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a
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
It was created by gmap configure 2021-12-17, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ ./configure --prefix=/opt/homebrew/Cellar/gmap-gsnap/2021-12-17 --with-simd-level=sse42
## --------- ##
## Platform. ##
## --------- ##
hostname = Alex-MacBook.fibertel.com.ar
uname -m = arm64
uname -r = 21.6.0
uname -s = Darwin
uname -v = Darwin Kernel Version 21.6.0: Mon Aug 22 20:19:52 PDT 2022; root:xnu-8020.140.49~2/RELEASE_ARM64_T6000
/usr/bin/uname -p = arm
/bin/uname -X = unknown
/bin/arch = unknown
/usr/bin/arch -k = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo = Mach kernel version:
Darwin Kernel Version 21.6.0: Mon Aug 22 20:19:52 PDT 2022; root:xnu-8020.140.49~2/RELEASE_ARM64_T6000
Kernel configured for up to 10 processors.
10 processors are physically available.
10 processors are logically available.
Processor type: arm64e (ARM64E)
Processors active: 0 1 2 3 4 5 6 7 8 9
Primary memory available: 64.00 gigabytes
Default processor set: 1033 tasks, 5815 threads, 10 processors
Load average: 6.58, Mach factor: 3.57
/bin/machine = unknown
/usr/bin/oslevel = unknown
/bin/universe = unknown
PATH: /opt/homebrew/Library/Homebrew/shims/mac/super
PATH: /opt/homebrew/opt/xz/bin
PATH: /opt/homebrew/opt/htslib/bin
PATH: /opt/homebrew/opt/samtools/bin
PATH: /usr/bin
PATH: /bin
PATH: /usr/sbin
PATH: /sbin
## ----------- ##
## Core tests. ##
## ----------- ##
configure:2526: checking package version
configure:2528: result: 2021-12-17
configure:2575: checking CFLAGS
configure:2579: result: not set by user so using default -O3 -fomit-frame-pointer
configure:2659: checking build system type
configure:2673: result: arm-apple-darwin21.6.0
configure:2693: checking host system type
configure:2706: result: arm-apple-darwin21.6.0
configure:2726: checking target system type
configure:2739: result: arm-apple-darwin21.6.0
configure:2767: checking for non-Intel CPU
configure:2784: result: no
configure:2838: checking for gcc
configure:2865: result: clang
configure:3094: checking for C compiler version
configure:3103: clang --version >&5
Apple clang version 14.0.0 (clang-1400.0.29.102)
Target: arm64-apple-darwin21.6.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
configure:3114: $? = 0
configure:3103: clang -v >&5
Apple clang version 14.0.0 (clang-1400.0.29.102)
Target: arm64-apple-darwin21.6.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
configure:3114: $? = 0
configure:3103: clang -V >&5
clang: error: unsupported option '-V -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk'
configure:3114: $? = 1
configure:3103: clang -qversion >&5
clang: error: unknown argument '-qversion'; did you mean '--version'?
configure:3114: $? = 1
configure:3134: checking whether the C compiler works
configure:3156: clang -O3 -fomit-frame-pointer conftest.c >&5
configure:3160: $? = 0
configure:3208: result: yes
configure:3211: checking for C compiler default output file name
configure:3213: result: a.out
configure:3219: checking for suffix of executables
configure:3226: clang -o conftest -O3 -fomit-frame-pointer conftest.c >&5
configure:3230: $? = 0
configure:3252: result:
configure:3274: checking whether we are cross compiling
configure:3282: clang -o conftest -O3 -fomit-frame-pointer conftest.c >&5
configure:3286: $? = 0
configure:3293: ./conftest
configure:3297: $? = 0
configure:3312: result: no
configure:3317: checking for suffix of object files
configure:3339: clang -c -O3 -fomit-frame-pointer conftest.c >&5
configure:3343: $? = 0
configure:3364: result: o
configure:3368: checking whether we are using the GNU C compiler
configure:3387: clang -c -O3 -fomit-frame-pointer conftest.c >&5
configure:3387: $? = 0
configure:3396: result: yes
configure:3405: checking whether clang accepts -g
configure:3425: clang -c -g conftest.c >&5
configure:3425: $? = 0
configure:3466: result: yes
configure:3483: checking for clang option to accept ISO C89
configure:3546: clang -c -O3 -fomit-frame-pointer conftest.c >&5
configure:3546: $? = 0
configure:3559: result: none needed
configure:3587: checking for special C compiler options needed for large files
configure:3632: result: no
configure:3638: checking for _FILE_OFFSET_BITS value needed for large files
configure:3663: clang -c -O3 -fomit-frame-pointer conftest.c >&5
configure:3663: $? = 0
configure:3695: result: no
configure:3809: checking for a BSD-compatible install
configure:3877: result: /usr/bin/install -c
configure:3888: checking whether build environment is sane
configure:3943: result: yes
configure:4084: checking for a thread-safe mkdir -p
configure:4123: result: config/install-sh -c -d
configure:4130: checking for gawk
configure:4160: result: no
configure:4130: checking for mawk
configure:4160: result: no
configure:4130: checking for nawk
configure:4160: result: no
configure:4130: checking for awk
configure:4146: found /usr/bin/awk
configure:4157: result: awk
configure:4168: checking whether make sets $(MAKE)
configure:4190: result: yes
configure:4220: checking for style of include used by make
configure:4248: result: GNU
configure:4282: checking whether make supports nested variables
configure:4299: result: yes
configure:4384: checking dependency style of clang
configure:4495: result: gcc3
configure:4512: checking whether to enable maintainer-specific portions of Makefiles
configure:4521: result: no
configure:4577: checking bindir
configure:4608: result: /opt/homebrew/Cellar/gmap-gsnap/2021-12-17/bin
configure:4616: checking for a working version of perl
configure:4648: result: /usr/bin/perl
configure:4707: checking for gcc
configure:4734: result: clang
configure:4963: checking for C compiler version
configure:4972: clang --version >&5
Apple clang version 14.0.0 (clang-1400.0.29.102)
Target: arm64-apple-darwin21.6.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
configure:4983: $? = 0
configure:4972: clang -v >&5
Apple clang version 14.0.0 (clang-1400.0.29.102)
Target: arm64-apple-darwin21.6.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
configure:4983: $? = 0
configure:4972: clang -V >&5
clang: error: unsupported option '-V -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk'
configure:4983: $? = 1
configure:4972: clang -qversion >&5
clang: error: unknown argument '-qversion'; did you mean '--version'?
configure:4983: $? = 1
configure:4987: checking whether we are using the GNU C compiler
configure:5015: result: yes
configure:5024: checking whether clang accepts -g
configure:5085: result: yes
configure:5102: checking for clang option to accept ISO C89
configure:5178: result: none needed
configure:5199: checking whether clang and cc understand -c and -o together
configure:5230: clang -c conftest.c -o conftest2.o >&5
configure:5234: $? = 0
configure:5240: clang -c conftest.c -o conftest2.o >&5
configure:5244: $? = 0
configure:5255: cc -c conftest.c >&5
configure:5259: $? = 0
configure:5267: cc -c conftest.c -o conftest2.o >&5
configure:5271: $? = 0
configure:5277: cc -c conftest.c -o conftest2.o >&5
configure:5281: $? = 0
configure:5299: result: yes
configure:5325: checking for C compiler vendor
configure:5372: clang -c -O3 -fomit-frame-pointer conftest.c >&5
conftest.c:17:9: error: use of undeclared identifier 'thisisanerror'
thisisanerror;
^
1 error generated.
configure:5372: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gmap"
| #define PACKAGE_TARNAME "gmap"
| #define PACKAGE_VERSION "2021-12-17"
| #define PACKAGE_STRING "gmap 2021-12-17"
| #define PACKAGE_BUGREPORT "Thomas Wu <twu@gene.com>"
| #define PACKAGE_URL ""
| #define PACKAGE "gmap"
| #define VERSION "2021-12-17"
| /* end confdefs.h. */
|
| int
| main ()
| {
|
| #if !(defined(__ICC) || defined(__ECC) || defined(__INTEL_COMPILER))
| thisisanerror;
| #endif
|
| ;
| return 0;
| }
configure:5372: clang -c -O3 -fomit-frame-pointer conftest.c >&5
conftest.c:17:9: error: use of undeclared identifier 'thisisanerror'
thisisanerror;
^
1 error generated.
configure:5372: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gmap"
| #define PACKAGE_TARNAME "gmap"
| #define PACKAGE_VERSION "2021-12-17"
| #define PACKAGE_STRING "gmap 2021-12-17"
| #define PACKAGE_BUGREPORT "Thomas Wu <twu@gene.com>"
| #define PACKAGE_URL ""
| #define PACKAGE "gmap"
| #define VERSION "2021-12-17"
| /* end confdefs.h. */
|
| int
| main ()
| {
|
| #if !(defined(__xlc__) || defined(__xlC__) || defined(__IBMC__) || defined(__IBMCPP__))
| thisisanerror;
| #endif
|
| ;
| return 0;
| }
configure:5372: clang -c -O3 -fomit-frame-pointer conftest.c >&5
conftest.c:17:9: error: use of undeclared identifier 'thisisanerror'
thisisanerror;
^
1 error generated.
configure:5372: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gmap"
| #define PACKAGE_TARNAME "gmap"
| #define PACKAGE_VERSION "2021-12-17"
| #define PACKAGE_STRING "gmap 2021-12-17"
| #define PACKAGE_BUGREPORT "Thomas Wu <twu@gene.com>"
| #define PACKAGE_URL ""
| #define PACKAGE "gmap"
| #define VERSION "2021-12-17"
| /* end confdefs.h. */
|
| int
| main ()
| {
|
| #if !(defined(__PATHCC__) || defined(__PATHSCALE__))
| thisisanerror;
| #endif
|
| ;
| return 0;
| }
configure:5372: clang -c -O3 -fomit-frame-pointer conftest.c >&5
configure:5372: $? = 0
configure:5380: result: clang
configure:5387: checking for rint in -lm
configure:5412: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
conftest.c:18:6: warning: incompatible redeclaration of library function 'rint' [-Wincompatible-library-redeclaration]
char rint ();
^
conftest.c:18:6: note: 'rint' is a builtin with type 'double (double)'
1 warning generated.
