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clojupyter / clojupyter

a Jupyter kernel for Clojure
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java-time error when using cljplot #131

Closed whewage closed 8 months ago

whewage commented 3 years ago

I am using Clojure for gaussian process (generateme/fastmath library ) and "cljplot" for graph visualization. It works well with fastmath but when I try to use cljplot it gives me the following error. Dependencies used --> [org.clojure/clojure "1.10.1"] [clojure2d "1.2.0-SNAPSHOT"] [generateme/fastmath "1.4.0-SNAPSHOT"] [clojure.java-time "0.3.2"] [cljplot "0.0.2-SNAPSHOT"] [org.clojure/data.json "1.0.0"] ;;;;;;;;;; java.lang.IllegalAccessError: tried to access field clojure.lang.APersistentVector._hash from class clojure.lang.PersistentUnrolledVector$Card1 at clojure.lang.PersistentUnrolledVector$Card1.hashCode(PersistentUnrolledVector.java:253) at java.util.concurrent.ConcurrentHashMap.get(ConcurrentHashMap.java:936) at java_time.potemkin.util$fast_memoize$fn15133.invoke(util.clj:48) at java_time.defconversion$combinations.invokeStatic(defconversion.clj:25) at java_time.defconversion$combinations.invoke(defconversion.clj:24) at java_time.defconversion$conversionBANG.invokeStatic(defconversion.clj:43) at java_time.defconversion$conversionBANG.invoke(defconversion.clj:39) at java_time.defconversion$conversionBANG.invokeStatic(defconversion.clj:40) at java_time.defconversion$conversionBANG.invoke(defconversion.clj:39) at java_time.temporal__init.load(Unknown Source) at java_time.temporalinit.(Unknown Source) at java.lang.Class.forName0(Native Method) at java.lang.Class.forName(Class.java:348) at clojure.lang.RT.classForName(RT.java:2204) at clojure.lang.RT.classForName(RT.java:2213) at clojure.lang.RT.loadClassForName(RT.java:2232) at clojure.lang.RT.load(RT.java:450) at clojure.lang.RT.load(RT.java:426) at clojure.core$load$fn6548.invoke(core.clj:6046) at clojure.core$load.invokeStatic(core.clj:6045) at clojure.core$load.doInvoke(core.clj:6029) at clojure.lang.RestFn.invoke(RestFn.java:408) at clojure.core$load_one.invokeStatic(core.clj:5848) at clojure.core$load_one.invoke(core.clj:5843) at clojure.core$load_lib$fn__6493.invoke(core.clj:5888) at clojure.core$load_lib.invokeStatic(core.clj:5887) at clojure.core$load_lib.doInvoke(core.clj:5868) at clojure.lang.RestFn.applyTo(RestFn.java:142) at clojure.core$apply.invokeStatic(core.clj:659) at clojure.core$load_libs.invokeStatic(core.clj:5929) at clojure.core$load_libs.doInvoke(core.clj:5909) at clojure.lang.RestFn.applyTo(RestFn.java:137) at clojure.core$apply.invokeStatic(core.clj:659) at clojure.core$require.invokeStatic(core.clj:5947) at clojure.core$require.doInvoke(core.clj:5947) at clojure.lang.RestFn.invoke(RestFn.java:436) at java_time$loading6721auto__14418.invoke(java_time.clj:1) at java_timeinit.load(Unknown Source) at java_timeinit.(Unknown Source) at java.lang.Class.forName0(Native Method) at java.lang.Class.forName(Class.java:348) at clojure.lang.RT.classForName(RT.java:2204) at clojure.lang.RT.classForName(RT.java:2213) at clojure.lang.RT.loadClassForName(RT.java:2232) at clojure.lang.RT.load(RT.java:450) at clojure.lang.RT.load(RT.java:426) at clojure.core$load$fn6548.invoke(core.clj:6046) at clojure.core$load.invokeStatic(core.clj:6045) at clojure.core$load.doInvoke(core.clj:6029) at clojure.lang.RestFn.invoke(RestFn.java:408) at clojure.core$load_one.invokeStatic(core.clj:5848) at clojure.core$load_one.invoke(core.clj:5843) at clojure.core$load_lib$fn6493.invoke(core.clj:5888) at clojure.core$load_lib.invokeStatic(core.clj:5887) at clojure.core$load_lib.doInvoke(core.clj:5868) at clojure.lang.RestFn.applyTo(RestFn.java:142) at clojure.core$apply.invokeStatic(core.clj:659) at clojure.core$load_libs.invokeStatic(core.clj:5925) at clojure.core$load_libs.doInvoke(core.clj:5909) at clojure.lang.RestFn.applyTo(RestFn.java:137) at clojure.core$apply.invokeStatic(core.clj:659) at clojure.core$require.invokeStatic(core.clj:5947) at clojure.core$require.doInvoke(core.clj:5947) at clojure.lang.RestFn.invoke(RestFn.java:930) at cljplot.common$loading6721auto__14282.invoke(common.clj:1) at cljplot.commoninit.load(Unknown Source) at cljplot.commoninit.