From patchwork Tue Apr 1 22:51:39 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Andreas Enge X-Patchwork-Id: 41144 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id E312C27BBE9; Tue, 1 Apr 2025 23:53:37 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-8.6 required=5.0 tests=BAYES_00,DKIMWL_WL_HIGH, DKIM_SIGNED,DKIM_VALID,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_MSPIKE_H2,RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL, RCVD_IN_VALIDITY_SAFE,SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 900E027BBE2 for ; Tue, 1 Apr 2025 23:53:36 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1tzkTu-0007sh-Ve; Tue, 01 Apr 2025 18:53:19 -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 1tzkTf-0007r7-OB for guix-patches@gnu.org; Tue, 01 Apr 2025 18:53:04 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1tzkTf-0006rK-5L for guix-patches@gnu.org; Tue, 01 Apr 2025 18:53:03 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=g9pRswPWyTAME46FeC2IvJJdXZDxWvvWwuN5jC/cOuA=; b=VrdTT9lGjXmjKSutxDfjri+MhimqP5qgzfXjdGmOLJujpHAG1n+fZyi0VgXRZxJvubhZDagEtl7AEQ2CtvYX7p57dFXJlIZFx832K1RO5Vp1QJX6Ou+00ezv75a+X/PQqBBWFtfc8hqcBr067ApTj5uPgGWbokwjF7LzCmyYIbsmPFGUItvC/7uBD4NBZ9VaomhqSACr2IeX8JNZZRdnmYQKcjn+WxxPtfLED7T7POV5X0+yhijEQiThKfhBwq+sRBwT5L0UL/Znuy+DezzPd7QTO6v0s1CSF5FoKyyvEihdOlFsECMtui8YK9gBLkGq2rIHSBwfiw/V9spOAItu3w==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1tzkTe-0008BV-Rp for guix-patches@gnu.org; Tue, 01 Apr 2025 18:53:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77442] [PATCH 1/2] gnu: Remove r-velocyto. Resent-From: Andreas Enge Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 01 Apr 2025 22:53:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 77442 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 77442@debbugs.gnu.org Cc: Andreas Enge Received: via spool by 77442-submit@debbugs.gnu.org id=B77442.174354793631129 (code B ref 77442); Tue, 01 Apr 2025 22:53:02 +0000 Received: (at 77442) by debbugs.gnu.org; 1 Apr 2025 22:52:16 +0000 Received: from localhost ([127.0.0.1]:52197 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tzkSs-00085k-5Z for submit@debbugs.gnu.org; Tue, 01 Apr 2025 18:52:16 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:60748) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tzkSp-00084g-7v for 77442@debbugs.gnu.org; Tue, 01 Apr 2025 18:52:12 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 252B22FF; Wed, 2 Apr 2025 00:52:05 +0200 (CEST) Authentication-Results: hera.aquilenet.fr; none X-Virus-Scanned: Debian amavis at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavis, port 10024) with ESMTP id 24pijB8CH4KB; Wed, 2 Apr 2025 00:52:04 +0200 (CEST) Received: from jurong.lan (176-179-191-150.abo.bbox.fr [176.179.191.150]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 8A492BF; Wed, 2 Apr 2025 00:51:57 +0200 (CEST) From: Andreas Enge Date: Wed, 2 Apr 2025 00:51:39 +0200 Message-ID: X-Mailer: git-send-email 2.49.0 In-Reply-To: References: MIME-Version: 1.0 X-Rspamd-Queue-Id: 252B22FF X-Spamd-Result: default: False [-3.60 / 15.00]; REPLY(-4.00)[]; BAYES_HAM(-3.00)[100.00%]; FORGED_RECIPIENTS(2.00)[m:andreas@enge.fr,s:andreas.enge@aquilenet.fr]; MID_CONTAINS_FROM(1.00)[]; R_MISSING_CHARSET(0.50)[]; MIME_GOOD(-0.10)[text/plain]; RCVD_TLS_ALL(0.00)[]; RCVD_COUNT_TWO(0.00)[2]; MIME_TRACE(0.00)[0:+]; FROM_EQ_ENVFROM(0.00)[]; TO_MATCH_ENVRCPT_SOME(0.00)[]; TO_DN_SOME(0.00)[]; RCPT_COUNT_TWO(0.00)[2]; RCVD_VIA_SMTP_AUTH(0.00)[]; FROM_HAS_DN(0.00)[]; ARC_NA(0.00)[] X-Rspamd-Action: no action X-Spamd-Bar: --- X-Rspamd-Server: hera X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches The package has not been updated since 2019 and depends on the deprecated r-h5. * gnu/packages/bioinformatics.scm (r-velocyto): Delete variable. Change-Id: I9783c67c92b5351647b964364c281a0d40319949 --- gnu/packages/bioinformatics.scm | 44 --------------------------------- 1 file changed, 44 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8fd7789028..226594d8ed 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -22632,50 +22632,6 @@ (define-public r-imagearray (description "@code{DelayedArray} based image operations.") (license license:expat)))) -(define-public r-velocyto - (let ((commit "d7790346cb99f49ab9c2b23ba70dcf9d2c9fc350") - (revision "1")) - (package - (name "r-velocyto") - (version (git-version "0.6" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/velocyto-team/velocyto.R") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "16wqf70j7rd7pay2q513iyz12i8n9vrpg1bisah4lddbcpx5dz1n")))) - (build-system r-build-system) - (inputs - (list boost)) - (propagated-inputs - (list r-hdf5r - r-mass - r-mgcv - r-pcamethods - r-rcpp - r-rcpparmadillo - ;; Suggested packages - r-rtsne - r-cluster - r-abind - r-h5 - r-biocgenerics - r-genomicalignments - r-rsamtools - r-edger - r-igraph)) - (home-page "https://velocyto.org") - (synopsis "RNA velocity estimation in R") - (description - "This package provides basic routines for estimation of gene-specific -transcriptional derivatives and visualization of the resulting velocity -patterns.") - (license license:gpl3)))) - (define-public r-voltron (let ((commit "21886d82292dc46521da2a03d978d78f3bd7210b") (revision "5")) From patchwork Tue Apr 1 22:51:40 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Andreas Enge X-Patchwork-Id: 41143 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 753CA27BBEA; Tue, 1 Apr 2025 23:53:32 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-8.6 required=5.0 tests=BAYES_00,DKIMWL_WL_HIGH, DKIM_SIGNED,DKIM_VALID,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_MSPIKE_H2,RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL, RCVD_IN_VALIDITY_SAFE,SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 29C6B27BBE2 for ; Tue, 1 Apr 2025 23:53:32 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1tzkTy-0007tm-OD; Tue, 01 Apr 2025 18:53:22 -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 1tzkTi-0007rb-Kv for guix-patches@gnu.org; Tue, 01 Apr 2025 18:53:13 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1tzkTh-0006rl-2p for guix-patches@gnu.org; Tue, 01 Apr 2025 18:53:05 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=Z0URK15KsMEH1DIrLOG1CEB+PXgwQNjK1ciPjtt79Bw=; b=Vdvc+VQMl/KcrdDuQ+kqSb/ECcPbfzI/wwRtep+7OoQjAWazv20q7C7kg++BcwpNtoeLLLrCxuvTp5OL5FeEd5xkjtpG7P212r7IGoQUbiZeZ5QlxG+Kk1OXnxkn0cYdUkjqfrzFgWRd33sXcPB5NL0gXEbYOEoHAkr+ew+rSeOrBgL4CQuebKlkTNHAbmwaycoysuRJe354uiMBEkaAfIOiqYlm61BEGdqVz8Ry2pSH3cLb3Ak1ED8zFMqAjjA8Xjn1IaWnr4k4vhLArBFFFzK8joX+pY2kyS0jRgKcWAIhyHZZjShlnVgvJW0cOMg4YDgN9idmEyFUDhwK8a0R6g==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1tzkTg-0008Bm-2k; Tue, 01 Apr 2025 18:53:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77442] [PATCH 2/2] gnu: Remove r-h5. Resent-From: Andreas Enge Original-Sender: "Debbugs-submit" Resent-CC: laurent.gatto@gmail.com, rekado@elephly.net, zimon.toutoune@gmail.com, guix-patches@gnu.org Resent-Date: Tue, 01 Apr 2025 22:53:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 77442 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 