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...
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(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.
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> library(akima)
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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santini@dsi.unimi.it writes:> 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...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.)> 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)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). -- O__ ---- Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard@biostat.ku.dk) FAX: (+45) 35327907 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-devel mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-devel-request@stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
Massimo Santini <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.) > > You are perfectly right. My system is an updated RedHat 6.2.Same here...> > > 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) > > > > 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). > > Non errors during the installation phase. The akima.so library is in > > /usr/lib/R/library/akima/libs/akima.so > > where it should be (with correct premissions), but is not in > > /usr/lib/R/library/base/libs/akima.so > > (the dir /usr/lib/R/library/base/libs is missing, to be precise).Oh. Didn't see that. Then that part is OK. Sorry.> Have you some hint about what to do now?Hmmm. Interesting: I can provoke the crash on *my other* RedHat6.2 computer (the one still running the egcs compiler). My stack trace says #0 _dl_lookup_symbol ( undef_name=0xcbf203b4 <Address 0xcbf203b4 out of bounds>, ref=0xbfffb234, symbol_scope=0x81d3cac, reference_name=0x81d3a60 "/usr/local/src/misc/r-release/BUILD/library/akima/libs/akima.so", reloc_type=64) at ../sysdeps/generic/dl-hash.h:31 #1 0x400096ad in _dl_relocate_object (l=0x81d3aa8, scope=0x81d3cac, lazy=0, consider_profiling=0) at ../sysdeps/i386/dl-machine.h:326 #2 0x40255be4 in dl_open_worker (a=0xbfffb3a0) at dl-open.c:182 #3 0x4000ac3b in _dl_catch_error (errstring=0xbfffb39c, operate=0x40255990 <dl_open_worker>, args=0xbfffb3a0) at dl-error.c:141 #4 0x40255d3d in _dl_open ( file=0xbfffc51c "/usr/local/src/misc/r-release/BUILD/library/akima/libs/akima.so", mode=2, caller=0xbfffb39c) at dl-open.c:232 #5 0x401323d3 in dlopen_doit (a=0xbfffb4b0) at dlopen.c:41 #6 0x4000ac3b in _dl_catch_error (errstring=0x40134080, operate=0x401323a8 <dlopen_doit>, args=0xbfffb4b0) at dl-error.c:141 #7 0x401328b9 in _dlerror_run (operate=0x401323a8 <dlopen_doit>, args=0xbfffb4b0) at dlerror.c:125 #8 0x40132393 in __dlopen_check ( file=0xbfffc51c "/usr/local/src/misc/r-release/BUILD/library/akima/libs/akima.so", mode=2) at dlopen.c:53 #9 0x80d9cc3 in AddDLL ( path=0xbfffc51c "/usr/local/src/misc/r-release/BUILD/library/akima/libs/akim a.so", asLocal=1, now=1) at ../../../R/src/unix/dynload.c:207 Looks like it is happening during the dynamic linking itself. Doesn't look nice. (But installing gcc 2.95.2 might fix your problem.) [diverted back to r-bugs] -- O__ ---- Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard@biostat.ku.dk) FAX: (+45) 35327907 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-devel mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-devel-request@stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._