From unknown Sun Jun 22 17:15:22 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#55615] [PATCH] gnu: Add r-pscbs. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: rekado@elephly.net, guix-patches@gnu.org Resent-Date: Tue, 24 May 2022 18:10:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 55615 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 55615@debbugs.gnu.org Cc: zimoun , rekado@elephly.net X-Debbugs-Original-To: guix-patches@gnu.org X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by submit@debbugs.gnu.org id=B.165341574912884 (code B ref -1); Tue, 24 May 2022 18:10:02 +0000 Received: (at submit) by debbugs.gnu.org; 24 May 2022 18:09:09 +0000 Received: from localhost ([127.0.0.1]:53296 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ntYxx-0003Lj-9I for submit@debbugs.gnu.org; Tue, 24 May 2022 14:09:09 -0400 Received: from lists.gnu.org ([209.51.188.17]:37426) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ntYxv-0003Lc-Vn for submit@debbugs.gnu.org; Tue, 24 May 2022 14:09:08 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:50542) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1ntYxv-0003KE-RL for guix-patches@gnu.org; Tue, 24 May 2022 14:09:07 -0400 Received: from mail-wr1-x432.google.com ([2a00:1450:4864:20::432]:38466) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1ntYxu-0005Et-2i for guix-patches@gnu.org; Tue, 24 May 2022 14:09:07 -0400 Received: by mail-wr1-x432.google.com with SMTP id k30so26842896wrd.5 for ; Tue, 24 May 2022 11:09:05 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=aL5ZvCy+yo7P6MMNwhEb1VrU6qtoR3Nm9vgq9zX0vz8=; b=NBZXDrObcI3qjIEFtghM79hq5dc1KRAh0Zvk0PsTg9o2ifh3EmG+OqtNMOmWi7Br3y 3N0l0YvLwbi8IAVmObRAMI4+5rJrZBWd+eqAM8oNQjOCS16chdgGsVQfcxtdO8vOSJww EnLxRBbXVGQB04Sw+3g4Jq6O5mYxzTJMhxNeCRMepP6bb75m1+fANnxea+bgH6v9Ve7x vJ/NKtTnsZjBWA6aDzt1FN0xpS6h5uKdub8Z4LP5TiPhfQ+66zbLF0BF4NXEUYWSjkwz ZLlfkv/FTW+Mza5NS+MfIdyDQV8SWzt4Bhu/o8059pSo8EjI7gSR+92yreKenCwrPNLF DLHw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=aL5ZvCy+yo7P6MMNwhEb1VrU6qtoR3Nm9vgq9zX0vz8=; b=d2glzb4AwQ3dNCNotJP2hbD5SoURKd4TnLxXM9BKVaVF4Tq/hL18rl9yC0mxXKrEKW zTVa9FPWFSiegT2mforPlhvK7hpfLx0kRY5U4OvJaNsh/vKSkOckortRLeo36mNHsD9T VapMyMQ1nQyUAg2bluIgXj+V/9KkWmeUeiNAEb2MGOFRW/x6aVWYNY61WnUZ0RiaghQ5 KGlPqko63FzHj4oB/7DLv4VjXA6U79uR7AqR8mCs1D6NVrTZ8nyy1Vv2JYZJCKIfxDQZ P8hB6hRMDMO6r8ZUPl6iwfVMmfTbpdTWQrrvvHkpolJS4GFPNOJlNtPQ1Ypp3/SxZjoM UWfQ== X-Gm-Message-State: AOAM530p9ind9yjcbiBd7Lve7LSyHaTTuC1hZMJVWal+jsNVZoLZNlJ3 Yar9ZsRThEbmkrCVg5yfSbXVo1jgw6w= X-Google-Smtp-Source: ABdhPJw4AbwZeiYfgG0ABr/Gr7/xRXLrnruqcpPJOaZ8830+P9QDdlefQ0/hkuI5pUX+PrDFj8fh8g== X-Received: by 2002:a05:6000:106:b0:20f:f96f:1072 with SMTP id o6-20020a056000010600b0020ff96f1072mr2255253wrx.159.1653415744206; Tue, 24 May 2022 11:09:04 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id o10-20020a5d648a000000b0020e66dbb9dbsm150729wri.81.2022.05.24.11.09.03 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 24 May 2022 11:09:03 -0700 (PDT) From: zimoun Date: Tue, 24 May 2022 20:08:50 +0200 Message-Id: <20220524180850.3381234-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.36.0 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=2a00:1450:4864:20::432; envelope-from=zimon.toutoune@gmail.com; helo=mail-wr1-x432.google.