From nobody Sun Jan 02 17:32:51 2022 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 56DC8192B3FA; Sun, 2 Jan 2022 17:32:52 +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 4JRmDN0928z3q0S; Sun, 2 Jan 2022 17:32:52 +0000 (UTC) (envelope-from git@FreeBSD.org) 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 D92E615DF8; Sun, 2 Jan 2022 17:32:51 +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 202HWpDA036987; Sun, 2 Jan 2022 17:32:51 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 202HWppa036986; Sun, 2 Jan 2022 17:32:51 GMT (envelope-from git) Date: Sun, 2 Jan 2022 17:32:51 GMT Message-Id: <202201021732.202HWppa036986@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: =?utf-8?Q?Fernando Apestegu=C3=ADa?= Subject: git: 59a8ef603d05 - main - biology/phyml: update to 3.3.20211231 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: fernape X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 59a8ef603d053f64e4067f3723feeeb60610bedb Auto-Submitted: auto-generated ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1641144772; 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=cSe9uFGC7qHAl3sGF/t8keRAk5SBKl+h35oJgLIA6I0=; b=g1/vq9zjeVTEaby67XyvKa16lLM032wsls9zO8fNBZt+8vBpOitvnJ0zLQmF60L6i61bUc i6J4ZZTLDc+AdtGTS50wevEy8bq0mj133GcjPftJB8JwfGiAgpgvofWAo+HyzV3s8epR5x DszX3JSDuXwhQnOjT7ysXXiU8Kl7SAjZFwOykQcPchPPPy2S4swOfhWwK2tQrVLN3hwh+f bjayyMEFsfBVwWctp0rqrodVBc850j8clZU3E9mU3izO/km9yzRy0nkVKCXcBa307rJrJY 2CLm39NyZBEgyOn6Mh0hbdfQgYMGNyFxqjmUXCQNfEzTzsv8gNJhGMm/OTBn1Q== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1641144772; a=rsa-sha256; cv=none; b=HWI8NLsyEiylAoYkHigkrO/Ufz7uXU+g0KA8l7gh+8RSdvbjSuMP/EBOEHveJsFw59/I58 /M2zIMY/mS7i5sass95l8oOY1yt8qDrG/V2cgFo3G6Q3C3zMnLPCBrNrzRYjklmh7NF0De AO57mj5XfR/q9oPldQxWUhJNNPH9HsvguPrablmHgfmfUrPZOC4yYbmkZ7N1by2WaseMel YRF1DZHq8x1AlYwWAbqhvKFhFRiv/JArjIXdJ7SvA7GBznYTHnK0+Uce6JVz1AiYpoP0ZM 46LsXXCTSGYcZ9+ol4RZaxgndhGSnjgENZXZL+ehq7pWDxfUjB8z82OpSuO6OQ== ARC-Authentication-Results: i=1; mx1.freebsd.org; none X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by fernape: URL: https://cgit.FreeBSD.org/ports/commit/?id=59a8ef603d053f64e4067f3723feeeb60610bedb commit 59a8ef603d053f64e4067f3723feeeb60610bedb Author: Fernando Apesteguía AuthorDate: 2022-01-02 16:45:30 +0000 Commit: Fernando Apesteguía CommitDate: 2022-01-02 17:31:24 +0000 biology/phyml: update to 3.3.20211231 ChangeLog: https://github.com/stephaneguindon/phyml/compare/v3.3.20211118...v3.3.20211231 Remove patches already merged into upstream. Reported by: portscout --- biology/phyml/Makefile | 4 +--- biology/phyml/distinfo | 6 +++--- biology/phyml/files/patch-configure.ac | 15 ++++++++------- biology/phyml/files/patch-src_io.c | 20 -------------------- biology/phyml/files/patch-src_phyrex.c | 11 ----------- biology/phyml/files/patch-src_utilities.c | 30 ------------------------------ biology/phyml/files/patch-src_utilities.h | 13 ------------- 7 files changed, 12 insertions(+), 87 deletions(-) diff --git a/biology/phyml/Makefile b/biology/phyml/Makefile index 0881c57ced44..4c659132117e 100644 --- a/biology/phyml/Makefile +++ b/biology/phyml/Makefile @@ -2,7 +2,7 @@ PORTNAME= phyml DISTVERSIONPREFIX= v -DISTVERSION= 3.3.20200621 +DISTVERSION= 3.3.20211231 PORTEPOCH= 1 CATEGORIES= biology @@ -44,8 +44,6 @@ BIN_SUFFIX= # none .endif post-patch: - @${REINPLACE_CMD} -e \ - 's|-O2 .* $${ARCH_flag}|$${CFLAGS}|' ${WRKSRC}/configure.ac .if ${ARCH} != amd64 && ${ARCH} != i386 @${REINPLACE_CMD} -e 's|VECTOR_FLAG=-march=native|dnl &|' ${WRKSRC}/configure.ac .endif diff --git a/biology/phyml/distinfo b/biology/phyml/distinfo index bb7619ad9861..1e98ab22af49 100644 --- a/biology/phyml/distinfo +++ b/biology/phyml/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1594372740 -SHA256 (stephaneguindon-phyml-v3.3.20200621_GH0.tar.gz) = ffbecbc716fe7dd3e25493d2ebc1aab42ff3c33fc6fffca0920a950d38d74e22 -SIZE (stephaneguindon-phyml-v3.3.20200621_GH0.tar.gz) = 2234125 +TIMESTAMP = 1641139689 +SHA256 (stephaneguindon-phyml-v3.3.20211231_GH0.tar.gz) = 5822c04f1b8ad7f9ef5aecaacc124f736b78344eb8cf459a230c727152734d99 +SIZE (stephaneguindon-phyml-v3.3.20211231_GH0.tar.gz) = 1802113 diff --git a/biology/phyml/files/patch-configure.ac b/biology/phyml/files/patch-configure.ac index c96d56cf91bc..ea8e872962a0 100644 --- a/biology/phyml/files/patch-configure.ac +++ b/biology/phyml/files/patch-configure.ac @@ -1,10 +1,11 @@ ---- configure.ac.orig 2020-07-09 11:49:16 UTC +--- configure.ac.orig 2022-01-02 16:39:46 UTC +++ configure.ac -@@ -10,7 +10,6 @@ AC_CONFIG_HEADERS([config.h]) - AC_DEFINE([UNIX],[1],[Unix tag on]) - AC_DEFINE([DEBUG],[1],[Debug tag on]) +@@ -67,7 +67,7 @@ dnl AC_PROG_LIBTOOL --AM_INIT_AUTOMAKE - AC_CANONICAL_HOST - AC_PROG_CC([gcc]) + dnl DEFAULT_C_FLAG="-fno-inline-functions -fno-inline-functions-called-once -fno-optimize-sibling-calls -O2 -fno-omit-frame-pointer -g ${VECTOR_FLAG}" +-DEFAULT_C_FLAG="-std=c99 -O3 -fomit-frame-pointer -funroll-loops -Wall -Winline -finline ${VECTOR_FLAG}" ++DEFAULT_C_FLAG="-std=c99 -O3 -fomit-frame-pointer -funroll-loops -msse3 -Wall -Winline -finline ${VECTOR_FLAG}" + dnl DEFAULT_C_FLAG="-O2 ${VECTOR_FLAG}" + dnl DEFAULT_C_FLAG="${VECTOR_FLAG}" + dnl DEFAULT_C_FLAG="-pthread -O3 -g -ffunction-sections -fdata-sections" diff --git a/biology/phyml/files/patch-src_io.c b/biology/phyml/files/patch-src_io.c deleted file mode 100644 index 00fdcf48030f..000000000000 --- a/biology/phyml/files/patch-src_io.c +++ /dev/null @@ -1,20 +0,0 @@ ---- src/io.c.orig 2020-07-09 11:49:16 UTC -+++ src/io.c -@@ -39,8 +39,6 @@ t_tree *Read_Tree(char **s_tree) - if((*s_tree)[i] == ',') n_otu++; - } - n_otu+=1; -- -- - - tree = Make_Tree_From_Scratch(n_otu,NULL); - subs = Sub_Trees((*s_tree),°ree); -@@ -2312,7 +2310,7 @@ void Print_Fp_Out(FILE *fp_out, time_t t_beg, time_t t - div_t hour,min; - int i, j; - -- if (precision > 0) snprintf (format, 8, "%%.