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Segfault in [.data.table #4892

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Kodiologist opened this issue Feb 4, 2021 · 10 comments · Fixed by #4944
Closed

Segfault in [.data.table #4892

Kodiologist opened this issue Feb 4, 2021 · 10 comments · Fixed by #4944
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@Kodiologist
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The following code (see attached file for the data)

library(data.table)
load("example.RData")
col = "ground.temp.min"
filter.zeros.thresh.K = 3
obs[.(check.regions$stn, check.regions$date), by = check.regions$g, (col) :=
     {v = get(col)
      if (!any(!is.na(v) &
              !zero &
              abs(v) <= filter.zeros.thresh.K))
          v[date == median(date)] = NA
      v}]

causes this segfault:

 *** caught segfault ***
address 0x56386f5fd8dc, cause 'memory not mapped'

Traceback:
 1: `[.data.table`(obs, .(check.regions$stn, check.regions$date),     by = check.regions$g, `:=`((col), {        v = get(col)        if (!any(!is.na(v) & !zero & abs(v) <= filter.zeros.thresh.K))             v[date == median(date)] = NA        v    }))
 2: obs[.(check.regions$stn, check.regions$date), by = check.regions$g,     `:=`((col), {        v = get(col)        if (!any(!is.na(v) & !zero & abs(v) <= filter.zeros.thresh.K))             v[date == median(date)] = NA        v    })]

sessionInfo is:

R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

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] data.table_1.13.6

loaded via a namespace (and not attached):
[1] compiler_4.0.2
@ColeMiller1

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@Kodiologist
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There are probably smaller datasets that could trigger the same segfault, but I haven't figured out how to make one. Here's a version that uses CSV instead of RData input if that helps; it does at least show that the problem isn't with binary loading or saving. Here are the two CSVs in a gzipped tarball.

library(data.table)
obs = fread("obs.csv")
setkey(obs, stn, date)
check.regions = fread("cr.csv")
col = "ground.temp.min"
filter.zeros.thresh.K = 3
obs[.(check.regions$stn, check.regions$date), by = check.regions$g, (col) :=
     {v = get(col)
      if (!any(!is.na(v) &
              !zero &
              abs(v) <= filter.zeros.thresh.K))
          v[date == median(date)] = NA
      v}]

@dantonnoriega

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@Kodiologist

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@chinsoon12
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Here is an option to lookup g into obs first before performing your desired operation:

obs[check.regions, on=.(stn, date), g := g]
obs[, (col) :=
    {
        v = get(col)
        if (!any(!is.na(v) & !zero & abs(v) <= filter.zeros.thresh.K))
            v[date == median(date)] = NA
        v
    },
    g]

I think using check.regions in the by of obs might be causing the issue.

@ColeMiller1
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Contributor

As @chinsoon12 notes, the problem is in the by. I have not fully tracked it down, but here is a self-contained example:

library(data.table)
x = data.table(id = 1:4, key = 'id')
y = data.table(id = 2:5, key = 'id')
x[y, by = .(1:4), .SD, verbose = TRUE]

## next line will segfault
x[y, by = .(c(2L, 1L, 2L, 1L)), .SD, verbose = TRUE]

The requirements are 1) a keyed join; 2) a non-column by that has at least 2 groups with multiple matches. I tried a gforce approach but it still segfaulted.

I have some other things to follow-up on, but if this is still around I'll look deeper.

@chackoge
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FWIW data.table has been crashing with segfault errors on my 128 Gb Centos machine that defaults to 128 threads. The input data file to the script has just over 99 million edges. The same script runs fine on a Fedora machine with 16 threads so I tried setDT(16) in the Centos machine and the error doesn't seem to have recurred since although there is, unsurprisingly, a performance hit.

sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS: /home/chackoge/R-4.1.2/lib/libRblas.so
LAPACK: /home/chackoge/R-4.1.2/lib/libRlapack.so

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] data.table_1.14.2

loaded via a namespace (and not attached):
[1] compiler_4.1.2

Error Message:

[path to dbid]$ nohup Rscript ~/repos/spring_2022_research/george/fmoy_test.R &
[1] 158635
[path to dbid]$ nohup: ignoring input and appending output to ‘nohup.out’

