From unknown Sun Jun 22 03:54:45 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#62098] [PATCH] gnu: Add r-hdcytodata. Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 10 Mar 2023 16:17:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 62098 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 62098@debbugs.gnu.org Cc: Navid Afkhami X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.16784649973600 (code B ref -1); Fri, 10 Mar 2023 16:17:02 +0000 Received: (at submit) by debbugs.gnu.org; 10 Mar 2023 16:16:37 +0000 Received: from localhost ([127.0.0.1]:55621 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pafQ4-0000w0-Ry for submit@debbugs.gnu.org; Fri, 10 Mar 2023 11:16:37 -0500 Received: from lists.gnu.org ([209.51.188.17]:49368) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pafQ2-0000vr-0D for submit@debbugs.gnu.org; Fri, 10 Mar 2023 11:16:35 -0500 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 1pafQ1-0001nF-Dm for guix-patches@gnu.org; Fri, 10 Mar 2023 11:16:33 -0500 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 1pafPy-0002TY-Vq for guix-patches@gnu.org; Fri, 10 Mar 2023 11:16:33 -0500 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=1678464977; x=1680279378; bh=mQSBWeE6N0/GTYj fhmR5mbshbQlHY2gYd8FsivvapXs=; b=TZ1FdiCfCZ04Rot+q/ykZrWZTjS30Lj btZ2yuRCw9BSTHhxFWepd7qQF1QXBMecOhYFlOgVs7lgCk+4zT9MJD/i60KEFpf9 aIoz1JuwskLFzZnnfxko3NgZUCB9YzZ0NdwiUeH1S7h+VcW2KTNhIYZA0f2w7NzG yxMeHn0EdTIQ= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id 76D6D1601BD for ; Fri, 10 Mar 2023 17:16:16 +0100 (CET) Received: from localhost (141.80.218.27) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.21; Fri, 10 Mar 2023 17:16:16 +0100 From: Navid Afkhami Date: Fri, 10 Mar 2023 16:16:12 +0000 Message-ID: <20230310161612.26795-1-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-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27496.000 X-TM-AS-Result: No-10--2.042600-5.000000 X-TMASE-MatchedRID: NGDYxnKYxb3/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeNLjXXGQy6nlIRM yN/ppM4nZfimYRvSI6PuNT8xdcEnQwE+dA3RWUSvDDzmS9l9fYoXivwflisSrMIubEPSkNnJy6W INJ1hC9u0xgJ2yHF4fkxV1hlPUX0zDN6rHhn+aUnX3j/lf1V8LN0pE2POjYg41ieOp+/Th7k0id jzp2+ZXmup/skFmke8WC+tM64OXB7ymVDB8yZElKubsOtSWY2QgDLqnrRlXrZ8nn9tnqel2MprJ P8FBOIaYp3pOsP+07HYJjTSOBXQX/kMDUcR1rUqJfXq4yHsT1SqgotqLJR5dSSGzg3BfsvRTVOb dqeve9+vbKx6IgNrB++Aax385P76+Bepavj7kpF4W/rV0NGdh/RzmpSOCosq9iVB5TfGsfRe0Ym bY3/fIg== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.042600-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27496.000 X-TM-SNTS-SMTP: 536B4E6EC2F26C4DAA770270B360E0F1C9FCA902F64F9ED533144C3B272409DA2002: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: -1.4 (-) 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: -2.4 (--) * gnu/packages/bioconductor.scm (r-hdcytodata): New variable. --- gnu/packages/bioconductor.scm | 40 +++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d603bd42c1..1cf33501d6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -560,6 +560,46 @@ (define-public r-hdo-db https://github.com/DiseaseOntology/HumanDiseaseOntology/tree/main/src/ontology}.") (license license:artistic2.0))) +(define-public r-hdcytodata + (package + (name "r-hdcytodata") + (version "1.18.