Ashim Kapoor
2021-Apr-07 05:05 UTC
[R] R does not start from (Debian) linux command line - error with doWithOneRestart() - segmentation fault
Dear R experts, Here is my problem : R startup FAILS with an error message. The error message is more meaningful when I do invoke R via sudo OR as root. I attach the startup messages when I invoke R as : 1. as non root user 2. with sudo 3. as Root user. The error messages ( mentioned in snippets below ) are more meaningful to me in the above mentioned order. When I google around for the error message, it looks like there is an .xlsx file which has non english characters which is messing with Java. I do not know how to fix this. I tried :- R --vanilla so that it would not use any startup scripts but that also does not work. ----------------- snip ---------------------------------------------------------------------------------------------------------------------------- When I try to start R from the command line : ~$ R *** caught segfault *** address (nil), cause 'unknown' Traceback: 1: NextMethod(.Generic) 2: Ops.numeric_version(R_version_built_under, "3.0.0") 3: testRversion(pkgInfo, package, pkgpath) 4: library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, warn.conflicts = warn.conflicts, quietly quietly, mask.ok = mask.ok, exclude = exclude, include.only include.only, attach.required = attach.required) 5: doTryCatch(return(expr), name, parentenv, handler) 6: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 7: tryCatchList(expr, classes, parentenv, handlers) 8: tryCatch(library(package, lib.loc = lib.loc, character.only TRUE, logical.return = TRUE, warn.conflicts = warn.conflicts, quietly = quietly, mask.ok = mask.ok, exclude = exclude, include.only = include.only, attach.required = attach.required), error = function(e) e) 9: require(pkg, quietly = TRUE, warn.conflicts = FALSE, character.only = TRUE) 10: .OptRequireMethods() Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Selection: Segmentation fault ----------------- snip ---------------------------------------------------------------------------------------------------------------------------- When I try to start R with sudo it gives a more clear message :- ~$ sudo R *** caught segfault *** address (nil), cause 'unknown' Traceback: 1: NextMethod(.Generic) 2: Ops.numeric_version(R_version_built_under, "3.0.0") 3: testRversion(pkgInfo, package, pkgpath) 4: library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, warn.conflicts = warn.conflicts, quietly quietly, mask.ok = mask.ok, exclude = exclude, include.only include.only, attach.required = attach.required) 5: doTryCatch(return(expr), name, parentenv, handler) 6: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 7: tryCatchList(expr, classes, parentenv, handlers) 8: tryCatch(library(package, lib.loc = lib.loc, character.only TRUE, logical.return = TRUE, warn.conflicts = warn.conflicts, quietly = quietly, mask.ok = mask.ok, exclude = exclude, include.only = include.only, attach.required = attach.required), error = function(e) e) 9: require(pkg, quietly = TRUE, warn.conflicts = FALSE, character.only = TRUE) 10: .OptRequireMethods() Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Selection: Error in doWithOneRestart(return(` \\x82\\x0ccPV`), restart) : not a proper file name R version 3.6.3 (2020-02-29) -- "Holding the Windsock" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. Error: not a proper file name Error in doWithOneRestart(return(` \\x82\\x0ccPV`), restart) : promise already under evaluation: recursive default argument reference or earlier problems? Segmentation fault ----------------- snip ---------------------------------------------------------------------------------------------------------------------------- Invoking R as a root user :- $ sudo -i root at crayshrimp ~ # R *** caught segfault *** address (nil), cause 'unknown' Traceback: 1: NextMethod(.Generic) 2: Ops.numeric_version(R_version_built_under, "3.0.0") 3: testRversion(pkgInfo, package, pkgpath) 4: library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, warn.conflicts = warn.conflicts, quietly quietly, mask.ok = mask.ok, exclude = exclude, include.only include.only, attach.required = attach.required) 5: doTryCatch(return(expr), name, parentenv, handler) 6: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 7: tryCatchList(expr, classes, parentenv, handlers) 8: tryCatch(library(package, lib.loc = lib.loc, character.only TRUE, logical.return = TRUE, warn.conflicts = warn.conflicts, quietly = quietly, mask.ok = mask.ok, exclude = exclude, include.only = include.only, attach.required = attach.required), error = function(e) e) 9: require(pkg, quietly = TRUE, warn.conflicts = FALSE, character.only = TRUE) 10: .OptRequireMethods() Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Selection: Error in doWithOneRestart(return(), restart) : not a proper file name R version 3.6.3 (2020-02-29) -- "Holding the Windsock" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. Error: not a proper file name Error in doWithOneRestart(return(), restart) : promise already under evaluation: recursive default argument reference or earlier problems? Error in tryCatchOne(, names, parentenv, handlers[[1L]]) : promise already under evaluation: recursive default argument reference or earlier problems? Error: not a proper file name Fatal error: unable to initialize the JIT ----------------- snip ---------------------------------------------------------------------------------------------------------------------------- Thank you, Ashim
Martin Maechler
2021-Apr-07 07:21 UTC
[R] R does not start from (Debian) linux command line - error with doWithOneRestart() - segmentation fault
>>>>> Ashim Kapoor >>>>> on Wed, 7 Apr 2021 10:35:14 +0530 writes:> Dear R experts, > Here is my problem : > R startup FAILS with an error message. The error message > is more meaningful when I do invoke R via sudo OR as > root. I attach the startup messages when I invoke R as : > 1. as non root user 2. with sudo 3. as Root user. > The error messages ( mentioned in snippets below ) are > more meaningful to me in the above mentioned order. Thank you, Ashim. Yes, the messages point to something really bad. OTOH ("On the other hand"), what we *can* see is that you try to start R version 3.6.3. While that is not extremely old, it may well be older than several other pieces of software (or even hardware) that you are running with. I very very *strongly* recommend to use an R version 4.0.x ... and why not use the latest 4.0.5 ? Then, it may also be caused by a mismatch of system libraries and your oldish version of R. ... but there I'd strongly recommend consulting with other Debian users, notably as there is a dedicated mailing list R-SIG-Debian --> do subscribe there, and ask -- with more details on how you got your R: Is it the default R on your Debian, which version of Debian, etc. Last but not least, Dirk Eddelbuettel, the maintainer of the official R Debian package maintains a nice web page -- part of the official CRAN web pages, but unfortunately a bit hidden nowadays, (not the least because CRAN still uses frames (w?rg!!)): https://cloud.r-project.org/bin/linux/debian/ A very nice and useful page, much underrated and underused, probably. Best regards, Martin Maechler ETH Zurich and R Core Team > When I google around for the error message, it looks like > there is an .xlsx file which has non english characters > which is messing with Java. > I do not know how to fix this. I tried :- > R --vanilla > so that it would not use any startup scripts but that also > does not work. > ----------------- snip > ---------------------------------------------------------------------------------------------------------------------------- > When I try to start R from the command line : > ~$ R > *** caught segfault *** address (nil), cause 'unknown' > Traceback: 1: NextMethod(.Generic) 2: > Ops.numeric_version(R_version_built_under, "3.0.0") 3: > testRversion(pkgInfo, package, pkgpath) 4: > library(package, lib.loc = lib.loc, character.only = TRUE, > logical.return = TRUE, warn.conflicts = warn.conflicts, > quietly = quietly, mask.ok = mask.ok, exclude = exclude, > include.only = include.only, attach.required > attach.required) 5: doTryCatch(return(expr), name, > parentenv, handler) 6: tryCatchOne(expr, names, parentenv, > handlers[[1L]]) 7: tryCatchList(expr, classes, parentenv, > handlers) 8: tryCatch(library(package, lib.loc = lib.loc, > character.only = TRUE, logical.return = TRUE, > warn.conflicts = warn.conflicts, quietly = quietly, > mask.ok = mask.ok, exclude = exclude, include.only > include.only, attach.required = attach.required), error > function(e) e) 9: require(pkg, quietly = TRUE, > warn.conflicts = FALSE, character.only = TRUE) 10: > .OptRequireMethods() > Possible actions: 1: abort (with core dump, if enabled) 2: > normal R exit 3: exit R without saving workspace 4: exit R > saving workspace Selection: Segmentation fault > ----------------- snip > ---------------------------------------------------------------------------------------------------------------------------- > When I try to start R with sudo it gives a more clear > message :- > ~$ sudo R > *** caught segfault *** address (nil), cause 'unknown' > Traceback: 1: NextMethod(.Generic) 2: > Ops.numeric_version(R_version_built_under, "3.0.0") 3: > testRversion(pkgInfo, package, pkgpath) 4: > library(package, lib.loc = lib.loc, character.only = TRUE, > logical.return = TRUE, warn.conflicts = warn.conflicts, > quietly = quietly, mask.ok = mask.ok, exclude = exclude, > include.only = include.only, attach.required > attach.required) 5: doTryCatch(return(expr), name, > parentenv, handler) 6: tryCatchOne(expr, names, parentenv, > handlers[[1L]]) 7: tryCatchList(expr, classes, parentenv, > handlers) 8: tryCatch(library(package, lib.loc = lib.loc, > character.only = TRUE, logical.return = TRUE, > warn.conflicts = warn.conflicts, quietly = quietly, > mask.ok = mask.ok, exclude = exclude, include.only > include.only, attach.required = attach.required), error > function(e) e) 9: require(pkg, quietly = TRUE, > warn.conflicts = FALSE, character.only = TRUE) 10: > .OptRequireMethods() > Possible actions: 1: abort (with core dump, if enabled) 2: > normal R exit 3: exit R without saving workspace 4: exit R > saving workspace Selection: Error in > doWithOneRestart(return(` \\x82\\x0ccPV`), restart) : not > a proper file name > R version 3.6.3 (2020-02-29) -- "Holding the Windsock" > Copyright (C) 2020 The R Foundation for Statistical > Computing Platform: x86_64-pc-linux-gnu (64-bit) > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain > conditions. Type 'license()' or 'licence()' for > distribution details. > Natural language support but running in an English > locale > R is a collaborative project with many contributors. Type > 'contributors()' for more information and 'citation()' on > how to cite R or R packages in publications. > Type 'demo()' for some demos, 'help()' for on-line help, > or 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > Error: not a proper file name Error in > doWithOneRestart(return(` \\x82\\x0ccPV`), restart) : > promise already under evaluation: recursive default > argument reference or earlier problems? Segmentation > fault > ----------------- snip > ---------------------------------------------------------------------------------------------------------------------------- > Invoking R as a root user :- > $ sudo -i root at crayshrimp ~ # R > *** caught segfault *** address (nil), cause 'unknown' > Traceback: 1: NextMethod(.Generic) 2: > Ops.numeric_version(R_version_built_under, "3.0.0") 3: > testRversion(pkgInfo, package, pkgpath) 4: > library(package, lib.loc = lib.loc, character.only = TRUE, > logical.return = TRUE, warn.conflicts = warn.conflicts, > quietly = quietly, mask.ok = mask.ok, exclude = exclude, > include.only = include.only, attach.required > attach.required) 5: doTryCatch(return(expr), name, > parentenv, handler) 6: tryCatchOne(expr, names, parentenv, > handlers[[1L]]) 7: tryCatchList(expr, classes, parentenv, > handlers) 8: tryCatch(library(package, lib.loc = lib.loc, > character.only = TRUE, logical.return = TRUE, > warn.conflicts = warn.conflicts, quietly = quietly, > mask.ok = mask.ok, exclude = exclude, include.only > include.only, attach.required = attach.required), error > function(e) e) 9: require(pkg, quietly = TRUE, > warn.conflicts = FALSE, character.only = TRUE) 10: > .OptRequireMethods() > Possible actions: 1: abort (with core dump, if enabled) 2: > normal R exit 3: exit R without saving workspace 4: exit R > saving workspace Selection: Error in > doWithOneRestart(return(), restart) : not a proper file > name > R version 3.6.3 (2020-02-29) -- "Holding the Windsock" > Copyright (C) 2020 The R Foundation for Statistical > Computing Platform: x86_64-pc-linux-gnu (64-bit) > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain > conditions. Type 'license()' or 'licence()' for > distribution details. > Natural language support but running in an English > locale > R is a collaborative project with many contributors. Type > 'contributors()' for more information and 'citation()' on > how to cite R or R packages in publications. > Type 'demo()' for some demos, 'help()' for on-line help, > or 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > Error: not a proper file name Error in > doWithOneRestart(return(), restart) : promise already > under evaluation: recursive default argument reference or > earlier problems? Error in tryCatchOne(, names, > parentenv, handlers[[1L]]) : promise already under > evaluation: recursive default argument reference or > earlier problems? Error: not a proper file name Fatal > error: unable to initialize the JIT > ----------------- snip > ---------------------------------------------------------------------------------------------------------------------------- > Thank you, Ashim > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and > more, see https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html and provide > commented, minimal, self-contained, reproducible code.