[path to dbid]$ tail -f nohup.out
[1] "2022-02-16 16:36:03 CST"
[1] "***********"
*** Error in `/software/R-4.0.3/lib64/R/bin/exec/R': double free or corruption (!prev): 0x0000000006e19670 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81329)[0x7fd076af6329]
/home/userid/R/x86_64-pc-linux-gnu-library/4.0/data.table/libs/datatable.so(+0x20fb0)[0x7fd06aeb4fb0]
/home/userid/R/x86_64-pc-linux-gnu-library/4.0/data.table/libs/datatable.so(forder+0xa7e)[0x7fd06aeb894e]
/software/R-4.0.3/lib64/R/lib/libR.so(+0xffaa4)[0x7fd0775b1aa4]
/software/R-4.0.3/lib64/R/lib/libR.so(+0x14174a)[0x7fd0775f374a]
/software/R-4.0.3/lib64/R/lib/libR.so(Rf_eval+0x178)[0x7fd077601028]
/software/R-4.0.3/lib64/R/lib/libR.so(+0x15088b)[0x7fd07760288b]
/software/R-4.0.3/lib64/R/lib/libR.so(Rf_applyClosure+0x1c1)[0x7fd077603611]
/software/R-4.0.3/lib64/R/lib/libR.so(+0x13d9b2)[0x7fd0775ef9b2]
/software/R-4.0.3/lib64/R/lib/libR.so(Rf_eval+0x178)[0x7fd077601028]
/software/R-4.0.3/lib64/R/lib/libR.so(+0x15088b)[0x7fd07760288b]
/software/R-4.0.3/lib64/R/lib/libR.so(Rf_applyClosure+0x1c1)[0x7fd077603611]
/software/R-4.0.3/lib64/R/lib/libR.so(+0x13d9b2)[0x7fd0775ef9b2]
/software/R-4.0.3/lib64/R/lib/libR.so(Rf_eval+0x178)[0x7fd077601028]
/software/R-4.0.3/lib64/R/lib/libR.so(+0x15088b)[0x7fd07760288b]
/software/R-4.0.3/lib64/R/lib/libR.so(Rf_applyClosure+0x1c1)[0x7fd077603611]
/software/R-4.0.3/lib64/R/lib/libR.so(+0x193fdd)[0x7fd077645fdd]
/software/R-4.0.3/lib64/R/lib/libR.so(+0x194468)[0x7fd077646468]
/software/R-4.0.3/lib64/R/lib/libR.so(+0x135ae7)[0x7fd0775e7ae7]
/software/R-4.0.3/lib64/R/lib/libR.so(+0x139cd4)[0x7fd0775ebcd4]
/software/R-4.0.3/lib64/R/lib/libR.so(+0x1568be)[0x7fd0776088be]
/software/R-4.0.3/lib64/R/lib/libR.so(+0x157c70)[0x7fd077609c70]
/software/R-4.0.3/lib64/R/lib/libR.so(Rf_eval+0x51f)[0x7fd0776013cf]
/software/R-4.0.3/lib64/R/lib/libR.so(Rf_ReplIteration+0x252)[0x7fd077635182]
/software/R-4.0.3/lib64/R/lib/libR.so(+0x1834e1)[0x7fd0776354e1]
/software/R-4.0.3/lib64/R/lib/libR.so(run_Rmainloop+0x4f)[0x7fd07763557f]
/software/R-4.0.3/lib64/R/bin/exec/R(main+0x1b)[0x40076b]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7fd076a97555]
/software/R-4.0.3/lib64/R/bin/exec/R[0x40079b]
======= Memory map: ========
00400000-00401000 r-xp 00000000 00:32 3304998407 /software/R-4.0.3/lib64/R/bin/exec/R
00600000-00601000 r--p 00000000 00:32 3304998407 /software/R-4.0.3/lib64/R/bin/exec/R
00601000-00602000 rw-p 00001000 00:32 3304998407 /software/R-4.0.3/lib64/R/bin/exec/R
00c25000-2add5000 rw-p 00000000 00:00 0 [heap]
7fcd30000000-7fcd3008d000 rw-p 00000000 00:00 0
7fcd3008d000-7fcd34000000 ---p 00000000 00:00 0
7fcd38000000-7fcd3808d000 rw-p 00000000 00:00 0
7fcd3808d000-7fcd3c000000 ---p 00000000 00:00 0
7fcd40000000-7fcd4008d000 rw-p 00000000 00:00 0
7fcd4008d000-7fcd44000000 ---p 00000000 00:00 0
7fcd48000000-7fcd4808d000 rw-p 00000000 00:00 0
