[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
Fri Apr 9 06:27:58 CEST 2021
Dear Henrik,
We upgraded R and rebooted the computer and the error went away. Hence
I do not think we will get any strange results anymore.
Still, I could be mistaken and I am still curious as to what happened
to my R installation. Please find the answers inline below.
On Thu, Apr 8, 2021 at 9:59 PM Henrik Bengtsson
<henrik.bengtsson using gmail.com> wrote:
>
> 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?
>
IIRC I installed R by doing:
apt-get install r-base r-base-dev
( following the instructions on this page :
https://cloud.r-project.org/ ) I went to this page and clicked on
"Download R for Linux" and then clicked on "debian". I think, since
the page uses frames, the url does not change when I do those 2 steps.
> 2. What happens if you call:
>
> $ Rscript --vanilla -e "1+2"
>
$ Rscript --vanilla -e "1+2"
[1] 3
> 3. What happens if you call:
>
> $ Rscript --vanilla --default-packages=base -e "1+2"
>
$ Rscript --vanilla --default-packages=base -e "1+2"
[1] 3
> 4. What happens if you call:
>
> $ Rscript --vanilla --default-packages=base,methods -e "1+2"
>
$ Rscript --vanilla --default-packages=base,methods -e "1+2"
[1] 3
> If any of 2-4 gives a different result, that's a first clue.
>
> /Henrik
>
Many thanks for your help,
Best Regards,
Ashim
> On Wed, Apr 7, 2021 at 1:17 AM Ashim Kapoor <ashimkapoor using gmail.com> wrote:
> >
> > 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
> > > > 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 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.
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