[Rd] *** buffer overflow detected ***: /usr/lib64/R/bin/exec/R terminated on R 2.6.2 to 2.8.0: logging a bug?

From: Corrado <ct529_at_york.ac.uk>
Date: Fri, 31 Oct 2008 11:17:17 +0000


Dear friends,

there is a serious problem with RODBC on R from 2.6.2 to 2.8.0 on a postgresql 8.3 database.

Let's say we define an empty dsn called "test", with user "postgres" and password "none". We test the connection with another application, and it works properly.

When you call the database using RODBC, you get the following:

> odbcConnect("test","postgres","none")
*** buffer overflow detected ***: /usr/lib64/R/bin/exec/R terminated ======= Backtrace: =========
/lib64/libc.so.6(__fortify_fail+0x37)[0x2ad38a3f4157]
/lib64/libc.so.6[0x2ad38a3f27e0]
/lib64/libc.so.6[0x2ad38a3f1db9]
/lib64/libc.so.6(_IO_default_xsputn+0x8e)[0x2ad38a379b5e]
/lib64/libc.so.6(_IO_vfprintf+0x3c22)[0x2ad38a351fa2]
/lib64/libc.so.6(__vsprintf_chk+0x9d)[0x2ad38a3f1e5d]
/lib64/libc.so.6(__sprintf_chk+0x80)[0x2ad38a3f1da0]
/usr/lib64/libodbcpsql.so.2(SQLGetInfo+0x973)[0x2ad38de11013]
/usr/lib64/libodbc.so.1(SQLGetInfo+0x624)[0x2ad38c5e91a4]
/usr/lib64/R/library/RODBC/libs/RODBC.so(RODBCGetInfo+0xbb)[0x2ad38c393a9b]
/usr/lib64/R/lib/libR.so[0x2ad389c2562d]

/usr/lib64/R/lib/libR.so(Rf_eval+0x6a1)[0x2ad389c4ef31]
/usr/lib64/R/lib/libR.so[0x2ad389c51dc3]
/usr/lib64/R/lib/libR.so(Rf_eval+0x474)[0x2ad389c4ed04]
/usr/lib64/R/lib/libR.so[0x2ad389c5014c]
/usr/lib64/R/lib/libR.so(Rf_eval+0x474)[0x2ad389c4ed04]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x2aa)[0x2ad389c5268a]
/usr/lib64/R/lib/libR.so(Rf_eval+0x38c)[0x2ad389c4ec1c]
/usr/lib64/R/lib/libR.so[0x2ad389c5014c]
/usr/lib64/R/lib/libR.so(Rf_eval+0x474)[0x2ad389c4ed04]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x2aa)[0x2ad389c5268a]
/usr/lib64/R/lib/libR.so(Rf_eval+0x38c)[0x2ad389c4ec1c]
/usr/lib64/R/lib/libR.so(Rf_ReplIteration+0x1c3)[0x2ad389c733c3]
/usr/lib64/R/lib/libR.so(run_Rmainloop+0xd1)[0x2ad389c736d1]
/usr/lib64/R/bin/exec/R(main+0x2b)[0x4008bb]
/lib64/libc.so.6(__libc_start_main+0xf4)[0x2ad38a32a074]
/usr/lib64/R/bin/exec/R[0x400769]


