From debbugs-submit-bounces@debbugs.gnu.org Mon May 29 08:16:27 2023 Received: (at submit) by debbugs.gnu.org; 29 May 2023 12:16:27 +0000 Received: from localhost ([127.0.0.1]:57308 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q3bnW-0005My-Oi for submit@debbugs.gnu.org; Mon, 29 May 2023 08:16:26 -0400 Received: from lists.gnu.org ([209.51.188.17]:54402) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q3bnU-0005Mq-5J for submit@debbugs.gnu.org; Mon, 29 May 2023 08:16:24 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1q3bnT-0000pV-8q for bug-guix@gnu.org; Mon, 29 May 2023 08:16:23 -0400 Received: from sender3-of-o58.zoho.com ([136.143.184.58]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1q3bnR-0004oF-Go for bug-guix@gnu.org; Mon, 29 May 2023 08:16:23 -0400 ARC-Seal: i=1; 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bh=RcuFnuxtcsYldLYmurmEm5lHkGPnO0AH5VcsD7ZOQmg=; b=Tw+FVN0wpKRK9RHr9TqR7DHWbL7pVMpLuvNLyEW2KjBhlcK8ikBf0PR9nMxry5H0 mTX4EJb+hvc4lF6HFRURGm2QWb9QoyEEj/FE7K18y+8ofUiFG6tdj6+5hpZjDx9lFfD 22tlm5qETyD7Nc0aq1753VkBro09G0Hs2OjfconA= Received: from localhost (78-108-142-46.pool.kielnet.net [46.142.108.78]) by mx.zohomail.com with SMTPS id 1685362576553858.3123891670713; Mon, 29 May 2023 05:16:16 -0700 (PDT) User-agent: mu4e 1.10.2; emacs 28.2 From: Ricardo Wurmus To: bug-guix@gnu.org Subject: r-dismo bundles pre-built jars Date: Mon, 29 May 2023 14:14:15 +0200 Message-ID: <87a5xnwcxf.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External Received-SPF: pass client-ip=136.143.184.58; envelope-from=rekado@elephly.net; helo=sender3-of-o58.zoho.com X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_NONE=-0.0001, RCVD_IN_MSPIKE_H5=0.001, RCVD_IN_MSPIKE_WL=0.001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.3 (-) X-Debbugs-Envelope-To: submit X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.3 (--) The files dismo.jar and maxent.jar in the r-dismo package don=E2=80=99t hav= e any associated source code and are not built from source. --=20 Ricardo From debbugs-submit-bounces@debbugs.gnu.org Thu Jun 01 17:10:00 2023 Received: (at 63783) by debbugs.gnu.org; 1 Jun 2023 21:10:00 +0000 Received: from localhost ([127.0.0.1]:38628 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q4pYV-0001P0-KJ for submit@debbugs.gnu.org; Thu, 01 Jun 2023 17:10:00 -0400 Received: from sender3-of-o57.zoho.com ([136.143.184.57]:21799) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q4pYR-0001Oq-UT for 63783@debbugs.gnu.org; Thu, 01 Jun 2023 17:09:57 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1685653793; cv=none; d=zohomail.com; s=zohoarc; b=O5uH52cbcIfDDJQoorcQMvFXcwk9LI/5VgYk0BuaihFaLEF6COPLp+5CHHG/9y27izhWrAdutlRdmOt8m/Mdtka4wzLd4C3q2NWKab9ZNFDEzg+aNfPLJIo2X9BSr97mqCcLcOMcHwm6X6t4nMzweSzz52EjmhttmXzhO9dGj/0= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1685653793; h=Content-Type:Content-Transfer-Encoding:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=S6plCPeudtafW+Mn2XyZILyvw2rTOf4cmXR7QprDt+E=; b=HGKiUMhaUz2YfGkGyDv7zd2gOs/UcKDvnsH4VpXT4PUQ8g1XiO660uBAdnyGCWEklR/vmJaxsdgMvNJM4a7tFf8P/yGIY4ycHXdgOwzzEFj0cGDfz6NBxmo8Zq3uJl1ipAwkUeeM5tYLrDazhxISwxZL/uj2AIDjOHygRMXSNU0= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1685653793; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:From:To:To:Subject:Subject:Date:Date:In-reply-to:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-Id:Reply-To:Cc; bh=S6plCPeudtafW+Mn2XyZILyvw2rTOf4cmXR7QprDt+E=; b=PiA/+SXH1gxRJWcbw4w9m6H0dPX7YLmsgIOGOBqi5K2ldW5A8tX9atoK/mAsg6Fz