configure:5412: $? = 0
configure:5421: result: yes
configure:5445: checking for pthreads feature
configure:5802: result: not specified so enabled by default
configure:5968: checking for the pthreads library -lpthreads
configure:6001: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lpthreads -lm >&5
conftest.c:17:41: warning: null passed to a callee that requires a non-null argument [-Wnonnull]
pthread_attr_init(0); pthread_cleanup_push(0, 0);
~^
conftest.c:18:44: warning: null passed to a callee that requires a non-null argument [-Wnonnull]
pthread_create(0,0,0,0); pthread_cleanup_pop(0);
~ ^
conftest.c:18:44: warning: null passed to a callee that requires a non-null argument [-Wnonnull]
pthread_create(0,0,0,0); pthread_cleanup_pop(0);
~ ^
3 warnings generated.
ld: library not found for -lpthreads
clang: error: linker command failed with exit code 1 (use -v to see invocation)
configure:6001: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gmap"
| #define PACKAGE_TARNAME "gmap"
| #define PACKAGE_VERSION "2021-12-17"
| #define PACKAGE_STRING "gmap 2021-12-17"
| #define PACKAGE_BUGREPORT "Thomas Wu <twu@gene.com>"
| #define PACKAGE_URL ""
| #define PACKAGE "gmap"
| #define VERSION "2021-12-17"
| #define HAVE_LIBM 1
| /* end confdefs.h. */
| #include <pthread.h>
| int
| main ()
| {
| pthread_t th; pthread_join(th, 0);
| pthread_attr_init(0); pthread_cleanup_push(0, 0);
| pthread_create(0,0,0,0); pthread_cleanup_pop(0);
| ;
| return 0;
| }
configure:6010: result: no
configure:5913: checking whether pthreads work without any flags
configure:6001: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
conftest.c:17:41: warning: null passed to a callee that requires a non-null argument [-Wnonnull]
pthread_attr_init(0); pthread_cleanup_push(0, 0);
~^
conftest.c:18:44: warning: null passed to a callee that requires a non-null argument [-Wnonnull]
pthread_create(0,0,0,0); pthread_cleanup_pop(0);
~ ^
conftest.c:18:44: warning: null passed to a callee that requires a non-null argument [-Wnonnull]
pthread_create(0,0,0,0); pthread_cleanup_pop(0);
~ ^
3 warnings generated.
configure:6001: $? = 0
configure:6010: result: yes
configure:6029: checking for joinable pthread attribute
configure:6044: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
configure:6044: $? = 0
configure:6050: result: PTHREAD_CREATE_JOINABLE
configure:6060: checking if more special flags are required for pthreads
configure:6067: result: -D_THREAD_SAFE
configure:6079: checking for cc_r
configure:6107: result: clang
configure:6150: checking how to run the C preprocessor
configure:6181: clang -E conftest.c
configure:6181: $? = 0
configure:6195: clang -E conftest.c
conftest.c:13:10: fatal error: 'ac_nonexistent.h' file not found
#include <ac_nonexistent.h>
^~~~~~~~~~~~~~~~~~
1 error generated.
configure:6195: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gmap"
| #define PACKAGE_TARNAME "gmap"
| #define PACKAGE_VERSION "2021-12-17"
| #define PACKAGE_STRING "gmap 2021-12-17"
| #define PACKAGE_BUGREPORT "Thomas Wu <twu@gene.com>"
| #define PACKAGE_URL ""
| #define PACKAGE "gmap"
| #define VERSION "2021-12-17"
| #define HAVE_LIBM 1
| #define HAVE_PTHREAD 1
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:6220: result: clang -E
configure:6240: clang -E conftest.c
configure:6240: $? = 0
configure:6254: clang -E conftest.c
conftest.c:13:10: fatal error: 'ac_nonexistent.h' file not found
#include <ac_nonexistent.h>
^~~~~~~~~~~~~~~~~~
1 error generated.
configure:6254: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gmap"
| #define PACKAGE_TARNAME "gmap"
| #define PACKAGE_VERSION "2021-12-17"
| #define PACKAGE_STRING "gmap 2021-12-17"
| #define PACKAGE_BUGREPORT "Thomas Wu <twu@gene.com>"
| #define PACKAGE_URL ""
| #define PACKAGE "gmap"
| #define VERSION "2021-12-17"
| #define HAVE_LIBM 1
| #define HAVE_PTHREAD 1
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:6283: checking for grep that handles long lines and -e
configure:6341: result: /usr/bin/grep
configure:6346: checking for egrep
configure:6408: result: /usr/bin/grep -E
configure:6413: checking for ANSI C header files
configure:6433: clang -c -O3 -fomit-frame-pointer conftest.c >&5
configure:6433: $? = 0
configure:6506: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
configure:6506: $? = 0
configure:6506: ./conftest
configure:6506: $? = 0
configure:6517: result: yes
configure:6528: checking for dirent.h that defines DIR
configure:6547: clang -c -O3 -fomit-frame-pointer conftest.c >&5
configure:6547: $? = 0
configure:6555: result: yes
configure:6568: checking for library containing opendir
configure:6599: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
configure:6599: $? = 0
configure:6616: result: none required
configure:6688: checking for sys/types.h
configure:6688: clang -c -O3 -fomit-frame-pointer conftest.c >&5
configure:6688: $? = 0
configure:6688: result: yes
configure:6688: checking for sys/stat.h
configure:6688: clang -c -O3 -fomit-frame-pointer conftest.c >&5
configure:6688: $? = 0
configure:6688: result: yes
configure:6688: checking for stdlib.h
configure:6688: clang -c -O3 -fomit-frame-pointer conftest.c >&5
configure:6688: $? = 0
configure:6688: result: yes
configure:6688: checking for string.h
configure:6688: clang -c -O3 -fomit-frame-pointer conftest.c >&5
configure:6688: $? = 0
configure:6688: result: yes
configure:6688: checking for memory.h
configure:6688: clang -c -O3 -fomit-frame-pointer conftest.c >&5
configure:6688: $? = 0
configure:6688: result: yes
configure:6688: checking for strings.h
configure:6688: clang -c -O3 -fomit-frame-pointer conftest.c >&5
configure:6688: $? = 0
configure:6688: result: yes
configure:6688: checking for inttypes.h
configure:6688: clang -c -O3 -fomit-frame-pointer conftest.c >&5
configure:6688: $? = 0
configure:6688: result: yes
configure:6688: checking for stdint.h
configure:6688: clang -c -O3 -fomit-frame-pointer conftest.c >&5
configure:6688: $? = 0
configure:6688: result: yes
configure:6688: checking for unistd.h
configure:6688: clang -c -O3 -fomit-frame-pointer conftest.c >&5
configure:6688: $? = 0
configure:6688: result: yes
configure:6703: checking fcntl.h usability
configure:6703: clang -c -O3 -fomit-frame-pointer conftest.c >&5
configure:6703: $? = 0
configure:6703: result: yes
configure:6703: checking fcntl.h presence
configure:6703: clang -E conftest.c
configure:6703: $? = 0
configure:6703: result: yes
configure:6703: checking for fcntl.h
configure:6703: result: yes
configure:6703: checking limits.h usability
configure:6703: clang -c -O3 -fomit-frame-pointer conftest.c >&5
configure:6703: $? = 0
configure:6703: result: yes
configure:6703: checking limits.h presence
configure:6703: clang -E conftest.c
configure:6703: $? = 0
configure:6703: result: yes
configure:6703: checking for limits.h
configure:6703: result: yes
configure:6703: checking stddef.h usability
configure:6703: clang -c -O3 -fomit-frame-pointer conftest.c >&5
configure:6703: $? = 0
configure:6703: result: yes
configure:6703: checking stddef.h presence
configure:6703: clang -E conftest.c
configure:6703: $? = 0
configure:6703: result: yes
configure:6703: checking for stddef.h
configure:6703: result: yes
configure:6703: checking for stdlib.h
configure:6703: result: yes
configure:6703: checking for string.h
configure:6703: result: yes
configure:6703: checking for strings.h
configure:6703: result: yes
configure:6703: checking for unistd.h
configure:6703: result: yes
configure:6703: checking for sys/types.h
configure:6703: result: yes
configure:6715: checking for inline
configure:6731: clang -c -O3 -fomit-frame-pointer conftest.c >&5
configure:6731: $? = 0
configure:6739: result: inline
configure:6764: checking whether byte ordering is bigendian
configure:6779: clang -c -O3 -fomit-frame-pointer conftest.c >&5
configure:6779: $? = 0
configure:6824: clang -c -O3 -fomit-frame-pointer conftest.c >&5
configure:6824: $? = 0
configure:6842: clang -c -O3 -fomit-frame-pointer conftest.c >&5
conftest.c:40:4: error: use of undeclared identifier 'not'
not big endian
^
1 error generated.
configure:6842: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gmap"
| #define PACKAGE_TARNAME "gmap"
| #define PACKAGE_VERSION "2021-12-17"
| #define PACKAGE_STRING "gmap 2021-12-17"
| #define PACKAGE_BUGREPORT "Thomas Wu <twu@gene.com>"
| #define PACKAGE_URL ""
| #define PACKAGE "gmap"
| #define VERSION "2021-12-17"
| #define HAVE_LIBM 1
| #define HAVE_PTHREAD 1
| #define STDC_HEADERS 1
| #define HAVE_DIRENT_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_INLINE 1
| /* end confdefs.h. */
| #include <sys/types.h>
| #include <sys/param.h>
|
| int
| main ()
| {
| #if BYTE_ORDER != BIG_ENDIAN
| not big endian
| #endif
|
| ;
| return 0;
| }
configure:6970: result: no
configure:6988: checking for an ANSI C-conforming const
configure:7054: clang -c -O3 -fomit-frame-pointer conftest.c >&5
configure:7054: $? = 0
configure:7061: result: yes
configure:7069: checking for working volatile
configure:7088: clang -c -O3 -fomit-frame-pointer conftest.c >&5
configure:7088: $? = 0
configure:7095: result: yes
configure:7103: checking for size_t
configure:7103: clang -c -O3 -fomit-frame-pointer conftest.c >&5
configure:7103: $? = 0
configure:7103: clang -c -O3 -fomit-frame-pointer conftest.c >&5
conftest.c:69:21: error: expected expression
if (sizeof ((size_t)))
^
1 error generated.
