From simon.urbanek at r-project.org  Sun Sep 25 22:06:07 2011
From: simon.urbanek at r-project.org (Simon Urbanek)
Date: Sun, 25 Sep 2011 16:06:07 -0400
Subject: [Rd] cbind() crashes on raw vectors
In-Reply-To: <4E7CF03F.7090100@fhcrc.org>
References: <4E7CF03F.7090100@fhcrc.org>
Message-ID: <22DD113B-230D-482C-9894-2EB0D6CC6B67@r-project.org>

Thanks, now fixed.
Simon


On Sep 23, 2011, at 4:46 PM, Herv? Pag?s wrote:

> Hi,
> 
> cbind() doesn't seem to like raw vectors:
> 
> > df <- cbind(a=integer(4000), b=raw(4000))
> > df
> *** glibc detected *** /home/hpages/R-2.13.1/bin/exec/R: malloc(): memory corruption: 0x0000000002d73ca0 ***
> ======= Backtrace: =========
> /lib/x86_64-linux-gnu/libc.so.6(+0x79d7a)[0x7f3592b91d7a]
> /lib/x86_64-linux-gnu/libc.so.6(__libc_malloc+0x6e)[0x7f3592b9431e]
> /lib/libreadline.so.5(xmalloc+0x6)[0x7f3592620ab6]
> /lib/libreadline.so.5(add_history+0xbe)[0x7f359262136e]
> /home/hpages/R-2.13.1/lib/libR.so(+0x1b6538)[0x7f35936bd538]
> /lib/libreadline.so.5(rl_callback_read_char+0x8c)[0x7f359261cb1c]
> /home/hpages/R-2.13.1/lib/libR.so(+0x1b6f74)[0x7f35936bdf74]
> /home/hpages/R-2.13.1/lib/libR.so(Rf_ReplIteration+0xe7)[0x7f3593610eb7]
> /home/hpages/R-2.13.1/lib/libR.so(+0x10a260)[0x7f3593611260]
> /home/hpages/R-2.13.1/lib/libR.so(run_Rmainloop+0x50)[0x7f3593611780]
> /home/hpages/R-2.13.1/bin/exec/R(main+0x1b)[0x40085b]
> /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xff)[0x7f3592b36eff]
> /home/hpages/R-2.13.1/bin/exec/R[0x400779]
> ======= Memory map: ========
> 00400000-00401000 r-xp 00000000 08:01 3811201  /home/hpages/R-2.13.1/bin/exec/R
> 00600000-00601000 r--p 00000000 08:01 3811201  /home/hpages/R-2.13.1/bin/exec/R
> 00601000-00602000 rw-p 00001000 08:01 3811201  /home/hpages/R-2.13.1/bin/exec/R
> 02583000-03b16000 rw-p 00000000 00:00 0  [heap]
> 7f358c000000-7f358c021000 rw-p 00000000 00:00 0
> 7f358c021000-7f3590000000 ---p 00000000 00:00 0
> 7f3590342000-7f3590357000 r-xp 00000000 08:06 8155  /lib/x86_64-linux-gnu/libgcc_s.so.1
> 7f3590357000-7f3590556000 ---p 00015000 08:06 8155  /lib/x86_64-linux-gnu/libgcc_s.so.1
> 7f3590556000-7f3590557000 r--p 00014000 08:06 8155  /lib/x86_64-linux-gnu/libgcc_s.so.1
> 7f3590557000-7f3590558000 rw-p 00015000 08:06 8155  /lib/x86_64-linux-gnu/libgcc_s.so.1
> 7f3590558000-7f35905c4000 r-xp 00000000 08:01 3818237  /home/hpages/R-2.13.1/library/stats/libs/stats.so
> 7f35905c4000-7f35907c3000 ---p 0006c000 08:01 3818237  /home/hpages/R-2.13.1/library/stats/libs/stats.so
> 7f35907c3000-7f35907c5000 r--p 0006b000 08:01 3818237  /home/hpages/R-2.13.1/library/stats/libs/stats.so
> 7f35907c5000-7f35907c7000 rw-p 0006d000 08:01 3818237  /home/hpages/R-2.13.1/library/stats/libs/stats.so
> 7f35907c7000-7f359083a000 rw-p 00000000 00:00 0
> 7f359083a000-7f359085c000 r-xp 00000000 08:01 3817784  /home/hpages/R-2.13.1/library/grDevices/libs/grDevices.so
> 7f359085c000-7f3590a5b000 ---p 00022000 08:01 3817784  /home/hpages/R-2.13.1/library/grDevices/libs/grDevices.so
> 7f3590a5b000-7f3590a5c000 r--p 00021000 08:01 3817784  /home/hpages/R-2.13.1/library/grDevices/libs/grDevices.so
> 7f3590a5c000-7f3590a5d000 rw-p 00022000 08:01 3817784  /home/hpages/R-2.13.1/library/grDevices/libs/grDevices.so
> 7f3590b61000-7f3590b63000 r-xp 00000000 08:07 671027  /usr/lib/x86_64-linux-gnu/gconv/ISO8859-1.so
> 7f3590b63000-7f3590d62000 ---p 00002000 08:07 671027  /usr/lib/x86_64-linux-gnu/gconv/ISO8859-1.so
> 7f3590d62000-7f3590d63000 r--p 00001000 08:07 671027  /usr/lib/x86_64-linux-gnu/gconv/ISO8859-1.so
