hadley wickham
2006-May-09 09:06 UTC
[Rd] Seg fault when installing package from bad repository
> install.packages("rggobi", repos="http://ggobi.org/r/")Warning in install.packages("rggobi", repos = "http://ggobi.org/r/") : argument 'lib' is missing: using /Users/hadley/Library/R/library/ Reading symbols for shared libraries . done Program received signal EXC_BAD_ACCESS, Could not access memory. Reason: KERN_INVALID_ADDRESS at address: 0x5f4d4550 0x90002f48 in strlen () (gdb) where #0 0x90002f48 in strlen () #1 0x9000d7d0 in __vfprintf$LDBL128 () #2 0x900273cc in vsnprintf$LDBL128 () #3 0x0108ea1c in Rvsnprintf (buf=0xbfff35f4 "B", size=1000, format=0x3 <Address 0x3 out of bounds>, ap=0x34 <Address 0x34 out of bounds>) at ../../../../R-2.3.0/src/main/errors.c:211 #4 0x01092e68 in Rf_warning (format=0x3 <Address 0x3 out of bounds>) at ../../../../R-2.3.0/src/main/errors.c:223 #5 0x023c39a8 in in_R_HTTPOpen (url=0x212c930 "/Library/Frameworks/R.framework/Resources/share/locale/en/LC_MESSAGES/R.mo", cacheOK=404) at ../../../../../R-2.3.0/src/modules/internet/internet.c:490 #6 0x023c3f00 in in_do_download (call=0x5f4d4553, op=0xbfff2a03, args=0x195d300, env=0x34) at ../../../../../R-2.3.0/src/modules/internet/internet.c:320 #7 0x010b6290 in do_download (call=0x18d0078, op=0x181c2a8, args=0x18c3b50, env=0x18cfd64) at ../../../../R-2.3.0/src/main/internet.c:99 #8 0x010cefc4 in do_internal (call=0x18c3b50, op=0xbfff2a03, args=0x0, env=0x18cfd64) at ../../../../R-2.3.0/src/main/names.c:1089 #9 0x0109d798 in Rf_eval (e=0x18d0040, rho=0x18cfd64) at ../../../../R-2.3.0/src/main/eval.c:391 #10 0x0109f87c in do_set (call=0x18d17b0, op=0x180a190, args=0x18d0008, rho=0x18cfd64) at ../../../../R-2.3.0/src/main/eval.c:1303 #11 0x0109d798 in Rf_eval (e=0x18d17b0, rho=0x18cfd64) at ../../../../R-2.3.0/src/main/eval.c:391 #12 0x0109d798 in Rf_eval (e=0x18d16b4, rho=0x18cfd64) at ../../../../R-2.3.0/src/main/eval.c:391 #13 0x0109f93c in do_begin (call=0x18d1920, op=0x180a0cc, args=0x18d1628, rho=0x18cfd64) at ../../../../R-2.3.0/src/main/eval.c:1067 #14 0x0109d798 in Rf_eval (e=0x18d1920, rho=0x18cfd64) at ../../../../R-2.3.0/src/main/eval.c:391 #15 0x010a0d34 in Rf_applyClosure (call=0x18f8cf4, op=0x18d2580, arglist=0x18cfb50, rho=0x18f61ac, suppliedenv=0x181d200) at ../../../../R-2.3.0/src/main/eval.c:581 #16 0x0109d634 in Rf_eval (e=0x18f8cf4, rho=0x18f61ac) at ../../../../R-2.3.0/src/main/eval.c:422 #17 0x0109d66c in Rf_eval (e=0x18d2894, rho=0x18d293c) at ../../../../R-2.3.0/src/main/eval.c:370 #18 0x0109d938 in Rf_eval (e=0x1826b18, rho=0x18d293c) at ../../../../R-2.3.0/src/main/eval.c:357 #19 0x0109f93c in do_begin (call=0x1a37720, op=0x180a0cc, args=0x1a38f2c, rho=0x18d293c) at ../../../../R-2.3.0/src/main/eval.c:1067 #20 0x0109d798 in Rf_eval (e=0x1a37720, rho=0x18d293c) at ../../../../R-2.3.0/src/main/eval.c:391 #21 0x0109d798 in Rf_eval (e=0x1a37800, rho=0x18d293c) at ../../../../R-2.3.0/src/main/eval.c:391 #22 0x0109f93c in do_begin (call=0x1a37838, op=0x180a0cc, args=0x1a3781c, rho=0x18d293c) at ../../../../R-2.3.0/src/main/eval.c:1067 #23 0x0109d798 in Rf_eval (e=0x1a37838, rho=0x18d293c) at ../../../../R-2.3.0/src/main/eval.c:391 #24 0x010a0d34 in Rf_applyClosure (call=0x18f8cbc, op=0x1a378c4, arglist=0x18d28b0, rho=0x18f61ac, suppliedenv=0x181d200) at ../../../../R-2.3.0/src/main/eval.c:581 #25 0x0109d634 in Rf_eval (e=0x18f8cbc, rho=0x18f61ac) at ../../../../R-2.3.0/src/main/eval.c:422 #26 0x0109f87c in do_set (call=0x18f8c68, op=0x180a190, args=0x18f8c84, rho=0x18f61ac) at ../../../../R-2.3.0/src/main/eval.c:1303 #27 0x0109d798 in Rf_eval (e=0x18f8c68, rho=0x18f61ac) at ../../../../R-2.3.0/src/main/eval.c:391 #28 0x0109f93c in do_begin (call=0x18f88e8, op=0x180a0cc, args=0x18f8c4c, rho=0x18f61ac) at ../../../../R-2.3.0/src/main/eval.c:1067 #29 0x0109d798 in Rf_eval (e=0x18f88e8, rho=0x18f61ac) at ../../../../R-2.3.0/src/main/eval.c:391 #30 0x0109d798 in Rf_eval (e=0x18f9724, rho=0x18f61ac) at ../../../../R-2.3.0/src/main/eval.c:391 #31 0x0109f93c in do_begin (call=0x18f94d8, op=0x180a0cc, args=0x18f9708, rho=0x18f61ac) at ../../../../R-2.3.0/src/main/eval.c:1067 #32 0x0109d798 in Rf_eval (e=0x18f94d8, rho=0x18f61ac) at ../../../../R-2.3.0/src/main/eval.c:391 #33 0x0109d798 in Rf_eval (e=0x18fa350, rho=0x18f61ac) at ../../../../R-2.3.0/src/main/eval.c:391 #34 0x0109f93c in do_begin (call=0x18fa174, op=0x180a0cc, args=0x18fa334, rho=0x18f61ac) at ../../../../R-2.3.0/src/main/eval.c:1067 #35 0x0109d798 in Rf_eval (e=0x18fa174, rho=0x18f61ac) at ../../../../R-2.3.0/src/main/eval.c:391 #36 0x010a0074 in do_for (call=0x18fa104, op=0x1808958, args=0x18fa120, rho=0x18f61ac) at ../../../../R-2.3.0/src/main/eval.c:963 #37 0x0109d798 in Rf_eval (e=0x18fa104, rho=0x18f61ac) at ../../../../R-2.3.0/src/main/eval.c:391 #38 0x0109f93c in do_begin (call=0x18fb2fc, op=0x180a0cc, args=0x18fa0e8, rho=0x18f61ac) at ../../../../R-2.3.0/src/main/eval.c:1067 #39 0x0109d798 in Rf_eval (e=0x18fb2fc, rho=0x18f61ac) at ../../../../R-2.3.0/src/main/eval.c:391 #40 0x010a0d34 in Rf_applyClosure (call=0x1910b18, op=0x18fbf5c, arglist=0x18f6120, rho=0x190c0cc, suppliedenv=0x181d200) at ../../../../R-2.3.0/src/main/eval.c:581 #41 0x0109d634 in Rf_eval (e=0x1910b18, rho=0x190c0cc) at ../../../../R-2.3.0/src/main/eval.c:422 #42 0x0109f87c in do_set (call=0x1910ac4, op=0x180a190, args=0x1910ae0, rho=0x190c0cc) at ../../../../R-2.3.0/src/main/eval.c:1303 #43 0x0109d798 in Rf_eval (e=0x1910ac4, rho=0x190c0cc) at ../../../../R-2.3.0/src/main/eval.c:391 #44 0x0109d798 in Rf_eval (e=0x1910a38, rho=0x190c0cc) at ../../../../R-2.3.0/src/main/eval.c:391 #45 0x0109f93c in do_begin (call=0x19161ac, op=0x180a0cc, args=0x1910a00, rho=0x190c0cc) at ../../../../R-2.3.0/src/main/eval.c:1067 #46 0x0109d798 in Rf_eval (e=0x19161ac, rho=0x190c0cc) at ../../../../R-2.3.0/src/main/eval.c:391 #47 0x010a0d34 in Rf_applyClosure (call=0x19376ec, op=0x1916c30, arglist=0x190cd2c, rho=0x192e698, suppliedenv=0x181d200) at ../../../../R-2.3.0/src/main/eval.c:581 #48 0x0109d634 in Rf_eval (e=0x19376ec, rho=0x192e698) at ../../../../R-2.3.0/src/main/eval.c:422 #49 0x0109f93c in do_begin (call=0x19374bc, op=0x180a0cc, args=0x19376d0, rho=0x192e698) at ../../../../R-2.3.0/src/main/eval.c:1067 #50 0x0109d798 in Rf_eval (e=0x19374bc, rho=0x192e698) at ../../../../R-2.3.0/src/main/eval.c:391 #51 0x0109d798 in Rf_eval (e=0x1937414, rho=0x192e698) at ../../../../R-2.3.0/src/main/eval.c:391 #52 0x0109f93c in do_begin (call=0x19373dc, op=0x180a0cc, args=0x19373f8, rho=0x192e698) at ../../../../R-2.3.0/src/main/eval.c:1067 #53 0x0109d798 in Rf_eval (e=0x19373dc, rho=0x192e698) at ../../../../R-2.3.0/src/main/eval.c:391 #54 0x0109d798 in Rf_eval (e=0x1938eb4, rho=0x192e698) at ../../../../R-2.3.0/src/main/eval.c:391 #55 0x0109f93c in do_begin (call=0x193ceec, op=0x180a0cc, args=0x1938e98, rho=0x192e698) at ../../../../R-2.3.0/src/main/eval.c:1067 #56 0x0109d798 in Rf_eval (e=0x193ceec, rho=0x192e698) at ../../../../R-2.3.0/src/main/eval.c:391 #57 0x010a0d34 in Rf_applyClosure (call=0x193dd64, op=0x193c85c, arglist=0x192e4d8, rho=0x181d1e4, suppliedenv=0x181d200) at ../../../../R-2.3.0/src/main/eval.c:581 #58 0x0109d634 in Rf_eval (e=0x193dd64, rho=0x181d1e4) at ../../../../R-2.3.0/src/main/eval.c:422 #59 0x010bcdac in Rf_ReplIteration (rho=0x181d1e4, savestack=0, browselevel=18992200, state=0xbffff068) at ../../../../R-2.3.0/src/main/main.c:254 #60 0x010bd0e0 in R_ReplConsole (rho=0x181d1e4, savestack=0, browselevel=0) at ../../../../R-2.3.0/src/main/main.c:302 #61 0x010bd3f8 in run_Rmainloop () at ../../../../R-2.3.0/src/main/main.c:905 #62 0x00002cd8 in main (ac=1598899539, av=0xbfff2a03) at ../../../../R-2.3.0/src/main/Rmain.c:33 platform powerpc-apple-darwin8.6.0 arch powerpc os darwin8.6.0 system powerpc, darwin8.6.0 status major 2 minor 3.0 year 2006 month 04 day 24 svn rev 37909 language R version.string Version 2.3.0 (2006-04-24) http://ggobi.org/r/ is currently returning a 403 Forbidden header, but it shouldn't segfault (not a high priority either, though) Regards, Hadley
hadley wickham
2006-May-09 09:19 UTC
[Rd] Seg fault when installing package from bad repository
