We are having problems building R on Red Hat Linux 6.0/Sparc. R compiles with no problem but then it fails "make tests". Specifically, the line eigen(cbind(-1,c(1:2,0),0:2)) # complex values causes a segmentation fault. Previous versions of Red Hat Linux did not give this problem. The eigen() function is one of the rare cases in the base library where Fortran code is called via the .Fortran interface, which suggests to me that the problem lies in the Fortran installation or flags. Vin Everett, who is actually doing the compiling, has provided output from gdb, which is given below. Any help would be greatly appreciated. Martyn> eigen(cbind(-1,c(1:2,0),0:2)) # complex valuesProgram received signal SIGSEGV, Segmentation fault. 0xb1dc8 in hqr2_ () (gdb) bt gives:- (gdb) bt #0 0xb1dc8 in hqr2_ () #1 0xb4bb4 in rg_ () #2 0x3909c in do_dotCode (call=0x70421f64, op=0x70421b90, args=0x70679f28, env=0x7067791c) at dotcode.c:386 #3 0x3fc7c in eval (e=0x70421f64, rho=0x7067791c) at eval.c:180 #4 0x41118 in do_set (call=0x70421fa0, op=0x702d4828, args=0x70421f8c, rho=0x7067791c) at eval.c:761 #5 0x3fc7c in eval (e=0x70421fa0, rho=0x7067791c) at eval.c:180 #6 0x40b58 in do_begin (call=0x70421fb4, op=0x702d48c8, args=0x70421fc8, rho=0x7067791c) at eval.c:588 #7 0x3fc7c in eval (e=0x70421fb4, rho=0x7067791c) at eval.c:180 #8 0x40280 in do_if (call=0x70422ef0, op=0x702d44b8, args=0x70422edc, rho=0x7067791c) at eval.c:379 #9 0x3fc7c in eval (e=0x70422ef0, rho=0x7067791c) at eval.c:180 #10 0x40b58 in do_begin (call=0x70422f04, op=0x702d48c8, args=0x70422f18, rho=0x7067791c) at eval.c:588 #11 0x3fc7c in eval (e=0x70422f04, rho=0x7067791c) at eval.c:180 #12 0x40280 in do_if (call=0x70423120, op=0x702d44b8, args=0x7042310c, rho=0x7067791c) at eval.c:379 #13 0x3fc7c in eval (e=0x70423120, rho=0x7067791c) at eval.c:180 #14 0x40b58 in do_begin (call=0x7041eddc, op=0x702d48c8, args=0x70423134, rho=0x7067791c) at eval.c:588 #15 0x3fc7c in eval (e=0x7041eddc, rho=0x7067791c) at eval.c:180 #16 0x3ffcc in applyClosure (call=0x70677868, op=0x7042347c, arglist=0x706778cc, rho=0x702dca50, suppliedenv=0x702d4008) at eval.c:293 #17 0x3fcf0 in eval (e=0x70677868, rho=0x702dca50) at eval.c:189 #18 0x5370c in R_ReplConsole (rho=0x702dca50, savestack=0, browselevel=0) at main.c:274 #19 0x53b74 in mainloop () at main.c:465 #20 0xa0adc in main (ac=0, av=0xeffffc84) at system.c:641 #21 0x701eb8d0 in __libc_start_main () at ../sysdeps/generic/libc-start.c:78 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- 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 _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
Martyn Plummer <plummer@iarc.fr> writes:> Vin Everett, who is actually doing the compiling, has provided output > from gdb, which is given below. Any help would be greatly appreciated. > > Martyn > > > eigen(cbind(-1,c(1:2,0),0:2)) # complex values > > Program received signal SIGSEGV, Segmentation fault. > 0xb1dc8 in hqr2_ () > (gdb) > > bt gives:- > (gdb) bt > #0 0xb1dc8 in hqr2_ () > #1 0xb4bb4 in rg_ ()You kind of forgot to tell us which version of R and which compiler.... The first thing I'd try would be to change the FFLAGS line in Makeconf to -g and recompile eigen.o. That way gdb would at least tell you exactly where it crashes. -- 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 _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
Hello Peter,
I hope this is more helpful ?
