Dear R Help, I work with the Sage project, and we are trying to improve the ability to use R through Sage. Most things work, but make check seems to cause problems on certain platforms, and now that we want to upgrade to 2.10.1 I thought we should ask for help! R builds just fine on both Mac and Linux, but some things in make check seem to break on certain Linux boxes that don't on Mac or other machines. Here is an example from (Red Hat?) in doing the basic tests, in src/tests/Examples/, where base-Ex.R seems to have a problem, at the end of base-Ex.Rout.fail:> ### Name: groupGeneric > ### Title: S3 Group Generic Functions > ### Aliases: S3groupGeneric .Group Math Math.data.frame Ops Ops.data.frame > ### Summary Summary.data.frame Complex 'group generic' > ### Keywords: methods > > ### ** Examples > > require(utils) > > d.fr <- data.frame(x=1:9, y=stats::rnorm(9)) > class(1 + d.fr) == "data.frame" ##-- add to d.f. ...[1] TRUE> > methods("Math")*** caught segfault *** address 0x4b8, cause 'memory not mapped' Traceback: 1: dyn.load(file, DLLpath = DLLpath, ...) 2: library.dynam(lib, package, package.lib) 3: loadNamespace(name) 4: doTryCatch(return(expr), name, parentenv, handler) 5: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 6: tryCatchList(expr, classes, parentenv, handlers) 7: tryCatch(loadNamespace(name), error = function(e) stop(e)) 8: getNamespace(ns) 9: asNamespace(pkg) 10: get(name, envir = asNamespace(pkg), inherits = FALSE) 11: tools:::.make_S3_methods_stop_list 12: methods("Math") aborting ... Segmentation fault Note that make check for R in Sage passes on Mac OSX, as far as I can tell. For this particular machine and build, earlier in the same fail file the methods package was listed as methods /home/.../sage-4.3-linux-sage.math.washington.edu-x86_64-Linux/spkg/build/r-2.10.1/src/library/methods/libs/methods.so so it seems that the recommended package methods did build and load properly. Any help would be greatly appreciated! Thank you.
Hi, On 1/19/10 12:05 PM, Karl-Dieter Crisman wrote:> I work with the Sage project, and we are trying to improve the ability > to use R through Sage. Most things work, but make check seems to > cause problems on certain platforms, and now that we want to upgrade > to 2.10.1 I thought we should ask for help!This discussion might be more appropriate for R-devel. I'm not all that familiar with the Sage project and it isn't clear to me whether what you are seeing is in any way Sage-specific. If you are getting this segfault from a basic configure/make/make check sequence and you can reproduce the crash, then further debugging steps will likely be of interest.> R builds just fine on both Mac and Linux, but some things in make > check seem to break on certain Linux boxes that don't on Mac or other > machines. Here is an example from (Red Hat?) in doing the basic > tests, in src/tests/Examples/, where base-Ex.R seems to have a > problem, at the end of base-Ex.Rout.fail: > >> ### Name: groupGeneric >> ### Title: S3 Group Generic Functions >> ### Aliases: S3groupGeneric .Group Math Math.data.frame Ops Ops.data.frame >> ### Summary Summary.data.frame Complex 'group generic' >> ### Keywords: methods >> >> ### ** Examples >> >> require(utils) >> >> d.fr<- data.frame(x=1:9, y=stats::rnorm(9)) >> class(1 + d.fr) == "data.frame" ##-- add to d.f. ... > [1] TRUE >> >> methods("Math") > > *** caught segfault *** > address 0x4b8, cause 'memory not mapped'You might be able to reproduce this and get some more information like this: R -d gdb run source("src/tests/Examples/base-Ex.R") Assuming you get a crash, type bt in the gdb console and send output. + seth -- Seth Falcon | @sfalcon | http://userprimary.net/user
Dear Seth,> You might be able to reproduce this and get some more information like > this: > > > R -d gdb > run > source("src/tests/Examples/base-Ex.R") > > Assuming you get a crash, type bt in the gdb console and send output.I think it may have ended up being related to different Fortrans being used or something like that, but if not I will definitely use this - it is very helpful to know how to try to debug in R! Thank you for the tip and guidance; we appreciate it!