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Tue, 16 Mar 2021 05:27:12 -0700 (PDT) MIME-Version: 1.0 References: <20210315180714.8233-1-zimon.toutoune@gmail.com> <87pn00m4ig.fsf@elephly.net> In-Reply-To: From: zimoun Date: Tue, 16 Mar 2021 13:27:01 +0100 Message-ID: Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable 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+larch=yhetil.org@gnu.org Sender: "Guix-patches" X-Migadu-Flow: FLOW_IN ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1615897742; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-type:content-type: content-transfer-encoding:content-transfer-encoding:resent-cc: resent-from:resent-sender:resent-message-id:in-reply-to:in-reply-to: references:references:list-id:list-help:list-unsubscribe: list-subscribe:list-post:dkim-signature; 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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: -1.30 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20161025 header.b=IOdAGKhG; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=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: B9A0618D1F X-Spam-Score: -1.30 X-Migadu-Scanner: scn0.migadu.com X-TUID: LPopOju+5rVT Hi Leo, On Tue, 16 Mar 2021 at 00:56, Leo Famulari wrote: > On Mon, Mar 15, 2021 at 11:33:11PM +0100, Ricardo Wurmus wrote: > > > zimoun (10): > > > gnu: r-limma: Move to (gnu packages bioconductor). > > > gnu: r-xvector: Move to (gnu packages bioconductor). > > > gnu: r-genomicranges: Move to (gnu packages bioconductor). > > > gnu: r-biobase: Move to (gnu packages bioconductor). > > > gnu: r-annotationdbi: Move to (gnu packages bioconductor). > > > gnu: r-biomart: Move to (gnu packages bioconductor). > > > gnu: r-biocparallel: Move to (gnu packages bioconductor). > > > gnu: r-biostrings: Move to (gnu packages bioconductor). > > > gnu: r-rsamtools: Move to (gnu packages bioconductor). > > > gnu: r-delayedarray: Move to (gnu packages bioconductor). > > > > Thanks, I=E2=80=99ve pushed them all. > > These commits caused `guix pull` to fail, as described here: > > https://git.savannah.gnu.org/cgit/guix.git/commit/?id=3D8ec0ca8faff62f194= 26f22aeb1bd59a8950ca05a > > I think we just needed to import the bioconductor module in the cran > module, but I wasn't sure so I reverted them in order to fix the problem > quickly. Sorry for the annoyance. I did "make as-derivation" and it reports nothing. But indeed, "./pre-inst-env guix pull -p /tmp/new --url=3D$(pwd) --disable-authentication --branch=3Dtest" breaks. I do not know if I do something wrong (run make in a worktree for the branc= h). 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? Cheers, simon