-g flag, using g77 version egcs-2.91.66 19990314/Linux (egcs-1.1.2 release)
(from FSF-g77 version 0.5.24-19981002)
And srpms R-base-0.64.1-6.src.rpm
Program received signal SIGSEGV, Segmentation fault.
hqr2_ (nm=0x1, n=0x70d99fc8, low=0xefffed94, igh=0xefffed90, h=0x70d99f80,
wr=0x70d99f68, wi=0x70d99f50, z=0x70d99f00, ierr=0x70d99ed0)
at eigen.f:2120
2120 RA = RA + H(I,J) * H(J,NA)
Current language: auto; currently fortran
(gdb) bt
#0 hqr2_ (nm=0x1, n=0x70d99fc8, low=0xefffed94, igh=0xefffed90, h=0x70d99f80,
wr=0x70d99f68, wi=0x70d99f50, z=0x70d99f00, ierr=0x70d99ed0)
at eigen.f:2120
#1 0xb4c10 in rg_ (nm=0x70d99fd0, n=0x70d99fc8, a=0x70d99f80, wr=0x70d99f68,
wi=0x70d99f50, matz=0x70d99f48, z=0x70d99f00, iv1=0x70d99ef0,
fv1=0x70d99ed8, ierr=0x70d99ed0) at eigen.f:3263
#2 0x3909c in do_dotCode (call=0x70421f64, op=0x70421b90, args=0x70679f28,
env=0x7067791c) at dotcode.c:386
#3 0x3fc7c in eval (e=0x70421f64, rho=0x7067791c) at eval.c:180
#4 0x41118 in do_set (call=0x70421fa0, op=0x702d4828, args=0x70421f8c,
rho=0x7067791c) at eval.c:761
#5 0x3fc7c in eval (e=0x70421fa0, rho=0x7067791c) at eval.c:180
#6 0x40b58 in do_begin (call=0x70421fb4, op=0x702d48c8, args=0x70421fc8,
rho=0x7067791c) at eval.c:588
#7 0x3fc7c in eval (e=0x70421fb4, rho=0x7067791c) at eval.c:180
#8 0x40280 in do_if (call=0x70422ef0, op=0x702d44b8, args=0x70422edc,
rho=0x7067791c) at eval.c:379
#9 0x3fc7c in eval (e=0x70422ef0, rho=0x7067791c) at eval.c:180
#10 0x40b58 in do_begin (call=0x70422f04, op=0x702d48c8, args=0x70422f18,
rho=0x7067791c) at eval.c:588
#11 0x3fc7c in eval (e=0x70422f04, rho=0x7067791c) at eval.c:180
#12 0x40280 in do_if (call=0x70423120, op=0x702d44b8, args=0x7042310c,
rho=0x7067791c) at eval.c:379
#13 0x3fc7c in eval (e=0x70423120, rho=0x7067791c) at eval.c:180
#14 0x40b58 in do_begin (call=0x7041eddc, op=0x702d48c8, args=0x70423134,
rho=0x7067791c) at eval.c:588
#15 0x3fc7c in eval (e=0x7041eddc, rho=0x7067791c) at eval.c:180
#16 0x3ffcc in applyClosure (call=0x70677868, op=0x7042347c,
arglist=0x706778cc, rho=0x702dca50, suppliedenv=0x702d4008) at eval.c:293
#17 0x3fcf0 in eval (e=0x70677868, rho=0x702dca50) at eval.c:189
#18 0x53768 in R_ReplConsole (rho=0x702dca50, savestack=0, browselevel=0)
at main.c:274
#19 0x53bd0 in mainloop () at main.c:465
#20 0xa0b38 in main (ac=0, av=0xeffffc84) at system.c:641
#21 0x701eb8d0 in __libc_start_main () at ../sysdeps/generic/libc-start.c:78
Cheers Vin
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Vin Everett email: vin.everett@mrc-bsu.cam.ac.uk
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