From nobody Wed Jun 07 04:45:28 2023 X-Original-To: dev-commits-ports-main@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 4QbZXS5KLqz4bYHk; Wed, 7 Jun 2023 04:45:28 +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 4QbZXS4swLz4R2R; Wed, 7 Jun 2023 04:45:28 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1686113128; 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=pv6/WZ4pCcVRVr1oWdcGZRXYpCLVmKCXuAAgPxxQX9g=; b=Z9t3G4CCgxyFkVXb2v/dDP81IShc8gM5TuokJmifzCJIiic/Z0fQD1v8AzIPovQVp+e8T9 CxibjwhYfT9iVXqtjtvYQ5ayyFGgQbKDkaHS4Icbq2RR7BpYkkbKS91jFfrR1K8EXLDdRE 39sh387hYGx3fvrv/1oMAslP2CtgC7nHZmeSS4WTUOhOA/ZadBBZ2Hoq2HB6P1tQwRIUyt DmTQGU6SwSK2k/V7IZC8eZe82bwrkxkRmyIyikj+t0JT129dAHdFVh3Ju3BbkAPnNst9Fa mn2QytuI4+hyj/t15mF2lhdQl1QZpImiZehCbZsBqRr3BEUT2EpnUX4MVhfHHA== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1686113128; 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=pv6/WZ4pCcVRVr1oWdcGZRXYpCLVmKCXuAAgPxxQX9g=; b=aqvbCJo/OX5KcW05ZFesxL7GfTJyaCw6YdZ6lgwXHfcLYRR6xajkf3AR3YeIe8s4n3wIKB l0/LiKxBxCSjhN5Skt+9vlA55tCGXtE2BuwDjIgIHLRNT1on/vaogtOlxe0mBtXjfoX1+5 x5k5kPp6QBBEUeazg4+cnE5FqsUYGKpoYHnFe1Fgpm3y19kUTyI6h4cUXpXpKasNgP0bH9 NquWBSluGnxjzEzXKh67rjrwW3vycE7VA6LCy9POE64waESROe8Sc2ltxGPF0n8F4LkY3G MfAN6fqumQZYr5MF+DxI3159rut3WfonG16Fe+MED8V6Enq1hquDAErpMZ97wA== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1686113128; a=rsa-sha256; cv=none; b=JjLTtAOAhVLDlYU/4LU7XamterPEXyk5ktq+oEbXeN0cOH25edUbRO70Txo6wDVfbPaWr/ yZPsC69p8YEUAdKCppKrOdq2yA++L7ZAnAIXLKUZSEloVWnzedazqJdbWbnOzzxwPURz94 T+XSOjI9lfiWfrn9iAT+BUmpPD6+3CHhWRYwr0MFnc4fYWmMXtarLvc5zpkKFehaQihG6t 80TlHLhVFmWiFYfNQZvJqh12V4XvcoeoH9j+6XiEMnZwpGF5RxxPtX0VX9f2gWdF0ZZ0ya 3Spk2lVIgK+vzuj99K2yZwXRBSJhR2BhCCmGuktWGJ8nXtQYOthp18LSYhTbpg== 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 4QbZXS3xFXzyVQ; Wed, 7 Jun 2023 04:45:28 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 3574jSat020934; Wed, 7 Jun 2023 04:45:28 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 3574jSCs020933; Wed, 7 Jun 2023 04:45:28 GMT (envelope-from git) Date: Wed, 7 Jun 2023 04:45:28 GMT Message-Id: <202306070445.3574jSCs020933@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Yuri Victorovich Subject: git: 31745d2619e6 - main - =?utf-8?Q?science/tinker:=20Update=208.10.2=20=E2=86=92=208.10.5?= List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-main@freebsd.org X-BeenThere: dev-commits-ports-main@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: yuri X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 31745d2619e6fb51e1c0f5c7e474bbf8e562b84d Auto-Submitted: auto-generated X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=31745d2619e6fb51e1c0f5c7e474bbf8e562b84d commit 31745d2619e6fb51e1c0f5c7e474bbf8e562b84d Author: Yuri Victorovich AuthorDate: 2023-06-07 03:36:03 +0000 Commit: Yuri Victorovich CommitDate: 2023-06-07 04:45:24 +0000 science/tinker: Update 8.10.2 → 8.10.5 Reported by: portscout --- science/tinker/Makefile | 5 ++--- science/tinker/distinfo | 6 +++--- science/tinker/files/patch-make_Makefile | 21 ++++++--------------- science/tinker/pkg-plist | 28 ++++++++++++++++++++++------ 