[R] R does not start from (Debian) linux command line - error with doWithOneRestart() - segmentation fault
Ashim Kapoor
@@h|mk@poor @end|ng |rom gm@||@com
Wed Apr 7 10:16:46 CEST 2021
On Wed, Apr 7, 2021 at 12:51 PM Martin Maechler
<maechler using 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 (würg!!)):
>
> 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 using 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 using r-project.org mailing list -- To UNSUBSCRIBE and
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> > PLEASE do read the posting guide
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