configure:7103: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gmap"
| #define PACKAGE_TARNAME "gmap"
| #define PACKAGE_VERSION "2021-12-17"
| #define PACKAGE_STRING "gmap 2021-12-17"
| #define PACKAGE_BUGREPORT "Thomas Wu <twu@gene.com>"
| #define PACKAGE_URL ""
| #define PACKAGE "gmap"
| #define VERSION "2021-12-17"
| #define HAVE_LIBM 1
| #define HAVE_PTHREAD 1
| #define STDC_HEADERS 1
| #define HAVE_DIRENT_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_INLINE 1
| /* end confdefs.h. */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| # include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| # include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| int
| main ()
| {
| if (sizeof ((size_t)))
| return 0;
| ;
| return 0;
| }
configure:7103: result: yes
configure:7114: checking for off_t
configure:7114: clang -c -O3 -fomit-frame-pointer conftest.c >&5
configure:7114: $? = 0
configure:7114: clang -c -O3 -fomit-frame-pointer conftest.c >&5
conftest.c:69:20: error: expected expression
if (sizeof ((off_t)))
^
1 error generated.
configure:7114: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gmap"
| #define PACKAGE_TARNAME "gmap"
| #define PACKAGE_VERSION "2021-12-17"
| #define PACKAGE_STRING "gmap 2021-12-17"
| #define PACKAGE_BUGREPORT "Thomas Wu <twu@gene.com>"
| #define PACKAGE_URL ""
| #define PACKAGE "gmap"
| #define VERSION "2021-12-17"
| #define HAVE_LIBM 1
| #define HAVE_PTHREAD 1
| #define STDC_HEADERS 1
| #define HAVE_DIRENT_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_INLINE 1
| /* end confdefs.h. */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| # include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| # include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| int
| main ()
| {
| if (sizeof ((off_t)))
| return 0;
| ;
| return 0;
| }
configure:7114: result: yes
configure:7125: checking for caddr_t
configure:7125: clang -c -O3 -fomit-frame-pointer conftest.c >&5
configure:7125: $? = 0
configure:7125: clang -c -O3 -fomit-frame-pointer conftest.c >&5
conftest.c:69:22: error: expected expression
if (sizeof ((caddr_t)))
^
1 error generated.
configure:7125: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gmap"
| #define PACKAGE_TARNAME "gmap"
| #define PACKAGE_VERSION "2021-12-17"
| #define PACKAGE_STRING "gmap 2021-12-17"
| #define PACKAGE_BUGREPORT "Thomas Wu <twu@gene.com>"
| #define PACKAGE_URL ""
| #define PACKAGE "gmap"
| #define VERSION "2021-12-17"
| #define HAVE_LIBM 1
| #define HAVE_PTHREAD 1
| #define STDC_HEADERS 1
| #define HAVE_DIRENT_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_INLINE 1
| /* end confdefs.h. */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| # include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| # include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| int
| main ()
| {
| if (sizeof ((caddr_t)))
| return 0;
| ;
| return 0;
| }
configure:7125: result: yes
configure:7139: checking size of unsigned long
configure:7144: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
configure:7144: $? = 0
configure:7144: ./conftest
configure:7144: $? = 0
configure:7158: result: 8
configure:7172: checking size of unsigned long long
configure:7177: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
configure:7177: $? = 0
configure:7177: ./conftest
configure:7177: $? = 0
configure:7191: result: 8
configure:7205: checking size of off_t
configure:7210: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
configure:7210: $? = 0
configure:7210: ./conftest
configure:7210: $? = 0
configure:7224: result: 8
configure:7241: checking for _LARGEFILE_SOURCE value needed for large files
configure:7260: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
configure:7260: $? = 0
configure:7288: result: no
configure:7313: checking whether alloca is enabled
configure:7520: result: not specified so disabled by default
configure:7526: checking whether mmap is enabled
configure:7871: result: not specified so enabled by default
configure:7884: checking for working mmap with MAP_FIXED
configure:8019: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
conftest.c:123:3: error: implicit declaration of function 'umask' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
umask (0);
^
1 error generated.
configure:8019: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gmap"
| #define PACKAGE_TARNAME "gmap"
| #define PACKAGE_VERSION "2021-12-17"
| #define PACKAGE_STRING "gmap 2021-12-17"
| #define PACKAGE_BUGREPORT "Thomas Wu <twu@gene.com>"
| #define PACKAGE_URL ""
| #define PACKAGE "gmap"
| #define VERSION "2021-12-17"
| #define HAVE_LIBM 1
| #define HAVE_PTHREAD 1
| #define STDC_HEADERS 1
| #define HAVE_DIRENT_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_INLINE 1
| #define HAVE_CADDR_T 1
| #define SIZEOF_UNSIGNED_LONG 8
| #define SIZEOF_UNSIGNED_LONG_LONG 8
| #define SIZEOF_OFF_T 8
| #define HAVE_FSEEKO 1
| /* end confdefs.h. */
|
| /* Thanks to Mike Haertel and Jim Avera for this test.
| Here is a matrix of mmap possibilities:
| mmap private not fixed
| mmap private fixed at somewhere currently unmapped
| mmap private fixed at somewhere already mapped
| mmap shared not fixed
| mmap shared fixed at somewhere currently unmapped
| mmap shared fixed at somewhere already mapped
| For private mappings, we should verify that changes cannot be read()
| back from the file, nor mmap's back from the file at a different
| address. (There have been systems where private was not correctly
| implemented like the infamous i386 svr4.0, and systems where the
| VM page cache was not coherent with the file system buffer cache
| like early versions of FreeBSD and possibly contemporary NetBSD.)
| For shared mappings, we should conversely verify that changes get
| propagated back to all the places they're supposed to be.
|
| Grep wants private fixed already mapped.
| The main things grep needs to know about mmap are:
| * does it exist and is it safe to write into the mmap'd area
| * how to use it (BSD variants) */
|
| #include <fcntl.h>
| #include <sys/mman.h>
| #include <stdlib.h>
| #include <unistd.h>
|
| #if !STDC_HEADERS && !HAVE_STDLIB_H
| char *malloc ();
| #endif
|
| /* This mess was copied from the GNU getpagesize.h. */
| #if !HAVE_GETPAGESIZE
| /* Assume that all systems that can run configure have sys/param.h. */
| # if !HAVE_SYS_PARAM_H
| # define HAVE_SYS_PARAM_H 1
| # endif
|
| # ifdef _SC_PAGESIZE
| # define getpagesize() sysconf(_SC_PAGESIZE)
| # else /* no _SC_PAGESIZE */
| # if HAVE_SYS_PARAM_H
| # include <sys/param.h>
| # ifdef EXEC_PAGESIZE
| # define getpagesize() EXEC_PAGESIZE
| # else /* no EXEC_PAGESIZE */
| # ifdef NBPG
| # define getpagesize() NBPG * CLSIZE
| # ifndef CLSIZE
| # define CLSIZE 1
| # endif /* no CLSIZE */
| # else /* no NBPG */
| # ifdef NBPC
| # define getpagesize() NBPC
| # else /* no NBPC */
| # ifdef PAGESIZE
| # define getpagesize() PAGESIZE
| # endif /* PAGESIZE */
| # endif /* no NBPC */
| # endif /* no NBPG */
| # endif /* no EXEC_PAGESIZE */
| # else /* no HAVE_SYS_PARAM_H */
| # define getpagesize() 8192 /* punt totally */
| # endif /* no HAVE_SYS_PARAM_H */
| # endif /* no _SC_PAGESIZE */
|
| #endif /* no HAVE_GETPAGESIZE */
|
| int
| main ()
| {
|
| char *data, *data2, *data3;
| size_t i, pagesize;
| int fd;
|
| pagesize = getpagesize ();
|
| /* First, make a file with some known garbage in it. */
| data = (char *) malloc (pagesize);
| if (!data)
| exit (1);
| for (i = 0; i < pagesize; ++i)
| *(data + i) = rand ();
| umask (0);
| fd = creat ("conftest.mmap", 0600);
| if (fd < 0)
| exit (1);
| if (write (fd, data, pagesize) != pagesize)
| exit (1);
| close (fd);
|
| /* Next, try to mmap the file at a fixed address which already has
| something else allocated at it. If we can, also make sure that
| we see the same garbage. */
| fd = open ("conftest.mmap", O_RDWR);
| if (fd < 0)
| exit (1);
| data2 = (char *) malloc (2 * pagesize);
| if (!data2)
| exit (1);
| data2 += (pagesize - ((size_t) data2 & (pagesize - 1))) & (pagesize - 1);
| if (data2 != mmap (data2, pagesize, PROT_READ | PROT_WRITE,
| MAP_PRIVATE | MAP_FIXED, fd, 0L))
| exit (1);
| for (i = 0; i < pagesize; ++i)
| if (*(data + i) != *(data2 + i))
| exit (1);
|
| /* Finally, make sure that changes to the mapped area do not
| percolate back to the file as seen by read(). (This is a bug on
| some variants of i386 svr4.0.) */
| for (i = 0; i < pagesize; ++i)
| *(data2 + i) = *(data2 + i) + 1;
| data3 = (char *) malloc (pagesize);
| if (!data3)
| exit (1);
| if (read (fd, data3, pagesize) != pagesize)
| exit (1);
| for (i = 0; i < pagesize; ++i)
| if (*(data + i) != *(data3 + i))
| exit (1);
| close (fd);
| exit (0);
|
| ;
| return 0;
| }
configure:8025: result: no
configure:8046: checking for working mmap with MAP_VARIABLE
configure:8181: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
conftest.c:123:3: error: implicit declaration of function 'umask' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
umask (0);
^
conftest.c:142:36: error: use of undeclared identifier 'MAP_VARIABLE'
MAP_PRIVATE | MAP_VARIABLE, fd, 0L))
^
2 errors generated.
configure:8181: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gmap"
| #define PACKAGE_TARNAME "gmap"
| #define PACKAGE_VERSION "2021-12-17"
| #define PACKAGE_STRING "gmap 2021-12-17"
| #define PACKAGE_BUGREPORT "Thomas Wu <twu@gene.com>"
| #define PACKAGE_URL ""
| #define PACKAGE "gmap"
| #define VERSION "2021-12-17"
| #define HAVE_LIBM 1
| #define HAVE_PTHREAD 1
| #define STDC_HEADERS 1
| #define HAVE_DIRENT_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_INLINE 1
| #define HAVE_CADDR_T 1
| #define SIZEOF_UNSIGNED_LONG 8
| #define SIZEOF_UNSIGNED_LONG_LONG 8
| #define SIZEOF_OFF_T 8
| #define HAVE_FSEEKO 1
| /* end confdefs.h. */
|
| /* This modified from a test by Mike Haertel and Jim Avera.
