svn commit: r522911 - in head/biology/muscle: . files
Fernando Apesteguía
fernape at FreeBSD.org
Mon Jan 13 17:42:23 UTC 2020
Author: fernape
Date: Mon Jan 13 17:42:22 2020
New Revision: 522911
URL: https://svnweb.freebsd.org/changeset/ports/522911
Log:
biology/muscle: update to 3.8.1551
* Bug fix for long sequences.
* Unbreak '/dev/tty' problem during a build
* Update maintainer's mail address
PR: 243206
Submitted by: mzaki at e-mail.ne.jp (maintainer)
Added:
head/biology/muscle/files/patch-Makefile (contents, props changed)
Deleted:
head/biology/muscle/files/patch-mk
Modified:
head/biology/muscle/Makefile
head/biology/muscle/distinfo
head/biology/muscle/files/patch-globalslinux.cpp
Modified: head/biology/muscle/Makefile
==============================================================================
--- head/biology/muscle/Makefile Mon Jan 13 17:42:18 2020 (r522910)
+++ head/biology/muscle/Makefile Mon Jan 13 17:42:22 2020 (r522911)
@@ -2,27 +2,21 @@
# $FreeBSD$
PORTNAME= muscle
-PORTVERSION= 3.8.31
+PORTVERSION= 3.8.1551
CATEGORIES= biology
-MASTER_SITES= http://www.drive5.com/muscle/downloads${PORTVERSION}/
-DISTNAME= ${PORTNAME}${PORTVERSION}_src
+MASTER_SITES= http://www.drive5.com/muscle/
+DISTNAME= ${PORTNAME}_src_${PORTVERSION}
-MAINTAINER= mzaki at m.u-tokyo.ac.jp
+MAINTAINER= mzaki at e-mail.ne.jp
COMMENT= MUltiple Sequence Comparison by Log-Expectation
-FETCH_ARGS= -A
+LICENSE= PD
-WRKSRC= ${WRKDIR}/${PORTNAME}${PORTVERSION}/src
-
-USES= dos2unix
+USES= dos2unix gmake
+NO_WRKSUBDIR= yes
DOS2UNIX_GLOB= *.cpp
-ALL_TARGET= muscle
-
PLIST_FILES= bin/muscle
-
-ONLY_FOR_ARCHS= amd64 i386
-ONLY_FOR_ARCHS_REASON= Fails to install: tries to modify /dev/tty
do-install:
${INSTALL_PROGRAM} ${WRKSRC}/muscle ${STAGEDIR}${PREFIX}/bin
Modified: head/biology/muscle/distinfo
==============================================================================
--- head/biology/muscle/distinfo Mon Jan 13 17:42:18 2020 (r522910)
+++ head/biology/muscle/distinfo Mon Jan 13 17:42:22 2020 (r522911)
@@ -1,2 +1,3 @@
-SHA256 (muscle3.8.31_src.tar.gz) = 43c5966a82133bd7da5921e8142f2f592c2b5f53d802f0527a2801783af809ad
-SIZE (muscle3.8.31_src.tar.gz) = 515267
+TIMESTAMP = 1578543217
+SHA256 (muscle_src_3.8.1551.tar.gz) = c70c552231cd3289f1bad51c9bd174804c18bb3adcf47f501afec7a68f9c482e
+SIZE (muscle_src_3.8.1551.tar.gz) = 190019
Added: head/biology/muscle/files/patch-Makefile
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/muscle/files/patch-Makefile Mon Jan 13 17:42:22 2020 (r522911)
@@ -0,0 +1,28 @@
+--- Makefile.orig 2014-07-12 16:42:52 UTC
++++ Makefile
+@@ -10,8 +10,8 @@
+ # this is fixed by deleting "-static" from the LDLIBS line.
+
+ CFLAGS = -O3 -funroll-loops -Winline -DNDEBUG=1
+-LDLIBS = -lm -static
+-# LDLIBS = -lm
++#LDLIBS = -lm -static
++LDLIBS = -lm
+
+ OBJ = .o
+ EXE =
+@@ -19,7 +19,7 @@ EXE =
+ RM = rm -f
+ CP = cp
+
+-GPP = g++
++GPP = $(CXX)
+ LD = $(GPP) $(CFLAGS)
+ CPP = $(GPP) -c $(CFLAGS)
+
+@@ -33,4 +33,4 @@ $(CPPOBJ): %.o: %.cpp
+
+ muscle: $(CPPOBJ)
+ $(LD) -o muscle $(CPPOBJ) $(LDLIBS)
+- strip muscle
++# strip muscle
Modified: head/biology/muscle/files/patch-globalslinux.cpp
==============================================================================
--- head/biology/muscle/files/patch-globalslinux.cpp Mon Jan 13 17:42:18 2020 (r522910)
+++ head/biology/muscle/files/patch-globalslinux.cpp Mon Jan 13 17:42:22 2020 (r522911)
@@ -1,5 +1,5 @@
---- globalslinux.cpp.orig Tue Nov 30 05:09:50 2004
-+++ globalslinux.cpp Mon Jul 4 11:13:18 2005
+--- globalslinux.cpp.orig 2020-01-09 04:20:25 UTC
++++ globalslinux.cpp
@@ -7,6 +7,12 @@
#include <errno.h>
#include <stdio.h>
@@ -13,7 +13,7 @@
const int ONE_MB = 1000000;
const int MEM_WARNING_THRESHOLD = 20*ONE_MB;
-@@ -39,6 +45,34 @@
+@@ -39,6 +45,34 @@ const char *GetCmdLine()
return szCmdLine;
}
@@ -48,7 +48,7 @@
double GetMemUseMB()
{
static char statm[64];
-@@ -83,6 +117,7 @@
+@@ -74,6 +108,7 @@ double GetMemUseMB()
return ((double) Pages * (double) PageSize)/1e6;
}
@@ -56,7 +56,7 @@
void SaveCmdLine(int argc, char *argv[])
{
-@@ -118,6 +153,28 @@
+@@ -109,6 +144,28 @@ void CheckMemUse()
dPeakMemUseMB = dMB;
}
@@ -85,7 +85,7 @@
double GetRAMSizeMB()
{
const double DEFAULT_RAM = 500;
-@@ -168,5 +225,6 @@
+@@ -159,5 +216,6 @@ double GetRAMSizeMB()
int Bytes = atoi(pMem+9)*1000;
return ((double) Bytes)/1e6;
}
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