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
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