From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp0 ([2001:41d0:8:6d80::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms11 with LMTPS id ILMhELHbUGDTDgAA0tVLHw (envelope-from ) for ; Tue, 16 Mar 2021 16:24:17 +0000 Received: from aspmx1.migadu.com ([2001:41d0:8:6d80::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp0 with LMTPS id YLEADLHbUGB3KwAA1q6Kng (envelope-from ) for ; Tue, 16 Mar 2021 16:24:17 +0000 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id D89B22D2D8 for ; Tue, 16 Mar 2021 17:24:16 +0100 (CET) Received: from localhost ([::1]:55942 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lMCUR-0005e6-J3 for larch@yhetil.org; Tue, 16 Mar 2021 12:24:15 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:38776) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lMCFn-00078v-PQ for guix-patches@gnu.org; Tue, 16 Mar 2021 12:09:09 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:57535) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lMCFi-0004ad-HZ for guix-patches@gnu.org; Tue, 16 Mar 2021 12:09:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lMCFi-0002kJ-Cw for guix-patches@gnu.org; Tue, 16 Mar 2021 12:09:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#47171] [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor). Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 16 Mar 2021 16:09:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 47171 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: zimoun Cc: 47171@debbugs.gnu.org, Leo Famulari Received: via spool by 47171-submit@debbugs.gnu.org id=B47171.161591091710522 (code B ref 47171); Tue, 16 Mar 2021 16:09:02 +0000 Received: (at 47171) by debbugs.gnu.org; 16 Mar 2021 16:08:37 +0000 Received: from localhost ([127.0.0.1]:40848 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lMCFJ-0002je-9J for submit@debbugs.gnu.org; Tue, 16 Mar 2021 12:08:37 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21151) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lMCFH-0002jW-MM for 47171@debbugs.gnu.org; Tue, 16 Mar 2021 12:08:36 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1615910911; cv=none; d=zohomail.com; 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aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=elephly.net header.s=zoho header.b=J5XLAyQi; arc=reject ("signature check failed: fail, {[1] = sig:zohomail.com:reject}"); dmarc=none; spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Spam-Score: 2.10 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=elephly.net header.s=zoho header.b=J5XLAyQi; arc=reject ("signature check failed: fail, {[1] = sig:zohomail.com:reject}"); dmarc=none; spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Queue-Id: D89B22D2D8 X-Spam-Score: 2.10 X-Migadu-Scanner: scn0.migadu.com X-TUID: x6TwlpdgwNOW zimoun writes: > Hi, > > On Tue, 16 Mar 2021 at 14:20, Ricardo Wurmus wrote: >> zimoun writes: >> >> > Well, thanks for the report and I confirm that adding the bioconductor >> > import in cran fixes "guix pull". But in my memories, this import >> > was adding circular dependency. Ricardo, WDYT? >> >> The point of having (gnu packages cran) and (gnu packages bioconductor) >> be separate modules is to separate independent packages. >> >> I=E2=80=99d like to keep it that way and not let (gnu packages cran) dep= end on >> (gnu packages bioconductor). > > Therefore, the fix is to move the CRAN r-bisquerna and r-absfiltergsea > packages from (gnu packages cran) to (gnu packages bioconductor) > because they depend on the Bioconductor package r-biobase (and > r-limma). Right? Correct. We don=E2=80=99t want any CRAN packages to depend on Bioconductor things. When this is unavoidable, though, we move them to (gnu packages bioconductor) with a comment. > How do I proceed? Submit a patch moving these 2 packages and then > another patch reverting the revert? Sounds good. (You could do this all in the same issue.) --=20 Ricardo