RGL issue

[PCK1992]

Hi,

I've got a new computer and installed the package from scratch - unfortunately, I can't get it to run despite following the instructions.

This is the error message that I get:

conda environment r-reticulate installed

 *** caught segfault ***
address 0x10, cause 'memory not mapped'

Traceback:
 1: py_module_import(module, convert = convert)
 2: import(module)
 3: doTryCatch(return(expr), name, parentenv, handler)
 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5: tryCatchList(expr, classes, parentenv, handlers)
 6: tryCatch({    import(module)    TRUE}, error = clear_error_handler(FALSE))
 7: reticulate::py_module_available("umap")
 8: install_python_modules()
 9: eval(expr, pf)
10: eval(expr, pf)
11: withVisible(eval(expr, pf))
12: evalVis(expr)
13: capture.output(expr, file = file)
14: withCallingHandlers(expr, packageStartupMessage = function(c) tryInvokeRestart("muffleMessage"))
15: suppressPackageStartupMessages(capture.output(expr, file = file))
16: withCallingHandlers(expr, message = function(c) if (inherits(c,     classes)) tryInvokeRestart("muffleMessage"))
17: suppressMessages(suppressPackageStartupMessages(capture.output(expr,     file = file)))
18: withCallingHandlers(expr, warning = function(w) if (inherits(w,     classes)) tryInvokeRestart("muffleWarning"))
19: suppressWarnings(suppressMessages(suppressPackageStartupMessages(capture.output(expr,     file = file))))
20: quiet(install_python_modules())
21: doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: tryCatch({    if (reticulate::py_available() || sum("r-reticulate" == reticulate::conda_list()$name) >=         1) {        install_python_modules <- function(method = "auto", conda = "auto") {            if (!is.null(reticulate::conda_binary())) {                reticulate::use_python(reticulate::conda_python())                if (!("r-reticulate" %in% reticulate::conda_list()$name)) {                  reticulate::conda_create(envname = "r-reticulate",                     )                  if (!reticulate::py_module_available("conda"))                     reticulate::conda_install(envname = "r-reticulate",                       packages = "conda")                }                suppressWarnings(suppressMessages(reticulate::use_condaenv("r-reticulate")))                if (.Platform$OS.type == "windows") {                  install.packages("devtools", quiet = TRUE)                  devtools::install_github("rstudio/reticulate",                     ref = "86ebb56", quiet = TRUE)                  if (!reticulate::py_module_available("numpy"))                     suppressWarnings(suppressMessages(reticulate::conda_install(envname = "r-reticulate",                       packages = "numpy")))                  if (!reticulate::py_module_available("pandas"))                     suppressWarnings(suppressMessages(reticulate::conda_install(envname = "r-reticulate",                       packages = "pandas")))                  if (!reticulate::py_module_available("igraph"))                     suppressWarnings(suppressMessages(reticulate::conda_install(envname = "r-reticulate",                       packages = "python-igraph")))                  if (!reticulate::py_module_available("mkl"))                     suppressWarnings(suppressMessages(reticulate::conda_install(envname = "r-reticulate",                       packages = "mkl", channel = "intel")))                  if (!reticulate::py_module_available("umap"))                     suppressWarnings(suppressMessages(reticulate::conda_install(envname = "r-reticulate",                       packages = "umap-learn", channel = "conda-forge")))                  if (!reticulate::py_module_available("leidenalg"))                     suppressWarnings(suppressMessages(reticulate::conda_install(envname = "r-reticulate",                       packages = "leidenalg", channel = "conda-forge")))                  install.packages("reticulate", quiet = TRUE)                  if (!reticulate::py_module_available("leidenalg"))                     suppressWarnings(suppressMessages(reticulate::conda_install(envname = "r-reticulate",                       packages = "leidenalg")))                  utils::install.packages("reticulate", quiet = TRUE)                }                else {                  if (!reticulate::py_module_available("numpy"))                     