From ripley at stats.ox.ac.uk  Tue May  9 15:01:59 2006
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Tue, 9 May 2006 14:01:59 +0100 (BST)
Subject: [Rd] Seg fault when installing package from bad repository
In-Reply-To: <f8e6ff050605090219l5819fb2era4209d44ebf17c1e@mail.gmail.com>
References: <f8e6ff050605090206j763a2438n914d6dd8f639cba@mail.gmail.com>
	<f8e6ff050605090219l5819fb2era4209d44ebf17c1e@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.0605091344000.12602@gannet.stats.ox.ac.uk>

On Tue, 9 May 2006, hadley wickham wrote:

> 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.

It seems to be corruption inside the intl library on your machine: note 
how the url has been changed to be a file path and the format is an 
invalid address.  This sort of thing works correctly on my systems:

> download.file("http://ggobi.org/r/bin/macosx/powerpc/contrib/2.2/PACKAGES", 
"/tmp/foo")
trying URL 'http://ggobi.org/r/bin/macosx/powerpc/contrib/2.2/PACKAGES'
Error in 
download.file("http://ggobi.org/r/bin/macosx/powerpc/contrib/2.2/PACKAGES", 
:
         cannot open URL 
'http://ggobi.org/r/bin/macosx/powerpc/contrib/2.2/PACKAGES'
In addition: Warning message:
cannot open: HTTP status was '404 Not Found'

so I surmise it is a MacOS-specific problem.


> Is there anyway to fall back
> to source automatically?

No.

>
> 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
>>
>
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> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595



[Rd] Seg fault when installing package from bad repository
Prof Brian Ripley