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.dalp...@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.dalp...@pacificedge.co.nz > <mailto:mark.dalphin@**pacificedge.co.nz<mark.dalp...@pacificedge.co.nz> > > > *Ph:* +64-3-479-5805 > *Cell:* +64-21-156-7625 > *Skype:* mark.dalphin.pel > <http://www.facebook.com/**pages/Pacific-Edge/**111356775582456<http://www.facebook.com/pages/Pacific-Edge/111356775582456>> > <http://twitter.com/#%21/**pacificEdgeLtd<http://twitter.com/#%21/pacificEdgeLtd>> > <http://www.youtube.com/**PacificEdgeLtd<http://www.youtube.com/PacificEdgeLtd> > > > > 87 St David St, PO Box 56, Dunedin, New Zealand 9016www.pacificedge.co.nz > > > ______________________________________________ > R-help@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. > > [[alternative HTML version deleted]] ______________________________________________ R-help@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.