77442@debbugs.gnu.org Cc: Andreas Enge , Laurent Gatto , Ricardo Wurmus , Simon Tournier X-Debbugs-Original-Xcc: Laurent Gatto , Ricardo Wurmus , Simon Tournier Received: via spool by 77442-submit@debbugs.gnu.org id=B77442.174354794131174 (code B ref 77442); Tue, 01 Apr 2025 22:53:03 +0000 Received: (at 77442) by debbugs.gnu.org; 1 Apr 2025 22:52:21 +0000 Received: from localhost ([127.0.0.1]:52199 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tzkSx-00086W-9o for submit@debbugs.gnu.org; Tue, 01 Apr 2025 18:52:20 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:60756) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tzkSr-00084y-FM for 77442@debbugs.gnu.org; Tue, 01 Apr 2025 18:52:14 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 6101E303; Wed, 2 Apr 2025 00:52:07 +0200 (CEST) Authentication-Results: hera.aquilenet.fr; none X-Virus-Scanned: Debian amavis at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavis, port 10024) with ESMTP id u418urDW0AjM; Wed, 2 Apr 2025 00:52:06 +0200 (CEST) Received: from jurong.lan (176-179-191-150.abo.bbox.fr [176.179.191.150]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 62CACBF; Wed, 2 Apr 2025 00:52:05 +0200 (CEST) From: Andreas Enge Date: Wed, 2 Apr 2025 00:51:40 +0200 Message-ID: <69744c9f90b8c87efd63c107654ac7818682fee9.1743547708.git.andreas@enge.fr> X-Mailer: git-send-email 2.49.0 In-Reply-To: References: MIME-Version: 1.0 X-Rspamd-Queue-Id: 6101E303 X-Spamd-Result: default: False [-3.60 / 15.00]; REPLY(-4.00)[]; BAYES_HAM(-3.00)[100.00%]; FORGED_RECIPIENTS(2.00)[m:andreas@enge.fr,s:andreas.enge@aquilenet.fr]; MID_CONTAINS_FROM(1.00)[]; R_MISSING_CHARSET(0.50)[]; MIME_GOOD(-0.10)[text/plain]; RCVD_TLS_ALL(0.00)[]; RCVD_COUNT_TWO(0.00)[2]; MIME_TRACE(0.00)[0:+]; FROM_EQ_ENVFROM(0.00)[]; TO_MATCH_ENVRCPT_SOME(0.00)[]; TO_DN_SOME(0.00)[]; RCPT_COUNT_TWO(0.00)[2]; RCVD_VIA_SMTP_AUTH(0.00)[]; FROM_HAS_DN(0.00)[]; ARC_NA(0.00)[] X-Rspamd-Action: no action X-Spamd-Bar: --- X-Rspamd-Server: hera X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches The package has been deprecated by its author in 2017 in favor of r-hdf5r. It does not build with current hdf5@1.14. * gnu/packages/cran.scm (r-h5): Delete variable. Change-Id: Iaceb59b31af870a1aea1630d74bb5c03932808b0 --- gnu/packages/cran.scm | 29 ----------------------------- 1 file changed, 29 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4e96d70849..8d80bc2091 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -14921,35 +14921,6 @@ (define-public r-heatmaply ;; Either version of the license. (license (list license:gpl2 license:gpl3)))) -(define-public r-h5 - (package - (name "r-h5") - (version "0.9.9") - (source - (origin - (method url-fetch) - (uri (cran-uri "h5" version)) - (sha256 - (base32 - "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx")))) - (build-system r-build-system) - (inputs - (list zlib hdf5-1.10)) - (native-inputs - (list r-knitr r-testthat which)) - (propagated-inputs - (list r-rcpp)) - (home-page "https://github.com/mannau/h5") - (synopsis "Interface to the HDF5 Library") - (description - "This package provides an S4 interface to the HDF5 library supporting -fast storage and retrieval of R-objects like vectors, matrices and arrays to -binary files in a language independent format. The HDF5 format can therefore -be used as an alternative to R's save/load mechanism. Since h5 is able to -access only subsets of stored data it can also handle data sets which do not -fit into memory.") - (license license:bsd-2))) - (define-public r-cgdsr (package (name "r-cgdsr")