Bug 16328 - Buffer overflow R function POSIXct
Summary: Buffer overflow R function POSIXct
Status: CLOSED FIXED
Alias: None
Product: R
Classification: Unclassified
Component: Misc (show other bugs)
Version: R 3.1.3
Hardware: x86_64/x64/amd64 (64-bit) Linux-Ubuntu
: P5 enhancement
Assignee: R-core
URL:
Depends on:
Blocks:
 
Reported: 2015-04-22 13:05 UTC by Maxime
Modified: 2015-12-14 13:47 UTC (History)
2 users (show)

See Also:


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Description Maxime 2015-04-22 13:05:28 UTC
I'm trying to run a simple R script on an Ubuntu virtual machine (with Oracle Virtual Box). Whenever I try to use the date formatting function as.POSIXct, I get a buffer overflow error (see example below). Any idea what might cause this buffer overflow? Is there a way I can increase the size of the buffer to avoid it?

Thanks for your help!

R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
Copyright (C) 2013 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> a<-as.POSIXct('2015-04-22')
*** buffer overflow detected ***: /usr/lib/R/bin/exec/R terminated
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x741cf)[0x7f152388e1cf]
/lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x5c)[0x7f1523925b2c]
/lib/x86_64-linux-gnu/libc.so.6(+0x10a9f0)[0x7f15239249f0]
/lib/x86_64-linux-gnu/libc.so.6(+0x10cd6a)[0x7f1523926d6a]
/usr/lib/R/lib/libR.so(+0x926c4)[0x7f1523e906c4]
/usr/lib/R/lib/libR.so(+0x9446b)[0x7f1523e9246b]
/usr/lib/R/lib/libR.so(+0xdcddb)[0x7f1523edaddb]
/usr/lib/R/lib/libR.so(Rf_eval+0xf8)[0x7f1523ee2d98]
/usr/lib/R/lib/libR.so(Rf_applyClosure+0x346)[0x7f1523ee4056]
/usr/lib/R/lib/libR.so(+0xdbfc6)[0x7f1523ed9fc6]
/usr/lib/R/lib/libR.so(Rf_eval+0xf8)[0x7f1523ee2d98]
/usr/lib/R/lib/libR.so(Rf_applyClosure+0x346)[0x7f1523ee4056]
/usr/lib/R/lib/libR.so(+0x11a3bb)[0x7f1523f183bb]
/usr/lib/R/lib/libR.so(+0x11a811)[0x7f1523f18811]
/usr/lib/R/lib/libR.so(+0xdcf50)[0x7f1523edaf50]
/usr/lib/R/lib/libR.so(Rf_eval+0xf8)[0x7f1523ee2d98]
/usr/lib/R/lib/libR.so(Rf_applyClosure+0x346)[0x7f1523ee4056]
/usr/lib/R/lib/libR.so(+0xdbfc6)[0x7f1523ed9fc6]
/usr/lib/R/lib/libR.so(Rf_eval+0xf8)[0x7f1523ee2d98]
/usr/lib/R/lib/libR.so(+0xe5530)[0x7f1523ee3530]
/usr/lib/R/lib/libR.so(Rf_eval+0x598)[0x7f1523ee3238]
/usr/lib/R/lib/libR.so(+0x11a955)[0x7f1523f18955]
/usr/lib/R/lib/libR.so(+0xdcf50)[0x7f1523edaf50]
/usr/lib/R/lib/libR.so(Rf_eval+0xf8)[0x7f1523ee2d98]
/usr/lib/R/lib/libR.so(Rf_applyClosure+0x346)[0x7f1523ee4056]
/usr/lib/R/lib/libR.so(+0xdbfc6)[0x7f1523ed9fc6]
/usr/lib/R/lib/libR.so(Rf_eval+0xf8)[0x7f1523ee2d98]
/usr/lib/R/lib/libR.so(Rf_applyClosure+0x346)[0x7f1523ee4056]
/usr/lib/R/lib/libR.so(+0x11a3bb)[0x7f1523f183bb]
/usr/lib/R/lib/libR.so(+0x11a811)[0x7f1523f18811]
/usr/lib/R/lib/libR.so(+0xdcf50)[0x7f1523edaf50]
/usr/lib/R/lib/libR.so(Rf_eval+0xf8)[0x7f1523ee2d98]
/usr/lib/R/lib/libR.so(Rf_applyClosure+0x346)[0x7f1523ee4056]
/usr/lib/R/lib/libR.so(Rf_eval+0x26d)[0x7f1523ee2f0d]
/usr/lib/R/lib/libR.so(+0xe7d18)[0x7f1523ee5d18]
/usr/lib/R/lib/libR.so(Rf_eval+0x42d)[0x7f1523ee30cd]
/usr/lib/R/lib/libR.so(Rf_ReplIteration+0x1bd)[0x7f1523f0bbbd]
/usr/lib/R/lib/libR.so(+0x10ded1)[0x7f1523f0bed1]
/usr/lib/R/lib/libR.so(run_Rmainloop+0x44)[0x7f1523f0bf64]
/usr/lib/R/bin/exec/R(main+0x1b)[0x40082b]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5)[0x7f152383bec5]
