From unknown Sun Jun 22 17:13:11 2025 X-Loop: help-debbugs@gnu.org Subject: bug#63783: r-dismo bundles pre-built jars Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: bug-guix@gnu.org Resent-Date: Mon, 29 May 2023 12:17:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 63783 X-GNU-PR-Package: guix X-GNU-PR-Keywords: To: 63783@debbugs.gnu.org X-Debbugs-Original-To: bug-guix@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.168536258720649 (code B ref -1); Mon, 29 May 2023 12:17:01 +0000 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; 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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-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 unknown Sun Jun 22 17:13:11 2025 X-Loop: help-debbugs@gnu.org Subject: bug#63783: r-dismo bundles pre-built jars Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: bug-guix@gnu.org Resent-Date: Thu, 01 Jun 2023 21:10:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 63783 X-GNU-PR-Package: guix X-GNU-PR-Keywords: To: 63783@debbugs.gnu.org Received: via spool by 63783-submit@debbugs.gnu.org id=B63783.16856538005425 (code B ref 63783); Thu, 01 Jun 2023 21:10:03 +0000 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 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-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 unknown Sun Jun 22 17:13:11 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: Ricardo Wurmus Subject: bug#63783: closed (Re: r-dismo bundles pre-built jars) Message-ID: References: <87fs7aryhc.fsf@elephly.net> <87a5xnwcxf.fsf@elephly.net> X-Gnu-PR-Message: they-closed 63783 X-Gnu-PR-Package: guix Reply-To: 63783@debbugs.gnu.org Date: Fri, 02 Jun 2023 09:44:03 +0000 Content-Type: multipart/mixed; boundary="----------=_1685699043-15188-1" This is a multi-part message in MIME format... ------------=_1685699043-15188-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #63783: r-dismo bundles pre-built jars which was filed against the guix package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 63783@debbugs.gnu.org. --=20 63783: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D63783 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1685699043-15188-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit 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; 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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 ------------=_1685699043-15188-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit 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; 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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 ------------=_1685699043-15188-1--