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.> 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 +++ -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- 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 _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
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 _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._