From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 16 08:27:58 2021 Received: (at 47171) by debbugs.gnu.org; 16 Mar 2021 12:28:06 +0000 Received: from localhost ([127.0.0.1]:38401 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lM8na-00047g-GH for submit@debbugs.gnu.org; Tue, 16 Mar 2021 08:27:55 -0400 Received: from mail-qk1-f182.google.com ([209.85.222.182]:35905) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lM8n8-00042u-12 for 47171@debbugs.gnu.org; Tue, 16 Mar 2021 08:27:40 -0400 Received: by mail-qk1-f182.google.com with SMTP id n79so34936546qke.3 for <47171@debbugs.gnu.org>; Tue, 16 Mar 2021 05:27:18 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:references:in-reply-to:from:date:message-id:subject:to :cc:content-transfer-encoding; bh=Kgiq94fgC1A/rCZSPOmoTQ4jr4ZzyGHagGdoOa/GxHk=; b=IOdAGKhGk1XTlEp8r99ZAxecJmlpreHiv5wJ1NGvgu2wbV2Bi8aGfyLjgxV+bkl8n7 Yak2Nzk1A2yQMMHXld3f6LWrk5g0+2a2h/dH6sNbq6CYaeE4QFscamxpDNTqGk5SZ8S3 kY4iMXoiPUZ/2TtknflaPxqJc8KA8niZs4WCQEhDcyPtu1QNYeEQ6YRdJZ2qqVbr79Uq yH15mjuItzp/opJwS6hE2ZEt9d+MjKRGpI00hwtVRCfrITnqOhSq+0t74sxIXEA9Ir6c l/WFh0A+NExC/LII0RRR8b0AwkabaYEN1OcrIo+9z26jeeHvNXrQILNZptZ3Lz8r5jxD dPIg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc:content-transfer-encoding; bh=Kgiq94fgC1A/rCZSPOmoTQ4jr4ZzyGHagGdoOa/GxHk=; b=qUIDEgQ2UpViCv25n4V/QQIAs2A+iaOwzz2vgp+1ZzZE3dXJ21p66OMwt6Lun1fhD/ YSzpO7kBIiPszPY8GrtUkf7AgARSoDOOv4KOdClRfH6HSMQMNHi/BlMbpUCxtTfNUiqY 7hV2+zYJLYZOsxkPJU9JSB2Tc532mvMNdcrf+L9hB9UdlIVjsq1xPO5lcRpvrb0+G7/W XijGik4jbV0T3B3gipuFKDl3mrvOp+AQTBMV2JiG7szCsPrsO8smErxJf4d9s94KyYzY 8kzmOH5euorwijxp61CzcB9hVQf90fhtrKFGnkprRDB0mo2sOZLHPZpf6/e26kAM6X53 8YGw== X-Gm-Message-State: AOAM530M3iFPNl1+LdQD+W+qZSoMr0CjvGearW/w2/AYrDuhyJ0OkIdS LGV9YXdTK1ce5F5SPhovCwo2toMZDaiBurmEaRv+xIavtWY= X-Google-Smtp-Source: ABdhPJy8+RUh8hH/EQyUp+5qdJRtLupCTc3tSJPs1Z2AXX+5p0KpjD+kVpH4bT750FKIi+3e2hqVvYoHXZ3uK5gFs0g= X-Received: by 2002:a05:620a:91b:: with SMTP id v27mr30592397qkv.201.1615897632334; 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: Subject: Re: bug#47171: [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor). To: Leo Famulari Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 47171 Cc: Ricardo Wurmus , 47171@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 (-) 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