smorabit
commented
3 months ago Hi,
I am sorry to hear that you are having problems installing hdWGCNA. I have personally never encountered this issue and I do not believe any user has reported this issue before. Are you using the recommended installation instructions?
Hi,
I am trying to install hdWGCNA on my macOS 10.15.7. I am using R version 4.2.2. While installing,
sh: line 1: 20681 Segmentation fault: 11 R_TESTS= '/Library/Frameworks/R.framework/Resources/bin/R' --no-save --no-restore --no-echo 2>&1 < '/var/folders/zk/2fw0xn4j2y35sfh8w72ckb99y89vh3/T//Rtmpo9qAtM/file50bf5f8e06d'
caught segfault address 0x0, cause 'unknown'
Traceback: 1: Module(module, mustStart = TRUE, where = env) 2: doTryCatch(return(expr), name, parentenv, handler) 3: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 4: tryCatchList(expr, classes, parentenv, handlers) 5: tryCatch(Module(module, mustStart = TRUE, where = env), error = function(e) e) 6: loadModule(module = "harmony_module", what = TRUE, env = ns, loadNow = TRUE) 7: (function (ns) loadModule(module = "harmony_module", what = TRUE, env = ns, loadNow = TRUE))()
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch((function (ns) loadModule(module = "harmony_module", what = TRUE, env = ns, loadNow = TRUE))(), error = function(e) e)
12: eval(substitute(tryCatch(FUN(WHERE), error = function(e) e), list(FUN = f, WHERE = where)), where)
13: eval(substitute(tryCatch(FUN(WHERE), error = function(e) e), list(FUN = f, WHERE = where)), where)
14: .doLoadActions(where, attach)
15: methods::cacheMetaData(ns, TRUE, ns)
16: loadNamespace(package, lib.loc)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: 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)})
21: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc, quietly = quietly)
22: .getRequiredPackages2(pkgInfo, quietly, lib.loc, useImports)
23: .getRequiredPackages(quietly = TRUE)
24: withCallingHandlers(expr, packageStartupMessage = function(c) tryInvokeRestart("muffleMessage"))
25: suppressPackageStartupMessages(.getRequiredPackages(quietly = TRUE))
An irrecoverable exception occurred. R is aborting now ...
ERROR: lazy loading failed for package ‘hdWGCNA’
sessionInfo() R version 4.2.3 (2023-03-15) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Catalina 10.15.7
Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages: [1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached): [1] Rcpp_1.0.12 magrittr_2.0.3 usethis_2.2.2 devtools_2.4.5
[5] pkgload_1.3.3 xtable_1.8-4 R6_2.5.1 rlang_1.1.3
[9] fastmap_1.1.1 urlchecker_1.0.1 stringr_1.5.1 tools_4.2.3
[13] pkgbuild_1.4.3 sessioninfo_1.2.2 miniUI_0.1.1.1 cli_3.6.2
[17] remotes_2.4.2.1 htmltools_0.5.7 ellipsis_0.3.2 digest_0.6.34
[21] lifecycle_1.0.4 processx_3.8.3 shiny_1.8.0 callr_3.7.3
[25] purrr_1.0.2 later_1.3.2 ps_1.7.5 profvis_0.3.8
[29] htmlwidgets_1.6.4 vctrs_0.6.5 fs_1.6.3 promises_1.2.1
[33] curl_5.2.0 memoise_2.0.1 glue_1.7.0 cachem_1.0.8
[37] mime_0.12 stringi_1.8.3 compiler_4.2.3 desc_1.4.3
[41] httpuv_1.6.13
I am not sure where it is going wrong. Could you please help me to fix this issue?
Many thanks, Anbarasu