4 files changed, 33 insertions(+), 27 deletions(-) diff --git a/science/tinker/Makefile b/science/tinker/Makefile index cad65ea47aa3..139976dfc474 100644 --- a/science/tinker/Makefile +++ b/science/tinker/Makefile @@ -1,6 +1,5 @@ PORTNAME= tinker -DISTVERSION= 8.10.2 -PORTREVISION= 2 +DISTVERSION= 8.10.5 CATEGORIES= science MASTER_SITES= https://dasher.wustl.edu/tinker/downloads/ @@ -22,7 +21,7 @@ BUILD_WRKSRC= ${WRKSRC}/source INSTALL_WRKSRC= ${WRKSRC}/source MAKE_ENV= HAVE_G2C=yes -MAKE_ARGS= RANLIB=ranlib BINDIR=${STAGEDIR}${PREFIX}/bin +MAKE_ARGS= RANLIB=ranlib BINDIR=${STAGEDIR}${PREFIX}/bin LIBS="${LOCALBASE}/lib/libfftw3.a ${LOCALBASE}/lib/libfftw3_threads.a" MAKEFILE= ${WRKSRC}/make/Makefile EXTRACT_AFTER_ARGS=--exclude fftw --exclude windows --exclude macosx diff --git a/science/tinker/distinfo b/science/tinker/distinfo index a4b276b6d825..3237f17d500a 100644 --- a/science/tinker/distinfo +++ b/science/tinker/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1649951980 -SHA256 (tinker-8.10.2.tar.gz) = 7481769f3d61f81ab98e6a0950520693a6d078c4048998f388efb72c20adde40 -SIZE (tinker-8.10.2.tar.gz) = 72009856 +TIMESTAMP = 1686102562 +SHA256 (tinker-8.10.5.tar.gz) = 4673783f1d8f369c9e90add6f8be4aeb8a6969525fd8c09b6f97b7ca93294e94 +SIZE (tinker-8.10.5.tar.gz) = 70068463 diff --git a/science/tinker/files/patch-make_Makefile b/science/tinker/files/patch-make_Makefile index 8e315337a050..5f647f400faf 100644 --- a/science/tinker/files/patch-make_Makefile +++ b/science/tinker/files/patch-make_Makefile @@ -1,22 +1,13 @@ ---- make/Makefile.orig 2022-01-13 23:40:10 UTC +--- make/Makefile.orig 2023-03-09 06:01:09 UTC +++ make/Makefile -@@ -68,7 +68,7 @@ APBS_LIBS = -lapbsmainroutines -lapbs -lmaloc -lapbsbl - - F77 = gfortran - F77FLAGS = -c --OPTFLAGS = -Ofast -march=native -fopenmp -+OPTFLAGS = -Ofast -fopenmp - #OPTFLAGS = -Ofast -msse3 -fopenmp - #OPTFLAGS = -Og -fbacktrace -fcheck=bounds -Wunused -Wmaybe-uninitialized - LIBDIR = -L. -L$(TINKER_LIBDIR)/linux -Wl,--no-as-needed -ldl -@@ -803,136 +803,136 @@ listing: +@@ -818,136 +818,136 @@ listing: cat *.f *.c > tinker.txt rename_bin: - mv alchemy.x $(BINDIR)/alchemy - mv analyze.x $(BINDIR)/analyze - mv anneal.x $(BINDIR)/anneal -- mv archive.x $(BINDIR)/archive +- mv arcedit.x $(BINDIR)/arcedit - mv bar.x $(BINDIR)/bar - mv correlate.x $(BINDIR)/correlate - mv critical.x $(BINDIR)/critical @@ -80,7 +71,7 @@ + ${BSD_INSTALL_PROGRAM} alchemy.x $(BINDIR)/alchemy + ${BSD_INSTALL_PROGRAM} analyze.x $(BINDIR)/analyze + ${BSD_INSTALL_PROGRAM} anneal.x $(BINDIR)/anneal -+ ${BSD_INSTALL_PROGRAM} archive.x $(BINDIR)/archive ++ ${BSD_INSTALL_PROGRAM} arcedit.x $(BINDIR)/arcedit + ${BSD_INSTALL_PROGRAM} bar.x $(BINDIR)/bar + ${BSD_INSTALL_PROGRAM} correlate.x $(BINDIR)/correlate + ${BSD_INSTALL_PROGRAM} critical.x $(BINDIR)/critical @@ -146,7 +137,7 @@ - mv alchemy.x $(BINDIR)/alchemy.exe - mv analyze.x $(BINDIR)/analyze.exe - mv anneal.x $(BINDIR)/anneal.exe -- mv archive.x $(BINDIR)/archive.exe +- mv arcedit.x $(BINDIR)/arcedit.exe - mv bar.x $(BINDIR)/bar.exe - mv correlate.x $(BINDIR)/correlate.exe - mv critical.x $(BINDIR)/critical.exe @@ -210,7 +201,7 @@ + ${BSD_INSTALL_PROGRAM} alchemy.x $(BINDIR)/alchemy.exe + ${BSD_INSTALL_PROGRAM} analyze.x $(BINDIR)/analyze.exe + ${BSD_INSTALL_PROGRAM} anneal.x $(BINDIR)/anneal.exe -+ ${BSD_INSTALL_PROGRAM} archive.x $(BINDIR)/archive.exe ++ ${BSD_INSTALL_PROGRAM} arcedit.x $(BINDIR)/arcedit.exe + ${BSD_INSTALL_PROGRAM} bar.x $(BINDIR)/bar.exe + ${BSD_INSTALL_PROGRAM} correlate.x $(BINDIR)/correlate.exe + ${BSD_INSTALL_PROGRAM} critical.x $(BINDIR)/critical.exe diff --git a/science/tinker/pkg-plist b/science/tinker/pkg-plist index cb3939f54c62..93c386919f9f 100644 --- a/science/tinker/pkg-plist +++ b/science/tinker/pkg-plist @@ -1,7 +1,7 @@ bin/alchemy bin/analyze bin/anneal -bin/archive +bin/arcedit bin/bar bin/correlate bin/critical @@ -63,6 +63,7 @@ bin/xyzint bin/xyzmol2 bin/xyzpdb %%DATADIR%%/params/0README +%%DATADIR%%/params/amber14sb.prm %%DATADIR%%/params/amber94.prm %%DATADIR%%/params/amber96.prm %%DATADIR%%/params/amber98.prm @@ -72,6 +73,7 @@ bin/xyzpdb %%DATADIR%%/params/amoeba09.prm %%DATADIR%%/params/amoebabio09.prm %%DATADIR%%/params/amoebabio18.prm +%%DATADIR%%/params/amoebail22.prm %%DATADIR%%/params/amoebanuc17.prm %%DATADIR%%/params/amoebaplus.prm %%DATADIR%%/params/amoebapro04.prm @@ -81,6 +83,7 @@ bin/xyzpdb %%DATADIR%%/params/charmm22.prm %%DATADIR%%/params/charmm22cmap.prm %%DATADIR%%/params/dang.prm +%%DATADIR%%/params/hippo19.prm %%DATADIR%%/params/hoch.prm %%DATADIR%%/params/iwater.prm %%DATADIR%%/params/mm2.prm @@ -89,6 +92,7 @@ bin/xyzpdb %%DATADIR%%/params/mmff.prm %%DATADIR%%/params/oplsaa.prm %%DATADIR%%/params/oplsaal.prm +%%DATADIR%%/params/oplsaam.prm %%DATADIR%%/params/oplsua.prm %%DATADIR%%/params/smoothaa.prm %%DATADIR%%/params/smoothua.prm @@ -107,6 +111,13 @@ bin/xyzpdb %%DATADIR%%/test/argon.key %%DATADIR%%/test/argon.log %%DATADIR%%/test/argon.run +%%DATADIR%%/test/cation.ckey +%%DATADIR%%/test/cation.cxyz +%%DATADIR%%/test/cation.log +%%DATADIR%%/test/cation.rkey +%%DATADIR%%/test/cation.run +%%DATADIR%%/test/cation.rxyz +%%DATADIR%%/test/clean.make %%DATADIR%%/test/cluster.dat %%DATADIR%%/test/cluster.key %%DATADIR%%/test/cluster.log @@ -116,11 +127,11 @@ bin/xyzpdb %%DATADIR%%/test/crambin.log %%DATADIR%%/test/crambin.pdb %%DATADIR%%/test/crambin.run -%%DATADIR%%/test/cyclohex.boat -%%DATADIR%%/test/cyclohex.chair -%%DATADIR%%/test/cyclohex.key -%%DATADIR%%/test/cyclohex.log -%%DATADIR%%/test/cyclohex.run +%%DATADIR%%/test/cyclohexane.boat +%%DATADIR%%/test/cyclohexane.chair +%%DATADIR%%/test/cyclohexane.key +%%DATADIR%%/test/cyclohexane.log +%%DATADIR%%/test/cyclohexane.run %%DATADIR%%/test/dhfr.dyn %%DATADIR%%/test/dhfr.key %%DATADIR%%/test/dhfr.log @@ -198,9 +209,14 @@ bin/xyzpdb %%DATADIR%%/test/salt.key %%DATADIR%%/test/salt.log %%DATADIR%%/test/salt.run +%%DATADIR%%/test/vasopressin.key +%%DATADIR%%/test/vasopressin.log +%%DATADIR%%/test/vasopressin.run +%%DATADIR%%/test/vasopressin.xyz %%DATADIR%%/test/water.amoeba %%DATADIR%%/test/water.hippo %%DATADIR%%/test/water.log %%DATADIR%%/test/water.pot %%DATADIR%%/test/water.run +%%DATADIR%%/test/water.tip3p %%DATADIR%%/test/water.xyz