7fcd4808d000-7fcd4c000000 ---p 00000000 00:00 0
7fcd50000000-7fcd5008d000 rw-p 00000000 00:00 0
7fcd5008d000-7fcd54000000 ---p 00000000 00:00 0
7fcd58000000-7fcd5808d000 rw-p 00000000 00:00 0
7fcd5808d000-7fcd5c000000 ---p 00000000 00:00 0
7fcd60000000-7fcd6008d000 rw-p 00000000 00:00 0
7fcd6008d000-7fcd64000000 ---p 00000000 00:00 0
7fcd64000000-7fcd6408d000 rw-p 00000000 00:00 0
7fcd6408d000-7fcd68000000 ---p 00000000 00:00 0
7fcd68000000-7fcd6808d000 rw-p 00000000 00:00 0
7fcd6808d000-7fcd6c000000 ---p 00000000 00:00 0
7fcd6c000000-7fcd6c08d000 rw-p 00000000 00:00 0
7fcd6c08d000-7fcd70000000 ---p 00000000 00:00 0
7fcd70000000-7fcd7008d000 rw-p 00000000 00:00 0
7fcd7008d000-7fcd74000000 ---p 00000000 00:00 0
7fcd78000000-7fcd7808d000 rw-p 00000000 00:00 0
7fcd7808d000-7fcd7c000000 ---p 00000000 00:00 0
7fcd80000000-7fcd8008d000 rw-p 00000000 00:00 0
7fcd8008d000-7fcd84000000 ---p 00000000 00:00 0
7fcd88000000-7fcd8808d000 rw-p 00000000 00:00 0
7fcd8808d000-7fcd8c000000 ---p 00000000 00:00 0
7fcd90000000-7fcd9008d000 rw-p 00000000 00:00 0
7fcd9008d000-7fcd94000000 ---p 00000000 00:00 0
7fcd98000000-7fcd9808d000 rw-p 00000000 00:00 0
7fcd9808d000-7fcd9c000000 ---p 00000000 00:00 0
7fcda0000000-7fcda008d000 rw-p 00000000 00:00 0
7fcda008d000-7fcda4000000 ---p 00000000 00:00 0
7fcda8000000-7fcda808d000 rw-p 00000000 00:00 0
7fcda808d000-7fcdac000000 ---p 00000000 00:00 0
7fcdb0000000-7fcdb008d000 rw-p 00000000 00:00 0
7fcdb008d000-7fcdb4000000 ---p 00000000 00:00 0
7fcdb8000000-7fcdb808d000 rw-p 00000000 00:00 0
7fcdb808d000-7fcdbc000000 ---p 00000000 00:00 0
7fcdc0000000-7fcdc008d000 rw-p 00000000 00:00 0
7fcdc008d000-7fcdc4000000 ---p 00000000 00:00 0
7fcdc8000000-7fcdc808d000 rw-p 00000000 00:00 0
7fcdc808d000-7fcdcc000000 ---p 00000000 00:00 0
7fcdd0000000-7fcdd008d000 rw-p 00000000 00:00 0
7fcdd008d000-7fcdd4000000 ---p 00000000 00:00 0
7fcdd8000000-7fcdd808d000 rw-p 00000000 00:00 0
7fcdd808d000-7fcddc000000 ---p 00000000 00:00 0
7fcddc000000-7fcddc08d000 rw-p 00000000 00:00 0
7fcddc08d000-7fcde0000000 ---p 00000000 00:00 0
7fcde4000000-7fcde408d000 rw-p 00000000 00:00 0
7fcde408d000-7fcde8000000 ---p 00000000 00:00 0
7fcdec000000-7fcdec08d000 rw-p 00000000 00:00 0
7fcdec08d000-7fcdf0000000 ---p 00000000 00:00 0
7fcdf4000000-7fcdf408d000 rw-p 00000000 00:00 0
7fcdf408d000-7fcdf8000000 ---p 00000000 00:00 0
7fcdfc000000-7fcdfc08d000 rw-p 00000000 00:00 0
7fcdfc08d000-7fce00000000 ---p 00000000 00:00 0
7fce04000000-7fce0408d000 rw-p 00000000 00:00 0
7fce0408d000-7fce08000000 ---p 00000000 00:00 0
7fce0c000000-7fce0c08d000 rw-p 00000000 00:00 0
7fce0c08d000-7fce10000000 ---p 00000000 00:00 0
7fce14000000-7fce1408d000 rw-p 00000000 00:00 0
7fce1408d000-7fce18000000 ---p 00000000 00:00 0
7fce18000000-7fce1808d000 rw-p 00000000 00:00 0
7fce1808d000-7fce1c000000 ---p 00000000 00:00 0
7fce1c000000-7fce1c08d000 rw-p 00000000 00:00 0
7fce1c08d000-7fce20000000 ---p 00000000 00:00 0