(Unknown Source) at java.lang.Class.forName0(Native Method) at java.lang.Class.forName(Class.java:348) at clojure.lang.RT.classForName(RT.java:2204) at clojure.lang.RT.classForName(RT.java:2213) at clojure.lang.RT.loadClassForName(RT.java:2232) at clojure.lang.RT.load(RT.java:450) at clojure.lang.RT.load(RT.java:426) at clojure.core$load$fn6548.invoke(core.clj:6046) at clojure.core$load.invokeStatic(core.clj:6045) at clojure.core$load.doInvoke(core.clj:6029) at clojure.lang.RestFn.invoke(RestFn.java:408) at clojure.core$load_one.invokeStatic(core.clj:5848) at clojure.core$load_one.invoke(core.clj:5843) at clojure.core$load_lib$fn6493.invoke(core.clj:5888) at clojure.core$load_lib.invokeStatic(core.clj:5887) at clojure.core$load_lib.doInvoke(core.clj:5868) at clojure.lang.RestFn.applyTo(RestFn.java:142) at clojure.core$apply.invokeStatic(core.clj:659) at clojure.core$load_libs.invokeStatic(core.clj:5925) at clojure.core$load_libs.doInvoke(core.clj:5909) at clojure.lang.RestFn.applyTo(RestFn.java:137) at clojure.core$apply.invokeStatic(core.clj:659) at clojure.core$require.invokeStatic(core.clj:5947) at clojure.core$require.doInvoke(core.clj:5947) at clojure.lang.RestFn.invoke(RestFn.java:1523) at cljplot.core$loading6721auto__9797.invoke(core.clj:1) at cljplot.coreinit.load(Unknown Source) at cljplot.coreinit.(Unknown Source) at java.lang.Class.forName0(Native Method) at java.lang.Class.forName(Class.java:348) at clojure.lang.RT.classForName(RT.java:2204) at clojure.lang.RT.classForName(RT.java:2213) at clojure.lang.RT.loadClassForName(RT.java:2232) at clojure.lang.RT.load(RT.java:450) at clojure.lang.RT.load(RT.java:426) at clojure.core$load$fn6548.invoke(core.clj:6046) at clojure.core$load.invokeStatic(core.clj:6045) at clojure.core$load.doInvoke(core.clj:6029) at clojure.lang.RestFn.invoke(RestFn.java:408) at clojure.core$load_one.invokeStatic(core.clj:5848) at clojure.core$load_one.invoke(core.clj:5843) at clojure.core$load_lib$fn__6493.invoke(core.clj:5888) at clojure.core$load_lib.invokeStatic(core.clj:5887) at clojure.core$load_lib.doInvoke(core.clj:5868) at clojure.lang.RestFn.applyTo(RestFn.java:142) at clojure.core$apply.invokeStatic(core.clj:659) at clojure.core$load_libs.invokeStatic(core.clj:5925) at clojure.core$load_libs.doInvoke(core.clj:5909) at clojure.lang.RestFn.applyTo(RestFn.java:137) at clojure.core$apply.invokeStatic(core.clj:659) at clojure.core$require.invokeStatic(core.clj:5947) at clojure.core$require.doInvoke(core.clj:5947) at clojure.lang.RestFn.invoke(RestFn.java:1289) at ppdsp.masking.data_fitting$loading6721auto__9573.invoke(data_fitting.cljc:1) at ppdsp.masking.data_fittinginit.load(Unknown Source) at ppdsp.masking.data_fittinginit.(Unknown Source) at java.lang.Class.forName0(Native Method) at java.lang.Class.forName(Class.java:348) at clojure.lang.RT.classForName(RT.java:2204) at clojure.lang.RT.classForName(RT.java:2213) at clojure.lang.RT.loadClassForName(RT.java:2232) at clojure.lang.RT.load(RT.java:450) at clojure.lang.RT.load(RT.java:426) at clojure.core$load$fn6548.invoke(core.clj:6046) at clojure.core$load.invokeStatic(core.clj:6045) at clojure.core$load.doInvoke(core.clj:6029) at clojure.lang.RestFn.invoke(RestFn.java:408) at clojure.core$load_one.invokeStatic(core.clj:5848) at clojure.core$load_one.invoke(core.clj:5843) at clojure.core$load_lib$fn6493.invoke(core.clj:5888) at clojure.core$load_lib.invokeStatic(core.clj:5887) at clojure.core$load_lib.doInvoke(core.clj:5868) at clojure.lang.RestFn.applyTo(RestFn.java:142) at clojure.core$apply.invokeStatic(core.clj:659) at clojure.core$load_libs.invokeStatic(core.clj:5925) at clojure.core$load_libs.doInvoke(core.clj:5909) at clojure.lang.RestFn.applyTo(RestFn.java:137) at clojure.core$apply.invokeStatic(core.clj:659) at clojure.core$require.invokeStatic(core.clj:5947) at clojure.core$require.doInvoke(core.clj:5947) at clojure.lang.RestFn.invoke(RestFn.java:930) at beaker_clojure_shell_5723778d_77a7_4224_a870_dd3f3dc5d4f4$eval1242.invokeStatic(Unknown Source) at beaker_clojure_shell_5723778d_77a7_4224_a870_dd3f3dc5d4f4$eval1242.invoke(Unknown Source) at clojure.lang.Compiler.eval(Compiler.java:7062) at clojure.lang.Compiler.load(Compiler.java:7514) at clojure.lang.Compiler.load(Compiler.java:7461) at clojure.core$load_reader.invokeStatic(core.clj:4053) at clojure.core$load_string.invokeStatic(core.clj:4055) at clojure.core$load_string.invoke(core.clj:4055) at beaker_clojure_shell_5723778d_77a7_4224_a870_dd3f3dc5d4f4$run_str_5723778d_77a7_4224_a870_dd3f3dc5d4f4.invokeStatic(Unknown Source) at beaker_clojure_shell_5723778d_77a7_4224_a870_dd3f3dc5d4f4$run_str_5723778d_77a7_4224_a870_dd3f3dc5d4f4.invoke(Unknown Source) at clojure.lang.Var.invoke(Var.java:381) at com.twosigma.beakerx.clojure.evaluator.ClojureEvaluator.runCode(ClojureEvaluator.java:168) at com.twosigma.beakerx.clojure.evaluator.ClojureCodeRunner.call(ClojureCodeRunner.java:47) at com.twosigma.beakerx.clojure.evaluator.ClojureCodeRunner.call(ClojureCodeRunner.java:28) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.lang.Thread.run(Thread.java:745)

