I have recently started to work with Clojure. When I run a program in lein, I get the below error:
Exception in thread "main" Syntax error compiling at (bioavailability.clj:79:36).
at clojure.lang.Compiler$InvokeExpr.eval(Compiler.java:3707)
at clojure.lang.Compiler$DefExpr.eval(Compiler.java:457)
at clojure.lang.Compiler.eval(Compiler.java:7181)
at clojure.lang.Compiler.load(Compiler.java:7635)
at clojure.lang.RT.loadResourceScript(RT.java:381)
at clojure.lang.RT.loadResourceScript(RT.java:372)
at clojure.lang.RT.load(RT.java:463)
at clojure.lang.RT.load(RT.java:428)
at clojure.core$load$fn__6824.invoke(core.clj:6126)
at clojure.core$load.invokeStatic(core.clj:6125)
at clojure.core$load.doInvoke(core.clj:6109)
at clojure.lang.RestFn.invoke(RestFn.java:408)
at clojure.core$load_one.invokeStatic(core.clj:5908)
at clojure.core$load_one.invoke(core.clj:5903)
at clojure.core$load_lib$fn__6765.invoke(core.clj:5948)
at clojure.core$load_lib.invokeStatic(core.clj:5947)
at clojure.core$load_lib.doInvoke(core.clj:5928)
at clojure.lang.RestFn.applyTo(RestFn.java:142)
at clojure.core$apply.invokeStatic(core.clj:667)
at clojure.core$load_libs.invokeStatic(core.clj:5985)
at clojure.core$load_libs.doInvoke(core.clj:5969)
at clojure.lang.RestFn.applyTo(RestFn.java:137)
at clojure.core$apply.invokeStatic(core.clj:667)
at clojure.core$require.invokeStatic(core.clj:6007)
at clojure.core$require.doInvoke(core.clj:6007)
at clojure.lang.RestFn.invoke(RestFn.java:408)
at clojush.core$_main.invokeStatic(core.clj:40)
at clojush.core$_main.doInvoke(core.clj:26)
at clojure.lang.RestFn.invoke(RestFn.java:408)
at clojure.lang.Var.invoke(Var.java:384)
at user$eval140.invokeStatic(form-init8949943542898746617.clj:1)
at user$eval140.invoke(form-init8949943542898746617.clj:1)
at clojure.lang.Compiler.eval(Compiler.java:7176)
at clojure.lang.Compiler.eval(Compiler.java:7166)
at clojure.lang.Compiler.load(Compiler.java:7635)
at clojure.lang.Compiler.loadFile(Compiler.java:7573)
at clojure.main$load_script.invokeStatic(main.clj:452)
at clojure.main$init_opt.invokeStatic(main.clj:454)
at clojure.main$init_opt.invoke(main.clj:454)
at clojure.main$initialize.invokeStatic(main.clj:485)
at clojure.main$null_opt.invokeStatic(main.clj:519)
at clojure.main$null_opt.invoke(main.clj:516)
at clojure.main$main.invokeStatic(main.clj:598)
at clojure.main$main.doInvoke(main.clj:561)
at clojure.lang.RestFn.applyTo(RestFn.java:137)
at clojure.lang.Var.applyTo(Var.java:705)
at clojure.main.main(main.java:37)
Caused by: java.lang.IllegalArgumentException: No matching method findResource found taking 1 args for class jdk.internal.loader.ClassLoaders$AppClassLoader
at clojure.lang.Reflector.invokeMatchingMethod(Reflector.java:127)
at clojure.lang.Reflector.invokeInstanceMethod(Reflector.java:102)
at local_file$find_resource.invokeStatic(local_file.clj:30)
at local_file$find_resource.invoke(local_file.clj:26)
at local_file$project_dir.invokeStatic(local_file.clj:39)
at local_file$project_dir.invoke(local_file.clj:34)
at local_file$project_dir.invokeStatic(local_file.clj:47)
at local_file$project_dir.invoke(local_file.clj:34)
at local_file$file_STAR_.invokeStatic(local_file.clj:55)
at local_file$file_STAR_.invoke(local_file.clj:51)
at local_file$slurp_STAR_.invokeStatic(local_file.clj:60)
at local_file$slurp_STAR_.doInvoke(local_file.clj:57)
at clojure.lang.RestFn.invoke(RestFn.java:410)
at clojush.problems.regression.bioavailability$read_data.invokeStatic(bioavailability.clj:51)
at clojush.problems.regression.bioavailability$read_data.invoke(bioavailability.clj:49)
at clojush.problems.regression.bioavailability$define_fitness_cases.invokeStatic(bioavailability.clj:63)
at clojush.problems.regression.bioavailability$define_fitness_cases.invoke(bioavailability.clj:57)
at clojure.lang.AFn.applyToHelper(AFn.java:152)
at clojure.lang.AFn.applyTo(AFn.java:144)
at clojure.lang.Compiler$InvokeExpr.eval(Compiler.java:3702)
... 46 more
The code I am trying to run is:
https://github.com/lspector/Clojush/blob/master/src/clojush/problems/regression/bioavailability.clj
and the command that I use is:
lein run clojush.problems.regression.bioavailability
Thanks in advance for your kind help.
I tried to run each section of the main code seperately to understand where the problem exactly is but it was not succesful.
The problem is that the code in bioavailability.clj calls the function find-resource that in turn calls a method findResource that (i) is protected and (ii) expects a string but is passed a File.
To fix this, I did two things:
First, copied the function find-resource from the local-file library and renamed it get-resource and replaced the call to findResource by a call to getResource which is public. I inserted this code just above the read-data function in bioavailability.clj.
Second, I changed a line in read-data that calls the slurp* (that was (slurp* "src/clojush/problems/regression/data/bioavailability.txt")) function to instead call (slurp (get-resource "../src/clojush/problems/regression/data/bioavailability.txt")) by calling slurp on the result of the get-resource function to which I pass a path that I have prepended with ../. The prepended path is relative to the default resources directory.
The modified code is
;; I added this function
(defn get-resource
[file]
(loop [cl (.. Thread currentThread getContextClassLoader)]
(when cl
(if-let [url (.getResource cl file)]
url
(recur (.getParent cl))))))
(defn read-data []
"Reads data from data/bioavailability.txt into a sequence of sequences."
;; This line has been updated:
(let [f (slurp (get-resource "../src/clojush/problems/regression/data/bioavailability.txt"))
lines (csv/parse-csv f :delimiter \tab)]
(map #(map (fn [x] (float (read-string x)))
%)
lines)))