better cflags
Michael R. Crusoe
4 years ago
| 47 | 47 | # -I/usr/include/mysql -DMYSQL_DB |
| 48 | 48 | # -DSUPERFAMNUM -DSFCHAR="'|'" |
| 49 | 49 | |
| 50 | diff --git a/make/Makefile.linux b/make/Makefile.linux | |
| 51 | index 7d9e7a8..4755e3f 100644 | |
| 52 | --- a/make/Makefile.linux | |
| 53 | +++ b/make/Makefile.linux | |
| 50 | --- fasta3.orig/make/Makefile.linux | |
| 51 | +++ fasta3/make/Makefile.linux | |
| 54 | 52 | @@ -12,7 +12,7 @@ |
| 55 | 53 | |
| 56 | 54 | SHELL=/bin/bash |
| 60 | 58 | LIB_DB= |
| 61 | 59 | |
| 62 | 60 | #CC= gcc -pg -g -O -msse2 -ffast-math |
| 63 | @@ -26,7 +26,7 @@ LIB_DB= | |
| 61 | @@ -26,7 +26,7 @@ | |
| 64 | 62 | |
| 65 | 63 | # standard options |
| 66 | 64 | |
| 69 | 67 | # -I/usr/include/mysql -DMYSQL_DB |
| 70 | 68 | # -DSUPERFAMNUM -DSFCHAR="'|'" |
| 71 | 69 | |
| 72 | diff --git a/make/Makefile.linux32 b/make/Makefile.linux32 | |
| 73 | index 6d4127f..7584b38 100644 | |
| 74 | --- a/make/Makefile.linux32 | |
| 75 | +++ b/make/Makefile.linux32 | |
| 76 | @@ -16,7 +16,7 @@ SHELL=/bin/bash | |
| 70 | --- fasta3.orig/make/Makefile.linux32 | |
| 71 | +++ fasta3/make/Makefile.linux32 | |
| 72 | @@ -16,7 +16,7 @@ | |
| 77 | 73 | #LIB_DB= |
| 78 | 74 | |
| 79 | 75 | #CC=gcc -Wall -pedantic -ansi -g -O |
| 82 | 78 | LIB_DB=-lz |
| 83 | 79 | |
| 84 | 80 | # EBI uses the following with pgcc, -O3 does not work: |
| 85 | @@ -25,7 +25,7 @@ LIB_DB=-lz | |
| 81 | @@ -25,7 +25,7 @@ | |
| 86 | 82 | # this file works for x86 LINUX |
| 87 | 83 | |
| 88 | 84 | # standard options |
| 91 | 87 | # -DSFCHAR="'|'" -dSUPERFAMNUM |
| 92 | 88 | |
| 93 | 89 | # -I/usr/local/include/mysql -DMYSQL_DB |
| 94 | diff --git a/make/Makefile.linux32_sse2 b/make/Makefile.linux32_sse2 | |
| 95 | index 6c2b081..f37956e 100644 | |
| 96 | --- a/make/Makefile.linux32_sse2 | |
| 97 | +++ b/make/Makefile.linux32_sse2 | |
| 90 | --- fasta3.orig/make/Makefile.linux32_sse2 | |
| 91 | +++ fasta3/make/Makefile.linux32_sse2 | |
| 98 | 92 | @@ -12,7 +12,7 @@ |
| 99 | 93 | |
| 100 | 94 | SHELL=/bin/bash |
| 104 | 98 | LIB_DB= |
| 105 | 99 | #CC = gcc -g -DDEBUG -msse2 |
| 106 | 100 | |
| 107 | @@ -28,7 +28,7 @@ LIB_DB= | |
| 101 | @@ -28,7 +28,7 @@ | |
| 108 | 102 | |
| 109 | 103 | # standard options |
| 110 | 104 | |
| 113 | 107 | |
| 114 | 108 | # -DSUPERFAMNUM -DSFCHAR="'|'" |
| 115 | 109 | |
| 116 | diff --git a/make/Makefile.linux64 b/make/Makefile.linux64 | |
| 117 | index 7d9e7a8..4755e3f 100644 | |
| 118 | --- a/make/Makefile.linux64 | |
| 119 | +++ b/make/Makefile.linux64 | |
| 110 | --- fasta3.orig/make/Makefile.linux64 | |
| 111 | +++ fasta3/make/Makefile.linux64 | |
| 120 | 112 | @@ -12,7 +12,7 @@ |
| 121 | 113 | |
| 122 | 114 | SHELL=/bin/bash |
| 126 | 118 | LIB_DB= |
| 127 | 119 | |
| 128 | 120 | #CC= gcc -pg -g -O -msse2 -ffast-math |
| 129 | @@ -26,7 +26,7 @@ LIB_DB= | |
| 121 | @@ -26,7 +26,7 @@ | |
| 130 | 122 | |
| 131 | 123 | # standard options |
| 132 | 124 | |
| 135 | 127 | # -I/usr/include/mysql -DMYSQL_DB |
| 136 | 128 | # -DSUPERFAMNUM -DSFCHAR="'|'" |
| 137 | 129 | |
| 130 | @@ -38,13 +38,13 @@ | |
| 131 | # for mySQL databases | |
| 132 | # LIB_M = -L/usr/lib64/mysql -lmysqlclient -lm | |
| 133 | ||
| 134 | -HFLAGS= -o | |
| 135 | +HFLAGS= $(LDFLAGS) $(CPPFLAGS) -o | |
| 136 | NFLAGS= -o | |
| 137 | ||
| 138 | # for Linux | |
| 139 | THR_SUBS = pthr_subs2 | |
| 140 | THR_LIBS = -lpthread | |
| 141 | -THR_CC = | |
| 142 | +THR_CC = $(LDFLAGS) $(CPPFLAGS) | |
| 143 | ||
| 144 | BIN = ../bin | |
| 145 | XDIR = /seqprg/bin | |
| 146 | --- fasta3.orig/make/Makefile.pcom_t | |
| 147 | +++ fasta3/make/Makefile.pcom_t | |
| 148 | @@ -171,14 +171,14 @@ | |
| 149 | $(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c pssm_asn_subs.c $(LIB_M) $(LIB_DB) | |
| 150 | ||
| 151 | map_db : map_db.c uascii.h ncbl2_head.h | |
| 152 | - $(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c | |
| 153 | + $(CC) $(LDFLAGS) $(CPPFLAGS) $(CFLAGS) -o $(BIN)/map_db map_db.c | |
| 154 | ||
| 155 | list_db : list_db.c | |
| 156 | - $(CC) $(CFLAGS) -o $(BIN)/list_db list_db.c | |
| 157 | + $(CC) $(LDFLAGS) $(CPPFLAGS) $(CFLAGS) -o $(BIN)/list_db list_db.c | |
| 158 | ||
| 159 | ||
| 160 | lav2ps : lav2plt.o lavplt_ps.o | |
| 161 | - $(CC) -DUNIX -o $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm | |
| 162 | + $(CC) $(LDFLAGS) $(CPPFLAGS) -DUNIX -o $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm | |
| 163 | ||
| 164 | lav2svg : lav2plt.o lavplt_svg.o | |
| 165 | - $(CC) -DUNIX -o $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm | |
| 166 | + $(CC) $(LDFLAGS) $(CPPFLAGS) -DUNIX -o $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm | |