From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: Re: [PATCH] Add Blast+. Date: Mon, 29 Jun 2015 16:15:39 +0200 Message-ID: References: <87zj3ze3ne.fsf@netris.org> <87egkxf1je.fsf@netris.org> Mime-Version: 1.0 Content-Type: text/plain Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:54696) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z9Zqi-0003jt-Qu for guix-devel@gnu.org; Mon, 29 Jun 2015 10:15:58 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Z9Zqe-0005MZ-Ft for guix-devel@gnu.org; Mon, 29 Jun 2015 10:15:52 -0400 Received: from pegasus.bbbm.mdc-berlin.de ([141.80.25.20]:33507) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z9Zqe-0005MF-2o for guix-devel@gnu.org; Mon, 29 Jun 2015 10:15:48 -0400 In-Reply-To: <87egkxf1je.fsf@netris.org> List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org To: Mark H Weaver Cc: guix-devel Mark H Weaver writes: >> + (snippet >> + '(begin >> + ;; Remove bundled bzip2 and zlib >> + (delete-file-recursively "c++/src/util/compress/bzip2") >> + (delete-file-recursively "c++/src/util/compress/zlib") >> + (substitute* "c++/src/util/compress/Makefile.in" >> + (("bzip2 zlib api") "api")) >> + ;; Remove useless msbuild directory >> + (delete-file-recursively >> + "c++/src/build-system/project_tree_builder/msbuild"))))) > > As with phase procedures, the snippet should return a boolean, so please > add #t here. Done. >> + ;; Proceed even though the weird build system says that generated >> + ;; files are out of date >> + (setenv "NCBICXX_RECONF_POLICY" "warn") >> + >> + ;; Rewrite hardcoded paths to various tools >> + (substitute* (append (find-files "scripts/common/check" "\\.sh$") >> + '("scripts/common/impl/if_diff.sh" >> + "scripts/common/impl/run_with_lock.sh" >> + "src/build-system/Makefile.configurables.real" >> + "src/build-system/Makefile.in.top" >> + "src/build-system/Makefile.meta.gmake=no" >> + "src/build-system/Makefile.meta.in" >> + "src/build-system/Makefile.meta_l" >> + "src/build-system/Makefile.meta_p" >> + "src/build-system/Makefile.meta_r" >> + "src/build-system/Makefile.mk.in" >> + "src/build-system/Makefile.requirements" >> + "src/build-system/Makefile.rules_with_autodep.in" >> + "src/build-system/configure" >> + "src/build-system/configure.ac")) >> + (("(/usr/bin/|/bin/)([a-z][-_.a-z]*)" all dir cmd) >> + (or (which* cmd) all))) > > It would be better to patch configure.ac first, and then configure, and > then the others. As you have it here, the modification times will > indicate that 'configure' is older than 'configure.ac' and thus out of > date. Perhaps this is why you needed to setenv NCBICXX_RECONF_POLICY? You were right. I reordered the patching and could remove the variable. Thank you for the review and sharing your insights! I updated to Blast 2.2.31, built successfully and just pushed. ~~ Ricardo