| Here is a matrix of mmap possibilities:
| mmap private not fixed
| mmap private fixed at somewhere currently unmapped
| mmap private fixed at somewhere already mapped
| mmap shared not fixed
| mmap shared fixed at somewhere currently unmapped
| mmap shared fixed at somewhere already mapped
|
| For private mappings, we should verify that changes cannot be read()
| back from the file, nor mmap's back from the file at a different
| address. (There have been systems where private was not correctly
| implemented like the infamous i386 svr4.0, and systems where the
| VM page cache was not coherent with the file system buffer cache
| like early versions of FreeBSD and possibly contemporary NetBSD.)
| For shared mappings, we should conversely verify that changes get
| propagated back to all the places they're supposed to be.
|
| Previous test was designed for grep, which needs private fixed already mapped.
| We want shared variable.
| */
|
| #include <fcntl.h>
| #include <sys/mman.h>
| #include <stdlib.h>
| #include <unistd.h>
|
| #if !STDC_HEADERS && !HAVE_STDLIB_H
| char *malloc ();
| #endif
|
| /* This mess was copied from the GNU getpagesize.h. */
| #if !HAVE_GETPAGESIZE
| /* Assume that all systems that can run configure have sys/param.h. */
| # if !HAVE_SYS_PARAM_H
| # define HAVE_SYS_PARAM_H 1
| # endif
|
| # ifdef _SC_PAGESIZE
| # define getpagesize() sysconf(_SC_PAGESIZE)
| # else /* no _SC_PAGESIZE */
| # if HAVE_SYS_PARAM_H
| # include <sys/param.h>
| # ifdef EXEC_PAGESIZE
| # define getpagesize() EXEC_PAGESIZE
| # else /* no EXEC_PAGESIZE */
| # ifdef NBPG
| # define getpagesize() NBPG * CLSIZE
| # ifndef CLSIZE
| # define CLSIZE 1
| # endif /* no CLSIZE */
| # else /* no NBPG */
| # ifdef NBPC
| # define getpagesize() NBPC
| # else /* no NBPC */
| # ifdef PAGESIZE
| # define getpagesize() PAGESIZE
| # endif /* PAGESIZE */
| # endif /* no NBPC */
| # endif /* no NBPG */
| # endif /* no EXEC_PAGESIZE */
| # else /* no HAVE_SYS_PARAM_H */
| # define getpagesize() 8192 /* punt totally */
| # endif /* no HAVE_SYS_PARAM_H */
| # endif /* no _SC_PAGESIZE */
|
| #endif /* no HAVE_GETPAGESIZE */
|
| int
| main ()
| {
|
| char *data, *data2, *data3;
| size_t i, pagesize;
| int fd;
|
| pagesize = getpagesize ();
|
| /* First, make a file with some known garbage in it. */
| data = (char *) malloc (pagesize);
| if (!data)
| exit (1);
| for (i = 0; i < pagesize; ++i)
| *(data + i) = rand ();
| umask (0);
| fd = creat ("conftest.mmap", 0600);
| if (fd < 0)
| exit (1);
| if (write (fd, data, pagesize) != pagesize)
| exit (1);
| close (fd);
|
| /* Next, try to mmap the file at a fixed address which already has
| something else allocated at it. If we can, also make sure that
| we see the same garbage. */
| fd = open ("conftest.mmap", O_RDWR);
| if (fd < 0)
| exit (1);
| data2 = (char *) malloc (2 * pagesize);
| if (!data2)
| exit (1);
| data2 += (pagesize - ((size_t) data2 & (pagesize - 1))) & (pagesize - 1);
| if (data2 != mmap (data2, pagesize, PROT_READ | PROT_WRITE,
| MAP_PRIVATE | MAP_VARIABLE, fd, 0L))
| exit (1);
| for (i = 0; i < pagesize; ++i)
| if (*(data + i) != *(data2 + i))
| exit (1);
|
| /* Finally, make sure that changes to the mapped area do not
| percolate back to the file as seen by read(). (This is a bug on
| some variants of i386 svr4.0.) */
| for (i = 0; i < pagesize; ++i)
| *(data2 + i) = *(data2 + i) + 1;
| data3 = (char *) malloc (pagesize);
| if (!data3)
| exit (1);
| if (read (fd, data3, pagesize) != pagesize)
| exit (1);
| for (i = 0; i < pagesize; ++i)
| if (*(data + i) != *(data3 + i))
| exit (1);
| close (fd);
| exit (0);
|
| ;
| return 0;
| }
configure:8187: result: no
configure:8222: checking for MAP_FILE in mmap
configure:8236: clang -c -O3 -fomit-frame-pointer conftest.c >&5
configure:8236: $? = 0
configure:8237: result: yes
configure:8248: checking for MAP_VARIABLE in mmap
configure:8262: clang -c -O3 -fomit-frame-pointer conftest.c >&5
conftest.c:44:13: error: use of undeclared identifier 'MAP_VARIABLE'
int flags = MAP_VARIABLE;
^
1 error generated.
configure:8262: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gmap"
| #define PACKAGE_TARNAME "gmap"
| #define PACKAGE_VERSION "2021-12-17"
| #define PACKAGE_STRING "gmap 2021-12-17"
| #define PACKAGE_BUGREPORT "Thomas Wu <twu@gene.com>"
| #define PACKAGE_URL ""
| #define PACKAGE "gmap"
| #define VERSION "2021-12-17"
| #define HAVE_LIBM 1
| #define HAVE_PTHREAD 1
| #define STDC_HEADERS 1
| #define HAVE_DIRENT_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_INLINE 1
| #define HAVE_CADDR_T 1
| #define SIZEOF_UNSIGNED_LONG 8
| #define SIZEOF_UNSIGNED_LONG_LONG 8
| #define SIZEOF_OFF_T 8
| #define HAVE_FSEEKO 1
| #define HAVE_MMAP_MAP_FILE 1
| /* end confdefs.h. */
| #include <sys/types.h>
| #include <sys/mman.h>
| int
| main ()
| {
| int flags = MAP_VARIABLE;
| ;
| return 0;
| }
configure:8269: result: no
configure:8274: checking for MAP_SHARED in mmap
configure:8288: clang -c -O3 -fomit-frame-pointer conftest.c >&5
configure:8288: $? = 0
configure:8289: result: yes
configure:8300: checking for MAP_PRIVATE in mmap
configure:8314: clang -c -O3 -fomit-frame-pointer conftest.c >&5
configure:8314: $? = 0
configure:8315: result: yes
configure:8326: checking for MAP_FAILED in mmap
configure:8340: clang -c -O3 -fomit-frame-pointer conftest.c >&5
configure:8340: $? = 0
configure:8341: result: yes
configure:8368: checking for MADV_DONTNEED in madvise
configure:8382: clang -c -O3 -fomit-frame-pointer conftest.c >&5
configure:8382: $? = 0
configure:8383: result: yes
configure:8394: checking for MADV_WILLNEED in madvise
configure:8408: clang -c -O3 -fomit-frame-pointer conftest.c >&5
configure:8408: $? = 0
configure:8409: result: yes
configure:8420: checking for MADV_RANDOM in madvise
configure:8434: clang -c -O3 -fomit-frame-pointer conftest.c >&5
configure:8434: $? = 0
configure:8435: result: yes
configure:8446: checking for MADV_SEQUENTIAL in madvise
configure:8460: clang -c -O3 -fomit-frame-pointer conftest.c >&5
configure:8460: $? = 0
configure:8461: result: yes
configure:8488: checking for SHM_NORESERVE in shmget
configure:8502: clang -c -O3 -fomit-frame-pointer conftest.c >&5
conftest.c:50:13: error: use of undeclared identifier 'SHM_NORESERVE'
int flags = SHM_NORESERVE;
^
1 error generated.
configure:8502: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gmap"
| #define PACKAGE_TARNAME "gmap"
| #define PACKAGE_VERSION "2021-12-17"
| #define PACKAGE_STRING "gmap 2021-12-17"
| #define PACKAGE_BUGREPORT "Thomas Wu <twu@gene.com>"
| #define PACKAGE_URL ""
| #define PACKAGE "gmap"
| #define VERSION "2021-12-17"
| #define HAVE_LIBM 1
| #define HAVE_PTHREAD 1
| #define STDC_HEADERS 1
| #define HAVE_DIRENT_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_INLINE 1
| #define HAVE_CADDR_T 1
| #define SIZEOF_UNSIGNED_LONG 8
| #define SIZEOF_UNSIGNED_LONG_LONG 8
| #define SIZEOF_OFF_T 8
| #define HAVE_FSEEKO 1
| #define HAVE_MMAP_MAP_FILE 1
| #define HAVE_MMAP_MAP_SHARED 1
| #define HAVE_MMAP_MAP_PRIVATE 1
| #define HAVE_MADVISE_MADV_DONTNEED 1
| #define HAVE_MADVISE_MADV_WILLNEED 1
| #define HAVE_MADVISE_MADV_RANDOM 1
| #define HAVE_MADVISE_MADV_SEQUENTIAL 1
| /* end confdefs.h. */
| #include <sys/ipc.h>
| #include <sys/shm.h>
| int
| main ()
| {
| int flags = SHM_NORESERVE;
| ;
| return 0;
| }
configure:8509: result: no
configure:8526: checking for ceil
configure:8526: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
conftest.c:68:6: warning: incompatible redeclaration of library function 'ceil' [-Wincompatible-library-redeclaration]
char ceil ();
^
conftest.c:68:6: note: 'ceil' is a builtin with type 'double (double)'
1 warning generated.
configure:8526: $? = 0
configure:8526: result: yes
configure:8526: checking for floor
configure:8526: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
conftest.c:69:6: warning: incompatible redeclaration of library function 'floor' [-Wincompatible-library-redeclaration]
char floor ();
^
conftest.c:69:6: note: 'floor' is a builtin with type 'double (double)'
1 warning generated.