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, FREEMAIL_FROM=0.001, RCVD_IN_DNSWL_NONE=-0.0001, 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 (--) * gnu/packages/bioconductor.scm (r-pscbs): New variable. --- gnu/packages/bioconductor.scm | 42 +++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 80cf28c954..7fed1aa18b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4560,6 +4560,48 @@ (define-public r-pcamethods structure (pcaRes) to provide a common interface to the PCA results.") (license license:gpl3+))) +;; This is a CRAN package, but it depends on a Bioconductor package: +;; r-aroma-light, r-dnacopy.. +(define-public r-pscbs + (package + (name "r-pscbs") + (version "0.66.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "PSCBS" version)) + (sha256 + (base32 "14rs2wywipbkia3dbzfhpnkmfgdvm2bf586lggsx63sywlv5d02q")))) + (properties `((upstream-name . "PSCBS"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'install 'change-home-dir + (lambda _ + ;; Change from /homeless-shelter to /tmp for write permission. + (setenv "HOME" "/tmp")))))) + (propagated-inputs + (list r-aroma-light + r-dnacopy + r-future + r-listenv + r-matrixstats + r-r-cache + r-r-methodss3 + r-r-oo + r-r-utils)) + (native-inputs + (list r-r-rsp ;used to build vignettes + r-r-devices)) + (home-page "https://github.com/HenrikBengtsson/PSCBS") + (synopsis "Analysis of Parent-Specific DNA Copy Numbers") + (description + "Segmentation of allele-specific DNA copy number data and detection of +regions with abnormal copy number within each parental chromosome. Both +tumor-normal paired and tumor-only analyses are supported.") + (license license:gpl2+))) + (define-public r-protgenerics (package (name "r-protgenerics") base-commit: 01793ed03e8aa0960bff7adc21fd270e1527e68e -- 2.36.0 From unknown Sun Jun 22 17:15:22 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: zimoun Subject: bug#55615: closed (Re: [bug#55615] [PATCH] gnu: Add r-pscbs.) Message-ID: References: <87wneahb5b.fsf@elephly.net> <20220524180850.3381234-1-zimon.toutoune@gmail.com> X-Gnu-PR-Message: they-closed 55615 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 55615@debbugs.gnu.org Date: Tue, 24 May 2022 21:30:03 +0000 Content-Type: multipart/mixed; boundary="----------=_1653427803-8995-1" This is a multi-part message in MIME format... ------------=_1653427803-8995-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #55615: [PATCH] gnu: Add r-pscbs. which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 55615@debbugs.gnu.org. --=20 55615: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D55615 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1653427803-8995-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 55615-done) by debbugs.gnu.org; 24 May 2022 21:30:01 +0000 Received: from localhost ([127.0.0.1]:53641 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ntc6L-0002Kb-EH for submit@debbugs.gnu.org; Tue, 24 May 2022 17:30:01 -0400 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21064) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ntc6J-0002KT-J1 for 55615-done@debbugs.gnu.org; Tue, 24 May 2022 17:30:00 