Hello,

Maybe the reason why:

http://www.cran.r-project.org/doc/manuals/R-admin.html#Compilation-flags

Regards,
Pascal



2013/7/11 Mark Dalphin <mark.dalphin@pacificedge.co.nz>

> I have found a solution to the repeated seg-faults below.
>
> If I set environment variables:
>    setenv CFLAGS -O2
>    setenv FFLAGS -O2
> rather than the default -O3, then R builds and "checks" successfully.
>
> A few more details about the Debian system on which I have been building:
>     gcc (Debian 4.7.2-5) 4.7.2
>
> My "configure" command is:
> ./configure                 \
>    --prefix=$my_R_path \
>    --with-readline     \
>    --without-x         \
>    --enable-R-shlib    \
>    --enable-BLAS-shlib \
>    --with-system-zlib  \
>    --with-system-bzlib \
>     --with-system-pcre
>
> So, I'm good for the time being and hope this helps others who have
> trouble building from source.
>
> Cheers,
> Mark
>
> Mark Dalphin wrote:
>
>> Hi,
>>
>> I have for many years build R from source for Linux. I have just run into
>> my first problem with this in ... I don't know how long.
>>
>> uname -a
>> Linux douglas 3.2.0-4-686-pae #1 SMP Debian 3.2.46-1 i686 GNU/Linux
>>
>> cat /etc/issue
>> Debian GNU/Linux 7 \n \l
>>
>>
>> The version of R is 2.15.3. I know it is old, but we are in a regulated
>> environment and changes to R versions are painful. I have built R 2.15.3
>> elsewhere and have it running on multiple Linux boxes around here, both
>> 32-bit and 64-bit; Ubuntu distributions, however, not Debian.
>>
>> This build is on a virtual machine under OpenBox. The host is a 64-bit
>> Debian; the guest is a 32-bit Debian installation.
>>
>> The symptoms are strange (to me). I get segfaults during the
>> byte-compiling phase of libraries. If I re-run 'make', the make proceeds as
>> if it finished the previous seg-faulted step, and then segfaults on the
>> next byte-compile. The "permissions" makes me wonder about file
>> permissions, but the whole 'make' is under my HOME. Furthermore, I have
>> scanned the unpacked tar-gz package for something I don't "own" and it
>> isn't there. I also think segfaults are usually in memory, though I don't
>> know what "permission" I have there (don't I own the RAM I request?).
>>
>> I have attached a section of the 'make' output  below, followed by a the
>> next "make" output:
>> ------------------------------**------------------------------**
>> ------------------------------**----------------
>> make[4]: Leaving directory `/home/mdalphin/src/R-2.15.3/**
>> src/library/splines'
>> make[4]: Entering directory `/home/mdalphin/src/R-2.15.3/**
>> src/library/splines'
>> byte-compiling package 'splines'
>>
>> *** caught segfault ***
>> address 0x403ac3dc, cause 'invalid permissions'
>>
>> Traceback:
>> 1: fun(libname, pkgname)
>> 2: doTryCatch(return(expr), name, parentenv, handler)
>> 3: tryCatchOne(expr, names, parentenv, handlers[[1L]])
>> 4: tryCatchList(expr, classes, parentenv, handlers)
>> 5: tryCatch(fun(libname, pkgname), error = identity)
>> 6: runHook(".onLoad", env, package.lib, package)
>> 7: loadNamespace(name)
>> 8: doTryCatch(return(expr), name, parentenv, handler)
>> 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
>> 10: tryCatchList(expr, classes, parentenv, handlers)
>> 11: tryCatch(loadNamespace(name), error = function(e) stop(e))
>> 12: getNamespace(ns)
>> 13: asNamespace(pkg)
>> 14: get(name, envir = asNamespace(pkg), inherits = FALSE)
>> 15: compiler:::tryCmpfun
>> 16: .Call("R_**lazyLoadDBinsertValue", x[[1L]], file, ascii, compress,
>>   hook, PACKAGE = "base")
>> 17: lazyLoadDBinsertVariable(vars[**i], from, datafile, ascii, compress,
>>     envhook)
>> 18: makeLazyLoadDB(ns, dbbase, compress = compress)
>> 19: code2LazyLoadDB(package, lib.loc = lib.loc, keep.source =
>> keep.source,     compress = compress)
>> 20: tools:::makeLazyLoading("**splines")
>> aborting ...
>> /bin/bash: line 8: 18709 Done                    echo
>> "tools:::makeLazyLoading(\"**splines\")"
>>     18710 Segmentation fault      | R_COMPILE_PKGS=1
>> R_COMPILER_SUPPRESS_ALL=1 R_DEFAULT_PACKAGES=NULL LC_ALL=C ../../../bin/R
>> --vanilla --slave > /dev/null
>> make[4]: *** [../../../library/splines/R/**splines.rdb] Error 139
>> make[4]: Leaving directory `/home/mdalphin/src/R-2.15.3/**