/usr/lib/R/bin/exec/R[0x40085b]
======= Memory map: ========
00400000-00401000 r-xp 00000000 08:01 301486                             /usr/lib/R/bin/exec/R
00600000-00601000 r--p 00000000 08:01 301486                             /usr/lib/R/bin/exec/R
00601000-00602000 rw-p 00001000 08:01 301486                             /usr/lib/R/bin/exec/R
02243000-03b82000 rw-p 00000000 00:00 0                                  [heap]
7f151f137000-7f151f172000 r-xp 00000000 08:01 274513                     /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f151f172000-7f151f371000 ---p 0003b000 08:01 274513                     /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f151f371000-7f151f372000 r--p 0003a000 08:01 274513                     /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f151f372000-7f151f373000 rw-p 0003b000 08:01 274513                     /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f151f373000-7f151f389000 r-xp 00000000 08:01 138163                     /lib/x86_64-linux-gnu/libgcc_s.so.1
7f151f389000-7f151f588000 ---p 00016000 08:01 138163                     /lib/x86_64-linux-gnu/libgcc_s.so.1
7f151f588000-7f151f589000 rw-p 00015000 08:01 138163                     /lib/x86_64-linux-gnu/libgcc_s.so.1
7f151f589000-7f151f69f000 r-xp 00000000 08:01 264669                     /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f151f69f000-7f151f89f000 ---p 00116000 08:01 264669                     /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f151f89f000-7f151f8a0000 r--p 00116000 08:01 264669                     /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f151f8a0000-7f151f8a2000 rw-p 00117000 08:01 264669                     /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f151f8a2000-7f151fe3a000 r-xp 00000000 08:01 300537                     /usr/lib/lapack/liblapack.so.3.0
7f151fe3a000-7f1520039000 ---p 00598000 08:01 300537                     /usr/lib/lapack/liblapack.so.3.0
7f1520039000-7f152003a000 r--p 00597000 08:01 300537                     /usr/lib/lapack/liblapack.so.3.0
7f152003a000-7f152003e000 rw-p 00598000 08:01 300537                     /usr/lib/lapack/liblapack.so.3.0
7f152003e000-7f15200fc000 r-xp 00000000 08:01 301108                     /usr/lib/R/library/stats/libs/stats.so
7f15200fc000-7f15202fc000 ---p 000be000 08:01 301108                     /usr/lib/R/library/stats/libs/stats.so
7f15202fc000-7f15202fe000 r--p 000be000 08:01 301108                     /usr/lib/R/library/stats/libs/stats.so
7f15202fe000-7f1520300000 rw-p 000c0000 08:01 301108                     /usr/lib/R/library/stats/libs/stats.so
7f1520300000-7f1520347000 r-xp 00000000 08:01 301217                     /usr/lib/R/library/graphics/libs/graphics.so
7f1520347000-7f1520546000 ---p 00047000 08:01 301217                     /usr/lib/R/library/graphics/libs/graphics.so
7f1520546000-7f1520547000 r--p 00046000 08:01 301217                     /usr/lib/R/library/graphics/libs/graphics.so
7f1520547000-7f1520548000 rw-p 00047000 08:01 301217                     /usr/lib/R/library/graphics/libs/graphics.so
7f1520548000-7f1520582000 r-xp 00000000 08:01 301256                     /usr/lib/R/library/grDevices/libs/grDevices.so
7f1520582000-7f1520782000 ---p 0003a000 08:01 301256                     /usr/lib/R/library/grDevices/libs/grDevices.so
7f1520782000-7f1520787000 r--p 0003a000 08:01 301256                     /usr/lib/R/library/grDevices/libs/grDevices.so
7f1520787000-7f1520789000 rw-p 0003f000 08:01 301256                     /usr/lib/R/library/grDevices/libs/grDevices.so
7f1520789000-7f152078a000 rw-p 00000000 00:00 0 
7f15208c7000-7f15208c9000 r-xp 00000000 08:01 400578                     /usr/lib/x86_64-linux-gnu/gconv/ISO8859-1.so
7f15208c9000-7f1520ac8000 ---p 00002000 08:01 400578                     /usr/lib/x86_64-linux-gnu/gconv/ISO8859-1.so
7f1520ac8000-7f1520ac9000 r--p 00001000 08:01 400578                     /usr/lib/x86_64-linux-gnu/gconv/ISO8859-1.so
7f1520ac9000-7f1520aca000 rw-p 00002000 08:01 400578                     /usr/lib/x86_64-linux-gnu/gconv/ISO8859-1.so
7f1520aca000-7f1520bd3000 rw-p 00000000 00:00 0 
7f1520bd3000-7f1520bdb000 r-xp 00000000 08:01 300959                     /usr/lib/R/library/methods/libs/methods.so
7f1520bdb000-7f1520dda000 ---p 00008000 08:01 300959                     /usr/lib/R/library/methods/libs/methods.so
7f1520dda000-7f1520ddb000 r--p 00007000 08:01 300959                     /usr/lib/R/library/methods/libs/methods.so
7f1520ddb000-7f1520ddc000 rw-p 00008000 08:01 300959                     /usr/lib/R/library/methods/libs/methods.so
7f1520ddc000-7f1520de8000 r-xp 00000000 08:01 301185                     /usr/lib/R/library/utils/libs/utils.so
7f1520de8000-7f1520fe7000 ---p 0000c000 08:01 301185                     /usr/lib/R/library/utils/libs/utils.so
7f1520fe7000-7f1520fe8000 r--p 0000b000 08:01 301185                     /usr/lib/R/library/utils/libs/utils.so
7f1520fe8000-7f1520fe9000 rw-p 0000c000 08:01 301185                     /usr/lib/R/library/utils/libs/utils.so
7f1520fe9000-7f1520fea000 rw-p 00000000 00:00 0 
7f1520fea000-7f1520ff5000 r-xp 00000000 08:01 138211                     /lib/x86_64-linux-gnu/libnss_files-2.19.so
7f1520ff5000-7f15211f4000 ---p 0000b000 08:01 138211                     /lib/x86_64-linux-gnu/libnss_files-2.19.so
7f15211f4000-7f15211f5000 r--p 0000a000 08:01 138211                     /lib/x86_64-linux-gnu/libnss_files-2.19.so
7f15211f5000-7f15211f6000 rw-p 0000b000 08:01 138211                     /lib/x86_64-linux-gnu/libnss_files-2.19.so
7f15211f6000-7f1521201000 r-xp 00000000 08:01 138221                     /lib/x86_64-linux-gnu/libnss_nis-2.19.so
7f1521201000-7f1521400000 ---p 0000b000 08:01 138221                     /lib/x86_64-linux-gnu/libnss_nis-2.19.so
7f1521400000-7f1521401000 r--p 0000a000 08:01 138221                     /lib/x86_64-linux-gnu/libnss_nis-2.19.so
7f1521401000-7f1521402000 rw-p 0000b000 08:01 138221                     /lib/x86_64-linux-gnu/libnss_nis-2.19.so
7f152147d000-7f1521494000 r-xp 00000000 08:01 138205                     /lib/x86_64-linux-gnu/libnsl-2.19.so
7f1521494000-7f1521693000 ---p 00017000 08:01 138205                     /lib/x86_64-linux-gnu/libnsl-2.19.so
7f1521693000-7f1521694000 r--p 00016000 08:01 138205                     /lib/x86_64-linux-gnu/libnsl-2.19.so
7f1521694000-7f1521695000 rw-p 00017000 08:01 138205                     /lib/x86_64-linux-gnu/libnsl-2.19.so
7f1521695000-7f1521697000 rw-p 00000000 00:00 0 
7f1521697000-7f15216a0000 r-xp 00000000 08:01 138207                     /lib/x86_64-linux-gnu/libnss_compat-2.19.so