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1653427797; cv=none; d=zohomail.com; s=zohoarc; b=noL+kBmpMIJ8IlsgFeR3TJo6irr/mj/kCxVDrvB8TpVfUrEBT0uKXlHQfiaAFAUQa8elkF3YnfuchXN4gl2fJo1EGAYLr949VZvxE7RPp8RU59bt6Ho+qWHkXgW+OxnRh8Xnq3gmrFO7daK9fnPs89g+K5MVtDUl7JLuXZWdtGc= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1653427797; h=Content-Type:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=KqkBPZOEnofqXaYjji0NVw+PHmlXMflKOfTTfmUeXxs=; b=iSDrLVhvKykBa7tVyWZE3IdTgmYRW6Udm4ecSb22HxUgBkB68ICKfYGgYyWoPF5pjBhy41MZK2kmpI5/mNthecS81ja7r1Anl2ocDAsUYlFIq3fe/NQKCDA36L8dyHxjEHxLbPT2jMkPBk5UUaurM2FlWJB+PBxYrCFYZEivewM= 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=1653427797; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:In-reply-to:Message-ID:MIME-Version:Content-Type:Message-Id:Reply-To; bh=KqkBPZOEnofqXaYjji0NVw+PHmlXMflKOfTTfmUeXxs=; b=GG3JncVY2bTgqOS5XmgIdpqXsI/VlnmGDFWQuprsuQodgBQuZqaxm22jaFDAX3r/ rB/3JFMO+R2sP4DqtdEZT1uHovez4m0z2I1aokuEcDoIc5V9wPVkwUOs3cXDA8eY3AZ iq/oRD8oE7E+EFq4g1Hztm1C8ZEcc7vguDvroMUs= Received: from localhost (187-110-142-46.pool.kielnet.net [46.142.110.187]) by mx.zohomail.com with SMTPS id 1653427795605696.4475313841555; Tue, 24 May 2022 14:29:55 -0700 (PDT) References: <20220524180850.3381234-1-zimon.toutoune@gmail.com> User-agent: mu4e 1.6.10; emacs 28.0.50 From: Ricardo Wurmus To: zimoun Subject: Re: [bug#55615] [PATCH] gnu: Add r-pscbs. Date: Tue, 24 May 2022 23:29:36 +0200 In-reply-to: <20220524180850.3381234-1-zimon.toutoune@gmail.com> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Message-ID: <87wneahb5b.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 55615-done Cc: 55615-done@debbugs.gnu.org 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 (-) zimoun writes: > * gnu/packages/bioconductor.scm (r-pscbs): New variable. Applied with formatting changes. Thanks! -- Ricardo ------------=_1653427803-8995-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 24 May 2022 18:09:09 +0000 Received: from localhost ([127.0.0.1]:53296 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ntYxx-0003Lj-9I for submit@debbugs.gnu.org; Tue, 24 May 2022 14:09:09 -0400 Received: from lists.gnu.org ([209.51.188.17]:37426) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ntYxv-0003Lc-Vn for submit@debbugs.gnu.org; Tue, 24 May 2022 14:09:08 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:50542) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1ntYxv-0003KE-RL for guix-patches@gnu.org; Tue, 24 May 2022 14:09:07 -0400 Received: from mail-wr1-x432.google.com ([2a00:1450:4864:20::432]:38466) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1ntYxu-0005Et-2i for guix-patches@gnu.org; Tue, 24 May 2022 14:09:07 -0400 Received: by mail-wr1-x432.google.com with SMTP id k30so26842896wrd.5 for ; Tue, 24 May 2022 11:09:05 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=aL5ZvCy+yo7P6MMNwhEb1VrU6qtoR3Nm9vgq9zX0vz8=; b=NBZXDrObcI3qjIEFtghM79hq5dc1KRAh0Zvk0PsTg9o2ifh3EmG+OqtNMOmWi7Br3y 3N0l0YvLwbi8IAVmObRAMI4+5rJrZBWd+eqAM8oNQjOCS16chdgGsVQfcxtdO8vOSJww EnLxRBbXVGQB04Sw+3g4Jq6O5mYxzTJMhxNeCRMepP6bb75m1+fANnxea+bgH6v9Ve7x vJ/NKtTnsZjBWA6aDzt1FN0xpS6h5uKdub8Z4LP5TiPhfQ+66zbLF0BF4NXEUYWSjkwz ZLlfkv/FTW+Mza5NS+MfIdyDQV8SWzt4Bhu/o8059pSo8EjI7gSR+92yreKenCwrPNLF DLHw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=aL5ZvCy+yo7P6MMNwhEb1VrU6qtoR3Nm9vgq9zX0vz8=; b=d2glzb4AwQ3dNCNotJP2hbD5SoURKd4TnLxXM9BKVaVF4Tq/hL18rl9yC0mxXKrEKW