1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
|
From: Michael R. Crusoe <crusoe@debian.org>
Subject: Don't stomp on Debian's CFLAGS
Forwarded: https://github.com/EddyRivasLab/hmmer/pull/216
--- hmmer.orig/configure.ac
+++ hmmer/configure.ac
@@ -78,12 +78,6 @@
AC_INIT(HMMER, 3.3.2, sean@eddylab.org, hmmer)
AC_MSG_NOTICE([Configuring HMMER3 for your system.])
-# remember if the user is overriding CFLAGS
-esl_cflags_env_set=no
-if test x"$CFLAGS" != x; then
- esl_cflags_env_set=yes
-fi
-
################################################################
# 3. Info on the package
################################################################
@@ -245,21 +239,15 @@
# --enable-gcov, --enable-gprof, and --enable-debugging are mutually exclusive.
#
if test "$enable_gcov" = "yes"; then
- if test "$esl_cflags_env_set" = "yes"; then
- AC_MSG_ERROR([--enable-gcov overrides CFLAGS, so don't set CFLAGS])
- fi
- CFLAGS="-g -Wall -fprofile-arcs -ftest-coverage"
+ CFLAGS="${CLFAGS} -g -Wall -fprofile-arcs -ftest-coverage"
elif test "$enable_gprof" = "yes"; then
- if test "$esl_cflags_env_set" = "yes"; then
- AC_MSG_ERROR([--enable-gprof overrides CFLAGS, so don't set CFLAGS])
- fi
- CFLAGS="-O -g -pg"
+ CFLAGS="${CFLAGS} -O -g -pg"
elif test "$enable_debugging" != "no"; then
if test "$GCC" = "yes"; then
- CFLAGS="-g -Wall"
+ CFLAGS="${CFLAGS} -g -Wall"
fi
-elif test "$esl_cflags_env_set" != "yes"; then
- CFLAGS="-O3"
+else
+ CFLAGS="${CFLAGS} -O3"
fi
--- hmmer.orig/easel/Makefile.in
+++ hmmer/easel/Makefile.in
@@ -587,10 +587,10 @@
else DFILE=${srcdir}/esl_$${BASENAME}.c ;\
fi;\
if test ${V} ;\
- then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\
+ then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\
else echo ' ' GEN $@ ;\
fi ;\
- ${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}
+ ${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}
${ALL_EXPERIMENTS}: libeasel.a
@BASENAME=`echo $@ | sed -e 's/_experiment//'| sed -e 's/^esl_//'` ;\
--- hmmer.orig/src/Makefile.in
+++ hmmer/src/Makefile.in
@@ -270,13 +270,13 @@
${AUXPROGOBJS}: ${HDRS} p7_config.h
${PROGS} ${AUXPROGS}: % : %.o libhmmer.a ../${ESLDIR}/libeasel.a
- ${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${DEFS} ${LDFLAGS} ${MYLIBDIRS} -o $@ $@.o ${LIBS}
+ ${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} ${MYLIBDIRS} -o $@ $@.o ${LIBS}
.c.o:
${QUIET_CC}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${DEFS} ${CPPFLAGS} ${MYINCDIRS} -o $@ -c $<
${ITESTS}: % : %.o libhmmer.a ${HDRS} p7_config.h
- ${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${DEFS} ${LDFLAGS} ${MYLIBDIRS} -o $@ $@.o ${LIBS}
+ ${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${DEFS} ${CPPFLAGS} ${LDFLAGS} ${MYLIBDIRS} -o $@ $@.o ${LIBS}
${UTESTS}: libhmmer.a ${HDRS} p7_config.h
@BASENAME=`echo $@ | sed -e 's/_utest//' | sed -e 's/^p7_//'` ;\
|