configure:8526: $? = 0
configure:8526: result: yes
configure:8526: checking for index
configure:8526: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
conftest.c:70:6: warning: incompatible redeclaration of library function 'index' [-Wincompatible-library-redeclaration]
char index ();
^
conftest.c:70:6: note: 'index' is a builtin with type 'char *(const char *, int)'
1 warning generated.
configure:8526: $? = 0
configure:8526: result: yes
configure:8526: checking for log
configure:8526: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
conftest.c:71:6: warning: incompatible redeclaration of library function 'log' [-Wincompatible-library-redeclaration]
char log ();
^
conftest.c:71:6: note: 'log' is a builtin with type 'double (double)'
1 warning generated.
configure:8526: $? = 0
configure:8526: result: yes
configure:8526: checking for madvise
configure:8526: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
configure:8526: $? = 0
configure:8526: result: yes
configure:8526: checking for memcpy
configure:8526: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
conftest.c:73:6: warning: incompatible redeclaration of library function 'memcpy' [-Wincompatible-library-redeclaration]
char memcpy ();
^
conftest.c:73:6: note: 'memcpy' is a builtin with type 'void *(void *, const void *, unsigned long)'
1 warning generated.
configure:8526: $? = 0
configure:8526: result: yes
configure:8526: checking for memmove
configure:8526: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
conftest.c:74:6: warning: incompatible redeclaration of library function 'memmove' [-Wincompatible-library-redeclaration]
char memmove ();
^
conftest.c:74:6: note: 'memmove' is a builtin with type 'void *(void *, const void *, unsigned long)'
1 warning generated.
configure:8526: $? = 0
configure:8526: result: yes
configure:8526: checking for memset
configure:8526: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
conftest.c:75:6: warning: incompatible redeclaration of library function 'memset' [-Wincompatible-library-redeclaration]
char memset ();
^
conftest.c:75:6: note: 'memset' is a builtin with type 'void *(void *, int, unsigned long)'
1 warning generated.
configure:8526: $? = 0
configure:8526: result: yes
configure:8526: checking for munmap
configure:8526: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
configure:8526: $? = 0
configure:8526: result: yes
configure:8526: checking for pow
configure:8526: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
conftest.c:77:6: warning: incompatible redeclaration of library function 'pow' [-Wincompatible-library-redeclaration]
char pow ();
^
conftest.c:77:6: note: 'pow' is a builtin with type 'double (double, double)'
1 warning generated.
configure:8526: $? = 0
configure:8526: result: yes
configure:8526: checking for rint
configure:8526: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
conftest.c:78:6: warning: incompatible redeclaration of library function 'rint' [-Wincompatible-library-redeclaration]
char rint ();
^
conftest.c:78:6: note: 'rint' is a builtin with type 'double (double)'
1 warning generated.
configure:8526: $? = 0
configure:8526: result: yes
configure:8526: checking for stat64
configure:8526: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
configure:8526: $? = 0
configure:8526: result: yes
configure:8526: checking for strtoul
configure:8526: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
conftest.c:80:6: warning: incompatible redeclaration of library function 'strtoul' [-Wincompatible-library-redeclaration]
char strtoul ();
^
conftest.c:80:6: note: 'strtoul' is a builtin with type 'unsigned long (const char *, char **, int)'
1 warning generated.
configure:8526: $? = 0
configure:8526: result: yes
configure:8526: checking for sysconf
configure:8526: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
configure:8526: $? = 0
configure:8526: result: yes
configure:8526: checking for sysctl
configure:8526: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
configure:8526: $? = 0
configure:8526: result: yes
configure:8526: checking for sigaction
configure:8526: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
configure:8526: $? = 0
configure:8526: result: yes
configure:8526: checking for shmget
configure:8526: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
configure:8526: $? = 0
configure:8526: result: yes
configure:8526: checking for shmctl
configure:8526: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
configure:8526: $? = 0
configure:8526: result: yes
configure:8526: checking for shmat
configure:8526: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
configure:8526: $? = 0
configure:8526: result: yes
configure:8526: checking for shmdt
configure:8526: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
configure:8526: $? = 0
configure:8526: result: yes
configure:8526: checking for semget
configure:8526: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
configure:8526: $? = 0
configure:8526: result: yes
configure:8526: checking for semctl
configure:8526: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
configure:8526: $? = 0
configure:8526: result: yes
configure:8526: checking for semop
configure:8526: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
configure:8526: $? = 0
configure:8526: result: yes
configure:8545: checking for struct stat64
configure:8558: clang -c -O3 -fomit-frame-pointer conftest.c >&5
conftest.c:72:15: error: variable has incomplete type 'struct stat64'
struct stat64 st; stat64("/tmp/foo",&st);
^
conftest.c:72:8: note: forward declaration of 'struct stat64'
struct stat64 st; stat64("/tmp/foo",&st);
^
conftest.c:72:19: error: implicit declaration of function 'stat64' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
struct stat64 st; stat64("/tmp/foo",&st);
^
conftest.c:72:19: note: did you mean 'stat'?
/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/usr/include/sys/stat.h:386:9: note: 'stat' declared here
int stat(const char *, struct stat *) __DARWIN_INODE64(stat);
^
2 errors generated.
configure:8558: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gmap"
| #define PACKAGE_TARNAME "gmap"
| #define PACKAGE_VERSION "2021-12-17"
| #define PACKAGE_STRING "gmap 2021-12-17"
| #define PACKAGE_BUGREPORT "Thomas Wu <twu@gene.com>"
| #define PACKAGE_URL ""
| #define PACKAGE "gmap"
| #define VERSION "2021-12-17"
| #define HAVE_LIBM 1
| #define HAVE_PTHREAD 1
| #define STDC_HEADERS 1
| #define HAVE_DIRENT_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_INLINE 1
| #define HAVE_CADDR_T 1
| #define SIZEOF_UNSIGNED_LONG 8
| #define SIZEOF_UNSIGNED_LONG_LONG 8
| #define SIZEOF_OFF_T 8
| #define HAVE_FSEEKO 1
| #define HAVE_MMAP_MAP_FILE 1
| #define HAVE_MMAP_MAP_SHARED 1
| #define HAVE_MMAP_MAP_PRIVATE 1
| #define HAVE_MADVISE_MADV_DONTNEED 1
| #define HAVE_MADVISE_MADV_WILLNEED 1
| #define HAVE_MADVISE_MADV_RANDOM 1
| #define HAVE_MADVISE_MADV_SEQUENTIAL 1
| #define HAVE_CEIL 1
| #define HAVE_FLOOR 1
| #define HAVE_INDEX 1
| #define HAVE_LOG 1
| #define HAVE_MADVISE 1
| #define HAVE_MEMCPY 1
| #define HAVE_MEMMOVE 1
| #define HAVE_MEMSET 1
| #define HAVE_MUNMAP 1
| #define HAVE_POW 1
| #define HAVE_RINT 1
| #define HAVE_STAT64 1
| #define HAVE_STRTOUL 1
| #define HAVE_SYSCONF 1
| #define HAVE_SYSCTL 1
| #define HAVE_SIGACTION 1
| #define HAVE_SHMGET 1
| #define HAVE_SHMCTL 1
| #define HAVE_SHMAT 1
| #define HAVE_SHMDT 1
| #define HAVE_SEMGET 1
| #define HAVE_SEMCTL 1
| #define HAVE_SEMOP 1
| /* end confdefs.h. */
| #include <sys/stat.h>
| int
| main ()
| {
| struct stat64 st; stat64("/tmp/foo",&st);
| ;
| return 0;
| }
configure:8565: result: no
configure:8586: checking for pagesize via sysconf
configure:8599: clang -c -O3 -fomit-frame-pointer conftest.c >&5
configure:8599: $? = 0
configure:8600: result: yes
configure:8611: checking for pagesize via sysctl
configure:8625: clang -c -O3 -fomit-frame-pointer conftest.c >&5
configure:8625: $? = 0
configure:8626: result: yes
configure:8646: checking whether fopen accepts "b" mode
configure:8666: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
configure:8666: $? = 0
configure:8666: ./conftest
configure:8666: $? = 0
configure:8676: result: yes
configure:8684: checking whether fopen accepts "t" mode
configure:8704: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
configure:8704: $? = 0
configure:8704: ./conftest
configure:8704: $? = 0
configure:8714: result: yes
configure:8768: checking whether C compiler accepts -O3 -fomit-frame-pointer -mpopcnt
configure:8787: clang -c -O3 -fomit-frame-pointer -O3 -fomit-frame-pointer -mpopcnt conftest.c >&5
clang: warning: argument unused during compilation: '-mpopcnt' [-Wunused-command-line-argument]
configure:8787: $? = 0
configure:8796: result: yes
configure:8821: clang -o conftest -O3 -fomit-frame-pointer -mpopcnt conftest.c -lm >&5
configure:8821: $? = 0
configure:8842: checking whether __builtin_popcount is declared
configure:8842: clang -c -O3 -fomit-frame-pointer -mpopcnt conftest.c >&5
clang: warning: argument unused during compilation: '-mpopcnt' [-Wunused-command-line-argument]
conftest.c:112:10: error: builtin functions must be directly called
(void) __builtin_popcount;
^
1 error generated.
