From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from eggs.gnu.org ([2001:470:142:3::10]:39702) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1iPl91-0006dg-N3 for guix-patches@gnu.org; Wed, 30 Oct 2019 06:24:04 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1iPl90-0000ep-J0 for guix-patches@gnu.org; Wed, 30 Oct 2019 06:24:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:40458) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1iPl90-0000eg-G4 for guix-patches@gnu.org; Wed, 30 Oct 2019 06:24:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1iPl90-0005N2-B3 for guix-patches@gnu.org; Wed, 30 Oct 2019 06:24:02 -0400 Subject: [bug#37988] [PATCH 0/6] Add flowWorkspace from BioConductor Resent-Message-ID: Received: from eggs.gnu.org ([2001:470:142:3::10]:39643) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1iPl8Y-0006NQ-QW for guix-patches@gnu.org; Wed, 30 Oct 2019 06:23:35 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1iPl8X-0008Va-Kp for guix-patches@gnu.org; Wed, 30 Oct 2019 06:23:34 -0400 Received: from mail-wr1-x42c.google.com ([2a00:1450:4864:20::42c]:37426) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1iPl8X-0008Th-D5 for guix-patches@gnu.org; Wed, 30 Oct 2019 06:23:33 -0400 Received: by mail-wr1-x42c.google.com with SMTP id e11so1641651wrv.4 for ; Wed, 30 Oct 2019 03:23:33 -0700 (PDT) From: zimoun Date: Wed, 30 Oct 2019 11:23:24 +0100 Message-Id: <20191030102324.12437-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+kyle=kyleam.com@gnu.org Sender: "Guix-patches" To: 37988@debbugs.gnu.org Cc: zimoun Dear, The aim of this serie is to add the package flowWorkspace. It is important to notice that the package RProtobuflib [1] from BioConductor is not packaged using the correct convention. RProtobuflib includes its dependency protobuf-2.6.0 as an archive tgz and compiles it using its ./configure [2]. Therefore, the file ./configure from the unarchived protobuf-2.6.0 needs to be patched to apply the correct shebang. It is clearly unconventional and we should distribute our own version of RProtobuflib using the correct way i.e., packaging protobuf-2.6.0. However, do we want to diverge to the official BioConductor and add maintenance burden when we are not fully able to already package all the BioConductor archive? All the best, simon [1] https://bioconductor.org/packages/release/bioc/html/RProtoBufLib.html [2] https://github.com/RGLab/RProtoBufLib/blob/trunk/configure#L2860-L2889 zimoun (6): gnu: Add r-idpmisc. gnu: Add r-flowviz. gnu: Add r-rprotobuflib. gnu: Add r-cytolib. gnu: Add r-ncdfflow. gnu: Add r-flowworkspace. gnu/packages/bioconductor.scm | 173 ++++++++++++++++++++++++++++++++++ gnu/packages/cran.scm | 30 ++++++ 2 files changed, 203 insertions(+) -- 2.23.0