7fce20000000-7fce2008d000 rw-p 00000000 00:00 0
7fce2008d000-7fce24000000 ---p 00000000 00:00 0
7fce24000000-7fce2408d000 rw-p 00000000 00:00 0
7fce2408d000-7fce28000000 ---p 00000000 00:00 0
7fce28000000-7fce2808d000 rw-p 00000000 00:00 0
7fce2808d000-7fce2c000000 ---p 00000000 00:00 0
7fce2c000000-7fce2c08d000 rw-p 00000000 00:00 0
7fce2c08d000-7fce30000000 ---p 00000000 00:00 0
7fce30000000-7fce3008d000 rw-p 00000000 00:00 0
7fce3008d000-7fce34000000 ---p 00000000 00:00 0
7fce34000000-7fce3408d000 rw-p 00000000 00:00 0
7fce3408d000-7fce38000000 ---p 00000000 00:00 0
7fce38000000-7fce3808d000 rw-p 00000000 00:00 0
7fce3808d000-7fce3c000000 ---p 00000000 00:00 0
7fce3c000000-7fce3c08d000 rw-p 00000000 00:00 0
7fce3c08d000-7fce40000000 ---p 00000000 00:00 0
7fce40000000-7fce4008d000 rw-p 00000000 00:00 0
7fce4008d000-7fce44000000 ---p 00000000 00:00 0
7fce44000000-7fce4408d000 rw-p 00000000 00:00 0
7fce4408d000-7fce48000000 ---p 00000000 00:00 0
7fce48000000-7fce4808d000 rw-p 00000000 00:00 0
7fce4808d000-7fce4c000000 ---p 00000000 00:00 0
7fce4c000000-7fce4c08d000 rw-p 00000000 00:00 0
7fce4c08d000-7fce50000000 ---p 00000000 00:00 0
7fce50000000-7fce5008d000 rw-p 00000000 00:00 0
7fce5008d000-7fce54000000 ---p 00000000 00:00 0
7fce54000000-7fce5408d000 rw-p 00000000 00:00 0
7fce5408d000-7fce58000000 ---p 00000000 00:00 0
7fce58000000-7fce5808d000 rw-p 00000000 00:00 0
7fce5808d000-7fce5c000000 ---p 00000000 00:00 0
7fce5c000000-7fce5c08d000 rw-p 00000000 00:00 0
7fce5c08d000-7fce60000000 ---p 00000000 00:00 0
7fce60000000-7fce6008d000 rw-p 00000000 00:00 0
7fce6008d000-7fce64000000 ---p 00000000 00:00 0
7fce64000000-7fce6408d000 rw-p 00000000 00:00 0
7fce6408d000-7fce68000000 ---p 00000000 00:00 0
7fce68000000-7fce6815f000 rw-p 00000000 00:00 0
7fce6815f000-7fce6c000000 ---p 00000000 00:00 0
7fce6c000000-7fce6c08d000 rw-p 00000000 00:00 0
7fce6c08d000-7fce70000000 ---p 00000000 00:00 0
7fce70000000-7fce7008d000 rw-p 00000000 00:00 0
7fce7008d000-7fce74000000 ---p 00000000 00:00 0
7fce74000000-7fce7415f000 rw-p 00000000 00:00 0
7fce7415f000-7fce78000000 ---p 00000000 00:00 0
7fce78000000-7fce7808d000 rw-p 00000000 00:00 0
7fce7808d000-7fce7c000000 ---p 00000000 00:00 0
7fce7c000000-7fce7c08d000 rw-p 00000000 00:00 0
7fce7c08d000-7fce80000000 ---p 00000000 00:00 0
7fce80000000-7fce8008d000 rw-p 00000000 00:00 0
7fce8008d000-7fce84000000 ---p 00000000 00:00 0
7fce84000000-7fce8408d000 rw-p 00000000 00:00 0
7fce8408d000-7fce88000000 ---p 00000000 00:00 0
7fce88000000-7fce8808d000 rw-p 00000000 00:00 0
7fce8808d000-7fce8c000000 ---p 00000000 00:00 0
7fce8c000000-7fce8c15f000 rw-p 00000000 00:00 0
7fce8c15f000-7fce90000000 ---p 00000000 00:00 0
7fce90000000-7fce9015f000 rw-p 00000000 00:00 0
7fce9015f000-7fce94000000 ---p 00000000 00:00 0
7fce94000000-7fce9415f000 rw-p 00000000 00:00 0
7fce9415f000-7fce98000000 ---p 00000000 00:00 0