7f15216a0000-7f152189f000 ---p 00009000 08:01 138207                     /lib/x86_64-linux-gnu/libnss_compat-2.19.so
7f152189f000-7f15218a0000 r--p 00008000 08:01 138207                     /lib/x86_64-linux-gnu/libnss_compat-2.19.so
7f15218a0000-7f15218a1000 rw-p 00009000 08:01 138207                     /lib/x86_64-linux-gnu/libnss_compat-2.19.so
7f15218a1000-7f1521f84000 r--p 00000000 08:01 271098                     /usr/lib/locale/locale-archive
7f1521f84000-7f1521fa9000 r-xp 00000000 08:01 138282                     /lib/x86_64-linux-gnu/libtinfo.so.5.9
7f1521fa9000-7f15221a8000 ---p 00025000 08:01 138282                     /lib/x86_64-linux-gnu/libtinfo.so.5.9
7f15221a8000-7f15221ac000 r--p 00024000 08:01 138282                     /lib/x86_64-linux-gnu/libtinfo.so.5.9
7f15221ac000-7f15221ad000 rw-p 00028000 08:01 138282                     /lib/x86_64-linux-gnu/libtinfo.so.5.9
7f15221ad000-7f15221ba000 r-xp 00000000 08:01 274120                     /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f15221ba000-7f15223ba000 ---p 0000d000 08:01 274120                     /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f15223ba000-7f15223bb000 r--p 0000d000 08:01 274120                     /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f15223bb000-7f15223bc000 rw-p 0000e000 08:01 274120                     /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f15223bc000-7f15223bf000 r-xp 00000000 08:01 138153                     /lib/x86_64-linux-gnu/libdl-2.19.so
7f15223bf000-7f15225be000 ---p 00003000 08:01 138153                     /lib/x86_64-linux-gnu/libdl-2.19.so
7f15225be000-7f15225bf000 r--p 00002000 08:01 138153                     /lib/x86_64-linux-gnu/libdl-2.19.so
7f15225bf000-7f15225c0000 rw-p 00003000 08:01 138153                     /lib/x86_64-linux-gnu/libdl-2.19.so
7f15225c0000-7f15225c7000 r-xp 00000000 08:01 138264                     /lib/x86_64-linux-gnu/librt-2.19.so
7f15225c7000-7f15227c6000 ---p 00007000 08:01 138264                     /lib/x86_64-linux-gnu/librt-2.19.so
7f15227c6000-7f15227c7000 r--p 00006000 08:01 138264                     /lib/x86_64-linux-gnu/librt-2.19.so
7f15227c7000-7f15227c8000 rw-p 00007000 08:01 138264                     /lib/x86_64-linux-gnu/librt-2.19.so
7f15227c8000-7f15227e0000 r-xp 00000000 08:01 138299                     /lib/x86_64-linux-gnu/libz.so.1.2.8
7f15227e0000-7f15229df000 ---p 00018000 08:01 138299                     /lib/x86_64-linux-gnu/libz.so.1.2.8
7f15229df000-7f15229e0000 r--p 00017000 08:01 138299                     /lib/x86_64-linux-gnu/libz.so.1.2.8
7f15229e0000-7f15229e1000 rw-p 00018000 08:01 138299                     /lib/x86_64-linux-gnu/libz.so.1.2.8
7f15229e1000-7f15229f0000 r-xp 00000000 08:01 138135                     /lib/x86_64-linux-gnu/libbz2.so.1.0.4
7f15229f0000-7f1522bef000 ---p 0000f000 08:01 138135                     /lib/x86_64-linux-gnu/libbz2.so.1.0.4
7f1522bef000-7f1522bf0000 r--p 0000e000 08:01 138135                     /lib/x86_64-linux-gnu/libbz2.so.1.0.4
7f1522bf0000-7f1522bf1000 rw-p 0000f000 08:01 138135                     /lib/x86_64-linux-gnu/libbz2.so.1.0.4
7f1522bf1000-7f1522c12000 r-xp 00000000 08:01 138183                     /lib/x86_64-linux-gnu/liblzma.so.5.0.0
7f1522c12000-7f1522e11000 ---p 00021000 08:01 138183                     /lib/x86_64-linux-gnu/liblzma.so.5.0.0
