[R] [SOLVED] Problem building R-2.15.3 from source

[Mark Dalphin]

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
>
>
> ------------------------------------------------------------------------
>
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>   

-- 
	


    Mark Dalphin Ph.D.

Director of Bioinformatics

mark.dalphin at pacificedge.co.nz <mailto:mark.dalphin at pacificedge.co.nz>
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