configure:8842: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gmap"
| #define PACKAGE_TARNAME "gmap"
| #define PACKAGE_VERSION "2021-12-17"
| #define PACKAGE_STRING "gmap 2021-12-17"
| #define PACKAGE_BUGREPORT "Thomas Wu <twu@gene.com>"
| #define PACKAGE_URL ""
| #define PACKAGE "gmap"
| #define VERSION "2021-12-17"
| #define HAVE_LIBM 1
| #define HAVE_PTHREAD 1
| #define STDC_HEADERS 1
| #define HAVE_DIRENT_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_INLINE 1
| #define HAVE_CADDR_T 1
| #define SIZEOF_UNSIGNED_LONG 8
| #define SIZEOF_UNSIGNED_LONG_LONG 8
| #define SIZEOF_OFF_T 8
| #define HAVE_FSEEKO 1
| #define HAVE_MMAP_MAP_FILE 1
| #define HAVE_MMAP_MAP_SHARED 1
| #define HAVE_MMAP_MAP_PRIVATE 1
| #define HAVE_MADVISE_MADV_DONTNEED 1
| #define HAVE_MADVISE_MADV_WILLNEED 1
| #define HAVE_MADVISE_MADV_RANDOM 1
| #define HAVE_MADVISE_MADV_SEQUENTIAL 1
| #define HAVE_CEIL 1
| #define HAVE_FLOOR 1
| #define HAVE_INDEX 1
| #define HAVE_LOG 1
| #define HAVE_MADVISE 1
| #define HAVE_MEMCPY 1
| #define HAVE_MEMMOVE 1
| #define HAVE_MEMSET 1
| #define HAVE_MUNMAP 1
| #define HAVE_POW 1
| #define HAVE_RINT 1
| #define HAVE_STAT64 1
| #define HAVE_STRTOUL 1
| #define HAVE_SYSCONF 1
| #define HAVE_SYSCTL 1
| #define HAVE_SIGACTION 1
| #define HAVE_SHMGET 1
| #define HAVE_SHMCTL 1
| #define HAVE_SHMAT 1
| #define HAVE_SHMDT 1
| #define HAVE_SEMGET 1
| #define HAVE_SEMCTL 1
| #define HAVE_SEMOP 1
| #define PAGESIZE_VIA_SYSCONF 1
| #define PAGESIZE_VIA_SYSCTL 1
| #define USE_FOPEN_BINARY 1
| #define USE_FOPEN_TEXT 1
| /* end confdefs.h. */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| # include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| # include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| int
| main ()
| {
| #ifndef __builtin_popcount
| #ifdef __cplusplus
| (void) __builtin_popcount;
| #else
| (void) __builtin_popcount;
| #endif
| #endif
|
| ;
| return 0;
| }
configure:8842: result: no
configure:8883: checking whether __builtin_clz is declared
configure:8883: clang -c -O3 -fomit-frame-pointer -mpopcnt conftest.c >&5
clang: warning: argument unused during compilation: '-mpopcnt' [-Wunused-command-line-argument]
conftest.c:112:10: error: builtin functions must be directly called
(void) __builtin_clz;
^
1 error generated.
configure:8883: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gmap"
| #define PACKAGE_TARNAME "gmap"
| #define PACKAGE_VERSION "2021-12-17"
| #define PACKAGE_STRING "gmap 2021-12-17"
| #define PACKAGE_BUGREPORT "Thomas Wu <twu@gene.com>"
| #define PACKAGE_URL ""
| #define PACKAGE "gmap"
| #define VERSION "2021-12-17"
| #define HAVE_LIBM 1
| #define HAVE_PTHREAD 1
| #define STDC_HEADERS 1
| #define HAVE_DIRENT_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_INLINE 1
| #define HAVE_CADDR_T 1
| #define SIZEOF_UNSIGNED_LONG 8
| #define SIZEOF_UNSIGNED_LONG_LONG 8
| #define SIZEOF_OFF_T 8
| #define HAVE_FSEEKO 1
| #define HAVE_MMAP_MAP_FILE 1
| #define HAVE_MMAP_MAP_SHARED 1
| #define HAVE_MMAP_MAP_PRIVATE 1
| #define HAVE_MADVISE_MADV_DONTNEED 1
| #define HAVE_MADVISE_MADV_WILLNEED 1
| #define HAVE_MADVISE_MADV_RANDOM 1
| #define HAVE_MADVISE_MADV_SEQUENTIAL 1
| #define HAVE_CEIL 1
| #define HAVE_FLOOR 1
| #define HAVE_INDEX 1
| #define HAVE_LOG 1
| #define HAVE_MADVISE 1
| #define HAVE_MEMCPY 1
| #define HAVE_MEMMOVE 1
| #define HAVE_MEMSET 1
| #define HAVE_MUNMAP 1
| #define HAVE_POW 1
| #define HAVE_RINT 1
| #define HAVE_STAT64 1
| #define HAVE_STRTOUL 1
| #define HAVE_SYSCONF 1
| #define HAVE_SYSCTL 1
| #define HAVE_SIGACTION 1
| #define HAVE_SHMGET 1
| #define HAVE_SHMCTL 1
| #define HAVE_SHMAT 1
| #define HAVE_SHMDT 1
| #define HAVE_SEMGET 1
| #define HAVE_SEMCTL 1
| #define HAVE_SEMOP 1
| #define PAGESIZE_VIA_SYSCONF 1
| #define PAGESIZE_VIA_SYSCTL 1
| #define USE_FOPEN_BINARY 1
| #define USE_FOPEN_TEXT 1
| /* end confdefs.h. */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| # include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| # include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| int
| main ()
| {
| #ifndef __builtin_clz
| #ifdef __cplusplus
| (void) __builtin_clz;
| #else
| (void) __builtin_clz;
| #endif
| #endif
|
| ;
| return 0;
| }
configure:8883: result: no
configure:8924: checking whether __builtin_ctz is declared
configure:8924: clang -c -O3 -fomit-frame-pointer -mpopcnt conftest.c >&5
clang: warning: argument unused during compilation: '-mpopcnt' [-Wunused-command-line-argument]
conftest.c:112:10: error: builtin functions must be directly called
(void) __builtin_ctz;
^
1 error generated.
configure:8924: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gmap"
| #define PACKAGE_TARNAME "gmap"
| #define PACKAGE_VERSION "2021-12-17"
| #define PACKAGE_STRING "gmap 2021-12-17"
| #define PACKAGE_BUGREPORT "Thomas Wu <twu@gene.com>"
| #define PACKAGE_URL ""
| #define PACKAGE "gmap"
| #define VERSION "2021-12-17"
| #define HAVE_LIBM 1
| #define HAVE_PTHREAD 1
| #define STDC_HEADERS 1
| #define HAVE_DIRENT_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_INLINE 1
| #define HAVE_CADDR_T 1
| #define SIZEOF_UNSIGNED_LONG 8
| #define SIZEOF_UNSIGNED_LONG_LONG 8
| #define SIZEOF_OFF_T 8
| #define HAVE_FSEEKO 1
| #define HAVE_MMAP_MAP_FILE 1
| #define HAVE_MMAP_MAP_SHARED 1
| #define HAVE_MMAP_MAP_PRIVATE 1
| #define HAVE_MADVISE_MADV_DONTNEED 1
| #define HAVE_MADVISE_MADV_WILLNEED 1
| #define HAVE_MADVISE_MADV_RANDOM 1
| #define HAVE_MADVISE_MADV_SEQUENTIAL 1
| #define HAVE_CEIL 1
| #define HAVE_FLOOR 1
| #define HAVE_INDEX 1
| #define HAVE_LOG 1
| #define HAVE_MADVISE 1
| #define HAVE_MEMCPY 1
| #define HAVE_MEMMOVE 1
| #define HAVE_MEMSET 1
| #define HAVE_MUNMAP 1
| #define HAVE_POW 1
| #define HAVE_RINT 1
| #define HAVE_STAT64 1
| #define HAVE_STRTOUL 1
| #define HAVE_SYSCONF 1
| #define HAVE_SYSCTL 1
| #define HAVE_SIGACTION 1
| #define HAVE_SHMGET 1
| #define HAVE_SHMCTL 1
| #define HAVE_SHMAT 1
| #define HAVE_SHMDT 1
| #define HAVE_SEMGET 1
| #define HAVE_SEMCTL 1
| #define HAVE_SEMOP 1
| #define PAGESIZE_VIA_SYSCONF 1
| #define PAGESIZE_VIA_SYSCTL 1
| #define USE_FOPEN_BINARY 1
| #define USE_FOPEN_TEXT 1
| /* end confdefs.h. */
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| # include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| # include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| int
| main ()
| {
| #ifndef __builtin_ctz
| #ifdef __cplusplus
| (void) __builtin_ctz;
| #else
| (void) __builtin_ctz;
| #endif
| #endif
|
| ;
| return 0;
| }
configure:8924: result: no
configure:8985: checking for bsr instruction in assembly
configure:8998: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
conftest.c:76:27: error: implicit declaration of function 'rand' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
int msb; unsigned int x = rand(); asm("bsr %1,%0" : "=r"(msb) : "r"(x));
^
conftest.c:76:69: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths]
int msb; unsigned int x = rand(); asm("bsr %1,%0" : "=r"(msb) : "r"(x));
^
conftest.c:76:44: note: use constraint modifier "w"
int msb; unsigned int x = rand(); asm("bsr %1,%0" : "=r"(msb) : "r"(x));
^~
%w1
conftest.c:76:58: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths]
int msb; unsigned int x = rand(); asm("bsr %1,%0" : "=r"(msb) : "r"(x));
^
conftest.c:76:47: note: use constraint modifier "w"
int msb; unsigned int x = rand(); asm("bsr %1,%0" : "=r"(msb) : "r"(x));
^~
%w0
2 warnings and 1 error generated.
