From nobody Sat Dec 16 14:00:58 2023 X-Original-To: dev-commits-ports-all@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4Ssnmq0c75z53yGB; Sat, 16 Dec 2023 14:00:59 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4Ssnmp4mrZz4f5m; Sat, 16 Dec 2023 14:00:58 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1702735258; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=fptnMBAhWApD1jzJb2QgB6T28clCf1f5JDXjN3Mom5I=; b=Pz9W3vyHJD5cl9H15BwUJ3tPR/BaM+62mkz6WrOIQ0+Dwyn3zIAx/wLxcWRuTJH6CCOgLG 2nG7dNuHEG8uS7lOkdWoRh0v6XJUfPlpjkgWb8z51XR48DgzZfHRh+1cWzQdKA5WCCbd+k CllBxjs0NYgsqqg8rwWWgMIyQ8mL+LMVndng46FWUWnVICTGshE5il8jAQKaO7MZgLZdnR +64UwS9iZ6h+dvgoQdszd13+/jP8uqx0YIQT3MJUJSs3oqjLShOQn8gARTmcD/BASKJJIp rP/dwYzdkXRbvq+9GJKqxBoBSDtZyjEzM7Oaqi/EKdhiZB3oC1YquXzYMatxxQ== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1702735258; a=rsa-sha256; cv=none; b=V/zeMbt/u2di6zjgJGiMVNina24jEffMELD3Ln7SRpacZVISinxBke/PoBhAmgFJMATYgy Lx4cqMQb06nUG8PLkKMw2w8cRHXH0i58bVXB28Uz7ZXB0+xHYp6xPu3YNuiyppFnldjvvG BgaUzwihOGhWlaQLxXcSKvuTN2gbF6H8xL1L2AY3Lc47lQeOSDpRNObMXn0oUE3zMi90Dt gQfT8JNyI2cgS5GGxd7urBppW+QiH+jRFd2AU2H2S1I4Q7WiATNqcWPwygES0yQHMVoTmk StPcaFkbVFuANhMvIbFYlCP4m4lTDYUJ35PsV9hbnt31DFcpSJKeOenKL3uRgg== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1702735258; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=fptnMBAhWApD1jzJb2QgB6T28clCf1f5JDXjN3Mom5I=; b=Fx+QwLpYnuhe+nndWAz7CQo+fEkCU0bJjTuUji36JgK2d44QwIhFWvoxTQcGa4IqwcrPkm uILbN+mzLBBcC4kFaRYgu6nabsTH/bynQpHcIt4XXdqSbbgsKzu7SqMwgYPmNVxN0nXjs8 2fRnNZf6NIcYuaUZf+Ffg4kt1pzyrASdlh6HYrSUt7MtpH7wqMDQPVAH6znU2DMgftKNiD Dy6tU0u2fM/996s4nqla14aJoJmpNiPi3HArpMkxoKowl5d+jd4dPo8nyYR8gM7bljB9HB 254UYWVg+10JnU7UqbJY38L/m1mmchKdVl1idQRUczWbHKihfA2T/zNAY/StaQ== Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 4Ssnmp3svVzx5R; Sat, 16 Dec 2023 14:00:58 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.17.1/8.17.1) with ESMTP id 3BGE0wjs040729; Sat, 16 Dec 2023 14:00:58 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.17.1/8.17.1/Submit) id 3BGE0wJf040726; Sat, 16 Dec 2023 14:00:58 GMT (envelope-from git) Date: Sat, 16 Dec 2023 14:00:58 GMT Message-Id: <202312161400.3BGE0wJf040726@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: "Jason W. Bacon" Subject: git: 0f12812f16d4 - main - biology/py-pybigwig: Update to 0.3.22 List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-all@freebsd.org X-BeenThere: dev-commits-ports-all@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 0f12812f16d40ac818faf4123086697a041313d2 Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=0f12812f16d40ac818faf4123086697a041313d2 commit 0f12812f16d40ac818faf4123086697a041313d2 Author: Jason W. Bacon AuthorDate: 2023-12-16 13:59:37 +0000 Commit: Jason W. Bacon CommitDate: 2023-12-16 13:59:37 +0000 biology/py-pybigwig: Update to 0.3.22 No real changes from 0.3.21 Add patch to resolve conflict with roundup() macro in sys/param.h Reported by: pkg-fallout --- biology/py-pybigwig/Makefile | 2 +- biology/py-pybigwig/distinfo | 6 ++--- .../py-pybigwig/files/patch-libBigWig_bwValues.c | 29 ++++++++++++++++++++++ 3 files changed, 33 insertions(+), 4 deletions(-) diff --git a/biology/py-pybigwig/Makefile b/biology/py-pybigwig/Makefile index 131ba5e45ca1..76d160a9e818 100644 --- a/biology/py-pybigwig/Makefile +++ b/biology/py-pybigwig/Makefile @@ -1,5 +1,5 @@ PORTNAME= pyBigWig -DISTVERSION= 0.3.21 +DISTVERSION= 0.3.22 CATEGORIES= biology python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/biology/py-pybigwig/distinfo b/biology/py-pybigwig/distinfo index 4d8222cfc082..44d8c0b8eead 100644 --- a/biology/py-pybigwig/distinfo +++ b/biology/py-pybigwig/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1680381155 -SHA256 (pyBigWig-0.3.21.tar.gz) = 5bff713fe3f8840e0fbe48cf8c8fe9d92c8af8ba107da0b845076164445d076e -SIZE (pyBigWig-0.3.21.tar.gz) = 73827 +TIMESTAMP = 1681053575 +SHA256 (pyBigWig-0.3.22.tar.gz) = 5d4426f754bd7b7f6dc21d6c3f93b58a96a65b6eb2e578ae03b31a71272d2243 +SIZE (pyBigWig-0.3.22.tar.gz) = 73864 diff --git a/biology/py-pybigwig/files/patch-libBigWig_bwValues.c b/biology/py-pybigwig/files/patch-libBigWig_bwValues.c new file mode 100644 index 000000000000..7b2fc3774b92 --- /dev/null +++ b/biology/py-pybigwig/files/patch-libBigWig_bwValues.c @@ -0,0 +1,29 @@ +--- libBigWig/bwValues.c.orig 2023-12-16 13:51:54 UTC ++++ libBigWig/bwValues.c +@@ -5,7 +5,7 @@ + #include + #include + +-static uint32_t roundup(uint32_t v) { ++static uint32_t bigwig_roundup(uint32_t v) { + v--; + v |= v >> 1; + v |= v >> 2; +@@ -346,7 +346,7 @@ static bwOverlappingIntervals_t *pushIntervals(bwOverl + //Returns NULL on error, in which case o has been free()d + static bwOverlappingIntervals_t *pushIntervals(bwOverlappingIntervals_t *o, uint32_t start, uint32_t end, float value) { + if(o->l+1 >= o->m) { +- o->m = roundup(o->l+1); ++ o->m = bigwig_roundup(o->l+1); + o->start = realloc(o->start, o->m * sizeof(uint32_t)); + if(!o->start) goto error; + o->end = realloc(o->end, o->m * sizeof(uint32_t)); +@@ -366,7 +366,7 @@ static bbOverlappingEntries_t *pushBBIntervals(bbOverl + + static bbOverlappingEntries_t *pushBBIntervals(bbOverlappingEntries_t *o, uint32_t start, uint32_t end, char *str, int withString) { + if(o->l+1 >= o->m) { +- o->m = roundup(o->l+1); ++ o->m = bigwig_roundup(o->l+1); + o->start = realloc(o->start, o->m * sizeof(uint32_t)); + if(!o->start) goto error; + o->end = realloc(o->end, o->m * sizeof(uint32_t));