>> src/library/splines'
>> make[3]: *** [all] Error 2
>> make[3]: Leaving directory `/home/mdalphin/src/R-2.15.3/**
>> src/library/splines'
>> make[2]: *** [R] Error 1
>> make[2]: Leaving directory `/home/mdalphin/src/R-2.15.3/**src/library'
>> make[1]: *** [R] Error 1
>> make[1]: Leaving directory `/home/mdalphin/src/R-2.15.3/**src'
>> make: *** [R] Error 1
>> ------------------------------**------------------------------**
>> ------------------------------**-
>> make[4]: Entering directory `/home/mdalphin/src/R-2.15.3/**
>> src/library/splines'
>> make[4]: Nothing to be done for `mklazycomp'.
>> make[4]: Leaving directory `/home/mdalphin/src/R-2.15.3/**
>> src/library/splines'
>> make[3]: Leaving directory `/home/mdalphin/src/R-2.15.3/**
>> src/library/splines'
>> make[3]: Entering directory `/home/mdalphin/src/R-2.15.3/**
>> src/library/stats4'
>> building package 'stats4'
>> mkdir -p -- ../../../library/stats4
>> make[4]: Entering directory `/home/mdalphin/src/R-2.15.3/**
>> src/library/stats4'
>> mkdir -p -- ../../../library/stats4/R
>> mkdir -p -- ../../../library/stats4/po
>> make[4]: Leaving directory `/home/mdalphin/src/R-2.15.3/**
>> src/library/stats4'
>> make[4]: Entering directory `/home/mdalphin/src/R-2.15.3/**
>> src/library/stats4'
>> byte-compiling package 'stats4'
>>
>> *** caught segfault ***
>> address 0x403ac3dc, cause 'invalid permissions'
>>
>> Traceback:
>> 1: fun(libname, pkgname)
>> 2: doTryCatch(return(expr), name, parentenv, handler)
>> 3: tryCatchOne(expr, names, parentenv, handlers[[1L]])
>> 4: tryCatchList(expr, classes, parentenv, handlers)
>> 5: tryCatch(fun(libname, pkgname), error = identity)
>> 6: runHook(".onLoad", env, package.lib, package)
>> 7: loadNamespace(name)
>> 8: doTryCatch(return(expr), name, parentenv, handler)
>> 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
>> 10: tryCatchList(expr, classes, parentenv, handlers)
>> 11: tryCatch(loadNamespace(name), error = function(e) stop(e))
>> 12: getNamespace(ns)
>> 13: asNamespace(pkg)
>> 14: get(name, envir = asNamespace(pkg), inherits = FALSE)
>> 15: compiler:::tryCmpfun
>> 16: .Call("R_**lazyLoadDBinsertValue", x[[1L]], file, ascii, compress,
>>   hook, PACKAGE = "base")
>> 17: lazyLoadDBinsertVariable(vars[**i], from, datafile, ascii, compress,
>>     envhook)
>> 18: makeLazyLoadDB(ns, dbbase, compress = compress)
>> 19: code2LazyLoadDB(package, lib.loc = lib.loc, keep.source =
>> keep.source,     compress = compress)
>> 20: tools:::makeLazyLoading("**stats4")
>> aborting ...
>> /bin/bash: line 8: 19554 Done                    echo
>> "tools:::makeLazyLoading(\"**stats4\")"
>>     19555 Segmentation fault      | R_COMPILE_PKGS=1
>> R_COMPILER_SUPPRESS_ALL=1 R_DEFAULT_PACKAGES="methods,**graphics,stats"
>> LC_ALL=C ../../../bin/R --vanilla --slave > /dev/null
>> make[4]: *** [../../../library/stats4/R/**stats4.rdb] Error 139
>> make[4]: Leaving directory `/home/mdalphin/src/R-2.15.3/**
>> src/library/stats4'
>> make[3]: *** [all] Error 2
>> make[3]: Leaving directory `/home/mdalphin/src/R-2.15.3/**
>> src/library/stats4'
>> make[2]: *** [R] Error 1
>> make[2]: Leaving directory `/home/mdalphin/src/R-2.15.3/**src/library'
>> make[1]: *** [R] Error 1
>> make[1]: Leaving directory `/home/mdalphin/src/R-2.15.3/**src'
>> make: *** [R] Error 1
>>
>>
>> ------------------------------**------------------------------**
>> ------------
>>
>> ______________________________**________________
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/**listinfo/r-help<https://stat.ethz.ch/mailman/listinfo/r-help>
>> PLEASE do read the posting guide http://www.R-project.org/**
>> posting-guide.html <http://www.R-project.org/posting-guide.html>
>> and provide commented, minimal, self-contained, reproducible code.
>>
>>
>
> --
>
>
>
>    Mark Dalphin Ph.D.
>
> Director of Bioinformatics
>
> mark.dalphin@pacificedge.co.nz <mailto:mark.dalphin@**pacificedge.co.nz<mark.dalphin@pacificedge.co.nz>
> >
> *Ph:* +64-3-479-5805
> *Cell:* +64-21-156-7625
> *Skype:* mark.dalphin.pel
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> >
>
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>
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>
>

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