7fce98000000-7fce9808d000 rw-p 00000000 00:00 0
7fce9808d000-7fce9c000000 ---p 00000000 00:00 0
7fce9c000000-7fce9c08d000 rw-p 00000000 00:00 0
7fce9c08d000-7fcea0000000 ---p 00000000 00:00 0
7fcea0000000-7fcea008d000 rw-p 00000000 00:00 0
7fcea008d000-7fcea4000000 ---p 00000000 00:00 0
7fcea4000000-7fcea415f000 rw-p 00000000 00:00 0
7fcea415f000-7fcea8000000 ---p 00000000 00:00 0
7fcea8000000-7fcea808d000 rw-p 00000000 00:00 0
7fcea808d000-7fceac000000 ---p 00000000 00:00 0
7fceac000000-7fceac08d000 rw-p 00000000 00:00 0
7fceac08d000-7fceb0000000 ---p 00000000 00:00 0
7fceb0000000-7fceb008d000 rw-p 00000000 00:00 0
7fceb008d000-7fceb4000000 ---p 00000000 00:00 0
7fceb4000000-7fceb408d000 rw-p 00000000 00:00 0
7fceb408d000-7fceb8000000 ---p 00000000 00:00 0
7fceb8000000-7fceb808d000 rw-p 00000000 00:00 0
7fceb808d000-7fcebc000000 ---p 00000000 00:00 0
7fcebc000000-7fcebc08d000 rw-p 00000000 00:00 0
7fcebc08d000-7fcec0000000 ---p 00000000 00:00 0
7fcec0000000-7fcec008d000 rw-p 00000000 00:00 0
7fcec008d000-7fcec4000000 ---p 00000000 00:00 0
7fcec4000000-7fcec408d000 rw-p 00000000 00:00 0
7fcec408d000-7fcec8000000 ---p 00000000 00:00 0
7fcec8000000-7fcec808d000 rw-p 00000000 00:00 0
7fcec808d000-7fcecc000000 ---p 00000000 00:00 0
7fcecc000000-7fcecc08d000 rw-p 00000000 00:00 0
7fcecc08d000-7fced0000000 ---p 00000000 00:00 0
7fced0000000-7fced008d000 rw-p 00000000 00:00 0
7fced008d000-7fced4000000 ---p 00000000 00:00 0
7fced4000000-7fced408d000 rw-p 00000000 00:00 0
7fced408d000-7fced8000000 ---p 00000000 00:00 0
7fced8000000-7fced808d000 rw-p 00000000 00:00 0
7fced808d000-7fcedc000000 ---p 00000000 00:00 0
7fcedc000000-7fcedc08d000 rw-p 00000000 00:00 0
7fcedc08d000-7fcee0000000 ---p 00000000 00:00 0
7fcee0000000-7fcee008d000 rw-p 00000000 00:00 0
7fcee008d000-7fcee4000000 ---p 00000000 00:00 0
7fcee4000000-7fcee408d000 rw-p 00000000 00:00 0
7fcee408d000-7fcee8000000 ---p 00000000 00:00 0
7fcee8000000-7fcee808d000 rw-p 00000000 00:00 0
7fcee808d000-7fceec000000 ---p 00000000 00:00 0
7fceec000000-7fceec08d000 rw-p 00000000 00:00 0
7fceec08d000-7fcef0000000 ---p 00000000 00:00 0
7fcef0000000-7fcef008d000 rw-p 00000000 00:00 0
7fcef008d000-7fcef4000000 ---p 00000000 00:00 0
7fcef4000000-7fcef408d000 rw-p 00000000 00:00 0
7fcef408d000-7fcef8000000 ---p 00000000 00:00 0
7fcef8000000-7fcef808d000 rw-p 00000000 00:00 0
7fcef808d000-7fcefc000000 ---p 00000000 00:00 0
7fcefc000000-7fcefc08d000 rw-p 00000000 00:00 0
7fcefc08d000-7fcf00000000 ---p 00000000 00:00 0
7fcf00000000-7fcf0008d000 rw-p 00000000 00:00 0
7fcf0008d000-7fcf04000000 ---p 00000000 00:00 0
7fcf04000000-7fcf0408d000 rw-p 00000000 00:00 0
7fcf0408d000-7fcf08000000 ---p 00000000 00:00 0
7fcf08000000-7fcf0808d000 rw-p 00000000 00:00 0
7fcf0808d000-7fcf0c000000 ---p 00000000 00:00 0
7fcf0c000000-7fcf0c08d000 rw-p 00000000 00:00 0
7fcf0c08d000-7fcf10000000 ---p 00000000 00:00 0