configure:8998: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gmap"
| #define PACKAGE_TARNAME "gmap"
| #define PACKAGE_VERSION "2021-12-17"
| #define PACKAGE_STRING "gmap 2021-12-17"
| #define PACKAGE_BUGREPORT "Thomas Wu <twu@gene.com>"
| #define PACKAGE_URL ""
| #define PACKAGE "gmap"
| #define VERSION "2021-12-17"
| #define HAVE_LIBM 1
| #define HAVE_PTHREAD 1
| #define STDC_HEADERS 1
| #define HAVE_DIRENT_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_INLINE 1
| #define HAVE_CADDR_T 1
| #define SIZEOF_UNSIGNED_LONG 8
| #define SIZEOF_UNSIGNED_LONG_LONG 8
| #define SIZEOF_OFF_T 8
| #define HAVE_FSEEKO 1
| #define HAVE_MMAP_MAP_FILE 1
| #define HAVE_MMAP_MAP_SHARED 1
| #define HAVE_MMAP_MAP_PRIVATE 1
| #define HAVE_MADVISE_MADV_DONTNEED 1
| #define HAVE_MADVISE_MADV_WILLNEED 1
| #define HAVE_MADVISE_MADV_RANDOM 1
| #define HAVE_MADVISE_MADV_SEQUENTIAL 1
| #define HAVE_CEIL 1
| #define HAVE_FLOOR 1
| #define HAVE_INDEX 1
| #define HAVE_LOG 1
| #define HAVE_MADVISE 1
| #define HAVE_MEMCPY 1
| #define HAVE_MEMMOVE 1
| #define HAVE_MEMSET 1
| #define HAVE_MUNMAP 1
| #define HAVE_POW 1
| #define HAVE_RINT 1
| #define HAVE_STAT64 1
| #define HAVE_STRTOUL 1
| #define HAVE_SYSCONF 1
| #define HAVE_SYSCTL 1
| #define HAVE_SIGACTION 1
| #define HAVE_SHMGET 1
| #define HAVE_SHMCTL 1
| #define HAVE_SHMAT 1
| #define HAVE_SHMDT 1
| #define HAVE_SEMGET 1
| #define HAVE_SEMCTL 1
| #define HAVE_SEMOP 1
| #define PAGESIZE_VIA_SYSCONF 1
| #define PAGESIZE_VIA_SYSCTL 1
| #define USE_FOPEN_BINARY 1
| #define USE_FOPEN_TEXT 1
| /* end confdefs.h. */
|
| int
| main ()
| {
| int msb; unsigned int x = rand(); asm("bsr %1,%0" : "=r"(msb) : "r"(x));
| ;
| return 0;
| }
configure:9005: result: no
configure:9030: checking compiler is defective and requires an immediate in sse2 shift commands
configure:9048: clang -c -O3 -fomit-frame-pointer conftest.c >&5
In file included from conftest.c:74:
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/emmintrin.h:14:2: error: "This header is only meant to be used on x86 and x64 architecture"
#error "This header is only meant to be used on x86 and x64 architecture"
^
In file included from conftest.c:74:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/emmintrin.h:17:
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/xmmintrin.h:14:2: error: "This header is only meant to be used on x86 and x64 architecture"
#error "This header is only meant to be used on x86 and x64 architecture"
^
In file included from conftest.c:74:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/emmintrin.h:17:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/xmmintrin.h:17:
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:14:2: error: "This header is only meant to be used on x86 and x64 architecture"
#error "This header is only meant to be used on x86 and x64 architecture"
^
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:54:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_vec_init_v2si(__i, 0);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:133:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_packsswb((__v4hi)__m1, (__v4hi)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:163:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_packssdw((__v2si)__m1, (__v2si)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:193:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_packuswb((__v4hi)__m1, (__v4hi)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:220:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_punpckhbw((__v8qi)__m1, (__v8qi)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:243:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_punpckhwd((__v4hi)__m1, (__v4hi)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:264:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_punpckhdq((__v2si)__m1, (__v2si)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:291:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_punpcklbw((__v8qi)__m1, (__v8qi)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:314:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_punpcklwd((__v4hi)__m1, (__v4hi)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:335:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_punpckldq((__v2si)__m1, (__v2si)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:356:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_paddb((__v8qi)__m1, (__v8qi)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:377:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_paddw((__v4hi)__m1, (__v4hi)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:398:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_paddd((__v2si)__m1, (__v2si)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:420:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_paddsb((__v8qi)__m1, (__v8qi)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:443:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_paddsw((__v4hi)__m1, (__v4hi)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:465:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_paddusb((__v8qi)__m1, (__v8qi)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
configure:9048: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gmap"
| #define PACKAGE_TARNAME "gmap"
| #define PACKAGE_VERSION "2021-12-17"
| #define PACKAGE_STRING "gmap 2021-12-17"
| #define PACKAGE_BUGREPORT "Thomas Wu <twu@gene.com>"
| #define PACKAGE_URL ""
| #define PACKAGE "gmap"
| #define VERSION "2021-12-17"
| #define HAVE_LIBM 1
| #define HAVE_PTHREAD 1
| #define STDC_HEADERS 1
| #define HAVE_DIRENT_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_INLINE 1
| #define HAVE_CADDR_T 1
| #define SIZEOF_UNSIGNED_LONG 8
| #define SIZEOF_UNSIGNED_LONG_LONG 8
| #define SIZEOF_OFF_T 8
| #define HAVE_FSEEKO 1
| #define HAVE_MMAP_MAP_FILE 1
| #define HAVE_MMAP_MAP_SHARED 1
| #define HAVE_MMAP_MAP_PRIVATE 1
| #define HAVE_MADVISE_MADV_DONTNEED 1
| #define HAVE_MADVISE_MADV_WILLNEED 1
| #define HAVE_MADVISE_MADV_RANDOM 1
| #define HAVE_MADVISE_MADV_SEQUENTIAL 1
| #define HAVE_CEIL 1
| #define HAVE_FLOOR 1
| #define HAVE_INDEX 1
| #define HAVE_LOG 1
| #define HAVE_MADVISE 1
| #define HAVE_MEMCPY 1
| #define HAVE_MEMMOVE 1
| #define HAVE_MEMSET 1
| #define HAVE_MUNMAP 1
| #define HAVE_POW 1
| #define HAVE_RINT 1
| #define HAVE_STAT64 1
| #define HAVE_STRTOUL 1
| #define HAVE_SYSCONF 1
| #define HAVE_SYSCTL 1
| #define HAVE_SIGACTION 1
| #define HAVE_SHMGET 1
| #define HAVE_SHMCTL 1
| #define HAVE_SHMAT 1
| #define HAVE_SHMDT 1
| #define HAVE_SEMGET 1
| #define HAVE_SEMCTL 1
| #define HAVE_SEMOP 1
| #define PAGESIZE_VIA_SYSCONF 1
| #define PAGESIZE_VIA_SYSCTL 1
| #define USE_FOPEN_BINARY 1
| #define USE_FOPEN_TEXT 1
| /* end confdefs.h. */
| #include <stdio.h>
| #include <stdlib.h>
| #include <emmintrin.h>
| int
| main ()
| {
| int nshift = rand() % 32;
| __m128i shifted;
| shifted = _mm_slli_epi32(_mm_set1_epi32(1),nshift);
|
| ;
| return 0;
| }
configure:9055: result: yes
configure:9079: checking for _mm_extract_epi64
configure:9092: clang -c -O3 -fomit-frame-pointer conftest.c >&5
In file included from conftest.c:73:
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/smmintrin.h:14:2: error: "This header is only meant to be used on x86 and x64 architecture"
#error "This header is only meant to be used on x86 and x64 architecture"
^
In file included from conftest.c:73:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/smmintrin.h:17:
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/tmmintrin.h:14:2: error: "This header is only meant to be used on x86 and x64 architecture"
#error "This header is only meant to be used on x86 and x64 architecture"
^
In file included from conftest.c:73:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/smmintrin.h:17:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/tmmintrin.h:17:
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/pmmintrin.h:14:2: error: "This header is only meant to be used on x86 and x64 architecture"
#error "This header is only meant to be used on x86 and x64 architecture"
^
In file included from conftest.c:73:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/smmintrin.h:17:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/tmmintrin.h:17:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/pmmintrin.h:17:
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/emmintrin.h:14:2: error: "This header is only meant to be used on x86 and x64 architecture"
#error "This header is only meant to be used on x86 and x64 architecture"
^
In file included from conftest.c:73:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/smmintrin.h:17:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/tmmintrin.h:17:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/pmmintrin.h:17:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/emmintrin.h:17:
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/xmmintrin.h:14:2: error: "This header is only meant to be used on x86 and x64 architecture"
#error "This header is only meant to be used on x86 and x64 architecture"
^
In file included from conftest.c:73:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/smmintrin.h:17:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/tmmintrin.h:17:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/pmmintrin.h:17:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/emmintrin.h:17:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/xmmintrin.h:17:
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:14:2: error: "This header is only meant to be used on x86 and x64 architecture"
#error "This header is only meant to be used on x86 and x64 architecture"
^
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:54:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_vec_init_v2si(__i, 0);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:133:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_packsswb((__v4hi)__m1, (__v4hi)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:163:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_packssdw((__v2si)__m1, (__v2si)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:193:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_packuswb((__v4hi)__m1, (__v4hi)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:220:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_punpckhbw((__v8qi)__m1, (__v8qi)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:243:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_punpckhwd((__v4hi)__m1, (__v4hi)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:264:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_punpckhdq((__v2si)__m1, (__v2si)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:291:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_punpcklbw((__v8qi)__m1, (__v8qi)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:314:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_punpcklwd((__v4hi)__m1, (__v4hi)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:335:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_punpckldq((__v2si)__m1, (__v2si)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:356:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_paddb((__v8qi)__m1, (__v8qi)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:377:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_paddw((__v4hi)__m1, (__v4hi)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:398:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_paddd((__v2si)__m1, (__v2si)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
