From unknown Sun Jun 15 09:00:34 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#66118] [PATCH] gnu: Add r-omixerrpm. Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 20 Sep 2023 10:41:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 66118 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 66118@debbugs.gnu.org Cc: Navid Afkhami X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.169520641819786 (code B ref -1); Wed, 20 Sep 2023 10:41:02 +0000 Received: (at submit) by debbugs.gnu.org; 20 Sep 2023 10:40:18 +0000 Received: from localhost ([127.0.0.1]:58428 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qiud0-000594-7u for submit@debbugs.gnu.org; Wed, 20 Sep 2023 06:40:18 -0400 Received: from lists.gnu.org ([2001:470:142::17]:49424) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qiucx-00058j-Hc for submit@debbugs.gnu.org; Wed, 20 Sep 2023 06:40:17 -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 1qiuci-0008M8-Mb for guix-patches@gnu.org; Wed, 20 Sep 2023 06:40:00 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1qiucf-0001tU-GP for guix-patches@gnu.org; Wed, 20 Sep 2023 06:40:00 -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=1695206364; x=1697020765; bh=YdM3aoab6x+PuwN YoYDFb7+cxMNBBpd4QP7PwQrMP6k=; b=qVIJQ1cmgjj5xkgA75rez8nqKS30EJs ZLwoHrjHM53fkBgnUYKdlmlG571Q/OVZa7+aYBfLeleeklhQyNIaZ2sRUFWoe/rF K/UofzMcZvQW3D323fXqTo/FuAaoXpo0kzviQtOwxizF2gclMrCZKM0dM/8TVso9 BFoiOAFYWFR0= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id ED8B9160171 for ; Wed, 20 Sep 2023 12:39:23 +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; Wed, 20 Sep 2023 12:39:23 +0200 From: Navid Afkhami Date: Wed, 20 Sep 2023 10:39:12 +0000 Message-ID: <5b11081be482875b9b4a1da4c892c8f6c5f07006.1695206352.git.navid.afkhami@mdc-berlin.de> 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-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27886.007 X-TM-AS-Result: No-10--2.820400-5.000000 X-TMASE-MatchedRID: I6rpFm0lrcN6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VICu qghmtWfXXt3JNptef3p4Zvg4N7yewiq+GZ9ZHxIhuW77/y896sj4qCLIu0mtIMIubEPSkNnJl1i peFKJNYV7MSP7SLpuGE/hQBftKoDg1pVckLHgk0JvTnqYKYXTRuuLFZZYlisfHxPMjOKY7A8Lbi gRnpKlKTpcQTtiHDgWHjCkLaWYZ2QgPTinL8C6wmCJGp28iuq7p2wz3wbcShyCrkjmrUz0BiHon v4c0EiVS4gT0lUFanq4V2EhtNy1pYLe0bg7vlvwt0oQIuj+SVeFEVfQxs3N6ZDgmt8QekvB5maC eNv/LIzVGQdqwsDiEg== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.820400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27886.007 X-TM-SNTS-SMTP: AFCD40719FF622B581007DE6B7CAE4CF4D47C6C8A0FA20F3188B33AB7EBE04142000:F Received-SPF: pass client-ip=194.95.234.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=b2062.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/bioinformatics.scm (r-omixerrpm): New variable. --- gnu/packages/bioinformatics.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6acf37b312..d4da92b6b6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15065,6 +15065,29 @@ (define-public r-dyngen dynamic cellular processes at single-cell resolution.") (license license:expat))) +(define-public r-omixerrpm + (let ((commit "184f1cc99aefed722e20eb00eda082348a064c4e") + (revision "1")) + (package + (name "r-omixerrpm") + (version (git-version "0.3.3" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/omixer/omixer-rpmR") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "10ipasg8zi4ln13a5zj2l4a35hd3sfy3p6gir0sw0vf3cbc11lnz")))) + (properties `((upstream-name . "omixerRpm"))) + (build-system r-build-system) + (home-page "https://github.com/omixer/omixer-rpmR") + (synopsis "Metabolic module profiling of microbiome samples") + (description + "An R interface for microbiome metabolic module profiling with omixer-rpm.") + (license license:gpl3)))) + ;; Needed for r-liana (define-public r-omnipathr/devel (let ((commit "679bb79e319af246a16968d27d64d8d6937a331a") base-commit: 6bd17a0806ad32d1493ac51a7443276f719c4224 -- 2.34.1 From unknown Sun Jun 15 09:00:34 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#66118: closed (Can not be added to Guix - The package contains a non-free binary) Message-ID: References: <5b11081be482875b9b4a1da4c892c8f6c5f07006.1695206352.git.navid.afkhami@mdc-berlin.de> X-Gnu-PR-Message: they-closed 66118 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 66118@debbugs.gnu.org Date: Wed, 20 Sep 2023 12:35:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1695213302-11050-1" This is a multi-part message in MIME format... ------------=_1695213302-11050-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #66118: [PATCH] gnu: Add r-omixerrpm. 