I had a stablize version of ananconda distribution installed on my Macbook (OS 10.15) for years.
I mainly program in Python 3 so everything was working smoothly.
However, today I followed the instructions on anacondo's website to install R (see here)
Once I completed the instructions on anacondo's website to install R I attempted to Open the environment with the R package using the Open with Jupyter Notebook option. as instructed in the link above.
When I do that I get the following error:
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The default interactive shell is now zsh.
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/Users/mycomputer/.anaconda/navigator/a.tool ; exit;
(base) mycomputers-MacBook-Air:~ mycomputer$ /Users/mycomputer/.anaconda/navigator/a.tool ; exit;
[W 11:29:35.377 NotebookApp] Error loading server extension jupyterlab
Traceback (most recent call last):
File "/Users/mycomputer/anaconda/envs/R_environment/lib/python3.6/site-packages/notebook/notebookapp.py", line 1271, in init_server_extensions
mod = importlib.import_module(modulename)
File "/Users/mycomputer/anaconda/envs/R_environment/lib/python3.6/importlib/__init__.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 978, in _gcd_import
File "<frozen importlib._bootstrap>", line 961, in _find_and_load
File "<frozen importlib._bootstrap>", line 948, in _find_and_load_unlocked
ModuleNotFoundError: No module named 'jupyterlab'
[I 11:29:35.390 NotebookApp] Serving notebooks from local directory: /Users/mycomputer
[I 11:29:35.390 NotebookApp] 0 active kernels
[I 11:29:35.390 NotebookApp] The Jupyter Notebook is running at: http://localhost:8888/?token=b0bbdfcb5934081d376514f0d5f68ff0eab87b935d557dce
The notebook server seems to launch.
So I click new to create a new notebook and select R as the language. It opens and in the first cell I type in library(ggplot2) and I try to execute the cell. I immediately get a kernal has died error.
The console tracebook is as follows:
*** caught segfault ***
address 0x10, cause 'memory not mapped'
Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
4: asNamespace(ns)
5: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
6: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
7: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
8: loadNamespace(package, lib.loc)
9: doTryCatch(return(expr), name, parentenv, handler)
10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
11: tryCatchList(expr, classes, parentenv, handlers)
12: tryCatch({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps)}, error = function(e) { P <- if (!is.null(cc <- conditionCall(e))) paste(" in", deparse(cc)[1L]) else "" msg <- gettextf("package or namespace load failed for %s%s:\n %s", sQuote(package), P, conditionMessage(e)) if (logical.return) message(paste("Error:", msg), domain = NA) else stop(msg, call. = FALSE, domain = NA)})
13: library(ggplot2)
14: eval(expr, envir, enclos)
15: eval(expr, envir, enclos)
16: withVisible(eval(expr, envir, enclos))
17: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
18: doTryCatch(return(expr), name, parentenv, handler)
19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
20: tryCatchList(expr, classes, parentenv, handlers)
21: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L msg <- conditionMessage(e) sm <- strsplit(msg, "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
22: try(f, silent = TRUE)
23: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
24: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
25: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing)
26: evaluate(request$content$code, envir = .GlobalEnv, output_handler = oh, stop_on_error = 1L)
27: doTryCatch(return(expr), name, parentenv, handler)
28: tryCatchOne(expr, names, parentenv, handlers[[1L]])
29: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
30: doTryCatch(return(expr), name, parentenv, handler)
31: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
32: tryCatchList(expr, classes, parentenv, handlers)
33: tryCatch(evaluate(request$content$code, envir = .GlobalEnv, output_handler = oh, stop_on_error = 1L), interrupt = function(cond) interrupted <<- TRUE, error = .self$handle_error)
34: executor$execute(msg)
35: handle_shell()
36: kernel$run()
37: IRkernel::main()
An irrecoverable exception occurred. R is aborting now ...
I then load up an existing python 3 notebook and attempt to run the first cell which has import numpy as np in it and I get the following error:
ModuleNotFoundError Traceback (most recent call last)
<ipython-input-2-2c671b621757> in <module>()
----> 1 import numpy as np
When I launch the jupyter notebook from the command line rather than from within Ananconda-Navigator the notebook launches fine without any errors HOWEVER when I click new to create new notebook it does NOT have R as an option. It only has R as an option when I launch the jupyter notebook from within the Ananconda-Navigator from the R environment I created.
Finally, the Ananconda-Navigator application icon fails to load HOWEVER, I can launch it from the command line via anaconda-navigator command.
So clearly, the installation of R environment described on anaconda's website has messed everything up.
I even re-installed ananconda python on top of everything I had to see if that would clear up any of the problems. Nope - same thing.
I downloaded Rstudio directly and tried to launch it - and I got the following error:
Unable to locate `R` binary by scanning standard locations.
How can the RStudio app NOT find what it just installed? Bizarre?
Does anyone have any ideas what is going on and how do I fix the various issues that are present?