suppressWarnings(suppressMessages(reticulate::conda_install("r-reticulate",                       "numpy")))                  if (!reticulate::py_module_available("pandas"))                     suppressWarnings(suppressMessages(reticulate::conda_install("r-reticulate",                       "pandas")))                  if (!reticulate::py_module_available("igraph"))                     suppressWarnings(suppressMessages(reticulate::conda_install("r-reticulate",                       "python-igraph")))                  if (!reticulate::py_module_available("umap"))                     suppressWarnings(suppressMessages(reticulate::conda_install("r-reticulate",                       "umap-learn", forge = TRUE)))                  if (!reticulate::py_module_available("leidenalg"))                     suppressWarnings(suppressMessages(reticulate::conda_install("r-reticulate",                       "leidenalg", forge = TRUE)))                  Sys.setenv(RETICULATE_PYTHON = reticulate::conda_python())                }            }            else {                if (!reticulate::py_module_available("numpy"))                   suppressWarnings(suppressMessages(reticulate::py_install("numpy")))                if (!reticulate::py_module_available("pandas"))                   suppressWarnings(suppressMessages(reticulate::py_install("pandas")))                if (!reticulate::py_module_available("igraph"))                   suppressWarnings(suppressMessages(reticulate::py_install("python-igraph",                     method = method, conda = conda)))                if (!reticulate::py_module_available("umap"))                   suppressWarnings(suppressMessages(reticulate::py_install("umap-learn")))                if (!reticulate::py_module_available("leidenalg"))                   suppressWarnings(suppressMessages(reticulate::py_install("leidenalg",                     method = method, conda = conda, forge = TRUE)))                Sys.setenv(RETICULATE_PYTHON = reticulate::py_config()$python)            }        }        quiet <- function(expr, all = TRUE) {            if (Sys.info()["sysname"] == "Windows") {                file <- "NUL"            }            else {                file <- "/dev/null"            }            if (all) {                suppressWarnings(suppressMessages(suppressPackageStartupMessages(capture.output(expr,                   file = file))))            }            else {                capture.output(expr, file = file)            }        }        quiet(install_python_modules())    }}, error = function(e) {    packageStartupMessage("Unable to install python modules igraph and leidenalg")    packageStartupMessage("run in terminal:")    packageStartupMessage("conda install -n r-reticulate -c conda-forge vtraag python-igraph pandas umap learn")}, finally = packageStartupMessage("python modules igraph and leidenalg installed"))
25: fun(libname, pkgname)
26: doTryCatch(return(expr), name, parentenv, handler)
27: tryCatchOne(expr, names, parentenv, handlers[[1L]])
28: tryCatchList(expr, classes, parentenv, handlers)
29: tryCatch(fun(libname, pkgname), error = identity)
30: runHook(".onAttach", ns, dirname(nspath), nsname)
31: attachNamespace(ns, pos = pos, deps, exclude, include.only)
32: doTryCatch(return(expr), name, parentenv, handler)
33: tryCatchOne(expr, names, parentenv, handlers[[1L]])
34: tryCatchList(expr, classes, parentenv, handlers)
35: tryCatch({    attr(package, "LibPath") <- which.lib.loc    ns <- loadNamespace(package, lib.loc)    env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)}, 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)})
36: library(leiden)

Possible actions:

Any idea what could be the issue here? Older versions of the the package worked flawlessly for me.

[PCK1992]

I was able to isolate the problem - it seems like it doesn't work well with the rgl package. If I don't load that part of the script the error does not appear. So I'm not sure if this is a Leiden problem or a rgl problem. I would still appreciate it if you have any input on how to solve this issue!

[TomKellyGenetics]

Thanks for reporting this. It seems to be an issue with installing dependencies in a conda environment. I'm a little confused by this since it has been over a year since significant changes were released on CRAN. It should not be different to when you installed it previously unless it was a long time ago.