get] Getting: http://rdp.cme.msu.edu/download/rdpclassifiertraindata/data.tgz
[get] To: /home/zihuiliu/software/RDPTools/classifier/build/classes/data.tgz
[get] Not modified - so not downloaded
[untar] Expanding: /home/zihuiliu/software/RDPTools/classifier/build/classes/data.tgz into /home/zihuiliu/software/RDPTools/classifier/build/classes
BUILD FAILED
/home/zihuiliu/software/RDPTools/classifier/build.xml:51: Error while expanding /home/zihuiliu/software/RDPTools/classifier/build/classes/data.tgz
java.io.EOFException: Unexpected end of ZLIB input stream
at java.util.zip.InflaterInputStream.fill(InflaterInputStream.java:240)
at java.util.zip.InflaterInputStream.read(InflaterInputStream.java:158)
at java.util.zip.GZIPInputStream.read(GZIPInputStream.java:117)
at org.apache.tools.tar.TarBuffer.readBlock(TarBuffer.java:253)
at org.apache.tools.tar.TarBuffer.readRecord(TarBuffer.java:220)
at org.apache.tools.tar.TarInputStream.read(TarInputStream.java:603)
at java.io.FilterInputStream.read(FilterInputStream.java:107)
at org.apache.tools.ant.taskdefs.Expand.extractFile(Expand.java:368)
at org.apache.tools.ant.taskdefs.Untar.expandStream(Untar.java:160)
at org.apache.tools.ant.taskdefs.Untar.expandFile(Untar.java:106)
at org.apache.tools.ant.taskdefs.Expand.execute(Expand.java:152)
at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:293)
at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
at org.apache.tools.ant.Task.perform(Task.java:352)
at org.apache.tools.ant.Target.execute(Target.java:437)
at org.apache.tools.ant.Target.performTasks(Target.java:458)
at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1406)
at org.apache.tools.ant.Project.executeTarget(Project.java:1377)
at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
at org.apache.tools.ant.Project.executeTargets(Project.java:1261)
at org.apache.tools.ant.Main.runBuild(Main.java:857)
at org.apache.tools.ant.Main.startAnt(Main.java:236)
at org.apache.tools.ant.launch.Launcher.run(Launcher.java:287)
at org.apache.tools.ant.launch.Launcher.main(Launcher.java:112)
Total time: 3 seconds
make: *** [classifier/dist/classifier.jar] ้่ฏฏ 1
(base) [zihuiliu@bogon RDPTools]$
######################################################################################################
(base) [zihuiliu@bogon RDPTools]$ java -version
openjdk version "1.8.0_212"
OpenJDK Runtime Environment (build 1.8.0_212-b04)
OpenJDK 64-Bit Server VM (build 25.212-b04, mixed mode)
(base) [zihuiliu@bogon RDPTools]$ javac -version
javac 1.8.0_212
(base) [zihuiliu@bogon RDPTools]$ ant -v
Apache Ant(TM) version 1.9.14 compiled on March 12 2019
Trying the default build file: build.xml
Buildfile: build.xml does not exist!
Build failed
(base) [zihuiliu@bogon RDPTools]$ lsb_release -a
LSB Version: :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch
Distributor ID: CentOS
Description: CentOS release 6.5 (Final)
Release: 6.5
Codename: Final
(base) [zihuiliu@bogon RDPTools]$
Need to download the database
I am fetching below information from RDP
Goto Hierarchy Browser>Search species> copy Strain type and Locus ID
Example:
S000413927 Bradyrhizobium oligotrophicum (T); JCM 1494; D78366
S000438365 Bradyrhizobium japonicum (T); USDA 6, 3I1b6, ATCC10324, SEMIA 5052, RCR 3425, ACCC 15032; original isolate received by USDA from Dr. K. Aso; U69638
Is there a way to fetch this information from the database directly by downloading the updated fasta/entire data base dump?
Please guide me steps if any way available as I will be requiring this sort of data to download monthly basis?
I downloaded bacteria aligned fasta file, but that does not serve the purpose
Just downloading the zip file is insufficient for installation.
A notification of some sort in the README documentation indicating that downloading a zip file from github is not enough for installation.
It all worked out though, just wanted to provide my 2 cents that this thing could be more clear.
Wonder full tools though.
rdpclassifiertraindata/data.tgz Missing. Build fail
Running make.. works till the mentioned file is tried to download.
jar:
[echo] To run this application from the command line without Ant, try:
[echo] java -jar "/home/clevergene/swdump/RDPTools/TaxonomyTree/dist/TaxonomyTree.jar"
-check-automatic-build:
-clean-after-automatic-build:
-verify-automatic-build:
-pre-pre-compile:
-pre-compile:
-copy-persistence-xml:
-compile-depend:
-do-compile:
-post-compile:
compile:
-pre-jar:
-post-jar:
download-traindata:
[get] Getting: http://rdp.cme.msu.edu/download/rdpclassifiertraindata/data.tgz
[get] To: /home/clevergene/swdump/RDPTools/classifier/build/classes/data.tgz
[get] Error opening connection java.io.IOException: Server returned HTTP response code: 502 for URL: http://rdp.cme.msu.edu/download/rdpclassifiertraindata/data.tgz
[get] Error opening connection java.io.IOException: Server returned HTTP response code: 502 for URL: http://rdp.cme.msu.edu/download/rdpclassifiertraindata/data.tgz
[get] Error opening connection java.io.IOException: Server returned HTTP response code: 502 for URL: http://rdp.cme.msu.edu/download/rdpclassifiertraindata/data.tgz
[get] Can't get http://rdp.cme.msu.edu/download/rdpclassifiertraindata/data.tgz to /home/clevergene/swdump/RDPTools/classifier/build/classes/data.tgz
BUILD FAILED
/home/clevergene/swdump/RDPTools/classifier/build.xml:50: Can't get http://rdp.cme.msu.edu/download/rdpclassifiertraindata/data.tgz to /home/clevergene/swdump/RDPTools/classifier/build/classes/data.tgz
Total time: 14 seconds
make: *** [classifier/dist/classifier.jar] Error 1
RDPTools cannot make.
make: ant: No such file or directory
make: *** [Clustering/dist/Clustering.jar] Error 1
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