7f1522e11000-7f1522e12000 r--p 00020000 08:01 138183                     /lib/x86_64-linux-gnu/liblzma.so.5.0.0
7f1522e12000-7f1522e13000 rw-p 00021000 08:01 138183                     /lib/x86_64-linux-gnu/liblzma.so.5.0.0
7f1522e13000-7f1522e50000 r-xp 00000000 08:01 138239                     /lib/x86_64-linux-gnu/libpcre.so.3.13.1
7f1522e50000-7f152304f000 ---p 0003d000 08:01 138239                     /lib/x86_64-linux-gnu/libpcre.so.3.13.1
7f152304f000-7f1523050000 r--p 0003c000 08:01 138239                     /lib/x86_64-linux-gnu/libpcre.so.3.13.1
7f1523050000-7f1523051000 rw-p 0003d000 08:01 138239                     /lib/x86_64-linux-gnu/libpcre.so.3.13.1
7f1523051000-7f152308e000 r-xp 00000000 08:01 138261                     /lib/x86_64-linux-gnu/libreadline.so.6.3
7f152308e000-7f152328e000 ---p 0003d000 08:01 138261                     /lib/x86_64-linux-gnu/libreadline.so.6.3
7f152328e000-7f1523290000 r--p 0003d000 08:01 138261                     /lib/x86_64-linux-gnu/libreadline.so.6.3
7f1523290000-7f1523296000 rw-p 0003f000 08:01 138261                     /lib/x86_64-linux-gnu/libreadline.so.6.3
7f1523296000-7f1523297000 rw-p 00000000 00:00 0 
7f1523297000-7f152339c000 r-xp 00000000 08:01 138186                     /lib/x86_64-linux-gnu/libm-2.19.so
7f152339c000-7f152359b000 ---p 00105000 08:01 138186                     /lib/x86_64-linux-gnu/libm-2.19.so
7f152359b000-7f152359c000 r--p 00104000 08:01 138186                     /lib/x86_64-linux-gnu/libm-2.19.so
7f152359c000-7f152359d000 rw-p 00105000 08:01 138186                     /lib/x86_64-linux-gnu/libm-2.19.so
7f152359d000-7f1523619000 r-xp 00000000 08:01 300518                     /usr/lib/libblas/libblas.so.3.0
7f1523619000-7f1523818000 ---p 0007c000 08:01 300518                     /usr/lib/libblas/libblas.so.3.0
7f1523818000-7f1523819000 r--p 0007b000 08:01 300518                     /usr/lib/libblas/libblas.so.3.0
7f1523819000-7f152381a000 rw-p 0007c000 08:01 300518                     /usr/lib/libblas/libblas.so.3.0
7f152381a000-7f15239d6000 r-xp 00000000 08:01 138136                     /lib/x86_64-linux-gnu/libc-2.19.so
7f15239d6000-7f1523bd5000 ---p 001bc000 08:01 138136                     /lib/x86_64-linux-gnu/libc-2.19.so
7f1523bd5000-7f1523bd9000 r--p 001bb000 08:01 138136                     /lib/x86_64-linux-gnu/libc-2.19.so
7f1523bd9000-7f1523bdb000 rw-p 001bf000 08:01 138136                     /lib/x86_64-linux-gnu/libc-2.19.so
7f1523bdb000-7f1523be0000 rw-p 00000000 00:00 0 
7f1523be0000-7f1523bf9000 r-xp 00000000 08:01 138256                     /lib/x86_64-linux-gnu/libpthread-2.19.so
7f1523bf9000-7f1523df8000 ---p 00019000 08:01 138256                     /lib/x86_64-linux-gnu/libpthread-2.19.so
7f1523df8000-7f1523df9000 r--p 00018000 08:01 138256                     /lib/x86_64-linux-gnu/libpthread-2.19.so
7f1523df9000-7f1523dfa000 rw-p 00019000 08:01 138256                     /lib/x86_64-linux-gnu/libpthread-2.19.so
7f1523dfa000-7f1523dfe000 rw-p 00000000 00:00 0 
7f1523dfe000-7f1524053000 r-xp 00000000 08:01 301472                     /usr/lib/R/lib/libR.so
7f1524053000-7f1524253000 ---p 00255000 08:01 301472                     /usr/lib/R/lib/libR.so
7f1524253000-7f1524258000 r--p 00255000 08:01 301472                     /usr/lib/R/lib/libR.so