zTVa9FPWFSiegT2mforPlhvK7hpfLx0kRY5U4OvJaNsh/vKSkOckortRLeo36mNHsD9T VapMyMQ1nQyUAg2bluIgXj+V/9KkWmeUeiNAEb2MGOFRW/x6aVWYNY61WnUZ0RiaghQ5 KGlPqko63FzHj4oB/7DLv4VjXA6U79uR7AqR8mCs1D6NVrTZ8nyy1Vv2JYZJCKIfxDQZ P8hB6hRMDMO6r8ZUPl6iwfVMmfTbpdTWQrrvvHkpolJS4GFPNOJlNtPQ1Ypp3/SxZjoM UWfQ== X-Gm-Message-State: AOAM530p9ind9yjcbiBd7Lve7LSyHaTTuC1hZMJVWal+jsNVZoLZNlJ3 Yar9ZsRThEbmkrCVg5yfSbXVo1jgw6w= X-Google-Smtp-Source: ABdhPJw4AbwZeiYfgG0ABr/Gr7/xRXLrnruqcpPJOaZ8830+P9QDdlefQ0/hkuI5pUX+PrDFj8fh8g== X-Received: by 2002:a05:6000:106:b0:20f:f96f:1072 with SMTP id o6-20020a056000010600b0020ff96f1072mr2255253wrx.159.1653415744206; Tue, 24 May 2022 11:09:04 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id o10-20020a5d648a000000b0020e66dbb9dbsm150729wri.81.2022.05.24.11.09.03 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 24 May 2022 11:09:03 -0700 (PDT) From: zimoun To: guix-patches@gnu.org Subject: [PATCH] gnu: Add r-pscbs. Date: Tue, 24 May 2022 20:08:50 +0200 Message-Id: <20220524180850.3381234-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.36.0 MIME-Version: 1.0 X-Debbugs-CC: rekado@elephly.net Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=2a00:1450:4864:20::432; envelope-from=zimon.toutoune@gmail.com; helo=mail-wr1-x432.google.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, FREEMAIL_FROM=0.001, RCVD_IN_DNSWL_NONE=-0.0001, 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 Cc: zimoun 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 (--) * gnu/packages/bioconductor.scm (r-pscbs): New variable. --- gnu/packages/bioconductor.scm | 42 +++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 80cf28c954..7fed1aa18b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4560,6 +4560,48 @@ (define-public r-pcamethods structure (pcaRes) to provide a common interface to the PCA results.") (license license:gpl3+))) +;; This is a CRAN package, but it depends on a Bioconductor package: +;; r-aroma-light, r-dnacopy.. +(define-public r-pscbs + (package + (name "r-pscbs") + (version "0.66.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "PSCBS" version)) + (sha256 + (base32 "14rs2wywipbkia3dbzfhpnkmfgdvm2bf586lggsx63sywlv5d02q")))) + (properties `((upstream-name . "PSCBS"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'install 'change-home-dir + (lambda _ + ;; Change from /homeless-shelter to /tmp for write permission. + (setenv "HOME" "/tmp")))))) + (propagated-inputs + (list r-aroma-light + r-dnacopy + r-future + r-listenv + r-matrixstats + r-r-cache + r-r-methodss3 + r-r-oo + r-r-utils)) + (native-inputs + (list r-r-rsp ;used to build vignettes + r-r-devices)) + (home-page "https://github.com/HenrikBengtsson/PSCBS") + (synopsis "Analysis of Parent-Specific DNA Copy Numbers") + (description + "Segmentation of allele-specific DNA copy number data and detection of +regions with abnormal copy number within each parental chromosome. Both +tumor-normal paired and tumor-only analyses are supported.") + (license license:gpl2+))) + (define-public r-protgenerics (package (name "r-protgenerics") base-commit: 01793ed03e8aa0960bff7adc21fd270e1527e68e -- 2.36.0 ------------=_1653427803-8995-1-- From unknown Sun Jun 22 17:15:22 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#55615] [PATCH] gnu: Add r-pscbs. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 25 May 2022 07:32:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 55615 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Ricardo Wurmus Cc: 55615-done@debbugs.gnu.org Received: via spool by 55615-done@debbugs.gnu.org id=D55615.165346389812327 (code D ref 55615); Wed, 25 May 2022 07:32:02 +0000 Received: (at 55615-done) by debbugs.gnu.org; 25 May 2022 07:31:38 +0000 Received: from localhost ([127.0.0.1]:54209 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ntlUX-0003Cj-Uk for submit@debbugs.gnu.org; Wed, 25 May 2022 03:31:38 -0400 Received: from mail-pj1-f47.google.com ([209.85.216.47]:56243) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ntlUV-0003CW-LH for 55615-done@debbugs.gnu.org; Wed, 25 May 2022 03:31:36 -0400 Received: by mail-pj1-f47.google.com with SMTP id n10so18938206pjh.5 for <55615-done@debbugs.gnu.org>; Wed, 25 May 2022 00:31:35 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=mime-version:references:in-reply-to:from:date:message-id:subject:to :cc; bh=pM7AyotNk0yXR8mmYKuevDSZo3L6zrf9eU1U3D51oBI=; b=Wqoft4BBKuOduGEx1rYJTy1UyjPmCaOXBHvCfulzfVlmanIDsBKrhwknY2VVwyF08s r26usIJRfv+UTkDtW2zDrKQB5jynDK6Y0Mxn+d4t+EZhx3YlStJXQDUMVZSLX/UCLOv4 Ia3jP1hypWae+XPyxEo8g+bYWRiVoPcRNcAJVMQZmjYp8h1LPSxSg58F2tNvqiWf4a0S 9Z65AQZ6D8DHMocYJkzZVRpoyTMqeeNk6eq71tU2X0DnM3xLVDwgFfXnsthhLT5Fa4dn ikTfAsqyXCcqYEAR2c2lqVFYgfBuz/Ag7Ga1uutR50hNyKhgn8yZWc9ZpicZlPDytR9u ImvA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=pM7AyotNk0yXR8mmYKuevDSZo3L6zrf9eU1U3D51oBI=; b=fbDpeRQKtEY17yRETHNqZ62t4tDvxns0R5EOIeofksu3xlnHahoAtJt8UKH/0DSODx ldhHzevPRNbdQDGjOn3v1Uc5nR0SDaFqegOAyYz5fesxmSXh+HgW89f8xexKZKZj6Ifc d3bnh0ZJEPrqdsbnt7N+koYrR1eH7VBy76j30f7UTAVpVfP+/YhpN6/GdOAXHpb2pUPb e2TECnbUD6T2nXB1toFRwvOOnC58DzLsCUa+ACk7PpGcn5NcZVEVV6PUOa6yMcvyINlw s7zxWsL8LrVezCTZImkwJSm7SYZW0MlnOuHMrDjcXExbEwBy5bHt0Hygq2eGt1BxH63c MB1g== X-Gm-Message-State: AOAM5302ta1Daxfq+IumU0RGdENfzJTjK9OaTdWBOSJMoMw0cknT0hZ7 Ppem88jGLzo8vwTccPz7HrVQtmOhHwAOQo5wUx2acwog X-Google-Smtp-Source: ABdhPJxwn53zj8wubxby8COUOJTfj7z61BNTMMlRnX/TRp526DlPHQQ1mE2w6M3fKsvVama6eUN+lsuVlfmLQPBeB7I= X-Received: by 2002:a17:902:da8c:b0:162:33b5:6aa1 with SMTP id j12-20020a170902da8c00b0016233b56aa1mr10105574plx.75.1653463889584; Wed, 25 May 2022 00:31:29 -0700 (PDT) MIME-Version: 1.0 References: <20220524180850.3381234-1-zimon.toutoune@gmail.com> <87wneahb5b.fsf@elephly.net> In-Reply-To: <87wneahb5b.fsf@elephly.net> From: zimoun Date: Wed, 25 May 2022 09:31:17 +0200 Message-ID: Content-Type: text/plain; charset="UTF-8" X-Spam-Score: -0.0 (/) 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 (-) Hi, On Tue, 24 May 2022 at 23:30, Ricardo Wurmus wrote: > Applied with formatting changes. Thanks! Indeed, sorry. I reformatted the output of "guix import" but then I forgot to reformat again the phase modification (my bad!). And I ran "guix lint" which reported nothing. But "guix style" reformats; which I do not use (yet). Well, it is many manual error-prone steps. My questions are : 1. Could we adapted "guix import cran" to output something using the format of "guix style"? 2. Could we add a checker in "guix lint" using "guix style" and warn? Cheers, simon From unknown Sun Jun 22 17:15:22 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#55615] [PATCH] gnu: Add r-pscbs. Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 27 May 2022 08:14:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 55615 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: zimoun Cc: 55615-done@debbugs.gnu.org Received: via spool by 55615-done@debbugs.gnu.org id=D55615.1653639239408 (code D ref 55615); Fri, 27 May 2022 08:14:01 +0000 Received: (at 55615-done) by debbugs.gnu.org; 27 May 2022 08:13:59 +0000 Received: from localhost ([127.0.0.1]:60864 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nuV6Z-00006T-V6 for submit@debbugs.gnu.org; Fri, 27 May 2022 04:13:59 -0400 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21044) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nuV6U-00006G-Nr for 55615-done@debbugs.gnu.org; Fri, 27 May 2022 04:13:54 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1653639228; cv=none; d=zohomail.com; s=zohoarc; b=IVuC8vpZUcqjyPi0y2bwxEE1xgHy+PfgfLQUoCim9t+J0sYBxBFsdBe5HKWwYC1f9k1NAzPHWUzrDGkxo6raCYCqHTTcQ7hiKEMguJrNeNjk2MNFmWIbdRw9XhNi70VFTpTHJO/cjghIoRkoFH6mXMFBnPHQUjnrwJfBdae0sfE= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1653639228; h=Content-Type:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=p8qobEBr/wT1stqG563gz0OiQsChMRrcDJXB53b33iU=; b=lu/2Rx7g4ovXQJrSTeBywn38dM8u27p9S+TIE+qOqK/lOWeT9pdoaV+uuWPtrda/zCtYmEypa83fwzEr00CJnp0qP1QSIQU4l9EWHTjJLudtNqds/FIb45/L3pTzykQDuCaIzgidLBtTHl0E4wHX5kLSK3G6eOpnHhe4YznGoqY= 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=1653639228; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:In-reply-to:Message-ID:MIME-Version:Content-Type:Message-Id:Reply-To; bh=p8qobEBr/wT1stqG563gz0OiQsChMRrcDJXB53b33iU=; b=GIUkk2OfyHgPrfnw5nocYNNBjkOc7o6Wo8CGAARLSTs3ey69nlwJ82F6SgxuAaap fmEsXpHM9zMbib8g2TnkJ1tkeV0FTaiM5azKPKardNQsjuObBfTvMGI1hxMpLEgjBSq PLj/5L7eXMTpfPgrB6pmCx4n/56hDTbw4SO2DOdc= Received: from localhost (180-111-142-46.pool.kielnet.net [46.142.111.180]) by mx.zohomail.com with SMTPS id 165363922596519.946472904024745; Fri, 27 May 2022 01:13:45 -0700 (PDT) References: <20220524180850.3381234-1-zimon.toutoune@gmail.com> <87wneahb5b.fsf@elephly.net> User-agent: mu4e 1.6.10; emacs 28.1 From: Ricardo Wurmus Date: Fri, 27 May 2022 10:12:51 +0200 In-reply-to: X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Message-ID: <87zgj3cs09.fsf@elephly.net> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" X-ZohoMailClient: External X-Zoho-Virus-Status: 1 X-Spam-Score: 1.6 (+) X-Spam-Report: Spam detection software, running on the system "debbugs.gnu.org", has NOT identified this incoming email as spam. The original message has been attached to this so you can view it or label similar future email. If you have any questions, see the administrator of that system for details. Content preview: zimoun writes: > Hi, > > On Tue, 24 May 2022 at 23:30, Ricardo Wurmus wrote: > >> Applied with formatting changes. Thanks! > > Indeed, sorry. I reformatted the output of "guix import" but then I [...] Content analysis details: (1.6 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- -0.0 SPF_PASS SPF: sender matches SPF record 0.0 SPF_HELO_NONE SPF: HELO does not publish an SPF Record 1.6 PDS_OTHER_BAD_TLD Untrustworthy TLDs [URI: yoctocell.xyz (xyz)] -0.0 RCVD_IN_DNSWL_NONE RBL: Sender listed at https://www.dnswl.org/, no trust [136.143.188.50 listed in list.dnswl.org] -0.0 RCVD_IN_MSPIKE_H2 RBL: Average reputation (+2) [136.143.188.50 listed in wl.mailspike.net] -0.0 T_SCC_BODY_TEXT_LINE No description available. 