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| author | miwi <miwi@FreeBSD.org> | 2008-01-21 05:56:24 +0800 |
|---|---|---|
| committer | miwi <miwi@FreeBSD.org> | 2008-01-21 05:56:24 +0800 |
| commit | fa74fada7c20e3cfc54010665d98cdd6c88309b5 (patch) | |
| tree | 6139464debc967196f8ea13ec6156f79d91aa1ee /biology | |
| parent | f219bbc302a4dad1b620e3778aba12f7aced01cb (diff) | |
| download | freebsd-ports-gnome-fa74fada7c20e3cfc54010665d98cdd6c88309b5.tar.gz freebsd-ports-gnome-fa74fada7c20e3cfc54010665d98cdd6c88309b5.tar.zst freebsd-ports-gnome-fa74fada7c20e3cfc54010665d98cdd6c88309b5.zip | |
- Update to 2.4.1
PR: 119719
Submitted by: KATO Tsuguru <tkato432@yahoo.com>
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/migrate/Makefile | 7 | ||||
| -rw-r--r-- | biology/migrate/distinfo | 6 | ||||
| -rw-r--r-- | biology/migrate/files/patch-Makefile.in | 40 | ||||
| -rw-r--r-- | biology/migrate/pkg-plist | 8 |
4 files changed, 46 insertions, 15 deletions
diff --git a/biology/migrate/Makefile b/biology/migrate/Makefile index fc2f5228ea2d..0b4f00327de2 100644 --- a/biology/migrate/Makefile +++ b/biology/migrate/Makefile @@ -6,9 +6,10 @@ # PORTNAME= migrate -PORTVERSION= 2.3 +PORTVERSION= 2.4.1 CATEGORIES= biology -MASTER_SITES= http://popgen.csit.fsu.edu/currentversion/ +MASTER_SITES= http://popgen.csit.fsu.edu/%SUBDIR%/ +MASTER_SITE_SUBDIR= currentversion oldversions/${PORTVERSION} DISTNAME= ${PORTNAME}-${PORTVERSION}.src MAINTAINER= ports@FreeBSD.org @@ -42,8 +43,6 @@ ALL_TARGET= all post-patch: @${REINPLACE_CMD} -e \ 's|-lpthread|${PTHREAD_LIBS}|g' ${WRKSRC}/configure - @${REINPLACE_CMD} -e 's|@CFLAGS@||g ; \ - s|make -f|$$(MAKE) -f|g' ${WRKSRC}/Makefile.in do-install: ${INSTALL_PROGRAM} ${WRKSRC}/migrate-n ${PREFIX}/bin diff --git a/biology/migrate/distinfo b/biology/migrate/distinfo index 5530898c1b28..c781822e7123 100644 --- a/biology/migrate/distinfo +++ b/biology/migrate/distinfo @@ -1,3 +1,3 @@ -MD5 (migrate-2.3.src.tar.gz) = 12dbf7bd9d69b6ba87a9ba16b68ff7e5 -SHA256 (migrate-2.3.src.tar.gz) = 3407a92b41f23d036a6ef5fd11f77e6d1aa8ee39fa4f61c65b0f71670b8b8f62 -SIZE (migrate-2.3.src.tar.gz) = 1952466 +MD5 (migrate-2.4.1.src.tar.gz) = cd0e1d2bb551d09b553d833bb90a5df5 +SHA256 (migrate-2.4.1.src.tar.gz) = 09cb370f6911794d94b721e0f2a1a26c5f3bde5b2e55256f52ad57e9a0c0cdee +SIZE (migrate-2.4.1.src.tar.gz) = 1950793 diff --git a/biology/migrate/files/patch-Makefile.in b/biology/migrate/files/patch-Makefile.in new file mode 100644 index 000000000000..deccc333af92 --- /dev/null +++ b/biology/migrate/files/patch-Makefile.in @@ -0,0 +1,40 @@ +--- Makefile.in.orig Thu Jan 10 10:33:23 2008 ++++ Makefile.in Sun Jan 13 04:43:42 2008 +@@ -56,11 +56,11 @@ + # machines or ./configure --enable-altivec on PowerPC architectures, this will then set the option + # correctly + HARDWARECFLAGS = @HARDWARECFLAGS@ +-COMMONFLAGS = $(ARCH) -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP $(CFLAGS_MT) $(HARDWARECFLAGS) ++COMMONFLAGS = -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP $(CFLAGS_MT) $(HARDWARECFLAGS) + # + # combine the common flags with the version number and subversion number + COMMONVFLAGS = $(COMMONFLAGS) -DMIGRATESUBVERSION=\"\\\"$(MIGRATESUBVERSION)\\\"\" +-CFLAGS = @CFLAGS@ $(COMMONVFLAGS) -DMIGRATEVERSION=\"\\\"$(MIGRATEVERSION)\\\"\" ++CFLAGS = $(COMMONVFLAGS) -DMIGRATEVERSION=\"\\\"$(MIGRATEVERSION)\\\"\" + # IBM xlc compiler + # CC = xlc + # CFLAGS_XLC = -O3 -Q -qunroll -qalloca -qhot -qipa -qthreaded +@@ -151,8 +151,8 @@ + @echo "----------------------------------------------------" + $(MAKE) all + +-all:: haru +- $(MAKE) $(NAME) "CFLAGS = $(CFLAGS) $(PRETTYCFLAGS)" "LIBS = $(PDFLIB) $(LIBS)" "LDFLAGS = $(LDFLAGS) -fexceptions" ++all:: ++ $(MAKE) $(NAME) "CFLAGS = $(CFLAGS)" "LIBS = $(LIBS)" "LDFLAGS = $(LDFLAGS) -fexceptions" + + debug:: + $(MAKE) $(NAME) "CFLAGS = $(DEBUGCFLAGS)" +@@ -274,10 +274,10 @@ + -/bin/chmod +x $(CONFIGUREEXEC) + + haru:: +- (cd ./haru ; make -f makefile.osx "CC=$(CC)" "CPP=$(CC)" "ARCH=$(ARCH)") ++ (cd ./haru ; $(MAKE) -f makefile.osx "CC=$(CC)" "CPP=$(CC)" "ARCH=") + + haru-clean:: +- (cd ./haru ; make -f makefile.osx clean) ++ (cd ./haru ; $(MAKE) -f makefile.osx clean) + + distrib:: + $(MAKE) srcdistrib; diff --git a/biology/migrate/pkg-plist b/biology/migrate/pkg-plist index 2d4ed78b2f2d..7f737002f50c 100644 --- a/biology/migrate/pkg-plist +++ b/biology/migrate/pkg-plist @@ -9,20 +9,12 @@ bin/migrate-n %%PORTDOCS%%%%DOCSDIR%%/graphics/packet.gif %%PORTDOCS%%%%DOCSDIR%%/migrate.html %%PORTEXAMPLES%%%%EXAMPLESDIR%%/README -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bayesfile -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.benchmark %%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.ep %%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.msat %%PORTEXAMPLES%%%%EXAMPLESDIR%%/infile.seq -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-bayes %%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-bayes-saved %%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile-ml-saved -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/outfile.pdf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.benchmark -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.ep -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.msat -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.seq %%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.testbayes %%PORTEXAMPLES%%%%EXAMPLESDIR%%/parmfile.testml %%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%% |