From 161e29f6d36d13b0fe53ab87a6ed8c8eb95497cc Mon Sep 17 00:00:00 2001 From: Kuoi Date: Wed, 12 Apr 2023 17:53:37 +0800 Subject: [PATCH] fix: makefile and fortran code except staden bap --- src/Misc/makefile-alpha | 2 +- src/abi/makefile-alpha | 4 +- src/alf/makefile-alpha | 4 +- src/bap/makefile-alpha | 63 +++++++++++++++-------------- src/bap/osp-bits/makefile-alpha | 2 +- src/convert/makefile-alpha | 6 +-- src/cop/makefile-alpha | 6 +-- src/expGetSeq/makefile-alpha | 4 +- src/frog/makefile-alpha | 4 +- src/getMCH/makefile-alpha | 4 +- src/indexseqlibs/makefile-alpha | 4 +- src/newted/Graph.c | 1 - src/newted/Graph.h | 1 - src/newted/GraphP.h | 1 - src/newted/makefile-alpha | 6 +-- src/scf/makefile-alpha | 4 +- src/staden/makefile-alpha | 50 ++++++++++++----------- src/ted/Graph.c | 1 - src/ted/Graph.h | 35 +++++++--------- src/ted/GraphP.h | 1 - src/ted/makefile-alpha | 11 ++--- src/update_subclones/makefile-alpha | 6 +-- src/vepe/makefile-alpha | 10 ++--- 23 files changed, 114 insertions(+), 116 deletions(-) diff --git a/src/Misc/makefile-alpha b/src/Misc/makefile-alpha index 7b8cbdb..aeaee45 100644 --- a/src/Misc/makefile-alpha +++ b/src/Misc/makefile-alpha @@ -16,7 +16,7 @@ INCLUDES = -I$(SRC) # Alpha Version # CC = cc -CFLAGS = -g -std1 -ieee_with_inexact $(INCLUDES) +CFLAGS = -g $(INCLUDES) ARFLAGS = rv # diff --git a/src/abi/makefile-alpha b/src/abi/makefile-alpha index f200d15..2310ebc 100644 --- a/src/abi/makefile-alpha +++ b/src/abi/makefile-alpha @@ -16,9 +16,9 @@ SRC = . # Alpha # CC = cc -CFLAGS = -g -std1 -ieee_with_inexact -I$(SRC)/../ted +CFLAGS = -g -I$(SRC)/../ted LD = cc -LDFLAGS = -g -non_shared +LDFLAGS = -g # # Make the programs diff --git a/src/alf/makefile-alpha b/src/alf/makefile-alpha index 7df578e..d7012d8 100644 --- a/src/alf/makefile-alpha +++ b/src/alf/makefile-alpha @@ -16,9 +16,9 @@ SRC = . # Alpha # CC = cc -CFLAGS = -g -std1 -ieee_with_inexact -I$(SRC)/../ted +CFLAGS = -g -I$(SRC)/../ted LD = cc -LDFLAGS = -g -non_shared +LDFLAGS = -g # diff --git a/src/bap/makefile-alpha b/src/bap/makefile-alpha index 7cf135b..c8a3b25 100644 --- a/src/bap/makefile-alpha +++ b/src/bap/makefile-alpha @@ -26,13 +26,13 @@ PROGS= $(NPROGS) $(LPROGS) $(XPROGS) # SRC = . STADENSRC=$(SRC)/../staden -STADENBIN=$(STADENSRC)/alpha-binaries +STADENBIN=$(STADENSRC) TEDSRC=$(SRC)/../ted -TEDBIN=$(STADENBIN) +TEDBIN=$(TEDSRC) OSPSRC=$(SRC)/osp-bits -OSPBIN=$(OSPSRC)/alpha-binaries +OSPBIN=$(OSPSRC) MISCSRC=$(SRC)/../Misc -MISCBIN=$(MISCSRC)/alpha-binaries +MISCBIN=$(MISCSRC) # Use the ted sources compiled for staden executables INCLUDES= -I$(SRC) -I$(STADENSRC) -I$(TEDSRC) -I$(OSPSRC) -I$(MISCSRC) @@ -41,18 +41,19 @@ INCLUDES= -I$(SRC) -I$(STADENSRC) -I$(TEDSRC) -I$(OSPSRC) -I$(MISCSRC) # Compilers and flags # CC= cc -CFLAGS= -g -std1 -ieee_with_inexact $(INCLUDES) -F77= f77 +CFLAGS= -g $(INCLUDES) +F77= gfortran FFLAGS= -g -C -FLIBS= -lfor -lutil -lUfor -lots -lFutil -lm -lfor -lutil -lUfor -lots -lFutil -ldnet_stub +#FLIBS= -lfor -lUfor -lots -lFutil +FLIBS = -lm -lutil XLIBS= -lXaw -lXt -lXmu -lXext -lX11 LFLAGS= $(FLIBS) XLFLAGS= $(XLIBS) $(FLIBS) -LD = f77 +LD = gfortran XLD = cc -LDFLAGS = -g -non_shared +LDFLAGS = -g # # Avoid compilation of objects in remote directories @@ -540,28 +541,30 @@ splitp3: $(SPLITP3OBJS) # avoid filling up the (small on this machine) /tmp directory # with compiler debugging information. # +#%.a: $(SRC)/%.f +# BINDIR=`pwd`; \ +# cd $(SRC); \ +# SRCDIR=`pwd`; \ +# TMPDIR=/tmp/staden$$$$; \ +# if test ! -d $$TMPDIR; \ +# then mkdir $$TMPDIR; \ +# fi; \ +# cd $$TMPDIR; \ +# rm -f *.f *.o; \ +# fsplit $$SRCDIR/`expr $< : '.*/\(.*\)' \| $<`; \ +# $(F77) $(FFLAGS) -c *.f; \ +# rm *.f; \ +# rm -f $$BINDIR/$@; \ +# ar rcv $$BINDIR/$@ *.o; \ +# ranlib $$BINDIR/$@; \ +# rm *.o; \ +# cd $$BINDIR; \ +# rm -r $$TMPDIR + + %.a: $(SRC)/%.f - BINDIR=`pwd`; \ - cd $(SRC); \ - SRCDIR=`pwd`; \ - TMPDIR=/tmp/staden$$$$; \ - if test ! -d $$TMPDIR; \ - then mkdir $$TMPDIR; \ - fi; \ - cd $$TMPDIR; \ - rm -f *.f *.o; \ - fsplit $$SRCDIR/`expr $< : '.*/\(.*\)' \| $<`; \ - $(F77) $(FFLAGS) -c *.f; \ - rm *.f; \ - rm -f $$BINDIR/$@; \ - ar rcv $$BINDIR/$@ *.o; \ - ranlib $$BINDIR/$@; \ - rm *.o; \ - cd $$BINDIR; \ - rm -r $$TMPDIR - - - + $(F77) $(FFLAGS) -c *.f; + ar rcv $$BINDIR/$@ *.o; diff --git a/src/bap/osp-bits/makefile-alpha b/src/bap/osp-bits/makefile-alpha index a3ccd57..a336b29 100644 --- a/src/bap/osp-bits/makefile-alpha +++ b/src/bap/osp-bits/makefile-alpha @@ -23,7 +23,7 @@ VERSION = SUBVERSION # Compiler - debug on # CC= cc -CFLAGS= -g -non_shared -std1 -ieee_with_inexact -D$(VERSION) +CFLAGS= -g -D$(VERSION) # diff --git a/src/convert/makefile-alpha b/src/convert/makefile-alpha index 30cf237..0a49ee8 100644 --- a/src/convert/makefile-alpha +++ b/src/convert/makefile-alpha @@ -4,12 +4,12 @@ SRC = . MISCSRC=$(SRC)/../Misc -MISCBIN=$(MISCSRC)/alpha-binaries +MISCBIN=$(MISCSRC) CC = cc -CFLAGS = -g -std1 -ieee_with_inexact -I$(MISCSRC) +CFLAGS = -g -I$(MISCSRC) LD = cc -LDFLAGS = -g -non_shared +LDFLAGS = -g LIBS = $(MISCBIN)/misc.a # diff --git a/src/cop/makefile-alpha b/src/cop/makefile-alpha index 26c2255..cc038fc 100644 --- a/src/cop/makefile-alpha +++ b/src/cop/makefile-alpha @@ -13,7 +13,7 @@ PROGS = cop cop-bap SRC = . TEDSRC = $(SRC)/../ted MISCSRC = $(SRC)/../Misc -MISCBIN = $(MISCSRC)/alpha-binaries +MISCBIN = $(MISCSRC) CONVERTSRC = $(SRC)/../convert INCLUDES = -I$(SRC) -I$(TEDSRC) -I$(MISCSRC) -I$(CONVERTSRC) @@ -21,9 +21,9 @@ INCLUDES = -I$(SRC) -I$(TEDSRC) -I$(MISCSRC) -I$(CONVERTSRC) # Alpha # CC = cc -CFLAGS = -g -std1 -ieee_with_inexact $(INCLUDES) +CFLAGS = -g $(INCLUDES) LD = cc -LDFLAGS = -g -non_shared +LDFLAGS = -g LIBFLAGS = # diff --git a/src/expGetSeq/makefile-alpha b/src/expGetSeq/makefile-alpha index af3252c..e1fb49b 100644 --- a/src/expGetSeq/makefile-alpha +++ b/src/expGetSeq/makefile-alpha @@ -42,9 +42,9 @@ INCLUDES = -I/usr/include/mit -I$(SRC) -I$(TEDSRC) # Compiler - debug on # CC= cc -CFLAGS= -g -ieee_with_inexact $(SWITCHES) $(INCLUDES) +CFLAGS= -g $(SWITCHES) $(INCLUDES) LD= cc -LDFLAGS= -g -non_shared +LDFLAGS= -g # diff --git a/src/frog/makefile-alpha b/src/frog/makefile-alpha index 3d8bef9..4133818 100644 --- a/src/frog/makefile-alpha +++ b/src/frog/makefile-alpha @@ -1,7 +1,7 @@ CC = cc -CFLAGS = -g -std1 -ieee_with_inexact +CFLAGS = -g LD = cc -LDFLAGS = -g -non_shared +LDFLAGS = -g LIBFLAGS = SRC = . diff --git a/src/getMCH/makefile-alpha b/src/getMCH/makefile-alpha index c8dcb14..085ab8c 100644 --- a/src/getMCH/makefile-alpha +++ b/src/getMCH/makefile-alpha @@ -35,9 +35,9 @@ INCLUDES = -I$(SRC) -I$(TEDSRC) # Compiler - debug on # CC= cc -CFLAGS= -g -std1 -ieee_with_inexact $(SWITCHES) $(INCLUDES) +CFLAGS= -g $(SWITCHES) $(INCLUDES) LD= cc -LDFLAGS= -g -non_shared +LDFLAGS= -g LIBFLAGS = diff --git a/src/indexseqlibs/makefile-alpha b/src/indexseqlibs/makefile-alpha index f150f63..86d0689 100644 --- a/src/indexseqlibs/makefile-alpha +++ b/src/indexseqlibs/makefile-alpha @@ -44,9 +44,9 @@ SRC = . # Alpha # CC = cc -CFLAGS = -g -std1 -ieee_with_inexact +CFLAGS = -g LD = cc -LDFLAGS = -g -non_shared +LDFLAGS = -g # # Shared objects diff --git a/src/newted/Graph.c b/src/newted/Graph.c index 0e69bc7..2bf4cac 100644 --- a/src/newted/Graph.c +++ b/src/newted/Graph.c @@ -1,4 +1,3 @@ -#include /* $XConsortium: Graph.c,v 1.2 88/10/25 17:40:25 swick Exp $ */ /* Copyright Massachusetts Institute of Technology 1987, 1988 */ diff --git a/src/newted/Graph.h b/src/newted/Graph.h index 99fe869..c4285c5 100644 --- a/src/newted/Graph.h +++ b/src/newted/Graph.h @@ -1,4 +1,3 @@ -#include /* $XConsortium: Graph.h,v 1.2 88/10/25 17:22:09 swick Exp $ */ /* Copyright Massachusetts Institute of Technology 1987, 1988 */ diff --git a/src/newted/GraphP.h b/src/newted/GraphP.h index 07c673f..62ff7f2 100644 --- a/src/newted/GraphP.h +++ b/src/newted/GraphP.h @@ -1,4 +1,3 @@ -#include /* $XConsortium: GraphP.h,v 1.2 88/10/25 17:37:59 swick Exp $ */ /* Copyright Massachusetts Institute of Technology 1987, 1988 */ diff --git a/src/newted/makefile-alpha b/src/newted/makefile-alpha index e6707b2..faab788 100644 --- a/src/newted/makefile-alpha +++ b/src/newted/makefile-alpha @@ -42,11 +42,11 @@ SRC = . # CC= cc INCLUDES = -I$(SRC) -CFLAGS= -g -std1 -ieee_with_inexact $(SWITCHES) $(INCLUDES) -LIBS= -lXaw -lXt -lXmu -lXext -lX11 -ldnet_stub +CFLAGS= -g $(SWITCHES) $(INCLUDES) +LIBS= -lXaw -lXt -lXmu -lXext -lX11 # LD= cc -LDFLAGS= -g -non_shared +LDFLAGS= -g # # Object files diff --git a/src/scf/makefile-alpha b/src/scf/makefile-alpha index 331c209..627ce01 100644 --- a/src/scf/makefile-alpha +++ b/src/scf/makefile-alpha @@ -22,9 +22,9 @@ TEDSRC = $(SRC)/../ted # alpha # CC= cc -CFLAGS= -g -std1 -ieee_with_inexact $(SWITCHES) -I$(TEDSRC) +CFLAGS= -g $(SWITCHES) -I$(TEDSRC) LD= cc -LDFLAGS= -g -non_shared +LDFLAGS= -g LIBFLAGS = %.o : $(SRC)/%.c diff --git a/src/staden/makefile-alpha b/src/staden/makefile-alpha index f9b9043..89af7fd 100644 --- a/src/staden/makefile-alpha +++ b/src/staden/makefile-alpha @@ -19,25 +19,25 @@ PROGS= $(NPROGS) $(LPROGS) $(XPROGS) SRC=. TEDSRC=$(SRC)/../ted MISCSRC=$(SRC)/../Misc -MISCBIN=$(MISCSRC)/alpha-binaries +MISCBIN=$(MISCSRC) INCLUDES= -I$(SRC) -I$(TEDSRC) -I$(MISCSRC) # # Compilers and flags # CC= cc -CFLAGS= -g -std1 -ieee_with_inexact $(INCLUDES) -F77= f77 -FFLAGS= -g -C +CFLAGS= -g $(INCLUDES) +F77= gfortran +FFLAGS= -g -fdec -C FLIBS= -lfor -lutil -lUfor -lots -lFutil -lm -lfor -lutil -lUfor -lots -lFutil XLIBS= -lXaw -lXt -lXmu -lXext -lX11 -ldnet_stub LFLAGS= $(FLIBS) XLFLAGS= $(FLIBS) $(XLIBS) -LD = f77 +LD = gfortran CLD = cc -LDFLAGS = -g -non_shared # Comment out for faster linking when debugging +LDFLAGS = -g # Comment out for faster linking when debugging @@ -549,25 +549,29 @@ vep: $(VEPOBJS) # avoid filling up the (small on this machine) /tmp directory # with compiler debugging information. # +#%.a: $(SRC)/%.f +# BINDIR=`pwd`; \ +# cd $(SRC); \ +# SRCDIR=`pwd`; \ +# TMPDIR=/tmp/staden$$$$; \ +# if test ! -d $$TMPDIR; \ +# then mkdir $$TMPDIR; \ +# fi; \ +# cd $$TMPDIR; \ +# rm -f *.f *.o; \ +# fsplit $$SRCDIR/`expr $< : '.