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 66118@debbugs.gnu.org. --=20 66118: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D66118 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1695213302-11050-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 66118-done) by debbugs.gnu.org; 20 Sep 2023 12:34:10 +0000 Received: from localhost ([127.0.0.1]:58499 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qiwPC-0002qk-3g for submit@debbugs.gnu.org; Wed, 20 Sep 2023 08:34:10 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:42891) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qiwP9-0002qA-Nr for 66118-done@debbugs.gnu.org; Wed, 20 Sep 2023 08:34:09 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= mime-version:content-type:content-type:content-language :accept-language:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1695213231; x=1697027632; bh=QXLvTYFgMc7CQTr/4agIwQ6tQDBRGOQhnYt79e39ySc=; b=L3/YyvGcHSnX s65jFF0wWGyNxkRi6k8SFfY5aaoea56RBtrQ/y8IcYfVj15aBGGxfprUqxcypEf/ jlk8QcscojeyvuU7S1uOvyYdo/TKTrR41Pz2R73nOP9ySSMnN+zZ9/gNcIN0kxmK dNq4xBBLyeXR3uC8TqvOVnyxGKqNfCE= Received: from SW-IT-P-EX3.mdc-berlin.net (mgw3.mdc-berlin.de [141.80.113.61]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id 270C7A013A for <66118-done@debbugs.gnu.org>; Wed, 20 Sep 2023 14:33:51 +0200 (CEST) Received: from Pickup by SW-IT-P-EX3.mdc-berlin.net with Microsoft SMTP Server id 15.1.2507.17; Wed, 20 Sep 2023 12:33:49 +0000 Received: from SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) by SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.32; Wed, 20 Sep 2023 14:31:45 +0200 Received: from SW-IT-P-EX2.mdc-berlin.net ([fe80::2d6f:a37c:491f:7c27]) by SW-IT-P-EX2.mdc-berlin.net ([fe80::2d6f:a37c:491f:7c27%9]) with mapi id 15.01.2507.032; Wed, 20 Sep 2023 14:31:45 +0200 From: "Navid.Afkhami@mdc-berlin.de" To: "'66118-done@debbugs.gnu.org'" <66118-done@debbugs.gnu.org> Subject: Can not be added to Guix - The package contains a non-free binary Thread-Topic: Can not be added to Guix - The package contains a non-free binary Thread-Index: AdnrvhkeVKbVpLVNQsWsynWBpSA4SA== Date: Wed, 20 Sep 2023 12:31:45 +0000 Message-ID: Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: yes X-MS-TNEF-Correlator: x-originating-ip: [141.80.113.51] x-tm-smex-dtas-header-uuid: 6BEBA9C8F13C66C7EB7FBF859E60F7C927447182 x-tm-smex-dtas-header-flag: 9DEDCD08FA76A8F0DFBE80A6013BC475F0755E060005bc3a d20f-25c9-4e97-aaf2-61d22094a603 x-tm-as-product-ver: SMEX-14.0.0.3092-9.0.1002-27886.007 x-tm-as-result: No-10--5.100300-5.000000 x-tmase-matchedrid: SIzKuw2hzSt5R2Gl50HJBQrcxrzwsv5uwZT3SPru0Oh0PA/ki2kI7N6x PDqO2Y+uSSTrJqBYoSygfHz5rL2UAuGs5Npil1mvUgKYbZFF6Gi87rU89eLPKXmeOVC2CyiTOCj ykMcvhP4LwTxkKC1upZLUCjvVPrk1dtedPuBQuZMiPTMUjkOgksJd4cnAlxP2rjF7vq7X6ogyAv goZdaWzyKGAlWs2eIFiX+goQx8wOlvrBnHW6XSnLxygpRxo469lHLUcNM85doNIbt2ZiH1um21W 1bdGQjTQrmtv577MSEHIRBpbdAUR3D0V6C6hpoAYZSH25Vymp0vrT9rCm6riBtD2wLcqqOwI4+t 56oGUPrOH38lNbOoTLg87mD/ceeH319rGX8jiaGrm7DrUlmNkIAy6p60ZV62v2ThXg3lx4AfZMP NHXeG7gP90fJP9eHt x-tm-as-user-approved-sender: Yes x-tm-as-user-blocked-sender: No x-tmase-result: 10--5.100300-5.000000 x-tmase-version: SMEX-14.0.0.3092-9.0.1002-27886.007 x-tm-snts-smtp: 112C44AB871AFC8ECDBED43AE57B9DD48B428BBBAFE83E719F695514431FB6732000:F Content-Type: multipart/signed; protocol="application/x-pkcs7-signature"; micalg=SHA1; boundary="----=_NextPart_000_011D_01D9EBCF.2E548930" MIME-Version: 1.0 X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 66118-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: -3.3 (---) ------=_NextPart_000_011D_01D9EBCF.2E548930 Content-Type: multipart/alternative; boundary="----=_NextPart_001_011E_01D9EBCF.2E548930" ------=_NextPart_001_011E_01D9EBCF.2E548930 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello, =20 This package cannot be added to Guix because it contains a non-free = binary. Therefore, please close the report. =20 Thank you, Navid =20 - - =20 Navid Afkhami IT Administration Max Delbr=FCck Center for Molecular Medicine (MDC) Berlin Institute for Medical Systems Biology (BIMSB) Hannoversche Str. 28, 10115 Berlin Phone: +49 30 9406 1316 Email: = navid.afkhami@mdc-berlin.de =20 ------=_NextPart_001_011E_01D9EBCF.2E548930 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hello,

