From owner-freebsd-ports@FreeBSD.ORG Thu Jan 30 05:32:33 2014 Return-Path: Delivered-To: freebsd-ports@freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [8.8.178.115]) (using TLSv1 with cipher ADH-AES256-SHA (256/256 bits)) (No client certificate requested) by hub.freebsd.org (Postfix) with ESMTPS id 1C53179A for ; Thu, 30 Jan 2014 05:32:33 +0000 (UTC) Received: from mst-rip5-missouri-out.um.umsystem.edu (mst-rip5-missouri-out.um.umsystem.edu [198.209.50.135]) (using TLSv1 with cipher RC4-SHA (128/128 bits)) (No client certificate requested) by mx1.freebsd.org (Postfix) with ESMTPS id C2DE11370 for ; Thu, 30 Jan 2014 05:32:32 +0000 (UTC) X-IronPort-Anti-Spam-Filtered: true X-IronPort-Anti-Spam-Result: AhkFAGjj6VLPoJ7S/2dsb2JhbABZDoJ+OFe9GoEEFnSCJQEBAQR4EQIBCA4KCRYPCQMCAQIBICUCBAEMCAEBiAHDGIhFF48GhDgEiRGQSZBtgm4/gio X-IPAS-Result: AhkFAGjj6VLPoJ7S/2dsb2JhbABZDoJ+OFe9GoEEFnSCJQEBAQR4EQIBCA4KCRYPCQMCAQIBICUCBAEMCAEBiAHDGIhFF48GhDgEiRGQSZBtgm4/gio Received: from um-ncas5.um.umsystem.edu ([207.160.158.210]) by mst-rip5-exch-relay.um.umsystem.edu with ESMTP; 29 Jan 2014 23:31:20 -0600 Received: from UM-MBX-N02.um.umsystem.edu ([169.254.5.41]) by UM-NCAS5.um.umsystem.edu ([207.160.158.210]) with mapi id 14.03.0174.001; Wed, 29 Jan 2014 23:31:20 -0600 From: "Montgomery-Smith, Stephen" To: Kostas Oikonomou , =?iso-8859-1?Q?Jouko_Lumij=E4rvi?= , ajtiM , Greg Rivers , "GeorgSWeber@googlemail.com" , Daniel Smith , FreeBSD Ports Subject: Re: Sage update Thread-Topic: Sage update Thread-Index: AQHPHVa0fIyQoDOuwUKjHLdt+PT80pqc3m0AgABEeAA= Date: Thu, 30 Jan 2014 05:31:19 +0000 Message-ID: <52E9E3A4.2030204@missouri.edu> References: <52E9A43A.7010006@missouri.edu> <52E9AA34.9060909@missouri.edu> In-Reply-To: <52E9AA34.9060909@missouri.edu> Accept-Language: en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: user-agent: Mozilla/5.0 (X11; Linux i686; rv:24.0) Gecko/20100101 Thunderbird/24.2.0 x-originating-ip: [207.160.158.205] Content-Type: text/plain; charset="iso-8859-1" Content-ID: <7E8A0A17D143F240A6F54AA180257DB6@missouri.edu> Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-BeenThere: freebsd-ports@freebsd.org X-Mailman-Version: 2.1.17 Precedence: list List-Id: Porting software to FreeBSD List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 30 Jan 2014 05:32:33 -0000 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.