7fcf10000000-7fcf1008d000 rw-p 00000000 00:00 0
7fcf1008d000-7fcf14000000 ---p 00000000 00:00 0
7fcf14000000-7fcf1408d000 rw-p 00000000 00:00 0
7fcf1408d000-7fcf18000000 ---p 00000000 00:00 0
7fcf18000000-7fcf1808d000 rw-p 00000000 00:00 0
7fcf1808d000-7fcf1c000000 ---p 00000000 00:00 0
7fcf1c000000-7fcf1c08d000 rw-p 00000000 00:00 0
7fcf1c08d000-7fcf20000000 ---p 00000000 00:00 0
7fcf20000000-7fcf2015f000 rw-p 00000000 00:00 0
7fcf2015f000-7fcf24000000 ---p 00000000 00:00 0
7fcf24000000-7fcf2408d000 rw-p 00000000 00:00 0
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7fd06b302000-7fd06b501000 ---p 001ee000 00:32 1206212960 /software/R-4.0.3/lib64/R/lib/libRlapack.so
7fd06b501000-7fd06b502000 r--p 001ed000 00:32 1206212960 /software/R-4.0.3/lib64/R/lib/libRlapack.so
7fd06b502000-7fd06b503000 rw-p 001ee000 00:32 1206212960 /software/R-4.0.3/lib64/R/lib/libRlapack.so
7fd06b503000-7fd06b51d000 rw-p 00000000 00:00 0
7fd06b51d000-7fd06b5c1000 r-xp 00000000 00:32 5594023640 /software/R-4.0.3/lib64/R/library/stats/libs/stats.so
7fd06b5c1000-7fd06b7c1000 ---p 000a4000 00:32 5594023640 /software/R-4.0.3/lib64/R/library/stats/libs/stats.so
7fd06b7c1000-7fd06b7c3000 r--p 000a4000 00:32 5594023640 /software/R-4.0.3/lib64/R/library/stats/libs/stats.so
7fd06b7c3000-7fd06b7c5000 rw-p 000a6000 00:32 5594023640 /software/R-4.0.3/lib64/R/library/stats/libs/stats.so
7fd06b7c5000-7fd06b80c000 r-xp 00000000 00:32 5594023452 /software/R-4.0.3/lib64/R/library/graphics/libs/graphics.so
7fd06b80c000-7fd06ba0c000 ---p 00047000 00:32 5594023452 /software/R-4.0.3/lib64/R/library/graphics/libs/graphics.so
7fd06ba0c000-7fd06ba0d000 r--p 00047000 00:32 5594023452 /software/R-4.0.3/lib64/R/library/graphics/libs/graphics.so
7fd06ba0d000-7fd06ba0e000 rw-p 00048000 00:32 5594023452 /software/R-4.0.3/lib64/R/library/graphics/libs/graphics.so
7fd06ba0e000-7fd06ba1a000 r-xp 00000000 00:32 3305000342 /software/R-4.0.3/lib64/R/library/utils/libs/utils.so
7fd06ba1a000-7fd06bc19000 ---p 0000c000 00:32 3305000342 /software/R-4.0.3/lib64/R/library/utils/libs/utils.so
7fd06bc19000-7fd06bc1a000 r--p 0000b000 00:32 3305000342 /software/R-4.0.3/lib64/R/library/utils/libs/utils.so
7fd06bc1a000-7fd06bc1b000 rw-p 0000c000 00:32 3305000342 /software/R-4.0.3/lib64/R/library/utils/libs/utils.so
7fd06bc1b000-7fd06bc1c000 rw-p 00000000 00:00 0
7fd06bdb5000-7fd06bdea000 r-xp 00000000 00:32 7640869845 /software/R-4.0.3/lib64/R/library/grDevices/libs/grDevices.so
7fd06bdea000-7fd06bfea000 ---p 00035000 00:32 7640869845 /software/R-4.0.3/lib64/R/library/grDevices/libs/grDevices.so
7fd06bfea000-7fd06bfef000 r--p 00035000 00:32 7640869845 /software/R-4.0.3/lib64/R/library/grDevices/libs/grDevices.so
7fd06bfef000-7fd06bff1000 rw-p 0003a000 00:32 7640869845 /software/R-4.0.3/lib64/R/library/grDevices/libs/grDevices.so
7fd06bff1000-7fd06c0d7000 rw-p 00000000 00:00 0
7fd06c1a3000-7fd06c2e4000 rw-p 00000000 00:00 0
