Loading minfi on MacOS

[mehmet-cay]

Hi, I installed minfi via Bioconductor, then I try to import it via library("minfi") command, but it did not work.

this is the error I get: Loading required package: bumphunter Loading required package: locfit locfit 1.5-9.9 2024-03-01

caught segfault address 0x600000020, cause 'invalid permissions'

Traceback: 1: H5Pcreate("H5P_FILE_ACCESS") 2: H5Fcreate(file) 3: h5createFile(filepath) 4: .get_dump_autofile() 5: setHDF5DumpDir() 6: fun(libname, pkgname) 7: doTryCatch(return(expr), name, parentenv, handler) 8: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 9: tryCatchList(expr, classes, parentenv, handlers) 10: tryCatch(fun(libname, pkgname), error = identity) 11: runHook(".onLoad", env, package.lib, package) 12: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) 13: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package) 14: loadNamespace(package, lib.loc) 15: doTryCatch(return(expr), name, parentenv, handler) 16: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 17: tryCatchList(expr, classes, parentenv, handlers) 18: 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 && !quietly) message(paste("Error:", msg), domain = NA) else stop(msg, call. = FALSE, domain = NA)}) 19: library(minfi)

Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace can you solve this?

What is wrong with it, normally I was using it without error, after this error, I deleted R studio, R and all related files then I reinstalled everything, even though that I am still getting same error.

I also get this error in DMRCate package but not other packages, what is common thing? What is the solution of it?

[PeteHaitch]

This appears to be an issue with the HDF5Array package. Can you please start a new R session, run library(HDF5Array), and report the results.

[mehmet-cay]

Hi, The result is attached. I am looking forward for your answer

[mehmet-cay]

When I run library(HDF5Array) command, it says R session is aborted, then restart R Studio

[kasperdanielhansen]

So that sounds like an HDF5Array problem.

I would start by reinstalling the package.

On Fri, Apr 19, 2024 at 6:06 AM Mehmet ÇAY @.***> wrote:

When I run library(HDF5Array) command, it says R session is aborted, then restart R Studio

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[mehmet-cay]

Okey I'll try it,then I will inform you

[mehmet-cay]

Hi, It says R session is aborted when I call HDF5Array package (even after I removed and reinstalled package)

[kasperdanielhansen]

This seems like an HDF5Array issue and I am not sure I can help further.