DELTA 535347 0 27 SVN  i3ZvtENDREP DELTA SVN`b``# $FreeBSD$ PORTNAME= vt DISTVERSION= 0.57721 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Discovers short variants from Next Generation Sequencing data LICENSE= MIT LIB_DEPENDS= libhts.so:biology/htslib \ libsvm.so:science/libsvm \ libdeflate.so:archivers/libdeflate \ libcurl.so:ftp/curl USES= gmake ssl USE_GITHUB= yes GH_ACCOUNT= atks PLIST_FILES= bin/vt do-install: ${INSTALL_PROGRAM} ${WRKSRC}/vt ${STAGEDIR}${PREFIX}/bin .include ENDREP DELTA SVN+-++TIMESTAMP = 1591286057 SHA256 (atks-vt-0.57721_GH0.tar.gz) = 8f06d464ec5458539cfa30f81a034f47fe7f801146fe8ca80c14a3816b704e17 SIZE (atks-vt-0.57721_GH0.tar.gz) = 20925247 ENDREP DELTA SVNK.KKx^T[o0~Q )$-SPLT@NQpT B]sPiڃ>>7Aӌ7E4Sf1 j- mB)]3I <8jBKw~u Zl7A+|8*g%Mof E)96+NLOGKg{TB'J l=gyNlpg%1<'IHbFn2ط#(WX]_sHή{NEY@xWwC6uv`㏆ѵÂqNq- ѵ(<7m:qz$Uk f1 s= $Jc| 6"ɼ ŪK0W2uNS,C&^*[!# µ;MEM T`l1V2GYm*j%FV\Bt:p)- GŌåc7X &;E# ^"P [׌I4ͨjyuAc aDUŖRXe [V ꨲqDWc9MꕼBR^ߑXrU|G |qY2pE&W^N +7ߎ+bo[IlS#ToA|}ENDREP DELTA SVNBDBB--- lib/Rmath/Make.inc.orig 2020-06-04 16:21:07 UTC +++ lib/Rmath/Make.inc @@ -3,21 +3,21 @@ OS = $(shell uname) ARCH = $(shell uname -m) -FC = gfortran -FFLAGS-add += -O3 +FC ?= gfortran +# FFLAGS-add += -O3 -USEGCC = 1 -USECLANG = 0 +USEGCC = 0 +USECLANG = 1 -CFLAGS-add += -Wall -O3 +# CFLAGS-add += -Wall -O3 ifeq ($(USECLANG),1) USEGCC = 0 -CC = clang +CC ?= clang endif ifeq ($(USEGCC),1) -CC = gcc +CC ?= gcc endif AR = ar ENDREP DELTA SVN[][[--- lib/pcre2/Makefile.orig 2020-06-04 16:13:50 UTC +++ lib/pcre2/Makefile @@ -28,7 +28,7 @@ TOOLSRC = $(SOURCES:=.c) TOOLOBJ = $(TOOLSRC:.c=.o) .c.o : - gcc -g -O3 -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o $@ -c $*.c + ${CC} ${CFLAGS} -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o $@ -c $*.c libpcre2.a: $(TOOLOBJ) @-rm -f $@ ENDREP DELTA SVN --- svm_predict.h.orig 2020-06-04 16:33:17 UTC +++ svm_predict.h @@ -25,8 +25,8 @@ #define SVM_PREDICT_H #include "program.h" -#include "libsvm/svm.h" +#include void svm_predict(int argc, char ** argv); -#endif \ No newline at end of file +#endif ENDREP DELTA SVN--- svm_train.h.orig 2020-06-04 16:32:44 UTC +++ svm_train.h @@ -25,9 +25,9 @@ #define SVM_TRAIN_H #include "program.h" -#include "libsvm/svm.h" +#include #include "Rmath/Rmath.h" void svm_train(int argc, char ** argv); -#endif \ No newline at end of file +#endif ENDREP DELTA SVN vt is a variant tool set that discovers short variants from Next Generation Sequencing data. 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