7f1524258000-7f1524262000 rw-p 0025a000 08:01 301472                     /usr/lib/R/lib/libR.so
7f1524262000-7f152434e000 rw-p 00000000 00:00 0 
7f152434e000-7f1524371000 r-xp 00000000 08:01 138112                     /lib/x86_64-linux-gnu/ld-2.19.so
7f15243a9000-7f152455a000 rw-p 00000000 00:00 0 
7f1524564000-7f1524565000 rw-p 00000000 00:00 0 
7f1524565000-7f1524566000 r--p 00000000 08:01 300955                     /usr/lib/R/library/translations/en/LC_MESSAGES/R.mo
7f1524566000-7f152456d000 r--s 00000000 08:01 400634                     /usr/lib/x86_64-linux-gnu/gconv/gconv-modules.cache
7f152456d000-7f1524570000 rw-p 00000000 00:00 0 
7f1524570000-7f1524571000 r--p 00022000 08:01 138112                     /lib/x86_64-linux-gnu/ld-2.19.so
7f1524571000-7f1524572000 rw-p 00023000 08:01 138112                     /lib/x86_64-linux-gnu/ld-2.19.so
7f1524572000-7f1524573000 rw-p 00000000 00:00 0 
7fffe1752000-7fffe177e000 rw-p 00000000 00:00 0                          [stack]
7fffe17fe000-7fffe1800000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
A
Comment 1 Brian Ripley 2015-04-22 14:15:24 UTC
R 3.0.2 is not R 3.1.3 and neither are current. Please try 3.2.0 and if that fails tell us all the information from sessionInfo().

[There are relevant fixes in R 3.2.0 for non-English locales.]
Comment 2 Harold Ship 2015-06-28 06:48:11 UTC
I seem to be experiencing the same root problem when I try to load library(spatstat) on my Ubuntu 12.04.5 VM under R 3.2.1.

I have had a conversation on R-sig-geo with Adrian Baddeley and Ege Rubak and we concluded that it the same issue, although the error message I get is different.

This is my Ubuntu version:
Distributor ID:	Ubuntu
Description:	Ubuntu 12.04.5 LTS
Release:	12.04
Codename:	precise

This is my R version:
R version 3.2.1 (2015-06-18) -- "World-Famous Astronaut"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

I can reproduce the error using:
a<-as.POSIXct('2015-06-26')
** stack smashing detected ***: /usr/lib/R/bin/exec/R terminated
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x37)[0x7f74d3ee5e57]
/lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x0)[0x7f74d3ee5e20]
/usr/lib/R/lib/libR.so(+0xc9825)[0x7f74d4480825]
/usr/lib/R/lib/libR.so(+0x10d212)[0x7f74d44c4212]
/usr/lib/R/lib/libR.so(+0x117d90)[0x7f74d44ced90]
/usr/lib/R/lib/libR.so(Rf_applyClosure+0x5e5)[0x7f74d44d4295]
/usr/lib/R/lib/libR.so(+0x110c28)[0x7f74d44c7c28]
/usr/lib/R/lib/libR.so(+0x117d90)[0x7f74d44ced90]
/usr/lib/R/lib/libR.so(Rf_applyClosure+0x5e5)[0x7f74d44d4295]
/usr/lib/R/lib/libR.so(+0x14dc3b)[0x7f74d4504c3b]
/usr/lib/R/lib/libR.so(+0x14e09d)[0x7f74d450509d]
/usr/lib/R/lib/libR.so(+0x14e35d)[0x7f74d450535d]
/usr/lib/R/lib/libR.so(+0x10cfed)[0x7f74d44c3fed]
/usr/lib/R/lib/libR.so(+0x117d90)[0x7f74d44ced90]
/usr/lib/R/lib/libR.so(Rf_applyClosure+0x5e5)[0x7f74d44d4295]
/usr/lib/R/lib/libR.so(+0x110c28)[0x7f74d44c7c28]
/usr/lib/R/lib/libR.so(+0x117d90)[0x7f74d44ced90]
/usr/lib/R/lib/libR.so(+0x11863b)[0x7f74d44cf63b]
/usr/lib/R/lib/libR.so(+0x117eec)[0x7f74d44ceeec]
/usr/lib/R/lib/libR.so(+0x14e5b3)[0x7f74d45055b3]
/usr/lib/R/lib/libR.so(+0x10cfed)[0x7f74d44c3fed]
/usr/lib/R/lib/libR.so(+0x117d90)[0x7f74d44ced90]
/usr/lib/R/lib/libR.so(Rf_applyClosure+0x5e5)[0x7f74d44d4295]
/usr/lib/R/lib/libR.so(+0x110c28)[0x7f74d44c7c28]