Have someone faced a similar situation?

nighcoder commented 2 years ago

@whewage, I'm not sure that your problem has anything to do with Clojupyter. What code did you try to execute when it failed?

@genmeblog, does this sound familiar to you? Are you aware of any issues with using cljplot in Clojupyter?

genmeblog commented 2 years ago

Looks like it's not related to cljplot. Here is some hint: https://github.com/dm3/clojure.java-time/issues/37 You can try also to bump java-time to 0.3.3

btw. I want to recommend to update cljplot (https://clojars.org/cljplot/versions/0.0.2a-SNAPSHOT). Also, remove clojure2d and fastmath dependencies since cljplot will load them in proper versions.

krukow commented 8 months ago

Apologies for the late reply - I'm maintaining this in my spare time.

I've been looking into this and unfortunately I can no longer support installation via conda. Instead I recommend building the latest version locally via the following commands (requires clojure CLI and deps tools):

Build

Checkout this repo on the master branch and build an uberjar:

Building an uberjar:

clj -T:build uber

WARNING: parse-boolean already refers to: #'clojure.core/parse-boolean in namespace: omniconf.core, being replaced by: #'omniconf.core/parse-boolean
target/clojupyter-0.4.321-standalone.jar

Install kernel

clj -M -m clojupyter.cmdline install --jarfile target/clojupyter-0.4.321-standalone.jar --ident clojupyter-0.4.321

Verify:

clj -M -m clojupyter.cmdline list-installs

WARNING: parse-boolean already refers to: #'clojure.core/parse-boolean in namespace: omniconf.core, being replaced by: #'omniconf.core/parse-boolean
Clojupyter v0.4.321@321 - All Clojupyter kernels

    |              IDENT |                                          DIR |
    |--------------------+----------------------------------------------|
    | clojupyter-0.4.321 | ~/Library/Jupyter/kernels/clojupyter-0.4.321 |

exit(0)

Check that everything works

Install jupyterlab if you haven't already. On MacOS you might do:

brew install jupyterlab

Validate that it's working:

jupyter lab --version
4.0.9

Now you can try a console:

jupyter-console --kernel=clojupyter-0.4.321
WARNING: parse-boolean already refers to: #'clojure.core/parse-boolean in namespace: omniconf.core, being replaced by: #'omniconf.core/parse-boolean
Jupyter console 6.6.3

Clojupyter (0.4.321)

Or you can run in jupyter lab (from this repo):

jupyter lab

then open a file like: examples/demo-clojupyter.ipynb and run all cells.

Use clojupyter as a library as part of another program/library

You can also use this as a library - here's an example: https://github.com/krukow/edmondson