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "HDCytoData" version + 'experiment)) + (sha256 + (base32 + "1fn8q6ds10z3ymdarkfyh88pcqnrry9yhzammp84vf86f0bl8mrc")))) + (properties `((upstream-name . "HDCytoData"))) + (build-system r-build-system) + (arguments + (list #:phases '(modify-phases %standard-phases + (add-after 'unpack 'set-HOME + (lambda _ + (setenv "HOME" "/tmp"))) + (add-after 'unpack 'avoid-internet-access + (lambda _ + (setenv "GUIX_BUILD" "yes") + (substitute* "R/zzz.R" + (("createHubAccessors.*" m) + (string-append + "if (Sys.getenv(\"GUIX_BUILD\") == \"\") {" m + "}")))))))) + (propagated-inputs (list r-experimenthub r-flowcore r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/lmweber/HDCytoData") + (synopsis + "Set of high-dimensional flow cytometry and mass cytometry benchmark datasets") + (description + "HDCytoData contains a set of high-dimensional cytometry benchmark datasets. +These datasets are formatted into SummarizedExperiment and flowSet +Bioconductor object formats, including all required metadata. Row metadata +includes sample IDs, group IDs, patient IDs, reference cell population or +cluster labels and labels identifying spiked in cells. Column metadata +includes channel names, protein marker names, and protein marker classes.") + (license license:expat))) + (define-public r-homo-sapiens (package (name "r-homo-sapiens") -- 2.34.1 From unknown Sun Jun 22 03:54:45 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#62098: closed (Re: [bug#62098] [PATCH] gnu: Add r-hdcytodata.) Message-ID: References: <87o7lw6bla.fsf@cbaines.net> <20230310161612.26795-1-navid.afkhami@mdc-berlin.de> X-Gnu-PR-Message: they-closed 62098 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 62098@debbugs.gnu.org Date: Sat, 03 Jun 2023 11:16:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1685790962-8015-1" This is a multi-part message in MIME format... ------------=_1685790962-8015-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #62098: [PATCH] gnu: Add r-hdcytodata. 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 62098@debbugs.gnu.org. --=20 62098: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D62098 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1685790962-8015-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 62098-done) by debbugs.gnu.org; 3 Jun 2023 11:15:38 +0000 Received: from localhost ([127.0.0.1]:41652 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q5PEQ-00024P-BK for submit@debbugs.gnu.org; Sat, 03 Jun 2023 07:15:38 -0400 Received: from mira.cbaines.net ([212.71.252.8]:42590) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q5PEM-000249-EF for 62098-done@debbugs.gnu.org; Sat, 03 Jun 2023 07:15:36 -0400 Received: from localhost (unknown [IPv6:2a02:8010:68c1:0:54d1:d5d4:280e:f699]) by mira.cbaines.net (Postfix) with ESMTPSA id 641C727BBE2; Sat, 3 Jun 2023 12:15:33 +0100 (BST) Received: from felis (localhost [127.0.0.1]) by localhost (OpenSMTPD) with ESMTP id 6cf11e48; Sat, 3 Jun 2023 11:15:31 +0000 (UTC) References: <20230310161612.26795-1-navid.afkhami@mdc-berlin.de> User-agent: mu4e 1.10.2; emacs 28.2 From: Christopher Baines To: Navid Afkhami