 

This = package cannot be added to Guix because it contains a non-free binary. = Therefore, please close the report.

 

Thank = you,

Navid

 

- -  =

Navid = Afkhami

IT = Administration

Max Delbr=FCck = Center for Molecular Medicine (MDC)

Berlin Institute for = Medical Systems Biology (BIMSB)

Hannoversche Str. 28, 10115 = Berlin

Phone: +49 30 9406 = 1316

Email:   = navid.afkhami@mdc-berlin.de=

 

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Date: Wed, 20 Sep 2023 10:39:12 +0000 Message-ID: <5b11081be482875b9b4a1da4c892c8f6c5f07006.1695206352.git.navid.afkhami@mdc-berlin.de> 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-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27886.007 X-TM-AS-Result: No-10--2.820400-5.000000 X-TMASE-MatchedRID: I6rpFm0lrcN6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VICu qghmtWfXXt3JNptef3p4Zvg4N7yewiq+GZ9ZHxIhuW77/y896sj4qCLIu0mtIMIubEPSkNnJl1i peFKJNYV7MSP7SLpuGE/hQBftKoDg1pVckLHgk0JvTnqYKYXTRuuLFZZYlisfHxPMjOKY7A8Lbi gRnpKlKTpcQTtiHDgWHjCkLaWYZ2QgPTinL8C6wmCJGp28iuq7p2wz3wbcShyCrkjmrUz0BiHon v4c0EiVS4gT0lUFanq4V2EhtNy1pYLe0bg7vlvwt0oQIuj+SVeFEVfQxs3N6ZDgmt8QekvB5maC eNv/LIzVGQdqwsDiEg== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.820400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27886.007 X-TM-SNTS-SMTP: AFCD40719FF622B581007DE6B7CAE4CF4D47C6C8A0FA20F3188B33AB7EBE04142000:F Received-SPF: pass client-ip=194.95.234.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=b2062.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/bioinformatics.scm (r-omixerrpm): New variable. --- gnu/packages/bioinformatics.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6acf37b312..d4da92b6b6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15065,6 +15065,29 @@ (define-public r-dyngen dynamic cellular processes at single-cell resolution.") (license license:expat))) +(define-public r-omixerrpm + (let ((commit "184f1cc99aefed722e20eb00eda082348a064c4e") + (revision "1")) + (package + (name "r-omixerrpm") + (version (git-version "0.3.3" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/omixer/omixer-rpmR") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "10ipasg8zi4ln13a5zj2l4a35hd3sfy3p6gir0sw0vf3cbc11lnz")))) + (properties `((upstream-name . "omixerRpm"))) + (build-system r-build-system) + (home-page "https://github.com/omixer/omixer-rpmR") + (synopsis "Metabolic module profiling of microbiome samples") + (description + "An R interface for microbiome metabolic module profiling with omixer-rpm.") + (license license:gpl3)))) + ;; Needed for r-liana (define-public r-omnipathr/devel (let ((commit "679bb79e319af246a16968d27d64d8d6937a331a") base-commit: 6bd17a0806ad32d1493ac51a7443276f719c4224 -- 2.34.1 ------------=_1695213302-11050-1--