From nobody Tue Mar 19 10:47:22 2024 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 44F9CDC0116 for ; Tue, 26 Jan 2016 00:53:26 +0000 (UTC) Received: from mail-wm0-f44.google.com (mail-wm0-f44.google.com [74.125.82.44]) (using TLSv1 with cipher ECDHE-RSA-RC4-SHA (128/128 bits)) (No client certificate requested) by mail.alpinelinux.org (Postfix) with ESMTPS id B7B8BDC00A4 for ; Tue, 26 Jan 2016 00:53:25 +0000 (UTC) Received: by mail-wm0-f44.google.com with SMTP id n5so106726085wmn.0 for ; Mon, 25 Jan 2016 16:53:25 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:date:message-id:subject:from:to:content-type; bh=D0zAxvusLGDvqDOa9f6fXwXvR6QN9ck7m0u5b8MTCFg=; b=KUOWxJR6HIJ1CIRaa+CGQvH9ao3RX87ijHrOZb7HwlT+/jpRSInpmNtjl+15c4JwsV zwM24SqFiiFeukRjfcHfD6+5g1SRNl1ZhYuD6uvr3sSD9qCfJ6P+JYxgdR0FpzPdL/Mr pRpCkboDUHd2GjBU095C91vDgNWAKem8uUtCxs+iWQPWrJy1ZI8y22HppiuWBU4xwTnb Y2QbCE3Mu3jQaWY4Zu8a1VTW7MrInWAhTIN4rDXK9/v6M2cabcGNGERYjhnRCohUL9C6 ViQxUkvZRAwFy3bUno9ZypJOg5/ka+FbqEHC9RlEVStw/YuJrulmYGx49eJdmedcZduT ygkw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20130820; h=x-gm-message-state:mime-version:date:message-id:subject:from:to :content-type; bh=D0zAxvusLGDvqDOa9f6fXwXvR6QN9ck7m0u5b8MTCFg=; b=PSbH5rcmKFIQjvJj7oUkASVXiidPq/zfu+aOW490hbW+ytOhXbO30+LxA1oRNrBAj/ nQSDxqHUO2vYXhTP9usBFJw5bQOIlVOdFoYwF/dwOukJswazTLHv1VQ5f//pHsB1Ztaz R8YvYX8bIeBxfxN84H/ywIqWwiLWiPGKAmEwGDS+NXVEhXA6KA/lunMyCfRMoEJI9gCX nUXm5LQLkzzXh83OGdPKNjGSn22j1ZImohH2rRyPntwxcNDoG+9WbI/WRurXD+sPTl4D yOyu+/Ev0OcqG6gaw/gRqwhHoK1POz2k8VnsZ5/mKx7WwC3sb/VDG5K0hkB8D3O9P8Se kbNw== X-Gm-Message-State: AG10YOTyTczQCsdSf1BoVXIWdDOkXBQLNmlbJiBrR0UDs+/K21Yo7YPjpF6MhoIUaR0Lxl6mneOVgfYABMm78g== X-Mailinglist: alpine-devel Precedence: list List-Id: Alpine Development List-Unsubscribe: List-Post: List-Help: List-Subscribe: MIME-Version: 1.0 X-Received: by 10.28.68.214 with SMTP id r205mr21947342wma.23.1453769604315; Mon, 25 Jan 2016 16:53:24 -0800 (PST) Received: by 10.27.177.156 with HTTP; Mon, 25 Jan 2016 16:53:24 -0800 (PST) Date: Mon, 25 Jan 2016 22:53:24 -0200 Message-ID: Subject: [alpine-devel] Package request: R From: Alba Pompeo To: alpine-devel@lists.alpinelinux.org Content-Type: text/plain; charset=UTF-8 X-Virus-Scanned: ClamAV using ClamSMTP I like to request the package R from https://www.r-project.org/ It's very important for my work in statistics and I would be happy if we had it on Alpine. Thanks. Ciao. --- Unsubscribe: alpine-devel+unsubscribe@lists.alpinelinux.org Help: alpine-devel+help@lists.alpinelinux.org --- From nobody Tue Mar 19 10:47:22 2024 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 B5036DC0240 for ; Tue, 26 Jan 2016 13:17:57 +0000 (UTC) Received: from mail-wm0-f50.google.com (mail-wm0-f50.google.com [74.125.82.50]) (using TLSv1 with cipher ECDHE-RSA-RC4-SHA (128/128 bits)) (No client certificate requested) by mail.alpinelinux.org (Postfix) with ESMTPS id 5C362DC008F for ; Tue, 26 Jan 2016 13:17:57 +0000 (UTC) Received: by mail-wm0-f50.google.com with SMTP id u188so105840186wmu.1 for ; Tue, 26 Jan 2016 