[SOLVED] Problem building R-2.15.3 from source

Hello,

Maybe the reason why:

http://www.cran.r-project.org/doc/manuals/R-admin.html#Compilation-flags
And since this is a ix86 system, you really should be using -mtune=native.

I do not believe the default in 2.15.3 was -O3: it is not in current R, 
and it certainly included -g .
Regards,
Pascal

2013/7/11 Mark Dalphin <mark.dalphin at 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.
Others who do not follow the instructions?  As the manual says at the end

'Beware of using high levels of optimization, at least initially. On 
many compilers these reduce the degree of compliance to the IEEE model.'
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@**pacificedge.co.nz<mark.dalphin at pacificedge.co.nz>

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______________________________________________
R-help at r-project.org mailing list
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

	[[alternative HTML version deleted]]

______________________________________________
R-help at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

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

[SOLVED] Problem building R-2.15.3 from source

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