======= Memory map: ========
00400000-00401000 r-xp 00000000 08:02

815595                             /usr/lib64/R/bin/exec/R
00600000-00601000 rw-p 00000000 08:02 
815595                             /usr/lib64/R/bin/exec/R
00601000-01bf3000 rw-p 00601000 00:00 0                                  
[heap]
2ad38995c000-2ad389976000 r-xp 00000000 08:02
2044002                    /lib64/ld-2.7.so
2ad389976000-2ad389978000 rw-p 2ad389976000 00:00 0 2ad389b75000-2ad389b76000 r--p 00019000 08:02
2044002                    /lib64/ld-2.7.so
2ad389b76000-2ad389b77000 rw-p 0001a000 08:02 
2044002                    /lib64/ld-2.7.so
2ad389b77000-2ad389e03000 r-xp 00000000 08:02 
878425                     /usr/lib64/R/lib/libR.so
2ad389e03000-2ad38a002000 ---p 0028c000 08:02 
878425                     /usr/lib64/R/lib/libR.so
2ad38a002000-2ad38a016000 rw-p 0028b000 08:02 
878425                     /usr/lib64/R/lib/libR.so
2ad38a016000-2ad38a0af000 rw-p 2ad38a016000 00:00 0 2ad38a0af000-2ad38a0db000 r-xp 00000000 08:02
878426                     /usr/lib64/R/lib/libRblas.so
2ad38a0db000-2ad38a2da000 ---p 0002c000 08:02 
878426                     /usr/lib64/R/lib/libRblas.so
2ad38a2da000-2ad38a2db000 rw-p 0002b000 08:02 
878426                     /usr/lib64/R/lib/libRblas.so
2ad38a2db000-2ad38a2dc000 r--p 00000000 08:02 
892499                     /usr/share/locale/en_GB.UTF-8/LC_MESSAGES/SYS_LC_MESSAGES
2ad38a2dc000-2ad38a2e3000 r--s 00000000 08:02 
654700                     /usr/lib64/gconv/gconv-modules.cache
2ad38a30b000-2ad38a30c000 rw-p 2ad38a30b000 00:00 0 2ad38a30c000-2ad38a457000 r-xp 00000000 08:02
2044009                    /lib64/libc-2.7.so
2ad38a457000-2ad38a656000 ---p 0014b000 08:02 
2044009                    /lib64/libc-2.7.so
2ad38a656000-2ad38a65a000 r--p 0014a000 08:02 
2044009                    /lib64/libc-2.7.so
2ad38a65a000-2ad38a65b000 rw-p 0014e000 08:02 
2044009                    /lib64/libc-2.7.so
2ad38a65b000-2ad38a660000 rw-p 2ad38a65b000 00:00 0 2ad38a660000-2ad38a718000 r-xp 00000000 08:02
2396466                    /usr/lib64/libgfortran.so.2.0.0
2ad38a718000-2ad38a917000 ---p 000b8000 08:02 
2396466                    /usr/lib64/libgfortran.so.2.0.0
2ad38a917000-2ad38a919000 rw-p 000b7000 08:02 
2396466                    /usr/lib64/libgfortran.so.2.0.0
2ad38a919000-2ad38a998000 r-xp 00000000 08:02 
2044017                    /lib64/libm-2.7.so
2ad38a998000-2ad38ab98000 ---p 0007f000 08:02 
2044017                    /lib64/libm-2.7.so
2ad38ab98000-2ad38ab99000 r--p 0007f000 08:02 
2044017                    /lib64/libm-2.7.so
2ad38ab99000-2ad38ab9a000 rw-p 00080000 08:02 
2044017                    /lib64/libm-2.7.so
2ad38ab9a000-2ad38ab9b000 rw-p 2ad38ab9a000 00:00 0 2ad38ab9b000-2ad38abd1000 r-xp 00000000 08:02
2044184                    /lib64/libreadline.so.5.2
2ad38abd1000-2ad38add0000 ---p 00036000 08:02 
2044184                    /lib64/libreadline.so.5.2
2ad38add0000-2ad38add8000 rw-p 00035000 08:02 
2044184                    /lib64/libreadline.so.5.2
2ad38add8000-2ad38add9000 rw-p 2ad38add8000 00:00 0 2ad38add9000-2ad38ae23000 r-xp 00000000 08:02
2044157                    /lib64/libncurses.so.5.6
2ad38ae23000-2ad38b022000 ---p 0004a000 08:02 
2044157                    /lib64/libncurses.so.5.6
2ad38b022000-2ad38b027000 rw-p 00049000 08:02 
2044157                    /lib64/libncurses.so.5.6
2ad38b027000-2ad38b04d000 r-xp 00000000 08:02 
2044050                    /lib64/libpcre.so.0.0.1
2ad38b04d000-2ad38b24c000 ---p 00026000 08:02 
2044050                    /lib64/libpcre.so.0.0.1
2ad38b24c000-2ad38b24d000 rw-p 00025000 08:02 
2044050                    /lib64/libpcre.so.0.0.1
2ad38b24d000-2ad38b24e000 rw-p 2ad38b24d000 00:00 0 2ad38b24e000-2ad38b262000 r-xp 00000000 08:02
2044118                    /lib64/libz.so.1.2.3
2ad38b262000-2ad38b461000 ---p 00014000 08:02 
2044118                    /lib64/libz.so.1.2.3
2ad38b461000-2ad38b462000 rw-p 00013000 08:02 
2044118                    /lib64/libz.so.1.2.3
2ad38b462000-2ad38b464000 r-xp 00000000 08:02 
2044015                    /lib64/libdl-2.7.so
2ad38b464000-2ad38b664000 ---p 00002000 08:02 
2044015                    /lib64/libdl-2.7.so
2ad38b664000-2ad38b665000 r--p 00002000 08:02 
2044015                    /lib64/libdl-2.7.so
2ad38b665000-2ad38b666000 rw-p 00003000 08:02 
2044015                    /lib64/libdl-2.7.so
2ad38b666000-2ad38b668000 rw-p 2ad38b666000 00:00 0 2ad38b668000-2ad38b6a7000 r--p 00000000 08:02
720800                     /usr/share/locale/UTF-8/LC_CTYPE
2ad38b6a7000-2ad38b78b000 r--p 00000000 08:02 
720801                     /usr/share/locale/UTF-8/LC_COLLATE
2ad38b78b000-2ad38b78c000 r--p 00000000 08:02 
892249                     /usr/share/locale/en_GB.UTF-8/LC_TIME
2ad38b78c000-2ad38b78d000 r--p 00000000 08:02 
892496                     /usr/share/locale/en_GB.UTF-8/LC_PAPER
2ad38b78d000-2ad38b78e000 r--p 00000000 08:02 
892500                     /usr/share/locale/en_GB.UTF-8/LC_MAborted
ct529_at_localhost:~$                                     

OS: Mandriva 2008.1 x86_64
Postgresql: 8.3.1 (PostGIS enabled)
R: from 2.6.2 from repository to 2.8.0 repackaged

Is it my doing, or R's doing?

Best,

-- 
Corrado Topi

Global Climate Change & Biodiversity Indicators
Area 18,Department of Biology
University of York, York, YO10 5YW, UK
Phone: + 44 (0) 1904 328645, E-mail: ct529_at_york.ac.uk

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Received on Fri 31 Oct 2008 - 11:24:36 GMT

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