X-Original-To: alpine-devel@mail.alpinelinux.org Delivered-To: alpine-devel@mail.alpinelinux.org Received: from mail.alpinelinux.org (dallas-a1.alpinelinux.org [127.0.0.1]) by mail.alpinelinux.org (Postfix) with ESMTP id 57561DC0741 for ; Thu, 28 Jan 2016 03:19:17 +0000 (UTC) Received: from mail-pa0-f54.google.com (mail-pa0-f54.google.com [209.85.220.54]) (using TLSv1 with cipher ECDHE-RSA-RC4-SHA (128/128 bits)) (No client certificate requested) by mail.alpinelinux.org (Postfix) with ESMTPS id 1E0E6DC003D for ; Thu, 28 Jan 2016 03:19:16 +0000 (UTC) Received: by mail-pa0-f54.google.com with SMTP id ho8so15304142pac.2 for ; Wed, 27 Jan 2016 19:19:16 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=date:from:to:subject:message-id:reply-to:references:mime-version :content-type:content-disposition:in-reply-to:user-agent; bh=NmmxMSZ+fVBmD0aS2sKK89N9/p99A7vb1wzOq37fjJY=; b=HdmXKBIT1cAEpWmCE098bRF4Hxwpw4yxPw4fcVfPL6P5o9TKPGMFhqzGNjQFQDgbZc KA/pbwEdZZiYBRj9gvqlb/g7F4OH898ssgMszZxTIFmSpwkpHg3siL7W2sWFvQmsayNd Zlszww8BgudxDDtPYLkFYC0nUUUZS/aUnlYb3FI+NnC2pm1y3kNB8clIuU2FfmIAz1t1 9o0IWX5qjo2dDLgBoNspbLA2nSBAmClNoKAy6UPA2tTll8APLC/oyEEzTaDxJ1NQtUV6 9WafR+YMkIYQtH+BGAc4m+Sblt82AztjhTKyYzX/mvCiyWB0elEOfzs3ereA7y/4NUL0 9bXg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20130820; h=x-gm-message-state:date:from:to:subject:message-id:reply-to :references:mime-version:content-type:content-disposition :in-reply-to:user-agent; bh=NmmxMSZ+fVBmD0aS2sKK89N9/p99A7vb1wzOq37fjJY=; b=cu1CfN4aL/p2Xp2al8+3GnwqVRLtwfze1jLUR281v8wqA9oFKoaK+D/kT6CKh4Ij1I M3nz6yTGxBcNQgFjQvEyN6eLiMTYzzED7/tRVzqsBktbWFOrgpqrA1Mfqmy8I9TwSLX8 uvLqa4CdFMDUaDx/S78gGE+ZfC49wbAyYjmgkFambJGpoUmqtKSq2hmKsgoNqYCHGlKT VB+dtkEbfy/kRrz5shV53M0Jeg7bOnXIzJ5QSq2QWOqzqJJSQ/MneimmgDw+YmUX7mEw jDMOQjcgz2cxz6QiMgBNmvdLIiJe/8uNUZ0++1EUbKopnYiuHgOJiga5nv8v/IfWShW4 dBYA== X-Gm-Message-State: AG10YOSaqSCmA4FXhGZEHr8vaiXmFcpMP0r8iXSFxH9WGA87wPd4kCXGe6iXQiXlGk8g3g== X-Received: by 10.66.234.8 with SMTP id ua8mr1112015pac.45.1453951155604; Wed, 27 Jan 2016 19:19:15 -0800 (PST) Received: from newbook ([50.0.225.136]) by smtp.gmail.com with ESMTPSA id l14sm12046142pfb.73.2016.01.27.19.19.14 for (version=TLS1_2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128/128); Wed, 27 Jan 2016 19:19:15 -0800 (PST) Date: Wed, 27 Jan 2016 19:19:11 -0800 From: Isaac Dunham To: alpine-devel@lists.alpinelinux.org Subject: Re: [alpine-devel] Re: Package request: R Message-ID: <20160128031908.GA23427@newbook> Reply-To: alpine-devel@lists.alpinelinux.org References: X-Mailinglist: alpine-devel Precedence: list List-Id: Alpine Development List-Unsubscribe: List-Post: List-Help: List-Subscribe: MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: User-Agent: Mutt/1.5.24 (2015-08-30) X-Virus-Scanned: ClamAV using ClamSMTP On Tue, Jan 26, 2016 at 11:17:55AM -0200, Alba Pompeo wrote: > I tried to compile the source myself, but it appears R doesn't play > well with musl. > Can someone please help? If we can compile from source, then a > packager should easily make an APKBUILD for everyone. > The error. > ../unix/system.o: In function `Rf_initialize_R': > /home/albap/R-3.2.3/src/unix/system.c:185: undefined reference to > `__libc_stack_end' > /usr/lib/gcc/x86_64-alpine-linux-musl/5.3.0/../../../../x86_64-alpine-linux-musl/bin/ld: > ../unix/system.o: relocation R_X86_64_PC32 against undefined symbol > `__libc_stack_end' can not be used when making a shared object; > recompile with -fPIC Looking over things online, this is a (very longstanding) abuse of a private glibc symbol in R. When I tried building R, there was fallback code and a config.h 'feature guard', but no proper configure test (undef HAVE_LIBC_STACK_END). In R 3.2.3, it seems that configure is trying to test for it on Linux. It apparently fails to accurately test (as demonstrated by your link error), perhaps because the test program does not actually *use* __libc_stack_end so it gets optimized out. (See line 35500 or so in R-3.2.3/configure.) Ideally, the test program would check that a pointer to __libc_stack_end is non-null, but that's an autoconf bug. To work around the broken test, run: export r_cv_libc_stack_end=no before configuring R. Once you have it building, it would be good to report the issues you had with building--and results of "make check"--to the R mailing list. (And make *sure* that it *doesn't* pick up OpenBLAS; that would not help with getting support any.) Here, I'm seeing a couple little issues with non-ASCII text and a *lot* of math differences, many of which say "*no* convergence: NOTIFY R-core!" Until these are resolved, packaging R is not a good idea. But having only completed basic stats, I wouldn't have a clue about what to do; you would probably be the best person to bring these up. HTH, Isaac Dunham --- Unsubscribe: alpine-devel+unsubscribe@lists.alpinelinux.org Help: alpine-devel+help@lists.alpinelinux.org ---