Subject: Re: [bug#62098] [PATCH] gnu: Add r-hdcytodata. Date: Sat, 03 Jun 2023 12:15:11 +0100 In-reply-to: <20230310161612.26795-1-navid.afkhami@mdc-berlin.de> Message-ID: <87o7lw6bla.fsf@cbaines.net> MIME-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha512; protocol="application/pgp-signature" X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 62098-done Cc: 62098-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 (-) --=-=-= Content-Type: text/plain Navid Afkhami writes: > * gnu/packages/bioconductor.scm (r-hdcytodata): New variable. > --- > gnu/packages/bioconductor.scm | 40 +++++++++++++++++++++++++++++++++++ > 1 file changed, 40 insertions(+) > > diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm > index d603bd42c1..1cf33501d6 100644 > --- a/gnu/packages/bioconductor.scm > +++ b/gnu/packages/bioconductor.scm > @@ -560,6 +560,46 @@ (define-public r-hdo-db > https://github.com/DiseaseOntology/HumanDiseaseOntology/tree/main/src/ontology}.") > (license license:artistic2.0))) Looks like this was committed as f7682c247504d252cf86b274ffe7b8f62670b497. Thanks, Chris --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQKlBAEBCgCPFiEEPonu50WOcg2XVOCyXiijOwuE9XcFAmR7INFfFIAAAAAALgAo aXNzdWVyLWZwckBub3RhdGlvbnMub3BlbnBncC5maWZ0aGhvcnNlbWFuLm5ldDNF ODlFRUU3NDU4RTcyMEQ5NzU0RTBCMjVFMjhBMzNCMEI4NEY1NzcRHG1haWxAY2Jh aW5lcy5uZXQACgkQXiijOwuE9Xfn0hAAm9CuplO8nsk8pIecBHpXxArhbg+MTEzx kNllnkb/mFGgYEIc6UBArfeNjJ4b3SXjl/Ik+9btfUGiK0JHzKikU5ocdG53RHmG WRQ3uyzfN1JHpVQRxOXKX0pGMOg+m0KyAzEW3wPJ2QmVdb5MTgafxJ4xSOmLszNv w9EbAl0IyBAeJShZCGOTSKwnoe+UFlKixOR+eDJRgweWtfNrlaxPboPFkKPXt/9C eSvZw0WuOTegKGGiDvdmzAYh9Cgw5OMKyt+Kv7Q1Fen4s12O2TpCK88piW6Zi2Fk JElK8iI7szJUNe/r7bF/IOJqDZeE2Y4j+bm37m6QA4zDQ59tqbXX8zryQXflU6k9 Ahjy7K25FrkLhx9MqFmeyFHCKiU3IlTRawobBT90ZWhLfCx6c6EApmW/+ALuJQ4W cczPG25sh6GJa/1aatzgdat131hUCy+BnI+vA89bALGoUR601dWsFlL2ur90Hv4z BE/M7zJLGjcHjsLxVIRKT2LV4sCTJQbT10WdLfQmjxB19jKAukvJtyjsn/amAshT 0ZLc6mRdBhDJTAEVE7Itz6xas0aOfYB3FDu+IZ/F7VkXIu8XnK4sZR7ir2tHSnV+ pFXbXiYHTEGB6/xrwMuI65YiKN+kbiJDjdaYx/Ke0s58NqSnY7d67jiVYAAvsvqR pFTvk+D6q20= =NAYv -----END PGP SIGNATURE----- --=-=-=-- ------------=_1685790962-8015-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 10 Mar 2023 16:16:37 +0000 Received: from localhost ([127.0.0.1]:55621 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pafQ4-0000w0-Ry for submit@debbugs.gnu.org; Fri, 10 Mar 2023 11:16:37 -0500 Received: from lists.gnu.org ([209.51.188.17]:49368) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pafQ2-0000vr-0D for submit@debbugs.gnu.org; Fri, 10 Mar 2023 11:16:35 -0500 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 1pafQ1-0001nF-Dm for guix-patches@gnu.org; Fri, 10 Mar 2023 11:16:33 -0500 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 1pafPy-0002TY-Vq for guix-patches@gnu.org; Fri, 10 Mar 2023 11:16:33 -0500 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=1678464977; x=1680279378; bh=mQSBWeE6N0/GTYj fhmR5mbshbQlHY2gYd8FsivvapXs=; b=TZ1FdiCfCZ04Rot+q/ykZrWZTjS30Lj btZ2yuRCw9BSTHhxFWepd7qQF1QXBMecOhYFlOgVs7lgCk+4zT9MJD/i60KEFpf9 aIoz1JuwskLFzZnnfxko3NgZUCB9YzZ0NdwiUeH1S7h+VcW2KTNhIYZA0f2w7NzG yxMeHn0EdTIQ= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id 