From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from eggs.gnu.org ([2001:4830:134:3::10]:43102) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gRMft-00064u-NL for guix-patches@gnu.org; Mon, 26 Nov 2018 14:36:06 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gRMfq-0002U1-HE for guix-patches@gnu.org; Mon, 26 Nov 2018 14:36:05 -0500 Received: from debbugs.gnu.org ([208.118.235.43]:45882) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1gRMfq-0002Tv-E4 for guix-patches@gnu.org; Mon, 26 Nov 2018 14:36:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1gRMfq-0001Zx-59 for guix-patches@gnu.org; Mon, 26 Nov 2018 14:36:02 -0500 Subject: [bug#33308] [PATCH 1/2] gnu: mash: Update to 2.1. Resent-Message-ID: References: <87va58hdt1.fsf@cbaines.net> <20181107195654.22832-1-mail@cbaines.net> <20181107212327.2b3f7ded@centurylink.net> From: Christopher Baines In-reply-to: <20181107212327.2b3f7ded@centurylink.net> Date: Mon, 26 Nov 2018 19:35:42 +0000 Message-ID: <87o9abaay9.fsf@cbaines.net> MIME-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha512; protocol="application/pgp-signature" 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: Eric Bavier Cc: 33308@debbugs.gnu.org --=-=-= Content-Type: text/plain Eric Bavier writes: > On Wed, 7 Nov 2018 19:56:53 +0000 > Christopher Baines wrote: > > >> * gnu/packages/bioinformatics.scm (mash)[version]: Change to 2.1. >> [source]: Update sha256 hash. > > I think here we typically just say "(mash)[source]: Upgrade to 2.1." Ok, I've sent a new set of patches now, and updated the commit messages. >> [arguments]: Add new use-c++14 phase, to patch source to build using c++14. >> --- >> gnu/packages/bioinformatics.scm | 14 +++++++++++--- >> 1 file changed, 11 insertions(+), 3 deletions(-) >> >> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm >> index 9f0b8025da..93503d82b8 100644 >> --- a/gnu/packages/bioinformatics.scm >> +++ b/gnu/packages/bioinformatics.scm >> @@ -4012,7 +4012,15 @@ sequences).") >> (("^#include \"kseq\\.h\"") >> "#include \"htslib/kseq.h\"")) >> #t)) >> - (add-after 'fix-includes 'autoconf >> + (add-after 'fix-includes 'use-c++14 >> + (lambda _ >> + ;; capnproto 0.7 requires c++14 to build >> + (substitute* "configure.ac" >> + (("c\\+\\+11") "c++14")) >> + (substitute* "Makefile.in" >> + (("c\\+\\+11") "c++14")) > > I believe the configure.ac patch is sufficient for us here, since the > compile steps will pick up the CPPFLAGS set there. Too bad the > configure.ac is written so poorly... :( one should be able to just > pass "CPPFLAGS=-std=c++14" to `make`. I tried removing the Makefile.in change, but it didn't work for some reason. >> + #t)) >> + (add-after 'use-c++14 'autoconf >> (lambda _ (zero? (system* "autoconf"))))))) > > Maybe you could also update this step to use 'invoke'. This patch has now turned in to just fixing the package for the newer version of capnproto, as Ricardo did the upgrade a few weeks ago. This particular stage was removed in e35dce017090685d07aedf10c9899c0cdcc70d9e. Thanks for your comments Eric :) --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQKTBAEBCgB9FiEEPonu50WOcg2XVOCyXiijOwuE9XcFAlv8Sw5fFIAAAAAALgAo aXNzdWVyLWZwckBub3RhdGlvbnMub3BlbnBncC5maWZ0aGhvcnNlbWFuLm5ldDNF ODlFRUU3NDU4RTcyMEQ5NzU0RTBCMjVFMjhBMzNCMEI4NEY1NzcACgkQXiijOwuE 9XeabhAAtpiRDR+Qg+KaLOv7r/5LYJ2QveBeT6tGGZEdXMpB2zkD2jx1iUjzEUDx dlSpDzxP6WA9/l+siPocsRqg+OehwGLyFgMkRedRlaUv3DZlM9X30hfsOa2CbET3 OUGcTZDrkXIBMc6k9PqmJb4VyBp1LYCtSPeim2xR5yobZcgVhpgZhUZwmA4hSd7q fEcul9jisxxqGGsao9cH6szyYce+Bxo/yAw5o0qfbi5NCTHOHjxWMqhHEfiKim5R sPoCB+75q9kV1J1vDb23fOuRUlHzz/Wuw3TsowYvik1jVglZ6yVV+WmYtUrgwV56 eGOAsFEDhaGUyq/FvmRlvht+JCcsc1ln4G07WQlRqXWPP3QuV9tflJCA1IsreRkk Fpz/UAq0bW+2j4UUp3uCLnql3+IVO0wbRQTjobGkUDak+Z7EFf13hTYrViTazFlx EbzD/FBXKKhjktungrXFzBJgX5vCnllbIWqBQSDVytlrp4dXgLmdc/oqpfEIBvk9 A1wtzs9TcwSnkl/Md3G3De2FNlSnQyCNPpzBKnZcCMH0suhaUp0smM9EMBuFePPx EeIOjlr7ozYm92SLdVj4Wx87YLN0nOxTRk64Rbis6UtO16VOjvz5UBurbnVuddFc hUwmrdT4rQNAvQPB0JoamljLuX4EzgpcAzX/H2wMBN908hugxoU= =Ag6/ -----END PGP SIGNATURE----- --=-=-=--