> 7f3590d63000-7f3590d64000 rw-p 00002000 08:07 671027  /usr/lib/x86_64-linux-gnu/gconv/ISO8859-1.so
> 7f3590d64000-7f3590de6000 rw-p 00000000 00:00 0
> 7f3590de6000-7f3590ded000 r-xp 00000000 08:01 3818288  /home/hpages/R-2.13.1/library/methods/libs/methods.so
> 7f3590ded000-7f3590fec000 ---p 00007000 08:01 3818288  /home/hpages/R-2.13.1/library/methods/libs/methods.so
> 7f3590fec000-7f3590fed000 r--p 00006000 08:01 3818288  /home/hpages/R-2.13.1/library/methods/libs/methods.so
> 7f3590fed000-7f3590fee000 rw-p 00007000 08:01 3818288  /home/hpages/R-2.13.1/library/methods/libs/methods.so
> 7f3590fee000-7f3590ffa000 r-xp 00000000 08:06 8319  /lib/x86_64-linux-gnu/libnss_files-2.13.so
> 7f3590ffa000-7f35911f9000 ---p 0000c000 08:06 8319  /lib/x86_64-linux-gnu/libnss_files-2.13.so
> 7f35911f9000-7f35911fa000 r--p 0000b000 08:06 8319  /lib/x86_64-linux-gnu/libnss_files-2.13.so
> 7f35911fa000-7f35911fb000 rw-p 0000c000 08:06 8319  /lib/x86_64-linux-gnu/libnss_files-2.13.so
> 7f35911fb000-7f3591206000 r-xp 00000000 08:06 8321  /lib/x86_64-linux-gnu/libnss_nis-2.13.so
> 7f3591206000-7f3591405000 ---p 0000b000 08:06 8321  /lib/x86_64-linux-gnu/libnss_nis-2.13.so
> 7f3591405000-7f3591406000 r--p 0000a000 08:06 8321  /lib/x86_64-linux-gnu/libnss_nis-2.13.so
> 7f3591406000-7f3591407000 rw-p 0000b000 08:06 8321  /lib/x86_64-linux-gnu/libnss_nis-2.13.so
> 7f3591407000-7f359141e000 r-xp 00000000 08:06 8316  /lib/x86_64-linux-gnu/libnsl-2.13.so
> 7f359141e000-7f359161d000 ---p 00017000 08:06 8316  /lib/x86_64-linux-gnu/libnsl-2.13.so
> 7f359161d000-7f359161e000 r--p 00016000 08:06 8316  /lib/x86_64-linux-gnu/libnsl-2.13.so
> 7f359161e000-7f359161f000 rw-p 00017000 08:06 8316  /lib/x86_64-linux-gnu/libnsl-2.13.so
> 7f359161f000-7f3591621000 rw-p 00000000 00:00 0
> 7f3591621000-7f3591629000 r-xp 00000000 08:06 8317  /lib/x86_64-linux-gnu/libnss_compat-2.13.so
> 7f3591629000-7f3591828000 ---p 00008000 08:06 8317  /lib/x86_64-linux-gnu/libnss_compat-2.13.so
> 7f3591828000-7f3591829000 r--p 00007000 08:06 8317  /lib/x86_64-linux-gnu/libnss_compat-2.13.so
> 7f3591829000-7f359182a000 rw-p 00008000 08:06 8317  /lib/x86_64-linux-gnu/libnss_compat-2.13.so
> 7f359182a000-7f3591d21000 r--p 00000000 08:07 590549  /usr/lib/locale/locale-archive
> 7f3591d21000-7f3591d61000 r-xp 00000000 08:06 8139  /lib/libncurses.so.5.7
> 7f3591d61000-7f3591f60000 ---p 00040000 08:06 8139  /lib/libncurses.so.5.7
> 7f3591f60000-7f3591f64000 r--p 0003f000 08:06 8139  /lib/libncurses.so.5.7
> 7f3591f64000-7f3591f65000 rw-p 00043000 08:06 8139  /lib/libncurses.so.5.7
> 7f3591f65000-7f3591f6c000 r-xp 00000000 08:06 8326  /lib/x86_64-linux-gnu/librt-2.13.so
> 7f3591f6c000-7f359216b000 ---p 00007000 08:06 8326  /lib/x86_64-linux-gnu/librt-2.13.so
> 7f359216b000-7f359216c000 r--p 00006000 08:06 8326  /lib/x86_64-linux-gnu/librt-2.13.soAborted
> 
> This is with R 2.13.1 but it also crashes recent R devel.
> 
> Thanks,
> H.
> 
> > sessionInfo()
> R version 2.13.1 (2011-07-08)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> 
> locale:
> [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C
> [3] LC_TIME=en_CA.UTF-8        LC_COLLATE=en_CA.UTF-8
> [5] LC_MONETARY=C              LC_MESSAGES=en_CA.UTF-8
> [7] LC_PAPER=en_CA.UTF-8       LC_NAME=C
> [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_CA.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 fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
> 
> 



[Rd] cbind() crashes on raw vectors
Simon Urbanek