From unknown Fri Aug 15 17:19:14 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#65499] [PATCH 1/2] gnu: Add r-bumpymatrix. Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 24 Aug 2023 13:29:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 65499 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 65499@debbugs.gnu.org Cc: Navid Afkhami X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.169288373422237 (code B ref -1); Thu, 24 Aug 2023 13:29:02 +0000 Received: (at submit) by debbugs.gnu.org; 24 Aug 2023 13:28:54 +0000 Received: from localhost ([127.0.0.1]:36380 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qZAOM-0005ma-7f for submit@debbugs.gnu.org; Thu, 24 Aug 2023 09:28:54 -0400 Received: from lists.gnu.org ([2001:470:142::17]:38558) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qZAOK-0005mN-BX for submit@debbugs.gnu.org; Thu, 24 Aug 2023 09:28:53 -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 1qZAOA-0004cQ-Ar for guix-patches@gnu.org; Thu, 24 Aug 2023 09:28:42 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1qZAO7-0004H4-IE for guix-patches@gnu.org; Thu, 24 Aug 2023 09:28:42 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1692883711; x=1694698112; bh=2uKKU06f9iIOnwP WPN/bQneLN+rbCL4mIuhymLP0yiM=; b=G5XjZ5dQw0VkYSuiX4NRUHerbPBbs51 4XICsaM+EElrDoZeWqKoQ16AuNO2zv5ztsAhpKAa8/pfnL6wlAPjVDQEI8qFS57G yJTWcJCAmOWa0fRvr1/U5B3n950BrCGl/qNw3T6fOkIgOk9ckYFPNdcMoTfZByeg cjQxtOUIjPiw= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id DF4B7A02C9 for ; Thu, 24 Aug 2023 15:28:31 +0200 (CEST) Received: from localhost (141.80.218.27) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.32; Thu, 24 Aug 2023 15:28:31 +0200 From: Navid Afkhami Date: Thu, 24 Aug 2023 13:28:27 +0000 Message-ID: X-Mailer: git-send-email 2.34.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27832.007 X-TM-AS-Result: No-10--6.678300-5.000000 X-TMASE-MatchedRID: SzbEz7SZt2v/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeNTZ+DFCYZ6Lz/b Pm7tO5sURRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v9pkBMYDn8FeK9j7aNnpjtlmUD gikHuA07Ga3MOTq0sPzOU0DmKJatfWi8Qip68NgfdCok3ibXlQeuLFZZYlisfHxPMjOKY7A+6vV BUUydJCsRB0bsfrpPIFT1PBs+MVY3yU/oX+tpNmMNemkBN1aNy9gwOgJ18nxkwHwLpmah7BmhxU vc1FhawdNLEhCSvfmMchXTZ3Wukbw== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--6.678300-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27832.007 X-TM-SNTS-SMTP: F0A08225987C4BD0F992713D7159E1354A35F1F337329C02E363CA25C1974DF82000:F Received-SPF: pass client-ip=194.95.232.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=a2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 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_MED=-2.3, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 0.9 (/) 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: -0.1 (/) * gnu/packages/bioconductor.scm (r-bumpymatrix): New variable. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 74071900a3..6204173277 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12913,6 +12913,33 @@ (define-public r-siggenes Bayes Analyses of Microarrays} (EBAM).") (license license:lgpl2.0+))) +(define-public r-bumpymatrix + (package + (name "r-bumpymatrix") + (version "1.8.