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: 0.6 (/) --=-=-= Content-Type: text/plain zimoun writes: > Hi, > > On Tue, 24 May 2022 at 23:30, Ricardo Wurmus wrote: > >> Applied with formatting changes. Thanks! > > Indeed, sorry. I reformatted the output of "guix import" but then I > forgot to reformat again the phase modification (my bad!). And I ran > "guix lint" which reported nothing. But "guix style" reformats; > which I do not use (yet). > > Well, it is many manual error-prone steps. My questions are : > > 1. Could we adapted "guix import cran" to output something using the > format of "guix style"? How about this: --=-=-= Content-Type: text/x-patch; charset=utf-8 Content-Disposition: inline; filename=0001-scripts-import-Use-pretty-printer-from-guix-scripts-.patch Content-Transfer-Encoding: quoted-printable >From a10afc4c60ce734941c3c080cf13ec6636f0be33 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 27 May 2022 10:07:26 +0200 Subject: [PATCH] scripts/import: Use pretty printer from (guix scripts styl= e). * guix/scripts/import.scm (guix-import): Use pretty-print-with-comments. (newline-rewriting-port): Remove procedure. --- guix/scripts/import.scm | 39 +++------------------------------------ 1 file changed, 3 insertions(+), 36 deletions(-) diff --git a/guix/scripts/import.scm b/guix/scripts/import.scm index fa79f3211e..62aa7bdbc5 100644 --- a/guix/scripts/import.scm +++ b/guix/scripts/import.scm @@ -2,7 +2,7 @@ ;;; Copyright =C2=A9 2012, 2013, 2014, 2020, 2021 Ludovic Court=C3=A8s ;;; Copyright =C2=A9 2014 David Thompson ;;; Copyright =C2=A9 2018 Kyle Meyer -;;; Copyright =C2=A9 2019 Ricardo Wurmus +;;; Copyright =C2=A9 2019, 2022 Ricardo Wurmus ;;; Copyright =C2=A9 2021 Simon Tournier ;;; Copyright =C2=A9 2021 Xinglu Chen ;;; Copyright =C2=A9 2022 Philip McGrath @@ -25,6 +25,7 @@ (define-module (guix scripts import) #:use-module (guix ui) #:use-module (guix scripts) + #:use-module (guix scripts style) #:use-module (guix utils) #:use-module (srfi srfi-1) #:use-module (srfi srfi-11) @@ -32,41 +33,9 @@ (define-module (guix scripts import) #:use-module (srfi srfi-37) #:use-module (ice-9 format) #:use-module (ice-9 match) - #:use-module (ice-9 pretty-print) #:export (%standard-import-options guix-import)) =20 - -;;; -;;; Helper. -;;; - -(define (newline-rewriting-port output) - "Return an output port that rewrites strings containing the \\n escape -to an actual newline. This works around the behavior of `pretty-print' -and `write', which output these as \\n instead of actual newlines, -whereas we want the `description' field to contain actual newlines -rather than \\n." - (define (write-string str) - (let loop ((chars (string->list str))) - (match chars - (() - #t) - ((#\\ #\n rest ...) - (newline output) - (loop rest)) - ((chr rest ...) - (write-char chr output) - (loop rest))))) - - (make-soft-port (vector (cut write-char <>) - write-string - (lambda _ #t) ; flush - #f - (lambda _ #t) ; close - #f) - "w")) - ;;; ;;; Command line options. @@ -119,9 +88,7 @@ (define-command (guix-import . args) ((importer args ...) (if (member importer importers) (let ((print (lambda (expr) - (pretty-print expr (newline-rewriting-port - (current-output-port)) - #:max-expr-width 80)))) + (pretty-print-with-comments (current-output-port) = expr)))) (match (apply (resolve-importer importer) args) ((and expr (or ('package _ ...) ('let _ ...) --=20 2.36.1 --=-=-= Content-Type: text/plain -- Ricardo --=-=-=-- From unknown Sun Jun 22 17:15:22 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#55615] [PATCH] gnu: Add r-pscbs. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 01 Jun 2022 09:03:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 55615 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Ricardo Wurmus Cc: 55615-done@debbugs.gnu.org Received: via spool by 55615-done@debbugs.gnu.org id=D55615.165407415120595 (code D ref 55615); Wed, 01 Jun 2022 09:03:02 +0000 Received: (at 55615-done) by debbugs.gnu.org; 1 Jun 2022 09:02:31 +0000 Received: from localhost ([127.0.0.1]:49702 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nwKFL-0005M5-Hw for submit@debbugs.gnu.org; Wed, 01 Jun 2022 05:02:31 -0400 Received: from mail-pl1-f181.google.com ([209.85.214.181]:41738) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nwKFH-0005Ll-Qe for 55615-done@debbugs.gnu.org; Wed, 01 Jun 2022 05:02:29 -0400 Received: by mail-pl1-f181.google.com with SMTP id s14so1183349plk.8 for <55615-done@debbugs.gnu.org>; Wed, 01 Jun 2022 02:02:27 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=mime-version:references:in-reply-to:from:date:message-id:subject:to :cc; bh=c6gzV2QK2OuILlUuWCsRrcqdC6KPKeC+arSIKAZPDbg=; b=jHKEtxDXXu+xOVDVj46bSoEDg5kjqzaQHaj3uiQSvWPzV6xmxyb+rUqZNIigAFwOSL t8MBxPUxEGaoL1YyKf0wBoVzaZVAZzsQN/rGwbQ0KhE1nIxpSAEKmwJb7tCWJrDia4Yt FvTSOCsHNTI61T4n8k/vDKhKW4wBoRoW0o4Vy/hcl/eGTwKjc+IaKln4nVwBiGKKFHsD pAo1bqDEi+8OqEosE1Rom/J7efFbp+N5z3+ouU8YtDya1mCxhrafgsIOBGddDZcIFebB YL+Nr1WywFsSPouIId4yazHXDslDTJhmNvtJ2f6DvCJEJ/2x+cPcJqv5bd9hf/X7cPAk 22GA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=c6gzV2QK2OuILlUuWCsRrcqdC6KPKeC+arSIKAZPDbg=; b=U5XuQqbuWHF5+GvqiIAeDzvo+hy6xIIME+BJ0w46oyJ/hi+29HjB1aECY6aT2zsvzZ cQtjny6Oc0nwPhw8KIGrrSbERm9pLrdLsuAlqwbeiM+GyJbJxfqNMPD/5FOi8Q5GXOMA WncKkbHWEzS6XaJdCSfggO8NHJONHjA+1kqCo33lOyMxHJQYW0V7IsB+msDGC22vEvN/ RtL2uMBdY0UclGcrdnSgg+oRZeSoiGUkbU9DQG/xtlmQQDCcSk6h2DgrgL4eborvxt+T l/zwwZ+tSRNpBeMDQCWsYjmrOyi6jNG1X7YegII/kodcZkikcKzKScT6kZOHD/2ESWY9 MyJg== X-Gm-Message-State: AOAM5316LWEH1LESimObdtcD55Nv6qtvA3PnlepzOIJkNEegrr5G8uay OMf7Pw+/G898x9SszIsrvqyo86LOV9PKODtsNNc= X-Google-Smtp-Source: ABdhPJyZsBXAs694IAfu5zXlv3xiVoSsmsRKB0FldVUzRT4neV5iUBAHA8zEm+9OX9AAiOcFQ9At6KFP2lb85X1Ex0M= X-Received: by 2002:a17:902:d682:b0:163:cb15:dda1 with SMTP id v2-20020a170902d68200b00163cb15dda1mr16099989ply.36.1654074140732; Wed, 01 Jun 2022 02:02:20 -0700 (PDT) MIME-Version: 1.0 References: <20220524180850.3381234-1-zimon.toutoune@gmail.com> <87wneahb5b.fsf@elephly.net> <87zgj3cs09.fsf@elephly.net> In-Reply-To: <87zgj3cs09.fsf@elephly.net> From: zimoun Date: Wed, 1 Jun 2022 11:02:09 +0200 Message-ID: Content-Type: text/plain; charset="UTF-8" X-Spam-Score: -0.0 (/) 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 (-) Hi Ricardo, On Fri, 27 May 2022 at 10:13, Ricardo Wurmus wrote: > How about this: I am late and you already applied it. Cool! :-) Thanks, simon