R3aY0Kch61Vfefll3SFwJLZ0EcimmfuV7MZq5hGMnU702p1pvhMz85BEuU9ZNKuTbuc ToEAYcWZncrYcMSgHFl/B6VcEJEYxK8OLF2T3oHE= Received: from localhost (78-108-142-46.pool.kielnet.net [46.142.108.78]) by mx.zohomail.com with SMTPS id 1685653790988431.71330873332636; Thu, 1 Jun 2023 14:09:50 -0700 (PDT) References: <87a5xnwcxf.fsf@elephly.net> User-agent: mu4e 1.10.2; emacs 28.2 From: Ricardo Wurmus To: 63783@debbugs.gnu.org Subject: Re: r-dismo bundles pre-built jars Date: Thu, 01 Jun 2023 23:05:04 +0200 In-reply-to: <87a5xnwcxf.fsf@elephly.net> Message-ID: <87sfbasxd0.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: 0.7 (/) X-Debbugs-Envelope-To: 63783 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Ricardo Wurmus writes: > The files dismo.jar and maxent.jar in the r-dismo package don=E2=80=99t h= ave any > associated source code and are not built from source. The source code for maxent.jar is here: https://github.com/mrmaxent/Maxent Here=E2=80=99s a draft of a package definition: --8<---------------cut here---------------start------------->8--- (define-public java-maxent (package (name "java-maxent") (version "3.4.4") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/mrmaxent/Maxent") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "12q7hhly76l77vm8w8v9icga2gn6xs0bw33a7wb7zikcmvizcyp0")))) (build-system ant-build-system) (arguments (list #:tests? #false ;there are none #:jdk icedtea-8 #:phases #~(modify-phases %standard-phases (replace 'build (lambda _ (with-directory-excursion "gnu/getopt/" (invoke "make")) ;; See https://github.com/mrmaxent/Maxent/pull/11 (substitute* "density/Extractor.java" (("float") "double")) (apply invoke "javac" "-cp" (getcwd) "-g" (find-files "density" "\\.java$")) (apply invoke "javac" "-cp" (getcwd) "-g" (find-files "ptolemy/plot" "\\.java$")) (apply invoke "javac" "-cp" (getcwd) "-g" (find-files "com" "\\.java$")) (apply invoke "javac" "-cp" (getcwd) "-g" (find-files "gui" "\\.java$")) (apply invoke "jar" "cvfm" "maxent.jar" (cons* "density/mc.mf" "density/parameters.csv" (append (find-files "density" "\\.class$") (find-files "density" "\\.html$") (find-files "gnu/getopt" ".*") (find-files "gui/layouts" "\\.class$*") (find-files "com/macfaq/io" "\\.class$= *") (find-files "density/tools" "\\.class$= *") (find-files "ptolemy/plot" "\\.class$*= ")))))) (replace 'install (lambda _ (install-file "maxent.jar" (string-append #$output "/share/java/maxent/"))= ))))) (native-inputs (list gnu-make)) (home-page "http://biodiversityinformatics.amnh.org/open_source/maxent") (synopsis "Model species geographic distributions") (description "Maxent is a stand-alone Java application for modelling species geographic distributions.") (license license:expat))) --8<---------------cut here---------------end--------------->8--- The