[R] Problem building R-2.15.3 from source

[Mark Dalphin]

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


-- 
	


    Mark Dalphin Ph.D.

Director of Bioinformatics

mark.dalphin at pacificedge.co.nz <mailto:mark.dalphin at pacificedge.co.nz>
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*Skype:* mark.dalphin.pel
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