/usr/lib/R/lib/libR.so(+0x117d90)[0x7f74d44ced90]
/usr/lib/R/lib/libR.so(Rf_applyClosure+0x5e5)[0x7f74d44d4295]
/usr/lib/R/lib/libR.so(+0x14dc3b)[0x7f74d4504c3b]
/usr/lib/R/lib/libR.so(+0x14deef)[0x7f74d4504eef]
/usr/lib/R/lib/libR.so(+0x14e35d)[0x7f74d450535d]
/usr/lib/R/lib/libR.so(+0x10cfed)[0x7f74d44c3fed]
/usr/lib/R/lib/libR.so(+0x117d90)[0x7f74d44ced90]
/usr/lib/R/lib/libR.so(Rf_applyClosure+0x5e5)[0x7f74d44d4295]
/usr/lib/R/lib/libR.so(+0x117eb3)[0x7f74d44ceeb3]
/usr/lib/R/lib/libR.so(+0x11b7a6)[0x7f74d44d27a6]
/usr/lib/R/lib/libR.so(+0x118157)[0x7f74d44cf157]
/usr/lib/R/lib/libR.so(Rf_ReplIteration+0x1ea)[0x7f74d44f7c6a]
/usr/lib/R/lib/libR.so(+0x141030)[0x7f74d44f8030]
/usr/lib/R/lib/libR.so(run_Rmainloop+0x44)[0x7f74d44f8584]
/usr/lib/R/bin/exec/R(main+0x1b)[0x40074b]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7f74d3dfd76d]
/usr/lib/R/bin/exec/R[0x40077d]
======= Memory map: ========
00400000-00401000 r-xp 00000000 fc:00 3411492                            /usr/lib/R/bin/exec/R
00600000-00601000 r--p 00000000 fc:00 3411492                            /usr/lib/R/bin/exec/R
00601000-00602000 rw-p 00001000 fc:00 3411492                            /usr/lib/R/bin/exec/R
01711000-02d38000 rw-p 00000000 00:00 0                                  [heap]
7f74d00a0000-7f74d00d5000 r-xp 00000000 fc:00 2236075                    /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f74d00d5000-7f74d02d4000 ---p 00035000 fc:00 2236075                    /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f74d02d4000-7f74d02d5000 r--p 00034000 fc:00 2236075                    /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f74d02d5000-7f74d02d6000 rw-p 00035000 fc:00 2236075                    /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f74d02d6000-7f74d03ea000 r-xp 00000000 fc:00 2236078                    /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f74d03ea000-7f74d05ea000 ---p 00114000 fc:00 2236078                    /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f74d05ea000-7f74d05eb000 r--p 00114000 fc:00 2236078                    /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f74d05eb000-7f74d05ed000 rw-p 00115000 fc:00 2236078                    /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f74d05ed000-7f74d0ed2000 r-xp 00000000 fc:00 3542242                    /usr/lib/lapack/liblapack.so.3gf.0
7f74d0ed2000-7f74d10d1000 ---p 008e5000 fc:00 3542242                    /usr/lib/lapack/liblapack.so.3gf.0
7f74d10d1000-7f74d10d2000 r--p 008e4000 fc:00 3542242                    /usr/lib/lapack/liblapack.so.3gf.0
7f74d10d2000-7f74d10d6000 rw-p 008e5000 fc:00 3542242                    /usr/lib/lapack/liblapack.so.3gf.0
7f74d10d6000-7f74d11e3000 rw-p 00000000 00:00 0
7f74d11e3000-7f74d1284000 r-xp 00000000 fc:00 4066466                    /usr/lib/R/library/stats/libs/stats.so
7f74d1284000-7f74d1484000 ---p 000a1000 fc:00 4066466                    /usr/lib/R/library/stats/libs/stats.so
7f74d1484000-7f74d1486000 r--p 000a1000 fc:00 4066466                    /usr/lib/R/library/stats/libs/stats.so
7f74d1486000-7f74d1487000 rw-p 000a3000 fc:00 4066466                    /usr/lib/R/library/stats/libs/stats.so
7f74d1487000-7f74d15bb000 rw-p 00000000 00:00 0
