From hpages at fredhutch.org  Tue Nov 15 07:10:08 2016
From: hpages at fredhutch.org (=?UTF-8?B?SGVydsOpIFBhZ8Oocw==?=)
Date: Mon, 14 Nov 2016 22:10:08 -0800
Subject: [Rd] creating a long list puts R in a state where many things stop
	working
Message-ID: <3fc0697c-2c5b-f18c-22f8-76d0104ffefc@fredhutch.org>

Hi,

After I create a long list e.g. with

   x <- vector(mode="list", length=3e9)

many bad things start to happen e.g. some things stop working with a
spurious error message:

   gc()
   # Error in gc() :
   #   long vectors not supported yet: 
/home/hpages/src/R-3.3.2/src/main/memory.c:1137

   x_lens <- lengths(x)
   # Error in lengths(x) :
   #  long vectors not supported yet: 
/home/hpages/src/R-3.3.2/src/main/memory.c:1668

But then some of them work again:

   gc()
   #          used (Mb) gc trigger    (Mb)   max used    (Mb)
   # Ncells  57046  3.1     368000    19.7     350000    18.7
   # Vcells 138060  1.1 4320596678 32963.6 4500397915 34335.4

while others still fail but now with a different error message:

   x_lens <- lengths(x)
   # Error: evaluation nested too deeply: infinite recursion / 
options(expressions=)?

etc...

The more I go, the more weird things I see so clearly my session
got corrupted. Finally, and not too surprisingly, after playing a
little bit more, my session eventually crashed.

Thanks,
H.

 > sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.3 LTS

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


-- 
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319



[Rd] creating a long list puts R in a state where many things stop working
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