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BumpyMatrix" version)) + (sha256 + (base32 + "021xn5d08phmwv6g8a5d4ap5kcf5syhm6vpr784l4k54lflssr5i")))) + (properties `((upstream-name . "BumpyMatrix"))) + (build-system r-build-system) + (propagated-inputs (list r-iranges r-matrix r-s4vectors)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/BumpyMatrix") + (synopsis "Bumpy matrix of non-scalar objects") + (description + " +@code{BumpyMatrix} class and subclasses for storing non-scalar objects in matrix entries. +This is akin to a ragged array but the raggedness is in the third dimension, +much like a bumpy surface - hence the name. Of particular interest is the +@code{BumpyDataFrameMatrix,} where each entry is a Bioconductor data frame. +This allows us to naturally represent multivariate data in a format that is +compatible with two-dimensional containers like the @code{SummarizedExperiment} +and @code{MultiAssayExperiment} objects.") + (license license:expat))) + (define-public r-bumphunter (package (name "r-bumphunter") base-commit: 39fa1ef033fda82cb1d122e0d1675b51acb1db34 -- 2.34.1 From unknown Fri Aug 15 17:19:14 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: Navid Afkhami Subject: bug#65499: closed ([PATCH 1/2] gnu: Add r-bumpymatrix.) Message-ID: References: <87cyz7fuhq.fsf@elephly.net> X-Gnu-PR-Message: they-closed 65499 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 65499@debbugs.gnu.org Date: Mon, 28 Aug 2023 08:22:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1693210922-10277-1" This is a multi-part message in MIME format... ------------=_1693210922-10277-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #65499: [PATCH 1/2] gnu: Add r-bumpymatrix. 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 65499@debbugs.gnu.org. --=20 65499: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D65499 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1693210922-10277-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 65499-done) by debbugs.gnu.org; 28 Aug 2023 08:21:07 +0000 Received: from localhost ([127.0.0.1]:46874 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qaXUg-0002eE-Sc for submit@debbugs.gnu.org; Mon, 28 Aug 2023 04:21:07 -0400 Received: from sender3-of-o57.zoho.com ([136.143.184.57]:21709) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qaXUc-0002de-3f for 65499-done@debbugs.gnu.org; Mon, 28 Aug 2023 04:21:05 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1693210853; cv=none; d=zohomail.com; s=zohoarc; b=n5EWR99btFjsyA4+rc0YIJ6E6ACLPd2xZMNnFvhGmUH4KfWAdwZ1QLDTLwhyzX05PH2TloVejW+eXnYdsLQzNsJDb22K84F/py68E2YpLa8hWlzbZTyXI2vG4mSxNKt6dY80PBzyvu9TWR5sY5OW1MSiwS0xDARbE4dnq67corY= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1693210853; h=Content-Type:Date:Date:From:From:MIME-Version:Message-ID:Subject:Subject:To:To:Message-Id:Reply-To:Cc; bh=6MRBgA9hFv8LM+wOeuHRT38czJCMGVRlNPoUAXLAXbE=; b=WFE2WYWwF2iVVqzgvsySmri0JP9iuQf1E0w+WGeu881riQsn7s9880O9oFzROgXidNe4Y9SRO2dW6c4Ju/aXkw8UR6n5rJ+RrTZHdOMiUD2MxQf7HJbnMhys4zWGxpr2Fj2FbdIt86RwVWJiMgEte3e1THM+Y/mPFguEuZJJ8bA= 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=1693210853; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Subject:Subject:Date:Date:Message-ID:MIME-Version:Content-Type:Message-Id:Reply-To:Cc; bh=6MRBgA9hFv8LM+wOeuHRT38czJCMGVRlNPoUAXLAXbE=; b=FTQVsBdqggmyv3EUjYhkaRogl9bm+R9N7SGk2wTQWGx7wO6q+7xgdhAbsGfLo0wh qAg7NTPp2CMbwnjwqcNnpNzBfdfFZGzfsoo5Zbtv6MYznOZT3VPIPcO83AUN/Z+2+tJ EUE58JjgNm6US2tZj3RLeyNfDFuCJEZuZ4S4Ke78= Received: from localhost (113-111-142-46.pool.kielnet.net [46.142.111.113]) by mx.zohomail.com with SMTPS id 1693210852285289.7811227831521; Mon, 28 Aug 2023 01:20:52 -0700 (PDT) User-agent: mu4e 1.10.5; emacs 28.2 From: Ricardo Wurmus To: 65499-done@debbugs.gnu.org Subject: [PATCH 1/2] gnu: Add r-bumpymatrix. Date: Mon, 28 Aug 2023 10:20:22 +0200 Message-ID: <87cyz7fuhq.