[R] R does not start from (Debian) linux command line - error with doWithOneRestart() - segmentation fault

[Martin Maechler]

>>>>> 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 (würg!!)):

  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 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
    > 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.