Unable to create matrix in incanter 1.4.0 about incanter

[alexott]

Hmmm, very strange - I can't reproduce this on my machine. I deleted all incanter jars from ~/.m2/repository/ and used following project to get it from clojars:

(defproject in-test "0.1.0-SNAPSHOT"
    :dependencies [[incanter "1.4.0"]])

and in lein repl, I execute your commands without errors:

user=> (use 'incanter.io)
nil
user=> (use 'incanter.core)
nil
user=> (def A (matrix [[1 2 3] [4 5 6] [7 8 9]])) 
#'user/A
user=> A
[1.0000 2.0000 3.0000
4.0000 5.0000 6.0000
7.0000 8.0000 9.0000]

Can you provide more details on which java version are you using, which OS, etc.

[lionandoil]

I can reproduce this with incanter 1.4.* (clojure 1.4.0, JVM 1.6) even after completely wiping incanter/pcolt/jplasma from my local .m2 repositories:

(use '(incanter core io))
(def A (matrix [[1 2 3] [4 5 6] [7 8 9]])) 
user=> NoSuchMethodError edu.emory.mathcs.utils.ConcurrencyUtils.getThreadsBeginN_2D()I  cern.colt.matrix.tdouble.impl.DenseColumnDoubleMatrix2D.assign (DenseColumnDoubleMatrix2D.java:661)
user=> java.lang.NoSuchMethodError: edu.emory.mathcs.utils.ConcurrencyUtils.getThreadsBeginN_2D()I, compiling:(NO_SOURCE_FILE:2)
at clojure.lang.Compiler$InvokeExpr.eval(Compiler.java:3387)
at clojure.lang.Compiler$DefExpr.eval(Compiler.java:398)
at clojure.lang.Compiler.eval(Compiler.java:6516)
at clojure.lang.Compiler.eval(Compiler.java:6477)
at clojure.core$eval.invoke(core.clj:2797)
at clojure.main$repl$read_eval_print__6405.invoke(main.clj:245)
at clojure.main$repl$fn__6410.invoke(main.clj:266)
at clojure.main$repl.doInvoke(main.clj:266)
at clojure.lang.RestFn.invoke(RestFn.java:512)
at user$eval27$acc__3301__auto____30$fn__32.invoke(NO_SOURCE_FILE:1)
at clojure.lang.AFn.run(AFn.java:24)
at java.lang.Thread.run(Thread.java:680)
Caused by: java.lang.NoSuchMethodError: edu.emory.mathcs.utils.ConcurrencyUtils.getThreadsBeginN_2D()I
at cern.colt.matrix.tdouble.impl.DenseColumnDoubleMatrix2D.assign(DenseColumnDoubleMatrix2D.java:661)
at cern.colt.matrix.tdouble.impl.DenseColumnDoubleMatrix2D.<init>(DenseColumnDoubleMatrix2D.java:109)
at incanter.Matrix.<init>(Matrix.java:77)
at incanter.internal$make_matrix.invoke(internal.clj:41)
at incanter.core$matrix.invoke(core.clj:96)
at clojure.lang.AFn.applyToHelper(AFn.java:161)
at clojure.lang.AFn.applyTo(AFn.java:151)
at clojure.lang.Compiler$InvokeExpr.eval(Compiler.java:3382)
... 11 more

As in the stackoverflow Link above I can get it to work by either excluding jplasma or using jplasma-0.9.4 instead of 1.2.0. Excluding jplasma from the incanter.core deps should fix this, but if there's gonna be no 1.4.2 release I guess this issue is superfluous anyway?

[lionandoil]

The 0.9.4/exclude trick only fixes matrix and to-matrix, I still get the exception in other places, e.g. when calling non-linear-model:

java.lang.NoSuchMethodError: edu.emory.mathcs.utils.ConcurrencyUtils.getThreadsBeginN_1D()I
at cern.colt.matrix.tdouble.impl.DenseDoubleMatrix1D.assign(DenseDoubleMatrix1D.java:472)
at cern.colt.matrix.tdouble.algo.decomposition.DenseDoubleLUDecompositionQuick.decompose(DenseDoubleLUDecompositionQuick.java:145)
at cern.colt.matrix.tdouble.algo.decomposition.DenseDoubleLUDecomposition.<init>(DenseDoubleLUDecomposition.java:43)
at cern.colt.matrix.tdouble.algo.DenseDoubleAlgebra.lu(DenseDoubleAlgebra.java:202)
at cern.colt.matrix.tdouble.algo.DenseDoubleAlgebra.solve(DenseDoubleAlgebra.java:1119)
at cern.colt.matrix.tdouble.algo.DenseDoubleAlgebra.inverse(DenseDoubleAlgebra.java:195)
at incanter.core$solve.doInvoke(core.clj:726)
at clojure.lang.RestFn.invoke(RestFn.java:410)
at incanter.optimize$nls_gauss_newton.doInvoke(optimize.clj:563)
at clojure.lang.RestFn.invoke(RestFn.java:652)
at incanter.optimize$non_linear_model.doInvoke(optimize.clj:668)
at clojure.lang.RestFn.invoke(RestFn.java:470)
at inctest.core$logit_model.invoke(NO_SOURCE_FILE:55)
at inctest.core$eval3998.invoke(NO_SOURCE_FILE:98)
at clojure.lang.Compiler.eval(Compiler.java:6511)
at clojure.lang.Compiler.eval(Compiler.java:6477)
at clojure.core$eval.invoke(core.clj:2797)
at clojure.main$repl$read_eval_print__6405.invoke(main.clj:245)
at clojure.main$repl$fn__6410.invoke(main.clj:266)
at clojure.main$repl.doInvoke(main.clj:266)
at clojure.lang.RestFn.invoke(RestFn.java:512)
at user$eval27$acc__3301__auto____30$fn__32.invoke(NO_SOURCE_FILE:1)
at clojure.lang.AFn.run(AFn.java:24)
at java.lang.Thread.run(Thread.java:680)

