diff --git a/biology/muscle/Makefile b/biology/muscle/Makefile index dd6b31a9a07f..f243953b2e0e 100644 --- a/biology/muscle/Makefile +++ b/biology/muscle/Makefile @@ -1,25 +1,29 @@ PORTNAME= muscle -PORTVERSION= 3.8.1551 +PORTVERSION= 5.1 +DISTVERSIONPREFIX= v CATEGORIES= biology -MASTER_SITES= http://www.drive5.com/muscle/ -DISTNAME= ${PORTNAME}_src_${PORTVERSION} MAINTAINER= mzaki@e-mail.ne.jp COMMENT= MUltiple Sequence Comparison by Log-Expectation WWW= https://www.drive5.com/muscle/ -LICENSE= PD +LICENSE= GPLv3 -USES= dos2unix gmake -NO_WRKSUBDIR= yes -DOS2UNIX_GLOB= *.cpp +BUILD_DEPENDS= bash:shells/bash -PLIST_FILES= bin/muscle +USES= gmake +USE_GCC= yes + +USE_GITHUB= yes +GH_ACCOUNT= rcedgar +ALL_TARGET= ${OPSYS}/${PORTNAME} +BINARY_ALIAS= g++=g++14 +WRKSRC_SUBDIR= src -post-patch: - ${MV} ${WRKSRC}/subfams.cpp ${WRKSRC}/subfams.cpp.not_to_be_compiled +PLIST_FILES= bin/muscle do-install: - ${INSTALL_PROGRAM} ${WRKSRC}/muscle ${STAGEDIR}${PREFIX}/bin + cd ${WRKSRC} && \ + ${INSTALL} ${OPSYS}/muscle ${STAGEDIR}${PREFIX}/bin/ .include diff --git a/biology/muscle/distinfo b/biology/muscle/distinfo index a6687d526e2e..b7c853250e26 100644 --- a/biology/muscle/distinfo +++ b/biology/muscle/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1578543217 -SHA256 (muscle_src_3.8.1551.tar.gz) = c70c552231cd3289f1bad51c9bd174804c18bb3adcf47f501afec7a68f9c482e -SIZE (muscle_src_3.8.1551.tar.gz) = 190019 +TIMESTAMP = 1777062030 +SHA256 (rcedgar-muscle-v5.1_GH0.tar.gz) = 091d9f8733b92ff106c2a8eb274d1e5a57960d397a2068d8638d6002e8880dab +SIZE (rcedgar-muscle-v5.1_GH0.tar.gz) = 183891 diff --git a/biology/muscle/files/patch-Makefile b/biology/muscle/files/patch-Makefile deleted file mode 100644 index 1dc159c93a2c..000000000000 --- a/biology/muscle/files/patch-Makefile +++ /dev/null @@ -1,28 +0,0 @@ ---- 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 diff --git a/biology/muscle/files/patch-globalslinux.cpp b/biology/muscle/files/patch-globalslinux.cpp deleted file mode 100644 index d2b91bf23b06..000000000000 --- a/biology/muscle/files/patch-globalslinux.cpp +++ /dev/null @@ -1,94 +0,0 @@ ---- globalslinux.cpp.orig 2020-01-09 04:20:25 UTC -+++ globalslinux.cpp -@@ -7,6 +7,12 @@ - #include - #include - #include -+#if __FreeBSD__ > 2 -+#include -+#include -+#include -+#include -+#endif // __FreeBSD__ > 2 - - const int ONE_MB = 1000000; - const int MEM_WARNING_THRESHOLD = 20*ONE_MB; -@@ -39,6 +45,34 @@ const char *GetCmdLine() - return szCmdLine; - } - -+#if __FreeBSD__ > 2 -+double GetMemUseMB() -+ { -+ kvm_t *kd; -+ struct kinfo_proc *ki; -+ vm_size_t size; -+ int nproc; -+ -+ kd = kvm_open(NULL, "/dev/null", NULL, O_RDONLY, "kvm_open"); -+ if (kd == NULL) -+ { -+ static bool