Date: Thu, 30 Jan 2014 05:31:19 +0000 From: "Montgomery-Smith, Stephen" <stephen@missouri.edu> To: Kostas Oikonomou <k.oikonomou@att.net>, =?iso-8859-1?Q?Jouko_Lumij=E4rvi?= <jlumijar@sun3.oulu.fi>, ajtiM <lumiwa@gmail.com>, Greg Rivers <gcr+freebsd-ports@tharned.org>, "GeorgSWeber@googlemail.com" <GeorgSWeber@googlemail.com>, Daniel Smith <des006@ucsd.edu>, FreeBSD Ports <freebsd-ports@FreeBSD.org> Subject: Re: Sage update Message-ID: <52E9E3A4.2030204@missouri.edu> In-Reply-To: <52E9AA34.9060909@missouri.edu> References: <52E9A43A.7010006@missouri.edu> <52E9AA34.9060909@missouri.edu>
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On 01/29/2014 07:26 PM, Montgomery-Smith, Stephen wrote: > On 01/29/2014 07:00 PM, Montgomery-Smith, Stephen wrote: >> I have just updated sage to version 6.0. I have also made some changes >> to help it work with FreeBSD-10, using ideas given to me by Daniel >> Smith. Since I don't have a fast computer using FreeBSD-10, I would >> appreciate it if any of you guys could try it out and see if it works. >=20 > I meant math/sage (for those who don't normally use it.) So I tried it on my slow i386 computer. It dies on the subpackage r-3.0.2.p0. I would be interested if other people are seeing the same problem. I think it is because in the build, it creates libR.so using a command like this: cc -std=3Dgnu99 -shared -fopenmp -L/usr/home/stephen/sage/work/sage-6.0/local/lib/ -Wl,-rpath=3D/usr/home/stephen/sage/work/sage-6.0/local/lib -Wl,-rpath=3D/usr/local/lib/gcc46 -L/usr/local/lib/gcc46 -o libR.so CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o apply.o arithmetic.o array.o attrib.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cum.o dcf.o datetime.o debug.o deparse.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o edit.o engine.o envir.o errors.o eval.o format.o gevents.o gram.o gram-ex.o graphics.o grep.o identical.o inlined.o inspect.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o names.o objects.o options.o paste.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o qsort.o random.o raw.o registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o unique.o util.o version.o vfonts.o xxxpr.o `ls ../unix/*.o ../appl/*.o ../nmath/*.o` ../extra/zlib/libz.a ../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a ../extra/tre/libtre.a -L/usr/home/stephen/sage/work/sage-6.0/local/lib -lf77blas -latlas -lgfortran -lm -lquadmath -lintl -lreadline -llzma -lrt -lm -liconv Now -Wl,-rpath is set, so it should find libreadline in /usr/home/stephen/sage/work/sage-6.0/local/lib. But instead it finds libreadline in /lib. So later when it does the following compilation to build R.bin: gcc -std=3Dgnu99 -export-dynamic -fopenmp -L/usr/home/stephen/sage/work/sage-6.0/local/lib/ -Wl,-rpath=3D/usr/home/stephen/sage/work/sage-6.0/local/lib -Wl,-rpath=3D/usr/local/lib/gcc46 -L/usr/local/lib/gcc46 -o R.bin Rmain.o -L../../lib -lR ...it comes up with an error saying that rl_sort_completion_matches isn't found. And when I do an ldd or "readelf -d" on libR.so, I can see that it is trying to link to the wrong libreadline, and rl_sort_completion_matches is only defined in the other libreadline. I tried googling to find a fix. And it works fine with FreeBSD-8. This has me completely stumped. One web page suggested I added -Wl,-z,origin to the list of flags when building libR.so. But I really don't know what I am doing. Anyway, it didn't work.
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