It still segfaults even now that I've fixed the access error. Ah, but if I specify type="source", so it must be a problem with having a mac binary path but no packages in it. Is there anyway to fall back to source automatically? Thanks, Hadley On 5/9/06, hadley wickham <h.wickham at gmail.com> wrote:> > install.packages("rggobi", repos="http://ggobi.org/r/") > Warning in install.packages("rggobi", repos = "http://ggobi.org/r/") : > argument 'lib' is missing: using /Users/hadley/Library/R/library/ > Reading symbols for shared libraries . done > > Program received signal EXC_BAD_ACCESS, Could not access memory. > Reason: KERN_INVALID_ADDRESS at address: 0x5f4d4550 > 0x90002f48 in strlen () > (gdb) where > #0 0x90002f48 in strlen () > #1 0x9000d7d0 in __vfprintf$LDBL128 () > #2 0x900273cc in vsnprintf$LDBL128 () > #3 0x0108ea1c in Rvsnprintf (buf=0xbfff35f4 "B", size=1000, > format=0x3 <Address 0x3 out of bounds>, ap=0x34 <Address 0x34 out of > bounds>) at ../../../../R-2.3.0/src/main/errors.c:211 > #4 0x01092e68 in Rf_warning (format=0x3 <Address 0x3 out of bounds>) > at ../../../../R-2.3.0/src/main/errors.c:223 > #5 0x023c39a8 in in_R_HTTPOpen (url=0x212c930 > "/Library/Frameworks/R.framework/Resources/share/locale/en/LC_MESSAGES/R.mo", > cacheOK=404) at > ../../../../../R-2.3.0/src/modules/internet/internet.c:490 > #6 0x023c3f00 in in_do_download (call=0x5f4d4553, op=0xbfff2a03, > args=0x195d300, env=0x34) at > ../../../../../R-2.3.0/src/modules/internet/internet.c:320 > #7 0x010b6290 in do_download (call=0x18d0078, op=0x181c2a8, > args=0x18c3b50, env=0x18cfd64) at > ../../../../R-2.3.0/src/main/internet.c:99 > #8 0x010cefc4 in do_internal (call=0x18c3b50, op=0xbfff2a03, > args=0x0, env=0x18cfd64) at ../../../../R-2.3.0/src/main/names.c:1089 > #9 0x0109d798 in Rf_eval (e=0x18d0040, rho=0x18cfd64) at > ../../../../R-2.3.0/src/main/eval.c:391 > #10 0x0109f87c in do_set (call=0x18d17b0, op=0x180a190, > args=0x18d0008, rho=0x18cfd64) at > ../../../../R-2.3.0/src/main/eval.c:1303 > #11 0x0109d798 in Rf_eval (e=0x18d17b0, rho=0x18cfd64) at > ../../../../R-2.3.0/src/main/eval.c:391 > #12 0x0109d798 in Rf_eval (e=0x18d16b4, rho=0x18cfd64) at > ../../../../R-2.3.0/src/main/eval.c:391 > #13 0x0109f93c in do_begin (call=0x18d1920, op=0x180a0cc, > args=0x18d1628, rho=0x18cfd64) at > ../../../../R-2.3.0/src/main/eval.c:1067 > #14 0x0109d798 in Rf_eval (e=0x18d1920, rho=0x18cfd64) at > ../../../../R-2.3.0/src/main/eval.c:391 > #15 0x010a0d34 in Rf_applyClosure (call=0x18f8cf4, op=0x18d2580, > arglist=0x18cfb50, rho=0x18f61ac, suppliedenv=0x181d200) at > ../../../../R-2.3.0/src/main/eval.c:581 > #16 0x0109d634 in Rf_eval (e=0x18f8cf4, rho=0x18f61ac) at > ../../../../R-2.3.0/src/main/eval.c:422 > #17 0x0109d66c in Rf_eval (e=0x18d2894, rho=0x18d293c) at > ../../../../R-2.3.0/src/main/eval.c:370 > #18 0x0109d938 in Rf_eval (e=0x1826b18, rho=0x18d293c) at > ../../../../R-2.3.0/src/main/eval.c:357 > #19 0x0109f93c in do_begin (call=0x1a37720, op=0x180a0cc, > args=0x1a38f2c, rho=0x18d293c) at > ../../../../R-2.3.0/src/main/eval.c:1067 > #20 0x0109d798 in Rf_eval (e=0x1a37720, rho=0x18d293c) at > ../../../../R-2.3.0/src/main/eval.c:391 > #21 0x0109d798 in Rf_eval (e=0x1a37800, rho=0x18d293c) at > ../../../../R-2.3.0/src/main/eval.c:391 > #22 0x0109f93c in do_begin (call=0x1a37838, op=0x180a0cc, > args=0x1a3781c, rho=0x18d293c) at > ../../../../R-2.3.0/src/main/eval.c:1067 > #23 0x0109d798 in Rf_eval (e=0x1a37838, rho=0x18d293c) at > ../../../../R-2.3.0/src/main/eval.c:391 > #24 0x010a0d34 in Rf_applyClosure (call=0x18f8cbc, op=0x1a378c4, > arglist=0x18d28b0, rho=0x18f61ac, suppliedenv=0x181d200) at > ../../../../R-2.3.0/src/main/eval.c:581 > #25 0x0109d634 in Rf_eval (e=0x18f8cbc, rho=0x18f61ac) at > ../../../../R-2.3.0/src/main/eval.c:422 > #26 0x0109f87c in do_set (call=0x18f8c68, op=0x180a190, > args=0x18f8c84, rho=0x18f61ac) at > ../../../../R-2.3.0/src/main/eval.c:1303 > #27 0x0109d798 in Rf_eval (e=0x18f8c68, rho=0x18f61ac) at > ../../../../R-2.3.0/src/main/eval.c:391 > #28 0x0109f93c in do_begin (call=0x18f88e8, op=0x180a0cc, > args=0x18f8c4c, rho=0x18f61ac) at > ../../../../R-2.3.0/src/main/eval.c:1067 > #29 0x0109d798 in Rf_eval (e=0x18f88e8, rho=0x18f61ac) at > ../../../../R-2.3.0/src/main/eval.c:391 > #30 0x0109d798 in Rf_eval (e=0x18f9724, rho=0x18f61ac) at > ../../../../R-2.3.0/src/main/eval.c:391 > #31 0x0109f93c in do_begin (call=0x18f94d8, op=0x180a0cc, > args=0x18f9708, rho=0x18f61ac) at > ../../../../R-2.3.0/src/main/eval.c:1067 > #32 0x0109d798 in Rf_eval (e=0x18f94d8, rho=0x18f61ac) at > ../../../../R-2.3.0/src/main/eval.c:391 > #33 0x0109d798 in Rf_eval (e=0x18fa350, rho=0x18f61ac) at > ../../../../R-2.3.0/src/main/eval.c:391 > #34 0x0109f93c in do_begin (call=0x18fa174, op=0x180a0cc, > args=0x18fa334, rho=0x18f61ac) at > ../../../../R-2.3.0/src/main/eval.c:1067 > #35 0x0109d798 in Rf_eval (e=0x18fa174, rho=0x18f61ac) at > ../../../../R-2.3.0/src/main/eval.c:391 > #36 0x010a0074 in do_for (call=0x18fa104, op=0x1808958, > args=0x18fa120, rho=0x18f61ac) at > ../../../../R-2.3.0/src/main/eval.c:963 > #37 0x0109d798 in Rf_eval (e=0x18fa104, rho=0x18f61ac) at > ../../../../R-2.3.0/src/main/eval.c:391 > #38 0x0109f93c in do_begin (call=0x18fb2fc, op=0x180a0cc, > args=0x18fa0e8, rho=0x18f61ac) at > ../../../../R-2.3.0/src/main/eval.c:1067 > #39 0x0109d798 in Rf_eval (e=0x18fb2fc, rho=0x18f61ac) at > ../../../../R-2.3.0/src/main/eval.c:391 > #40 0x010a0d34 in Rf_applyClosure (call=0x1910b18, op=0x18fbf5c, > arglist=0x18f6120, rho=0x190c0cc, suppliedenv=0x181d200) at > ../../../../R-2.3.0/src/main/eval.c:581 > #41 0x0109d634 in Rf_eval (e=0x1910b18, rho=0x190c0cc) at > ../../../../R-2.3.0/src/main/eval.c:422 > #42 0x0109f87c in do_set (call=0x1910ac4, op=0x180a190, > args=0x1910ae0, rho=0x190c0cc) at > ../../../../R-2.3.0/src/main/eval.c:1303 > #43 0x0109d798 in Rf_eval (e=0x1910ac4, rho=0x190c0cc) at > ../../../../R-2.3.0/src/main/eval.c:391 > #44 0x0109d798 in Rf_eval (e=0x1910a38, rho=0x190c0cc) at > ../../../../R-2.3.0/src/main/eval.c:391 > #45 0x0109f93c in do_begin (call=0x19161ac, op=0x180a0cc, > args=0x1910a00, rho=0x190c0cc) at > ../../../../R-2.3.0/src/main/eval.c:1067 > #46 0x0109d798 in Rf_eval (e=0x19161ac, rho=0x190c0cc) at > ../../../../R-2.3.0/src/main/eval.c:391 > #47 0x010a0d34 in Rf_applyClosure (call=0x19376ec, op=0x1916c30, > arglist=0x190cd2c, rho=0x192e698, suppliedenv=0x181d200) at > ../../../../R-2.3.0/src/main/eval.c:581 > #48 0x0109d634 in Rf_eval (e=0x19376ec, rho=0x192e698) at > ../../../../R-2.3.0/src/main/eval.c:422 > #49 0x0109f93c in do_begin (call=0x19374bc, op=0x180a0cc, > args=0x19376d0, rho=0x192e698) at > ../../../../R-2.3.0/src/main/eval.c:1067 > #50 0x0109d798 in Rf_eval (e=0x19374bc, rho=0x192e698) at > ../../../../R-2.3.0/src/main/eval.c:391 > #51 0x0109d798 in Rf_eval (e=0x1937414, rho=0x192e698) at > ../../../../R-2.3.0/src/main/eval.c:391 > #52 0x0109f93c in do_begin (call=0x19373dc, op=0x180a0cc, > args=0x19373f8, rho=0x192e698) at > ../../../../R-2.3.0/src/main/eval.c:1067 > #53 0x0109d798 in Rf_eval (e=0x19373dc, rho=0x192e698) at > ../../../../R-2.3.0/src/main/eval.c:391 > #54 0x0109d798 in Rf_eval (e=0x1938eb4, rho=0x192e698) at > ../../../../R-2.3.0/src/main/eval.c:391 > #55 0x0109f93c in do_begin (call=0x193ceec, op=0x180a0cc, > args=0x1938e98, rho=0x192e698) at > ../../../../R-2.3.0/src/main/eval.c:1067 > #56 0x0109d798 in Rf_eval (e=0x193ceec, rho=0x192e698) at > ../../../../R-2.3.0/src/main/eval.c:391 > #57 0x010a0d34 in Rf_applyClosure (call=0x193dd64, op=0x193c85c, > arglist=0x192e4d8, rho=0x181d1e4, suppliedenv=0x181d200) at > ../../../../R-2.3.0/src/main/eval.c:581 > #58 0x0109d634 in Rf_eval (e=0x193dd64, rho=0x181d1e4) at > ../../../../R-2.3.0/src/main/eval.c:422 > #59 0x010bcdac in Rf_ReplIteration (rho=0x181d1e4, savestack=0, > browselevel=18992200, state=0xbffff068) at > ../../../../R-2.3.0/src/main/main.c:254 > #60 0x010bd0e0 in R_ReplConsole (rho=0x181d1e4, savestack=0, > browselevel=0) at ../../../../R-2.3.0/src/main/main.c:302 > #61 0x010bd3f8 in run_Rmainloop () at ../../../../R-2.3.0/src/main/main.c:905 > #62 0x00002cd8 in main (ac=1598899539, av=0xbfff2a03) at > ../../../../R-2.3.0/src/main/Rmain.c:33 > > platform powerpc-apple-darwin8.6.0 > arch powerpc > os darwin8.6.0 > system powerpc, darwin8.6.0 > status > major 2 > minor 3.0 > year 2006 > month 04 > day 24 > svn rev 37909 > language R > version.string Version 2.3.0 (2006-04-24) > > http://ggobi.org/r/ is currently returning a 403 Forbidden header, but > it shouldn't segfault (not a high priority either, though) > > Regards, > > Hadley >