%df", precision); -+ if (precision > 0) snprintf(format,8,"%%.%huf",(unsigned short)precision); - - if(n_data_set == 1) - { diff --git a/biology/phyml/files/patch-src_phyrex.c b/biology/phyml/files/patch-src_phyrex.c deleted file mode 100644 index 661ee785dd32..000000000000 --- a/biology/phyml/files/patch-src_phyrex.c +++ /dev/null @@ -1,11 +0,0 @@ ---- src/phyrex.c.orig 2020-07-09 11:49:16 UTC -+++ src/phyrex.c -@@ -958,7 +958,7 @@ phydbl *PHYREX_MCMC(t_tree *tree) - PHYREX_Label_Nodes_With_Locations(tree); - PHYREX_Label_Edges(tree); - char *s = Write_Tree(tree); -- PhyML_Fprintf(fp_tree,"\ntree %d [&lnP=%f,precision={1.e-1,1e-02,1e-01}] = [&R] %s",tree->mcmc->sample_num,tree->c_lnL,s); -+ PhyML_Fprintf(fp_tree,"\ntree %d [&lnP=%f,precision={1.e-1,1e-02,1e-01}] = [&R] %s",tree->mcmc->run,tree->c_lnL,s); - PhyML_Fprintf(fp_tree,"\nend;"); - fseek(fp_tree,-5,SEEK_END); - tree->write_tax_names = YES; diff --git a/biology/phyml/files/patch-src_utilities.c b/biology/phyml/files/patch-src_utilities.c deleted file mode 100644 index 99740e857571..000000000000 --- a/biology/phyml/files/patch-src_utilities.c +++ /dev/null @@ -1,30 +0,0 @@ ---- src/utilities.c.orig 2020-07-09 11:49:16 UTC -+++ src/utilities.c -@@ -17,6 +17,9 @@ the GNU public licence. See http://www.opensource.org - #include "beagle_utils.h" - #endif - -+int CALL; -+int TIME; -+ - ////////////////////////////////////////////////////////////// - ////////////////////////////////////////////////////////////// - -@@ -3066,7 +3069,7 @@ int Assign_State_With_Ambiguity(char *c, int datatype, - if(Is_Ambigu(c,GENERIC,stepsize)) state[0] = T_MAX_ALPHABET-1; - else - { -- char format[6]; -+ char format[20]; - sprintf(format,"%%%dd",stepsize); - if(!sscanf(c,format,state)) - { -@@ -4891,7 +4894,7 @@ int Are_Compatible(char *statea, char *stateb, int ste - else - { - int a,b; -- char format[6]; -+ char format[20]; - - sprintf(format,"%%%dd",stepsize); - diff --git a/biology/phyml/files/patch-src_utilities.h b/biology/phyml/files/patch-src_utilities.h deleted file mode 100644 index 14b65b1fff53..000000000000 --- a/biology/phyml/files/patch-src_utilities.h +++ /dev/null @@ -1,13 +0,0 @@ ---- src/utilities.h.orig 2020-08-29 08:31:23 UTC -+++ src/utilities.h -@@ -94,8 +94,8 @@ static inline int isinf_ld (long double x) { return is - #endif - - --int CALL; --int TIME; -+extern int CALL; -+extern int TIME; - - #define SLFV_GAUSSIAN 0 /* Spatial Lambda-Fleming-Viot model (Gaussian) */ - #define SLFV_UNIFORM 1 /* Spatial Lambda-Fleming-Viot model (Uniform) */