From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: Re: [PATCH 0/1] Update pardre source hash. Date: Thu, 8 Dec 2016 15:17:09 +0100 Message-ID: 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: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:56643) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1cEzVv-0003Ju-4j for guix-devel@gnu.org; Thu, 08 Dec 2016 09:17:39 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cEzVr-0006DE-Ql for guix-devel@gnu.org; Thu, 08 Dec 2016 09:17:35 -0500 Received: from venus.bbbm.mdc-berlin.de ([141.80.25.30]:59260) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1cEzVr-0006Cz-BZ for guix-devel@gnu.org; Thu, 08 Dec 2016 09:17:31 -0500 In-Reply-To: <8760muzgm2.fsf@kirby.i-did-not-set--mail-host-address--so-tickle-me> 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: Marius Bakke Cc: guix-devel@gnu.org Marius Bakke writes: > Ben Woodcroft writes: > >> Hi, >> >> It seems that the pardre source has been updated in place. I'm not su= re what >> the procedure is for verifying that nothing untoward has taken place, = since I >> cannot download and old version from the hydra content addressed mirro= r - >> 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 @@ -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 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; }