*/\(.*\)' \| $<`; \ +# $(F77) $(FFLAGS) -c *.f; \ +# rm *.f; \ +# rm -f $$BINDIR/$@; \ +# ar rcv $$BINDIR/$@ *.o; \ +# ranlib $$BINDIR/$@; \ +# rm *.o; \ +# cd $$BINDIR; \ +# rm -r $$TMPDIR + %.a: $(SRC)/%.f - BINDIR=`pwd`; \ - cd $(SRC); \ - SRCDIR=`pwd`; \ - TMPDIR=/tmp/staden$$$$; \ - if test ! -d $$TMPDIR; \ - then mkdir $$TMPDIR; \ - fi; \ - cd $$TMPDIR; \ - rm -f *.f *.o; \ - fsplit $$SRCDIR/`expr $< : '.*/\(.*\)' \| $<`; \ $(F77) $(FFLAGS) -c *.f; \ - rm *.f; \ - rm -f $$BINDIR/$@; \ - ar rcv $$BINDIR/$@ *.o; \ - ranlib $$BINDIR/$@; \ - rm *.o; \ - cd $$BINDIR; \ - rm -r $$TMPDIR + ar rcv *.o #.f.a: # $(F77) $(FFLAGS) -c $< diff --git a/src/ted/Graph.c b/src/ted/Graph.c index 0e69bc7..2bf4cac 100644 --- a/src/ted/Graph.c +++ b/src/ted/Graph.c @@ -1,4 +1,3 @@ -#include /* $XConsortium: Graph.c,v 1.2 88/10/25 17:40:25 swick Exp $ */ /* Copyright Massachusetts Institute of Technology 1987, 1988 */ diff --git a/src/ted/Graph.h b/src/ted/Graph.h index 99fe869..0b36bd0 100644 --- a/src/ted/Graph.h +++ b/src/ted/Graph.h @@ -1,5 +1,3 @@ -#include - /* $XConsortium: Graph.h,v 1.2 88/10/25 17:22:09 swick Exp $ */ /* Copyright Massachusetts Institute of Technology 1987, 1988 */ @@ -44,38 +42,35 @@ /* define any special resource names here that are not in */ -#define XtNgraphResource "graphResource" -#define XtCGraphResource "GraphResource" - -#define XtNdimBackground "dimBackground" -#define XtNexposeCallback "exposeCallback" -#define XtNgraphColour1 "graphColour1" -#define XtNgraphColour2 "graphColour2" -#define XtNgraphColour3 "graphColour3" -#define XtNgraphColour4 "graphColour4" -#define XtNresizeCallback "resizeCallback" +#define XtNgraphResource "graphResource" +#define XtCGraphResource "GraphResource" +#define XtNdimBackground "dimBackground" +#define XtNexposeCallback "exposeCallback" +#define XtNgraphColour1 "graphColour1" +#define XtNgraphColour2 "graphColour2" +#define XtNgraphColour3 "graphColour3" +#define XtNgraphColour4 "graphColour4" +#define XtNresizeCallback "resizeCallback" /* declare specific GraphWidget class and instance datatypes */ -typedef struct _GraphClassRec *GraphWidgetClass; -typedef struct _GraphRec *GraphWidget; - +typedef struct _GraphClassRec *GraphWidgetClass; +typedef struct _GraphRec *GraphWidget; /* declare the class constant */ extern WidgetClass graphWidgetClass; - /* ---- Exported procedures ---- */ extern Pixel GraphColour1(Widget