[alexott]

Can you try fresh 1.5.0 release?

[lionandoil]

Yes, it's all fixed now!

While not strictly related to the NoSuchMethodError problem, some of the matrix stuff within non-linear-model is still broken, in particular when using :method :newton-raphson, which always results in:

java.lang.ClassCastException: clatrix.core.Matrix cannot be cast to java.lang.Number
at incanter.core$symmetric_matrix.doInvoke(core.clj:2346)
at clojure.lang.RestFn.invoke(RestFn.java:439)
at incanter.optimize$nls_hessian.invoke(optimize.clj:456)
at incanter.optimize$nls_newton_raphson.doInvoke(optimize.clj:501)
at clojure.lang.RestFn.invoke(RestFn.java:866)
at incanter.optimize$non_linear_model.doInvoke(optimize.clj:667)
at clojure.lang.RestFn.invoke(RestFn.java:529)
at language_games.utils.math$eval4848.invoke(Unknown Source)
at clojure.lang.Compiler.eval(Compiler.java:6511)
at clojure.lang.Compiler.load(Compiler.java:6952)
at clojure.lang.Compiler.load(Compiler.java:6921)
at clojure.core$load_reader.invoke(core.clj:3627)
at clojure.core$load_string.invoke(core.clj:3637)
at user$eval4843.invoke(NO_SOURCE_FILE:90)
at clojure.lang.Compiler.eval(Compiler.java:6511)
at clojure.lang.Compiler.eval(Compiler.java:6477)
at clojure.core$eval.invoke(core.clj:2797)
at clojure.main$repl$read_eval_print__6405.invoke(main.clj:245)
at clojure.main$repl$fn__6410.invoke(main.clj:266)
at clojure.main$repl.doInvoke(main.clj:266)
at clojure.lang.RestFn.invoke(RestFn.java:512)
at user$eval27$acc__3301__auto____30$fn__32.invoke(NO_SOURCE_FILE:1)
at clojure.lang.AFn.run(AFn.java:24)
at java.lang.Thread.run(Thread.java:680)

:gauss-newton also still fails in many more cases than it did with 1.3, usually bailing out with:

org.jblas.exceptions.LapackException: LAPACK DGESV: Linear equation cannot be solved because the matrix was singular.
at org.jblas.SimpleBlas.gesv(SimpleBlas.java:274)
at org.jblas.Solve.solve(Solve.java:48)
at clatrix.core$solve.invoke(core.clj:790)
at clatrix.core$i.invoke(core.clj:801)
at incanter.core$solve.doInvoke(core.clj:695)
at clojure.lang.RestFn.invoke(RestFn.java:410)
at incanter.optimize$nls_gauss_newton.doInvoke(optimize.clj:563)
at clojure.lang.RestFn.invoke(RestFn.java:652)
at incanter.optimize$non_linear_model.doInvoke(optimize.clj:668)
at clojure.lang.RestFn.invoke(RestFn.java:470)
at language_games.utils.math$logistic_model.invoke(Unknown Source)
at language_games.utils.math$foo.invoke(Unknown Source)
at language_games.utils.math$eval4927.invoke(Unknown Source)
at clojure.lang.Compiler.eval(Compiler.java:6511)
at clojure.lang.Compiler.load(Compiler.java:6952)
at clojure.lang.Compiler.load(Compiler.java:6921)
at clojure.core$load_reader.invoke(core.clj:3627)
at clojure.core$load_string.invoke(core.clj:3637)
at user$eval4924.invoke(NO_SOURCE_FILE:117)
at clojure.lang.Compiler.eval(Compiler.java:6511)
at clojure.lang.Compiler.eval(Compiler.java:6477)
at clojure.core$eval.invoke(core.clj:2797)
at clojure.main$repl$read_eval_print__6405.invoke(main.clj:245)
at clojure.main$repl$fn__6410.invoke(main.clj:266)
at clojure.main$repl.doInvoke(main.clj:266)
at clojure.lang.RestFn.invoke(RestFn.java:512)
at user$eval27$acc__3301__auto____30$fn__32.invoke(NO_SOURCE_FILE:1)
at clojure.lang.AFn.run(AFn.java:24)
at java.lang.Thread.run(Thread.java:680)

but I guess that issue should go into its own thread.

[alexott]

yes, it's better to file separate bugs for these errors
thank you