7fd06c2e4000-7fd06c2ed000 r-xp 00000000 00:32 5594023552 /software/R-4.0.3/lib64/R/library/methods/libs/methods.so
7fd06c2ed000-7fd06c4ec000 ---p 00009000 00:32 5594023552 /software/R-4.0.3/lib64/R/library/methods/libs/methods.so
7fd06c4ec000-7fd06c4ed000 r--p 00008000 00:32 5594023552 /software/R-4.0.3/lib64/R/library/methods/libs/methods.so
7fd06c4ed000-7fd06c4ee000 rw-p 00009000 00:32 5594023552 /software/R-4.0.3/lib64/R/library/methods/libs/methods.so
7fd06c51d000-7fd06c92a000 rw-p 00000000 00:00 0
7fd06c92a000-7fd072e6d000 r--p 00000000 fd:00 41944138 /usr/lib/locale/locale-archive
7fd072e6d000-7fd072f56000 r-xp 00000000 fd:00 16778974 /usr/lib64/libstdc++.so.6.0.19
7fd072f56000-7fd073156000 ---p 000e9000 fd:00 16778974 /usr/lib64/libstdc++.so.6.0.19
7fd073156000-7fd07315e000 r--p 000e9000 fd:00 16778974 /usr/lib64/libstdc++.so.6.0.19
7fd07315e000-7fd073160000 rw-p 000f1000 fd:00 16778974 /usr/lib64/libstdc++.so.6.0.19
7fd073160000-7fd073175000 rw-p 00000000 00:00 0
7fd073175000-7fd074547000 r-xp 00000000 fd:00 17194507 /usr/lib64/libicudata.so.50.2
7fd074547000-7fd074746000 ---p 013d2000 fd:00 17194507 /usr/lib64/libicudata.so.50.2
7fd074746000-7fd074747000 r--p 013d1000 fd:00 17194507 /usr/lib64/libicudata.so.50.2
7fd074747000-7fd074748000 rw-p 013d2000 fd:00 17194507 /usr/lib64/libicudata.so.50.2
7fd074748000-7fd07476d000 r-xp 00000000 fd:00 16779003 /usr/lib64/libtinfo.so.5.9
7fd07476d000-7fd07496d000 ---p 00025000 fd:00 16779003 /usr/lib64/libtinfo.so.5.9
7fd07496d000-7fd074971000 r--p 00025000 fd:00 16779003 /usr/lib64/libtinfo.so.5.9
7fd074971000-7fd074972000 rw-p 00029000 fd:00 16779003 /usr/lib64/libtinfo.so.5.9
7fd074972000-7fd074987000 r-xp 00000000 fd:00 16777730 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7fd074987000-7fd074b86000 ---p 00015000 fd:00 16777730 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7fd074b86000-7fd074b87000 r--p 00014000 fd:00 16777730 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7fd074b87000-7fd074b88000 rw-p 00015000 fd:00 16777730 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7fd074b88000-7fd074d78000 r-xp 00000000 fd:00 17194509 /usr/lib64/libicui18n.so.50.2^C[1]+ Aborted

@MichaelChirico
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@chackoge note that this issue was closed by a commit in the current dev version 1.14.3, can you try installing that and making sure it solves your issue?

@chackoge
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@MichaelChirico thank you. This commit seems to have addressed the problem- I should have tried the dev version first,

data.table::update.dev.pkg()

other attached packages:
[1] data.table_1.14.3

@MichaelChirico
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glad it solved your issue!!

@jangorecki jangorecki modified the milestones: 1.14.9, 1.15.0 Oct 29, 2023
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