05:17:57 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:in-reply-to:references:date:message-id:subject:from:to :content-type; bh=gDKkE2rrJztYcN/I30wQLFk0qG3HZD8peQlgb0E/4Ho=; b=nEwrl8tcL0N7/pxtbRMi4bv7sYCDJmmUE56Y9UPrKLG3DwFp/A69s8eh+3srt1f+S9 6FaoiYZZ5yWSOgtM6iZ83iFYSgUtbW6tyd4DDOByquLmRWoiug7Oz4M6Vx3vg1gne6Nr SH4Zg5i4Q3av9rYCwD4jVcLAsrViyigdtwFcCH38EHAQ2aJw4pcWO+xjSknJ2d/5U1PF uqC+MNQVMCg7GCUyjvjjdTujVnSeByvL/baa/FU2+1CW73II7YYU+JCp0AswT3jY3M4W pyluQNASGx+xMf1aCbEaoC67ZlLEe8Fqk8N5TCX8iTRwWM48vHfhoDQIuVquTLGDYUq3 giGA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20130820; h=x-gm-message-state:mime-version:in-reply-to:references:date :message-id:subject:from:to:content-type; bh=gDKkE2rrJztYcN/I30wQLFk0qG3HZD8peQlgb0E/4Ho=; b=WhqX7CH7SQ6nQQxFIh3DDT3JbMUNexuP3FZpPQjI3g68P8+KprCiEaVQFo1+LS2jHi 5XueyuGSRaqD7OYGXJpV8OYqli4SAFrtoDCpb6h6ZG4eT0oqqxZOOGyaCfvK/RLaozWj MZNDPyxDgnvenddaQAOX7Uxc6WOlveJhkBciMtCUved66nMrsf8sGNRjsJWTtYNEGgwu 9SQK9E3lFE81XnzfdmWbaEjJWffvVJOQNCsrpiceuDa7YBK/Ljfnw8yghkqHBC56CnoL BRzA49WdOauVi2OY1vRBfodEuI1pU8zJJAnXIw1fBwLoNpVabjRVoTP8CdAnGKo9pKYR e56g== X-Gm-Message-State: AG10YORJ+yb3YShjSWz15WaXXSwqjfyErKRKibNG9VNm7UJUls1uVYHvxG5uzzvI+ba1U6pWoC0JgaXSv7x9tA== X-Mailinglist: alpine-devel Precedence: list List-Id: Alpine Development List-Unsubscribe: List-Post: List-Help: List-Subscribe: MIME-Version: 1.0 X-Received: by 10.194.103.198 with SMTP id fy6mr27336103wjb.48.1453814275732; Tue, 26 Jan 2016 05:17:55 -0800 (PST) Received: by 10.27.177.156 with HTTP; Tue, 26 Jan 2016 05:17:55 -0800 (PST) In-Reply-To: References: Date: Tue, 26 Jan 2016 11:17:55 -0200 Message-ID: Subject: [alpine-devel] Re: Package request: R From: Alba Pompeo To: alpine-devel@lists.alpinelinux.org Content-Type: text/plain; charset=UTF-8 X-Virus-Scanned: ClamAV using ClamSMTP 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 /usr/lib/gcc/x86_64-alpine-linux-musl/5.3.0/../../../../x86_64-alpine-linux-musl/bin/ld: final link failed: Bad value collect2: error: ld returned 1 exit status Ciao. On Mon, Jan 25, 2016 at 10:53 PM, Alba Pompeo wrote: > I like to request the package R from https://www.r-project.org/ > It's very important for my work in statistics and I would be happy if > we had it on Alpine. Thanks. > > Ciao. --- Unsubscribe: alpine-devel+unsubscribe@lists.alpinelinux.org Help: alpine-devel+help@lists.alpinelinux.org --- From nobody Tue Mar 19 10:47:22 2024 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 6123EDC06E1 for ; Tue, 26 Jan 2016 14:54:53 +0000 (UTC) Received: from mail-pf0-f175.google.com (mail-pf0-f175.google.com [209.85.192.175]) (using TLSv1 with cipher ECDHE-RSA-RC4-SHA (128/128 bits)) (No client certificate requested) by mail.alpinelinux.org (Postfix) with ESMTPS id 1DCD8DC008F for ; Tue, 26 Jan 2016 14:54:52 +0000 (UTC) Received: by mail-pf0-f175.google.com with SMTP id q63so102750935pfb.1 for ; Tue, 26 Jan 2016 06:54:52 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=date:from:to:subject:message-id:references:mime-version :content-type:content-disposition:in-reply-to:user-agent; bh=PzospesFd2sLU/02nVlDIP5dvIkIIo8+85IvRjTKlqg=; b=R/288stdPacniE1jrajzD35LyoQhrCSX59tT/2BJ5sVOQqB0p1z4cBNSO5sQ4ZhHlH E8k/t33XBOYLEXtwgb8EhLKPf4Ig4JYJou7BbSWMEFKMlG56JtLeS8NNusrSxDP7oX2L dhuul1L5zwGRU771P8z/5H5HOx8ZBna3neSVlP44paSan82NN7RNP7IFz/92uxgpjaio TTwWMe3dZWAtS6gkWh2UzykU+DliZoM05Qb6SSMCQmSnhsXGloj9ONfQlaH2j94YO/Mt TXtMRbOAnfspQhITgqqYier22PGrBuR3mzLLmNW4FnQ/SmOYTWiTiKtN8llxMCSjcO1m INUg== 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:references :mime-version:content-type:content-disposition:in-reply-to :user-agent; bh=PzospesFd2sLU/02nVlDIP5dvIkIIo8+85IvRjTKlqg=; b=iYz+M7TE3igpvd9zm4W2LFTfkRHyqOQvhDPYMfLiNs7g9piePNiCXj1WZvZmM2XjXu BzUgdR6RT+UR7tMSm1OoLCqFoC3q8QeFGZDzkC/5hfotIe9I467j1WmtMrTZVm8Qdc6I 1mwzppNBV/vvRo2xb/UCPWNtEsvv7/34fZdddSmtiantZ0jXhoa5XhAzOQmm8P2H4Ucp 607aTU3c4d+WB9J9WJD3TRJwF0ueW992ZlwhyjJ40CSm7DOz2d4hDv29Q1wi/sAt7wQl wK2NxQ6uzrHyZ0s4r2NF4ts0Km+HxJD2M55zMnCOiLL1CEM7Tr4arFt2gqFWdC9p7Mxu 4wDg== X-Gm-Message-State: AG10YORIlv0UUzWJ7o3bvicBtLBfr/aLaR3ribiXqxJ2nzTmzyCBXxVWqWhxgORD0FqVPQ== X-Received: by 10.98.42.83 with SMTP id q80mr33923067pfq.19.1453820091406; Tue, 26 Jan 2016 06:54:51 -0800 (PST) Received: from newbook ([50.0.225.136]) by smtp.gmail.com with ESMTPSA id 76sm2455953pfl.36.2016.01.26.06.54.50 for (version=TLS1_2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128/128); Tue, 26 Jan 2016 06:54:50 -0800 (PST) Date: Tue, 26 Jan 2016 06:54:47 -0800 From: Isaac Dunham To: alpine-devel@lists.alpinelinux.org Subject: Re: [alpine-devel] Re: Package request: R Message-ID: <20160126145445.GA23152@newbook> 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. I've tried building R for musl in the past; however, that was a few years ago, and it failed some of the tests. (IIRC, I was using gcc/gfortran 4.2 or a 3.4.x-based toolchain.) Because of that, I figured my build was unreliable. Passing 'make test' is an important step, despite being optional (not to mention impossible for cross-compiling). > The error. You missed the command; there's no way to help without it. (It's also good to know what configure options, CFLAGS, and LDFLAGS you used.) There should be something along the lines of with 'gcc ... .o .o ... -l -lc' . > ../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 > /usr/lib/gcc/x86_64-alpine-linux-musl/5.3.0/../../../../x86_64-alpine-linux-musl/bin/ld: > final link failed: Bad value > collect2: error: ld returned 1 exit status > > Ciao. > > > On Mon, Jan 25, 2016 at 10:53 PM, Alba Pompeo wrote: > > I like to request the package R from https://www.r-project.org/ > > It's very important for my work in statistics and I would be happy if > > we had it on Alpine. Thanks. > > > > Ciao. > > > --- > Unsubscribe: alpine-devel+unsubscribe@lists.alpinelinux.org > Help: alpine-devel+help@lists.alpinelinux.org > --- > --- Unsubscribe: alpine-devel+unsubscribe@lists.alpinelinux.org Help: alpine-devel+help@lists.alpinelinux.org --- From nobody Tue Mar 19 10:47:22 2024 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 ---