w); extern Pixel GraphColour2(Widget w); extern Pixel GraphColour3(Widget w); extern Pixel GraphColour4(Widget w); -extern GC GraphGC1(Widget w); -extern GC GraphGC2(Widget w); -extern GC GraphGC3(Widget w); -extern GC GraphGC4(Widget w); +extern GC GraphGC1(Widget w); +extern GC GraphGC2(Widget w); +extern GC GraphGC3(Widget w); +extern GC GraphGC4(Widget w); #endif /* _Graph_h */ diff --git a/src/ted/GraphP.h b/src/ted/GraphP.h index 07c673f..62ff7f2 100644 --- a/src/ted/GraphP.h +++ b/src/ted/GraphP.h @@ -1,4 +1,3 @@ -#include /* $XConsortium: GraphP.h,v 1.2 88/10/25 17:37:59 swick Exp $ */ /* Copyright Massachusetts Institute of Technology 1987, 1988 */ diff --git a/src/ted/makefile-alpha b/src/ted/makefile-alpha index e571a12..dbcc3c2 100644 --- a/src/ted/makefile-alpha +++ b/src/ted/makefile-alpha @@ -33,13 +33,14 @@ SRC = . # # Compiler - debug on # -CC= cc +CC= gfortran INCLUDES = -I$(SRC) -CFLAGS= -g -std1 -ieee_with_inexact $(SWITCHES) $(INCLUDES) -LIBS= -lXaw -lXt -lXmu -lXext -lX11 -ldnet_stub +CFLAGS= -g $(SWITCHES) $(INCLUDES) +LIBS= -lXaw -lXt -lXmu -lXext -lX11 +#-ldnet_stub # -LD= cc -LDFLAGS= -g -non_shared +LD= gfortran +LDFLAGS= -g # # Object files diff --git a/src/update_subclones/makefile-alpha b/src/update_subclones/makefile-alpha index 7f1782d..a24c246 100644 --- a/src/update_subclones/makefile-alpha +++ b/src/update_subclones/makefile-alpha @@ -12,16 +12,16 @@ PROGS = update_subclones # SRC = . MISCSRC = $(SRC)/../Misc -MISCBIN = $(MISCSRC)/alpha-binaries +MISCBIN = $(MISCSRC) INCLUDES = -I$(SRC) -I$(MISCSRC) # # Alpha # CC = cc -CFLAGS = -g -std1 -ieee_with_inexact $(INCLUDES) +CFLAGS = -g $(INCLUDES) LD = cc -LDFLAGS = -g -non_shared +LDFLAGS = -g # # Here they are diff --git a/src/vepe/makefile-alpha b/src/vepe/makefile-alpha index ff9fb35..f06a9f8 100644 --- a/src/vepe/makefile-alpha +++ b/src/vepe/makefile-alpha @@ -21,7 +21,7 @@ all: $(PROGS) SRC = . #STADENSRC=/nfs/rutland/home3/pubseq/inhouse/share/src/staden STADENSRC=$(SRC)/../staden -STADENBIN=$(STADENSRC)/alpha-binaries +STADENBIN=$(STADENSRC) # Use the ted sources compiled for staden executables INCLUDES= -I$(STADENSRC) @@ -31,11 +31,11 @@ INCLUDES= -I$(STADENSRC) # # debug on CC= cc -CFLAGS= -g -std1 -ieee_with_inexact $(INCLUDES) -F77= f77 +CFLAGS= -g $(INCLUDES) +F77= gfortran FFLAGS= -g -LD= f77 -LDFLAGS= -g -non_shared +LD= gfortran +LDFLAGS= -g FLIBS= -lfor -lutil -lUfor -lots -lFutil -lm -lfor -lutil -lUfor -lots -lFutil XLIBS= -lXaw -lXt -lXmu -lXext -lX11