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 65499-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 (-) Applied with minor changes. Thanks! -- Ricardo ------------=_1693210922-10277-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 24 Aug 2023 13:28:54 +0000 Received: from localhost ([127.0.0.1]:36380 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qZAOM-0005ma-7f for submit@debbugs.gnu.org; Thu, 24 Aug 2023 09:28:54 -0400 Received: from lists.gnu.org ([2001:470:142::17]:38558) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qZAOK-0005mN-BX for submit@debbugs.gnu.org; Thu, 24 Aug 2023 09:28:53 -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 1qZAOA-0004cQ-Ar for guix-patches@gnu.org; Thu, 24 Aug 2023 09:28:42 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1qZAO7-0004H4-IE for guix-patches@gnu.org; Thu, 24 Aug 2023 09:28:42 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1692883711; x=1694698112; bh=2uKKU06f9iIOnwP WPN/bQneLN+rbCL4mIuhymLP0yiM=; b=G5XjZ5dQw0VkYSuiX4NRUHerbPBbs51 4XICsaM+EElrDoZeWqKoQ16AuNO2zv5ztsAhpKAa8/pfnL6wlAPjVDQEI8qFS57G yJTWcJCAmOWa0fRvr1/U5B3n950BrCGl/qNw3T6fOkIgOk9ckYFPNdcMoTfZByeg cjQxtOUIjPiw= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id DF4B7A02C9 for ; Thu, 24 Aug 2023 15:28:31 +0200 (CEST) Received: from localhost (141.80.218.27) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.32; Thu, 24 Aug 2023 15:28:31 +0200 From: Navid Afkhami To: Subject: [PATCH 1/2] gnu: Add r-bumpymatrix. Date: Thu, 24 Aug 2023 13:28:27 +0000 Message-ID: X-Mailer: git-send-email 2.34.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27832.007 X-TM-AS-Result: No-10--6.678300-5.000000 X-TMASE-MatchedRID: SzbEz7SZt2v/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeNTZ+DFCYZ6Lz/b Pm7tO5sURRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v9pkBMYDn8FeK9j7aNnpjtlmUD gikHuA07Ga3MOTq0sPzOU0DmKJatfWi8Qip68NgfdCok3ibXlQeuLFZZYlisfHxPMjOKY7A+6vV BUUydJCsRB0bsfrpPIFT1PBs+MVY3yU/oX+tpNmMNemkBN1aNy9gwOgJ18nxkwHwLpmah7BmhxU vc1FhawdNLEhCSvfmMchXTZ3Wukbw== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--6.678300-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27832.007 X-TM-SNTS-SMTP: F0A08225987C4BD0F992713D7159E1354A35F1F337329C02E363CA25C1974DF82000:F Received-SPF: pass client-ip=194.95.232.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=a2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 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_MED=-2.3, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 0.9 (/) X-Debbugs-Envelope-To: submit Cc: Navid Afkhami 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: -0.1 (/) * gnu/packages/bioconductor.scm (r-bumpymatrix): New variable. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 74071900a3..6204173277 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12913,6 +12913,33 @@ (define-public r-siggenes Bayes Analyses of Microarrays} (EBAM).") (license license:lgpl2.0+))) +(define-public r-bumpymatrix + (package + (name "r-bumpymatrix") + (version "1.8.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BumpyMatrix" version)) + (sha256 + (base32 + "021xn5d08phmwv6g8a5d4ap5kcf5syhm6vpr784l4k54lflssr5i")))) + (properties `((upstream-name . "BumpyMatrix"))) + (build-system r-build-system) + (propagated-inputs (list r-iranges r-matrix r-s4vectors)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/BumpyMatrix") + (synopsis "Bumpy matrix of non-scalar objects") + (description + " +@code{BumpyMatrix} class and subclasses for storing non-scalar objects in matrix entries. +This is akin to a ragged array but the raggedness is in the third dimension, +much like a bumpy surface - hence the name. Of particular interest is the +@code{BumpyDataFrameMatrix,} where each entry is a Bioconductor data frame. +This allows us to naturally represent multivariate data in a format that is +compatible with two-dimensional containers like the @code{SummarizedExperiment} +and @code{MultiAssayExperiment} objects.") + (license license:expat))) + (define-public r-bumphunter (package (name "r-bumphunter") base-commit: 39fa1ef033fda82cb1d122e0d1675b51acb1db34 -- 2.34.1 ------------=_1693210922-10277-1--