Ashim Kapoor
2021-Apr-07 08:16 UTC
[R] R does not start from (Debian) linux command line - error with doWithOneRestart() - segmentation fault
On Wed, Apr 7, 2021 at 12:51 PM Martin Maechler <maechler at stat.math.ethz.ch> wrote:> > >>>>> 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. >My apologies for not being clear. I would like to clarify : 1. The error message from the incantation `R` is not very informative. 2. The error message from the incantation `sudo R` says (among other things which don't seem significant to me): Error in doWithOneRestart(return(` \\x82\\x0ccPV`), restart) : not a proper file name 3. The error message from invoking R as a root user says: Error: not a proper file name Fatal error: unable to initialize the JIT I found this on the internet : https://stackoverflow.com/questions/19512165/error-in-dowithonerestart The error messages and the above link point to issues with JAVA, but it does not say how to fix them. That is why I thought : there is an .xlsx file which has non english characters which is messing with Java. Query : is there a way to do JAVA garbage collection when R is not starting ?> 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 ? >We upgraded to 4.0.5 but it did not make a difference. We restarted the computer and that fixed the error. I think the JAVA garbage collection kicked in when we reset the computer and that is why it was fixed on rebooting. Not sure though.> 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. >Thank you for this.> 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.
Henrik Bengtsson
2021-Apr-08 16:28 UTC
[R] R does not start from (Debian) linux command line - error with doWithOneRestart() - segmentation fault
Ashim, as Martin says, there's something really weird going on with your core R installation. This is definitely not expected, and I don't know think if I've every seen this reported before. Here are some questions/comments that might help you move forward and for others to pitch in: 1. How did you install R? 2. What happens if you call: $ Rscript --vanilla -e "1+2" 3. What happens if you call: $ Rscript --vanilla --default-packages=base -e "1+2" 4. What happens if you call: $ Rscript --vanilla --default-packages=base,methods -e "1+2" If any of 2-4 gives a different result, that's a first clue. /Henrik On Wed, Apr 7, 2021 at 1:17 AM Ashim Kapoor <ashimkapoor at gmail.com> wrote:> > On Wed, Apr 7, 2021 at 12:51 PM Martin Maechler > <maechler at stat.math.ethz.ch> wrote: > > > > >>>>> 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. > > > > My apologies for not being clear. > > I would like to clarify : > > 1. The error message from the incantation `R` is not very informative. > > 2. The error message from the incantation `sudo R` says (among other > things which don't seem significant to me): > Error in doWithOneRestart(return(` \\x82\\x0ccPV`), restart) : > not a proper file name > > 3. The error message from invoking R as a root user says: > > Error: not a proper file name > Fatal error: unable to initialize the JIT > > I found this on the internet : > https://stackoverflow.com/questions/19512165/error-in-dowithonerestart > > The error messages and the above link point to issues with JAVA, but > it does not say how to fix them. > > That is why I thought : there is an .xlsx file which has non english > characters which is messing with > Java. > > Query : is there a way to do JAVA garbage collection when R is not starting ? > > > 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 ? > > > > We upgraded to 4.0.5 but it did not make a difference. We restarted > the computer and that fixed the error. > I think the JAVA garbage collection kicked in when we reset the > computer and that is why it was fixed on rebooting. Not sure though. > > > 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. > > > > Thank you for this. > > > 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. > > ______________________________________________ > 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.