Warned = false; -+ if (!Warned) -+ { -+ Warned = true; -+ Warning("*Warning* Cannot open KVM"); -+ } -+ return 0; -+ } -+ -+ ki = kvm_getprocs(kd, KERN_PROC_PID, getpid(), &nproc); -+ size = ki->ki_size; -+ -+ kvm_close(kd); -+ -+ return ((double) size)/1e6; -+ } -+#else // __FreeBSD__ > 2 - double GetMemUseMB() - { - static char statm[64]; -@@ -74,6 +108,7 @@ double GetMemUseMB() - - return ((double) Pages * (double) PageSize)/1e6; - } -+#endif // __FreeBSD__ > 2 - - void SaveCmdLine(int argc, char *argv[]) - { -@@ -109,6 +144,28 @@ void CheckMemUse() - dPeakMemUseMB = dMB; - } - -+#if __FreeBSD__ > 2 -+double GetRAMSizeMB() -+ { -+ const double DEFAULT_RAM = 500; -+ unsigned int physmem; -+ size_t len = sizeof physmem; -+ static int mib[2] = { CTL_HW, HW_PHYSMEM }; -+ -+ if (sysctl(mib, 2, &physmem, &len, NULL, 0)) -+ { -+ static bool Warned = false; -+ if (!Warned) -+ { -+ Warned = true; -+ Warning("*Warning* Cannot get hw.physmem"); -+ } -+ return DEFAULT_RAM; -+ } -+ -+ return ((double) physmem)/1e6; -+ } -+#else // __FreeBSD__ > 2 - double GetRAMSizeMB() - { - const double DEFAULT_RAM = 500; -@@ -159,5 +216,6 @@ double GetRAMSizeMB() - int Bytes = atoi(pMem+9)*1000; - return ((double) Bytes)/1e6; - } -+#endif // __FreeBSD__ > 2 - - #endif // !WIN32 diff --git a/biology/muscle/files/patch-src__myutils.cpp b/biology/muscle/files/patch-src__myutils.cpp new file mode 100644 index 000000000000..68b2a4eacfed --- /dev/null +++ b/biology/muscle/files/patch-src__myutils.cpp @@ -0,0 +1,65 @@ +--- myutils.cpp.orig 2022-01-13 23:29:59 UTC ++++ myutils.cpp +@@ -1050,7 +1050,62 @@ + g_PeakMemUseBytes = Bytes; + return Bytes; + } ++#elif defined(__FreeBSD__) ++ ++#include ++#include ++#include ++#include + ++double GetMemUseBytes() ++ { ++ static int initialized = 0; ++ static int mib[4]; ++ static size_t len; ++ ++ if (!initialized) ++ { ++ mib[0] = CTL_KERN; ++ mib[1] = KERN_PROC; ++ mib[2] = KERN_PROC_PID; ++ mib[3] = getpid(); ++ len = sizeof(struct kinfo_proc); ++ initialized = 1; ++ } ++ ++ struct kinfo_proc kp; ++ if (sysctl(mib, 4, &kp, &len, NULL, 0) == -1) ++ return 0.0; ++ ++ // Resident set size in pages → convert to bytes ++ long page_size = getpagesize(); ++ double bytes = (double)kp.ki_rssize * page_size; ++ ++ if (bytes > g_PeakMemUseBytes) ++ g_PeakMemUseBytes = bytes; ++ ++ return bytes; ++ ++ } ++ ++double GetPhysMemBytes() ++ { ++ #if BITS == 32 ++ unsigned int physmem32 = 0; ++ #else ++ uint64_t physmem = 0; ++ #endif ++ ++ size_t len = sizeof(physmem); ++ ++ static int mib[2] = { CTL_HW, HW_PHYSMEM }; ++ if (sysctl(mib, 2, &physmem, &len, NULL, 0) == -1) ++ return 0.0; ++ ++ return (double)physmem; ++ ++ } ++ + #elif defined(__MACH__) + #include + #include