From mboxrd@z Thu Jan 1 00:00:00 1970 From: Marius Bakke Subject: Re: [PATCH 0/1] Update pardre source hash. Date: Thu, 08 Dec 2016 15:45:43 +0100 Message-ID: <87wpfaxyw8.fsf@kirby.i-did-not-set--mail-host-address--so-tickle-me> References: <20161208131215.1205-1-donttrustben@gmail.com> <8760muzgm2.fsf@kirby.i-did-not-set--mail-host-address--so-tickle-me> Mime-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha512; protocol="application/pgp-signature" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:38489) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1cEzxH-0000D1-U5 for guix-devel@gnu.org; Thu, 08 Dec 2016 09:45:54 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cEzxC-0008WJ-7L for guix-devel@gnu.org; Thu, 08 Dec 2016 09:45:52 -0500 Received: from out4-smtp.messagingengine.com ([66.111.4.28]:55007) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1cEzxB-0008WC-WA for guix-devel@gnu.org; Thu, 08 Dec 2016 09:45:46 -0500 In-Reply-To: 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" To: Ricardo Wurmus Cc: guix-devel@gnu.org --=-=-= Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Ricardo Wurmus writes: > Marius Bakke writes: > >> Ben Woodcroft writes: >> >>> Hi, >>> >>> It seems that the pardre source has been updated in place. I'm not sur= e what >>> the procedure is for verifying that nothing untoward has taken place, s= ince I >>> cannot download and old version from the hydra content addressed mirror= - >>> it does not seem to exist there either. >> >> "diffoscope" has native support for tarballs and can quickly point out >> any differences. Perhaps Ricardo has a copy at the MDC? > > I do! I still have a copy of > /gnu/store/xp2yzil11yk9askvpp56a8jjqynqb12k-ParDRe-rel1.1.5.tar.gz > > The diff looks very familiar. Could it be that this has happened > before? Or maybe I noticed the changed hash before and forgot to submit > an update...? > > Anyway, here=E2=80=99s the full diff: > > > diff -ur ParDRe-rel1.1.5* > diff -ur ParDRe-rel1.1.5/.cproject ParDRe-rel1.1.5-new/.cproject > --- ParDRe-rel1.1.5/.cproject 2015-12-21 13:02:38.000000000 +0100 > +++ ParDRe-rel1.1.5-new/.cproject 2016-07-05 14:10:22.000000000 +0200 > @@ -1,8 +1,8 @@ > > > > - > - > + > + > > > > @@ -14,23 +14,23 @@ > > > > - > - > - > - > - > - > - > - > + > + > + > + > + > + > + > + > > - > - > + > + > > - > - > + > + > > - > - > + > + > > > > @@ -41,41 +41,44 @@ > > > > - > + > > > > - > - > - > > > > - > + > + > + > + > > > - > + > > > + > + > + > > > > - > + > > > - > - > + > + > > > > > - > + > > > > > > - > + > > > > diff -ur ParDRe-rel1.1.5/PairedEnd.cpp ParDRe-rel1.1.5-new/PairedEnd.cpp > --- ParDRe-rel1.1.5/PairedEnd.cpp 2016-05-18 11:46:38.000000000 +0200 > +++ ParDRe-rel1.1.5-new/PairedEnd.cpp 2016-07-06 12:15:02.000000000 +0200 > @@ -210,6 +210,7 @@ > } > } > } > + fflush(NULL); > } > MPI::COMM_WORLD.Barrier(); > } > diff -ur ParDRe-rel1.1.5/SingleEnd.cpp ParDRe-rel1.1.5-new/SingleEnd.cpp > --- ParDRe-rel1.1.5/SingleEnd.cpp 2016-05-18 11:47:07.000000000 +0200 > +++ ParDRe-rel1.1.5-new/SingleEnd.cpp 2016-07-06 12:13:13.000000000 +0200 > @@ -27,12 +27,12 @@ > if(!myRank){ > Utils::log("Process %d/%d: To print in %s\n", myRank, MPI::COMM_WORLD.= Get_size(), outPath.c_str()); > } > - if(myRank){ > + /*if(myRank){ > outPath.append("_id"); > outPath.append(to_string(myRank)); > } > _parserOut =3D new SeqFileParser(options, outPath.c_str(), true, false); > - _parserOut->setFormat(_parser->getFormat()); > + _parserOut->setFormat(_parser->getFormat());*/ > } > } >=20=20 > @@ -186,6 +186,7 @@ > } > } > } > + fflush(NULL); > } > MPI::COMM_WORLD.Barrier(); > } > diff -ur ParDRe-rel1.1.5/Utils.cpp ParDRe-rel1.1.5-new/Utils.cpp > --- ParDRe-rel1.1.5/Utils.cpp 2015-11-17 16:16:54.000000000 +0100 > +++ ParDRe-rel1.1.5-new/Utils.cpp 2016-05-27 14:03:38.000000000 +0200 > @@ -62,5 +62,12 @@ > } >=20=20 > uint64_t Utils::popcount(uint64_t v){ > - return __builtin_popcount(v); > + uint64_t b =3D (v & 0x5555555555555555LU) + (v >> 1 & 0x55555555555= 55555LU); > + b =3D (b & 0x3333333333333333LU) + (b >> 2 & 0x3333333333333333LU); > + b =3D b + (b >> 4) & 0x0F0F0F0F0F0F0F0FLU; > + b =3D b + (b >> 8); > + b =3D b + (b >> 16); > + b =3D b + (b >> 32) & 0x0000007F; > + > + return b; > } Looks like a portability fix, although I can't really tell what that bitshifting is about. Assuming it's the same as the GCC builtin :-) --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQEzBAEBCgAdFiEEu7At3yzq9qgNHeZDoqBt8qM6VPoFAlhJchcACgkQoqBt8qM6 VPowzwgAzCq6UsNRQhEK/eAwCJL8M/q4c2HDa2s1/NumHikONj8cTjBn7Tn/DvFm Z+Pln9oT+dTJ9TRydvthcKqV5/K4SRwKlVTCiazJtW53vjLSLxalf1mwkn/j1mT3 wQvN3zTzYKm8cT5NxS3fjUBZfLWuPyuosKggSOjRvxkRAitdDDvVzQvTqAXzwIc+ l/evZ55pMD8AMU7nj8p+lcmOakOZyqV8cuN5IOv4rXxmUaPM+acNlBtu90T8KMYr 3SsfLp6cCnWe4FSibyed6atO+JjkymCjWqCoDRuDfTRB0nMEn/bwEQfVg7BDYol1 +LcpYshHk4ITMcDOPJz6gqh4ceJxCg== =eAV+ -----END PGP SIGNATURE----- --=-=-=--