76D6D1601BD for ; Fri, 10 Mar 2023 17:16:16 +0100 (CET) Received: from localhost (141.80.218.27) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.21; Fri, 10 Mar 2023 17:16:16 +0100 From: Navid Afkhami To: Subject: [PATCH] gnu: Add r-hdcytodata. Date: Fri, 10 Mar 2023 16:16:12 +0000 Message-ID: <20230310161612.26795-1-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-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27496.000 X-TM-AS-Result: No-10--2.042600-5.000000 X-TMASE-MatchedRID: NGDYxnKYxb3/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeNLjXXGQy6nlIRM yN/ppM4nZfimYRvSI6PuNT8xdcEnQwE+dA3RWUSvDDzmS9l9fYoXivwflisSrMIubEPSkNnJy6W INJ1hC9u0xgJ2yHF4fkxV1hlPUX0zDN6rHhn+aUnX3j/lf1V8LN0pE2POjYg41ieOp+/Th7k0id jzp2+ZXmup/skFmke8WC+tM64OXB7ymVDB8yZElKubsOtSWY2QgDLqnrRlXrZ8nn9tnqel2MprJ P8FBOIaYp3pOsP+07HYJjTSOBXQX/kMDUcR1rUqJfXq4yHsT1SqgotqLJR5dSSGzg3BfsvRTVOb dqeve9+vbKx6IgNrB++Aax385P76+Bepavj7kpF4W/rV0NGdh/RzmpSOCosq9iVB5TfGsfRe0Ym bY3/fIg== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.042600-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27496.000 X-TM-SNTS-SMTP: 536B4E6EC2F26C4DAA770270B360E0F1C9FCA902F64F9ED533144C3B272409DA2002: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: -1.4 (-) 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: -2.4 (--) * gnu/packages/bioconductor.scm (r-hdcytodata): New variable. --- gnu/packages/bioconductor.scm | 40 +++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d603bd42c1..1cf33501d6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -560,6 +560,46 @@ (define-public r-hdo-db https://github.com/DiseaseOntology/HumanDiseaseOntology/tree/main/src/ontology}.") (license license:artistic2.0))) +(define-public r-hdcytodata + (package + (name "r-hdcytodata") + (version "1.18.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "HDCytoData" version + 'experiment)) + (sha256 + (base32 + "1fn8q6ds10z3ymdarkfyh88pcqnrry9yhzammp84vf86f0bl8mrc")))) + (properties `((upstream-name . "HDCytoData"))) + (build-system r-build-system) + (arguments + (list #:phases '(modify-phases %standard-phases + (add-after 'unpack 'set-HOME + (lambda _ + (setenv "HOME" "/tmp"))) + (add-after 'unpack 'avoid-internet-access + (lambda _ + (setenv "GUIX_BUILD" "yes") + (substitute* "R/zzz.R" + (("createHubAccessors.*" m) + (string-append + "if (Sys.getenv(\"GUIX_BUILD\") == \"\") {" m + "}")))))))) + (propagated-inputs (list r-experimenthub r-flowcore r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/lmweber/HDCytoData") + (synopsis + "Set of high-dimensional flow cytometry and mass cytometry benchmark datasets") + (description + "HDCytoData contains a set of high-dimensional cytometry benchmark datasets. +These datasets are formatted into SummarizedExperiment and flowSet +Bioconductor object formats, including all required metadata. Row metadata +includes sample IDs, group IDs, patient IDs, reference cell population or +cluster labels and labels identifying spiked in cells. Column metadata +includes channel names, protein marker names, and protein marker classes.") + (license license:expat))) + (define-public r-homo-sapiens (package (name "r-homo-sapiens") -- 2.34.1 ------------=_1685790962-8015-1--