sources in ptolemy/plot cannot be built yet, because we=E2=80=99re miss= ing a package for either https://ptolemy.berkeley.edu/ptolemyII/index.htm or https://ptolemy.berkeley.edu/ptolemyclassic/pt0.7.1/index.htm. We cannot use the Makefile to =E2=80=9Cmake compile=E2=80=9D or =E2=80=9Cma= ke distribution=E2=80=9D because it starts by building ParamPre.java, which can only be built when Parameters.java has been compiled. So perhaps there=E2=80=99s a need = for bootstrapping. In the above package definition we=E2=80=99re using some .j= ava files that have been generated through unknown means. The very small sources for dismo.jar are actually included in the dismo package itself, they just have unexpected names. --=20 Ricardo From debbugs-submit-bounces@debbugs.gnu.org Fri Jun 02 05:43:21 2023 Received: (at 63783-done) by debbugs.gnu.org; 2 Jun 2023 09:43:21 +0000 Received: from localhost ([127.0.0.1]:39093 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q51JY-0003vk-Vb for submit@debbugs.gnu.org; Fri, 02 Jun 2023 05:43:21 -0400 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21066) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q51JV-0003va-Tz for 63783-done@debbugs.gnu.org; Fri, 02 Jun 2023 05:43:19 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1685698995; cv=none; d=zohomail.com; s=zohoarc; b=ERyS05IDUZ6InlevURcMoFAFR0SoYr9Ii7HhpgbwCBJ620c0Ge/Odn8y/olyMWndEYLKA0yW1ysaSn7QnnUNB6e0dSJhAvBJRMf7ZPfMRW/GZG5vWsHxpsh7OYU44bBxtHE0777oks1yJ1eLWe26ESmcQJcoZjHd+t0+j8API4w= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1685698995; h=Content-Type:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=j/M+Xc3lG9WU4DfWA9fEYI0ds+RzlNpsQt5kH4qKHgA=; b=L+m/DK/Oy+om8zUzpBNMPOGpm7w75lY71TAXzmECqFniIgy3ZflIneIBKs4Jd8IQYRjOom2jkUimCvvS0FGK8plwfLHGYq+VHdRdZR+zyiF7QTMXOQ0tvQSzBwKkGzxSHmFaHSauWt3y7wraVreduDJgmMt+GR9rjU6g5vLsTY8= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1685698995; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:From:To:To:Subject:Subject:Date:Date:In-reply-to:Message-ID:MIME-Version:Content-Type:Message-Id:Reply-To:Cc; bh=j/M+Xc3lG9WU4DfWA9fEYI0ds+RzlNpsQt5kH4qKHgA=; b=OJ/LNTMFq7F7mAAVhM2i8FAQM133kCGeCD/M94WgEy7rR6USYkVlekuk9e/ZI8yp D/owuIpjYbWrc9RiA4meOfJ0tAntdRJLGOiTwotJB4y2rm+odVu6+ALGxdmQf6DGmXB wWtFBa8JWXDxDRWGrkWl+Dt+9iI0MJ0td8WP6NQg= Received: from localhost (78-108-142-46.pool.kielnet.net [46.142.108.78]) by mx.zohomail.com with SMTPS id 1685698994236827.5173533088233; Fri, 2 Jun 2023 02:43:14 -0700 (PDT) References: <87a5xnwcxf.fsf@elephly.net> <87sfbasxd0.fsf@elephly.net> User-agent: mu4e 1.10.2; emacs 28.2 From: Ricardo Wurmus To: 63783-done@debbugs.gnu.org Subject: Re: r-dismo bundles pre-built jars Date: Fri, 02 Jun 2023 11:42:57 +0200 In-reply-to: <87sfbasxd0.fsf@elephly.net> Message-ID: <87fs7aryhc.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 63783-done X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Fixed with commit bb27e3b8b13b4dbbb698b3ff5a4f6cf5793e9d5c. -- Ricardo From unknown Sun Jun 22 17:12:33 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. 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