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akima core dumps on loading (PR#521)

2 messages · santini@dsi.unimi.it, Peter Dalgaard

Original
santini@dsi.unimi.it
# 
Full_Name: Massimo santini
Version: 1.0.1
OS: Linux
Submission from: (NULL) (159.149.147.89)


I've just dl the .rpm of R 1.0.1, installed it and then launched 

	insatll.packages("akima")

after re-launching R [--vanilla], the command

	library(akima)

has the only effect to coredump the program. Here is the output of gdb and
strace...

--- GDB (commands given can be seen from the except)

$ R -d gdb
GNU gdb 19991004
Copyright 1998 Free Software Foundation, Inc.
GDB is free software, covered by the GNU General Public License, and you are
welcome to change it and/or distribute copies of it under certain conditions.
Type "show copying" to see the conditions.
There is absolutely no warranty for GDB.  Type "show warranty" for details.
This GDB was configured as "i386-redhat-linux"...
(gdb) run --vanilla
Starting program: /usr/lib/R/bin/R.X11 --vanilla

R : Copyright 2000, The R Development Core Team
Version 1.0.1  (April 14, 2000)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type	"?license" or "?licence" for distribution details.

R is a collaborative project with many contributors.
Type	"?contributors" for a list.

Type	"demo()" for some demos, "help()" for on-line help, or
    	"help.start()" for a HTML browser interface to help.
Type	"q()" to quit R.
Program received signal SIGSEGV, Segmentation fault.
_dl_lookup_symbol (undef_name=0x2d2e3b3 <Address 0x2d2e3b3 out of bounds>,
ref=0xbfffabb4, 
    symbol_scope=0x81ec65c, reference_name=0x81e8b20
"/usr/lib/R/library/akima/libs/akima.so", reloc_type=208)
    at ../sysdeps/generic/dl-hash.h:31
31	../sysdeps/generic/dl-hash.h: No such file or directory.
(gdb) 

--- STRACE (echo "library(akima)" | strace R --vanilla)

[...]
rt_sigprocmask(SIG_BLOCK, NULL, [], 8)  = 0
stat("/usr/lib/R/library/akima/libs/akima.so", {st_mode=S_IFREG|0755,
st_size=289367, ...}) = 0
stat("/usr/lib/R/library/base/libs/akima.so", 0xbfffdb60) = -1 ENOENT (No such
file or directory)
rt_sigprocmask(SIG_BLOCK, NULL, [], 8)  = 0
rt_sigprocmask(SIG_BLOCK, NULL, [], 8)  = 0
rt_sigprocmask(SIG_BLOCK, NULL, [], 8)  = 0
rt_sigprocmask(SIG_BLOCK, NULL, [], 8)  = 0
rt_sigprocmask(SIG_BLOCK, NULL, [], 8)  = 0
rt_sigprocmask(SIG_BLOCK, NULL, [], 8)  = 0
rt_sigprocmask(SIG_SETMASK, [], NULL, 8) = 0
rt_sigprocmask(SIG_BLOCK, NULL, [], 8)  = 0
rt_sigprocmask(SIG_BLOCK, NULL, [], 8)  = 0
rt_sigprocmask(SIG_SETMASK, [], NULL, 8) = 0
open("/usr/lib/R/library/akima/libs/akima.so", O_RDONLY) = 4
fstat(4, {st_mode=S_IFREG|0755, st_size=289367, ...}) = 0
read(4, "\177ELF\1\1\1\0\0\0\0\0\0\0\0\0\3\0\3\0\1\0\0\0000F\0\000"..., 4096) =
4096
old_mmap(NULL, 115364, PROT_READ|PROT_EXEC, MAP_PRIVATE, 4, 0) = 0x40f3d000
mprotect(0x40f55000, 17060, PROT_NONE)  = 0
old_mmap(0x40f55000, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED, 4,
0x17000) = 0x40f55000
old_mmap(0x40f57000, 8868, PROT_READ|PROT_WRITE,
MAP_PRIVATE|MAP_FIXED|MAP_ANONYMOUS, -1, 0) = 0x40f57000
close(4)                                = 0
mprotect(0x40f3d000, 98304, PROT_READ|PROT_WRITE) = 0
--- SIGSEGV (Segmentation fault) ---
+++ killed by SIGSEGV +++

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Peter Dalgaard
# 
santini@dsi.unimi.it writes:
Hmm. Doesn't happen here. (BTW: Remember to include as much
information about your system as you can think of. It's not obvious
whether you're running RedHat or SuSE for instance and in what
version.)
This would seem to be the problem: the dynamic library isn't there.
Did you get any error messages while compiling the package? (Except
for "...might be used uninitialized..." of which there are quite a few
here too).