[Rd] [External] memory consumption of nested (un)serialize of sys.frames()

Thu Apr 8 16:15:21 CEST 2021

I see that now also. Not sure yet what is going on.

One work-around that may work for you is to create a fresh crash dump
in a .onLoad function; somehting like

crash_dumps <- NULL
.onLoad <- function(...) crash_dumps <<- new.env()

Best,

luke

On Wed, 7 Apr 2021, Andreas Kersting wrote:

> Hi Dirk, hi Luke,
>
> Thanks for checking!
>
> I could narrow it down further. I have the issue only if I install --with-keep.source, i.e.
>
> R CMD INSTALL --with-keep.source dumpTest
>
> Since this is the default in RStudio when clicking "Install and Restart", I was always having the issue - also from base R. If I install using e.g. devtools::install_github() directly it is also fine for me.
>
> Could you please confirm? Thanks!
>
> Regards,
> Andreas
>
> 2021-04-07 16:20 GMT+02:00 "Dirk Eddelbuettel" <edd using debian.org>:
>>
>> On 7 April 2021 at 16:06, Andreas Kersting wrote:
>> | Hi Luke,
>> |
>> | Please see https://github.com/akersting/dumpTest for the package.
>> |
>> | Here a session showing my issue:
>> |
>> | > library(dumpTest)
>> | > sessionInfo()
>> | R version 4.0.5 (2021-03-31)
>> | Platform: x86_64-pc-linux-gnu (64-bit)
>> | Running under: Debian GNU/Linux 10 (buster)
>> |
>> | Matrix products: default
>> | BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.8.0
>> | LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.8.0
>> |
>> | locale:
>> |  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>> |  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>> |  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>> |  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>> |  [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> | [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>> |
>> | attached base packages:
>> | [1] stats     graphics  grDevices utils     datasets  methods   base
>> |
>> | other attached packages:
>> | [1] dumpTest_0.1.0
>> |
>> | loaded via a namespace (and not attached):
>> | [1] compiler_4.0.5
>> | > for (i in 1:100) {
>> | +   print(i)
>> | +   print(system.time(f()))
>> | + }
>> | [1] 1
>> |    user  system elapsed
>> |   0.028   0.004   0.034
>> | [1] 2
>> |    user  system elapsed
>> |   0.067   0.008   0.075
>> | [1] 3
>> |    user  system elapsed
>> |   0.176   0.000   0.176
>> | [1] 4
>> |    user  system elapsed
>> |   0.335   0.012   0.349
>> | [1] 5
>> |    user  system elapsed
>> |   0.745   0.023   0.770
>> | [1] 6
>> |    user  system elapsed
>> |   1.495   0.060   1.572
>> | [1] 7
>> |    user  system elapsed
>> |   2.902   0.136   3.040
>> | [1] 8
>> |    user  system elapsed
>> |   5.753   0.272   6.034
>> | [1] 9
>> |    user  system elapsed
>> |  11.807   0.708  12.597
>> | [1] 10
>> | ^C
>> | Timing stopped at: 6.638 0.549 7.214
>> |
>> | I had to interrupt in iteration 10 because I was running low on RAM.
>>
>> No issue here.  Ubuntu 20.10, R 4.0.5 'from CRAN' i.e. Michael's PPA build
>> off my Debian package, hence instrumentation as in the Debian package.
>>
>> edd using rob:~$ installGithub.r akersting/dumpTest
>> Using github PAT from envvar GITHUB_PAT
>> Downloading GitHub repo akersting/dumpTest using HEAD
>> ✔  checking for file ‘/tmp/remotes3f9af733166ccd/akersting-dumpTest-3bed8e2/DESCRIPTION’ ...
>> ─  preparing ‘dumpTest’:
>> ✔  checking DESCRIPTION meta-information ...
>> ─  checking for LF line-endings in source and make files and shell scripts
>> ─  checking for empty or unneeded directories
>> ─  building ‘dumpTest_0.1.0.tar.gz’
>>
>> Installing package into ‘/usr/local/lib/R/site-library’
>> (as ‘lib’ is unspecified)
>> * installing *source* package ‘dumpTest’ ...
>> ** using staged installation
>> ** R
>> ** byte-compile and prepare package for lazy loading
>> ** help
>> No man pages found in package  ‘dumpTest’
>> *** installing help indices
>> ** building package indices
>> ** testing if installed package can be loaded from temporary location
>> ** testing if installed package can be loaded from final location
>> ** testing if installed package keeps a record of temporary installation path
>> * DONE (dumpTest)
>> edd using rob:~$ Rscript -e 'system.time({for (i in 1:100) dumpTest::f()})'
>>    user  system elapsed
>>   0.481   0.019   0.500
>> edd using rob:~$
>>
>> (I also ran the variant you showed with the dual print statements, it just
>> consumes more screen real estate and ends on
>>
>> [...]
>> [1] 97
>>    user  system elapsed
>>   0.004   0.000   0.005
>> [1] 98
>>    user  system elapsed
>>   0.004   0.000   0.005
>> [1] 99
>>    user  system elapsed
>>   0.004   0.000   0.004
>> [1] 100
>>    user  system elapsed
>>   0.005   0.000   0.005
>> edd using rob:~$ )
>>
>> Dirk
>>
>> --
>> https://dirk.eddelbuettel.com | @eddelbuettel | edd using debian.org
>>

-- 
Luke Tierney
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa                  Phone:             319-335-3386
Department of Statistics and        Fax:               319-335-3017
    Actuarial Science
241 Schaeffer Hall                  email:   luke-tierney using uiowa.edu
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