7f74d15bb000-7f74d15f7000 r-xp 00000000 fc:00 4065986                    /usr/lib/R/library/graphics/libs/graphics.so
7f74d15f7000-7f74d17f7000 ---p 0003c000 fc:00 4065986                    /usr/lib/R/library/graphics/libs/graphics.so
7f74d17f7000-7f74d17f8000 r--p 0003c000 fc:00 4065986                    /usr/lib/R/library/graphics/libs/graphics.so
7f74d17f8000-7f74d17f9000 rw-p 0003d000 fc:00 4065986                    /usr/lib/R/library/graphics/libs/graphics.so
7f74d17f9000-7f74d1836000 r-xp 00000000 fc:00 4065800                    /usr/lib/R/library/grDevices/libs/grDevices.so
7f74d1836000-7f74d1a35000 ---p 0003d000 fc:00 4065800                    /usr/lib/R/library/grDevices/libs/grDevices.so
7f74d1a35000-7f74d1a3a000 r--p 0003c000 fc:00 4065800                    /usr/lib/R/library/grDevices/libs/grDevices.so
7f74d1a3a000-7f74d1a3c000 rw-p 00041000 fc:00 4065800                    /usr/lib/R/library/grDevices/libs/grDevices.so
7f74d1a3c000-7f74d1a3d000 rw-p 00000000 00:00 0
7f74d1a96000-7f74d1aab000 r-xp 00000000 fc:00 917548                     /lib/x86_64-linux-gnu/libgcc_s.so.1
7f74d1aab000-7f74d1caa000 ---p 00015000 fc:00 917548                     /lib/x86_64-linux-gnu/libgcc_s.so.1
7f74d1caa000-7f74d1cab000 r--p 00014000 fc:00 917548                     /lib/x86_64-linux-gnu/libgcc_s.so.1
7f74d1cab000-7f74d1cac000 rw-p 00015000 fc:00 917548                     /lib/x86_64-linux-gnu/libgcc_s.so.1
7f74d1cb5000-7f74d1cdc000 rw-p 00000000 00:00 0
7f74d1cdc000-7f74d1cde000 r-xp 00000000 fc:00 2238567                    /usr/lib/x86_64-linux-gnu/gconv/ISO8859-1.so
7f74d1cde000-7f74d1edd000 ---p 00002000 fc:00 2238567                    /usr/lib/x86_64-linux-gnu/gconv/ISO8859-1.so
7f74d1edd000-7f74d1ede000 r--p 00001000 fc:00 2238567                    /usr/lib/x86_64-linux-gnu/gconv/ISO8859-1.so
7f74d1ede000-7f74d1edf000 rw-p 00002000 fc:00 2238567                    /usr/lib/x86_64-linux-gnu/gconv/ISO8859-1.so
7f74d1edf000-7f74d1fd5000 rw-p 00000000 00:00 0
7f74d1fd5000-7f74d1fdd000 r-xp 00000000 fc:00 4066544                    /usr/lib/R/library/methods/libs/methods.so
7f74d1fdd000-7f74d21dc000 ---p 00008000 fc:00 4066544                    /usr/lib/R/library/methods/libs/methods.soAborted (core dumped)
Comment 3 Ege Rubak 2015-06-28 08:27:57 UTC
FYI: I cannot reproduce the error on my laptop running Linux Mint 17 (based on Ubuntu 14.04) 64 bit

I also tried installing Ubuntu 12.04.5 LTS in VMware Workstation and in VirtualBox and the bug wasn't reproducible there either.
Comment 4 Brian Ripley 2015-06-28 13:00:53 UTC
Please do not report on obsolete versions of R: since R 3.0.2 we have discovered issues with undefined-by-C99 behaviour of glibc that in some locales did overrun the stack.

We need to know at least the timezone you are using and the locale settings.  The output of sessionInfo() will show the latter.
Comment 5 Harold Ship 2015-06-28 13:52:32 UTC
this is my TZ
TZ=IST-2IDT,J86/02:00,J298/02:00

this is sessionInfo():
R version 3.2.1 (2015-06-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu precise (12.04.5 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
Comment 6 Brian Ripley 2015-06-28 21:59:03 UTC
So the issue is your timezone.  I suggest you use one of the simpler forms described in ?Sys.timezone.

We've worked around this in R-devel, and will port to R-patched in due course.