install error
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remotes::install_github("liamrevell/phytools")
Downloading GitHub repo liamrevell/phytools@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?
1: All
2: CRAN packages only
3: None
4: cpp11 (0.4.2 -> 0.4.6 ) [CRAN]
5: rlang (1.1.0 -> 1.1.1 ) [CRAN]
6: cli (3.4.1 -> 3.6.1 ) [CRAN]
7: digest (0.6.29 -> 0.6.33 ) [CRAN]
8: Rcpp (1.0.10 -> 1.0.11 ) [CRAN]
9: igraph (1.3.5 -> 1.5.1 ) [CRAN]
10: fastmatch (1.1-3 -> 1.1-4 ) [CRAN]
11: scatterpl... (0.3-43 -> 0.3-44 ) [CRAN]
12: phangorn (2.9.0 -> 2.11.1 ) [CRAN]
13: expm (0.999-6 -> 0.999-7) [CRAN]
14: maps (3.4.0 -> 3.4.1 ) [CRAN]
Enter one or more numbers, or an empty line to skip updates:
✔ checking for file ‘/tmp/RtmpBiYxcw/remotes323cd4c8706c1/liamrevell-phytools-d2e7481/DESCRIPTION’ (369ms)
─ preparing ‘phytools’:
✔ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ looking to see if a ‘data/datalist’ file should be added
─ building ‘phytools_1.9-23.tar.gz’
Installing package into ‘/home/wanggl/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
- installing source package ‘phytools’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
sh: line 1: 207081 Segmentation fault R_TESTS= '/opt/R/4.3.0/lib/R/bin/R' --no-save --no-restore --no-echo 2>&1 < '/tmp/RtmpLBSETc/file328b2249a71d6'
*** caught segfault ***
address 0x20, cause 'memory not mapped'
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 = "Fitch_mod", what = TRUE, env = ns, loadNow = TRUE)
7: (function (ns) loadModule(module = "Fitch_mod", 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 = "Fitch_mod", 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(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
17: asNamespace(ns)
18: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
19: loadNamespace(package = package, lib.loc = lib.loc, keep.source = keep.source, keep.parse.data = keep.parse.data, partial = TRUE)
20: withCallingHandlers(expr, packageStartupMessage = function(c) tryInvokeRestart("muffleMessage"))
21: suppressPackageStartupMessages(loadNamespace(package = package, lib.loc = lib.loc, keep.source = keep.source, keep.parse.data = keep.parse.data, partial = TRUE))
22: code2LazyLoadDB(package, lib.loc = lib.loc, keep.source = keep.source, keep.parse.data = keep.parse.data, compress = compress, set.install.dir = set.install.dir)
23: tools:::makeLazyLoading("phytools", "/home/wanggl/R/x86_64-pc-linux-gnu-library/4.2/00LOCK-phytools/00new", keep.source = FALSE, keep.parse.data = FALSE, set.install.dir = "/home/wanggl/R/x86_64-pc-linux-gnu-library/4.2/phytools")
**An irrecoverable exception occurred. R is aborting now ...
ERROR: lazy loading failed for package ‘phytools’
- removing ‘/home/wanggl/R/x86_64-pc-linux-gnu-library/4.2/phytools’
Warning message:
In i.p(...) :
installation of package ‘/tmp/RtmpBiYxcw/file323cd53ad1693/phytools_1.9-23.tar.gz’ had non-zero exit status**
Today remotes::install_github("liamrevell/phytools") seems to be working. Please let me know if this continues to be a problem for you & I can re-open the issue.