configure:9092: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gmap"
| #define PACKAGE_TARNAME "gmap"
| #define PACKAGE_VERSION "2021-12-17"
| #define PACKAGE_STRING "gmap 2021-12-17"
| #define PACKAGE_BUGREPORT "Thomas Wu <twu@gene.com>"
| #define PACKAGE_URL ""
| #define PACKAGE "gmap"
| #define VERSION "2021-12-17"
| #define HAVE_LIBM 1
| #define HAVE_PTHREAD 1
| #define STDC_HEADERS 1
| #define HAVE_DIRENT_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_INLINE 1
| #define HAVE_CADDR_T 1
| #define SIZEOF_UNSIGNED_LONG 8
| #define SIZEOF_UNSIGNED_LONG_LONG 8
| #define SIZEOF_OFF_T 8
| #define HAVE_FSEEKO 1
| #define HAVE_MMAP_MAP_FILE 1
| #define HAVE_MMAP_MAP_SHARED 1
| #define HAVE_MMAP_MAP_PRIVATE 1
| #define HAVE_MADVISE_MADV_DONTNEED 1
| #define HAVE_MADVISE_MADV_WILLNEED 1
| #define HAVE_MADVISE_MADV_RANDOM 1
| #define HAVE_MADVISE_MADV_SEQUENTIAL 1
| #define HAVE_CEIL 1
| #define HAVE_FLOOR 1
| #define HAVE_INDEX 1
| #define HAVE_LOG 1
| #define HAVE_MADVISE 1
| #define HAVE_MEMCPY 1
| #define HAVE_MEMMOVE 1
| #define HAVE_MEMSET 1
| #define HAVE_MUNMAP 1
| #define HAVE_POW 1
| #define HAVE_RINT 1
| #define HAVE_STAT64 1
| #define HAVE_STRTOUL 1
| #define HAVE_SYSCONF 1
| #define HAVE_SYSCTL 1
| #define HAVE_SIGACTION 1
| #define HAVE_SHMGET 1
| #define HAVE_SHMCTL 1
| #define HAVE_SHMAT 1
| #define HAVE_SHMDT 1
| #define HAVE_SEMGET 1
| #define HAVE_SEMCTL 1
| #define HAVE_SEMOP 1
| #define PAGESIZE_VIA_SYSCONF 1
| #define PAGESIZE_VIA_SYSCTL 1
| #define USE_FOPEN_BINARY 1
| #define USE_FOPEN_TEXT 1
| #define DEFECTIVE_SSE2_COMPILER 1
| /* end confdefs.h. */
| #include <smmintrin.h>
| int
| main ()
| {
| __m128i a;
| ;
| return 0;
| }
configure:9099: result: no
configure:9104: checking for _mm_popcnt_u64
configure:9117: clang -c -O3 -fomit-frame-pointer conftest.c >&5
In file included from conftest.c:73:
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/smmintrin.h:14:2: error: "This header is only meant to be used on x86 and x64 architecture"
#error "This header is only meant to be used on x86 and x64 architecture"
^
In file included from conftest.c:73:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/smmintrin.h:17:
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/tmmintrin.h:14:2: error: "This header is only meant to be used on x86 and x64 architecture"
#error "This header is only meant to be used on x86 and x64 architecture"
^
In file included from conftest.c:73:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/smmintrin.h:17:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/tmmintrin.h:17:
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/pmmintrin.h:14:2: error: "This header is only meant to be used on x86 and x64 architecture"
#error "This header is only meant to be used on x86 and x64 architecture"
^
In file included from conftest.c:73:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/smmintrin.h:17:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/tmmintrin.h:17:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/pmmintrin.h:17:
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/emmintrin.h:14:2: error: "This header is only meant to be used on x86 and x64 architecture"
#error "This header is only meant to be used on x86 and x64 architecture"
^
In file included from conftest.c:73:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/smmintrin.h:17:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/tmmintrin.h:17:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/pmmintrin.h:17:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/emmintrin.h:17:
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/xmmintrin.h:14:2: error: "This header is only meant to be used on x86 and x64 architecture"
#error "This header is only meant to be used on x86 and x64 architecture"
^
In file included from conftest.c:73:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/smmintrin.h:17:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/tmmintrin.h:17:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/pmmintrin.h:17:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/emmintrin.h:17:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/xmmintrin.h:17:
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:14:2: error: "This header is only meant to be used on x86 and x64 architecture"
#error "This header is only meant to be used on x86 and x64 architecture"
^
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:54:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_vec_init_v2si(__i, 0);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:133:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_packsswb((__v4hi)__m1, (__v4hi)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:163:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_packssdw((__v2si)__m1, (__v2si)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:193:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_packuswb((__v4hi)__m1, (__v4hi)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:220:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_punpckhbw((__v8qi)__m1, (__v8qi)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:243:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_punpckhwd((__v4hi)__m1, (__v4hi)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:264:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_punpckhdq((__v2si)__m1, (__v2si)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:291:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_punpcklbw((__v8qi)__m1, (__v8qi)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:314:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_punpcklwd((__v4hi)__m1, (__v4hi)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:335:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_punpckldq((__v2si)__m1, (__v2si)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:356:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_paddb((__v8qi)__m1, (__v8qi)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:377:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_paddw((__v4hi)__m1, (__v4hi)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:398:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
return (__m64)__builtin_ia32_paddd((__v2si)__m1, (__v2si)__m2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
configure:9117: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gmap"
| #define PACKAGE_TARNAME "gmap"
| #define PACKAGE_VERSION "2021-12-17"
| #define PACKAGE_STRING "gmap 2021-12-17"
| #define PACKAGE_BUGREPORT "Thomas Wu <twu@gene.com>"
| #define PACKAGE_URL ""
| #define PACKAGE "gmap"
| #define VERSION "2021-12-17"
| #define HAVE_LIBM 1
| #define HAVE_PTHREAD 1
| #define STDC_HEADERS 1
| #define HAVE_DIRENT_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_INLINE 1
| #define HAVE_CADDR_T 1
| #define SIZEOF_UNSIGNED_LONG 8
| #define SIZEOF_UNSIGNED_LONG_LONG 8
| #define SIZEOF_OFF_T 8
| #define HAVE_FSEEKO 1
| #define HAVE_MMAP_MAP_FILE 1
| #define HAVE_MMAP_MAP_SHARED 1
| #define HAVE_MMAP_MAP_PRIVATE 1
| #define HAVE_MADVISE_MADV_DONTNEED 1
| #define HAVE_MADVISE_MADV_WILLNEED 1
| #define HAVE_MADVISE_MADV_RANDOM 1
| #define HAVE_MADVISE_MADV_SEQUENTIAL 1
| #define HAVE_CEIL 1
| #define HAVE_FLOOR 1
| #define HAVE_INDEX 1
| #define HAVE_LOG 1
| #define HAVE_MADVISE 1
| #define HAVE_MEMCPY 1
| #define HAVE_MEMMOVE 1
| #define HAVE_MEMSET 1
| #define HAVE_MUNMAP 1
| #define HAVE_POW 1
| #define HAVE_RINT 1
| #define HAVE_STAT64 1
| #define HAVE_STRTOUL 1
| #define HAVE_SYSCONF 1
| #define HAVE_SYSCTL 1
| #define HAVE_SIGACTION 1
| #define HAVE_SHMGET 1
| #define HAVE_SHMCTL 1
| #define HAVE_SHMAT 1
| #define HAVE_SHMDT 1
| #define HAVE_SEMGET 1
| #define HAVE_SEMCTL 1
| #define HAVE_SEMOP 1
| #define PAGESIZE_VIA_SYSCONF 1
| #define PAGESIZE_VIA_SYSCTL 1
| #define USE_FOPEN_BINARY 1
| #define USE_FOPEN_TEXT 1
| #define DEFECTIVE_SSE2_COMPILER 1
| /* end confdefs.h. */
| #include <smmintrin.h>
| int
| main ()
| {
| int a;
| ;
| return 0;
| }
configure:9124: result: no
configure:9137: checking for whether simd is enabled
configure:9160: result: not specified so enabled by default
configure:9428: checking for sse2 support
configure:9454: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
conftest.c:76:22: error: invalid output constraint '+b' in asm
__asm__ ("cpuid" : "+b" (ebx), "+a" (eax), "+c" (ecx), "=d" (edx));
^
1 error generated.
configure:9454: $? = 1
configure: program exited with status 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gmap"
| #define PACKAGE_TARNAME "gmap"
| #define PACKAGE_VERSION "2021-12-17"
| #define PACKAGE_STRING "gmap 2021-12-17"
| #define PACKAGE_BUGREPORT "Thomas Wu <twu@gene.com>"
| #define PACKAGE_URL ""
| #define PACKAGE "gmap"
| #define VERSION "2021-12-17"
| #define HAVE_LIBM 1
| #define HAVE_PTHREAD 1
| #define STDC_HEADERS 1
| #define HAVE_DIRENT_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_INLINE 1
| #define HAVE_CADDR_T 1
| #define SIZEOF_UNSIGNED_LONG 8
| #define SIZEOF_UNSIGNED_LONG_LONG 8
| #define SIZEOF_OFF_T 8
| #define HAVE_FSEEKO 1
| #define HAVE_MMAP_MAP_FILE 1
| #define HAVE_MMAP_MAP_SHARED 1
| #define HAVE_MMAP_MAP_PRIVATE 1
| #define HAVE_MADVISE_MADV_DONTNEED 1
| #define HAVE_MADVISE_MADV_WILLNEED 1
| #define HAVE_MADVISE_MADV_RANDOM 1
| #define HAVE_MADVISE_MADV_SEQUENTIAL 1
| #define HAVE_CEIL 1
| #define HAVE_FLOOR 1
| #define HAVE_INDEX 1
| #define HAVE_LOG 1
| #define HAVE_MADVISE 1
| #define HAVE_MEMCPY 1
| #define HAVE_MEMMOVE 1
| #define HAVE_MEMSET 1
| #define HAVE_MUNMAP 1
| #define HAVE_POW 1
| #define HAVE_RINT 1
| #define HAVE_STAT64 1
| #define HAVE_STRTOUL 1
| #define HAVE_SYSCONF 1
| #define HAVE_SYSCTL 1
| #define HAVE_SIGACTION 1
| #define HAVE_SHMGET 1
| #define HAVE_SHMCTL 1
| #define HAVE_SHMAT 1
| #define HAVE_SHMDT 1
| #define HAVE_SEMGET 1
| #define HAVE_SEMCTL 1
| #define HAVE_SEMOP 1
| #define PAGESIZE_VIA_SYSCONF 1
| #define PAGESIZE_VIA_SYSCTL 1
| #define USE_FOPEN_BINARY 1
| #define USE_FOPEN_TEXT 1
| #define DEFECTIVE_SSE2_COMPILER 1
| /* end confdefs.h. */
| #include <stdint.h>
| static void run_cpuid (uint32_t eax, uint32_t ecx, uint32_t *abcd) {
| uint32_t ebx, edx;
| __asm__ ("cpuid" : "+b" (ebx), "+a" (eax), "+c" (ecx), "=d" (edx));
| abcd[0] = eax; abcd[1] = ebx; abcd[2] = ecx; abcd[3] = edx;}
| int
| main ()
| {
| uint32_t abcd[4];
| uint32_t sse2_mask = (1 << 26);
| run_cpuid(1, 0, abcd);
| return ((abcd[/*EDX*/3] & sse2_mask) == sse2_mask) ? 0 : 9;
| ;
| return 0;
| }
configure:9459: result: no
configure:9468: checking for ssse3 support
configure:9494: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
conftest.c:76:22: error: invalid output constraint '+b' in asm
__asm__ ("cpuid" : "+b" (ebx), "+a" (eax), "+c" (ecx), "=d" (edx));
^
1 error generated.
configure:9494: $? = 1
configure: program exited with status 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gmap"
| #define PACKAGE_TARNAME "gmap"
| #define PACKAGE_VERSION "2021-12-17"
| #define PACKAGE_STRING "gmap 2021-12-17"
| #define PACKAGE_BUGREPORT "Thomas Wu <twu@gene.com>"
| #define PACKAGE_URL ""
| #define PACKAGE "gmap"
| #define VERSION "2021-12-17"
| #define HAVE_LIBM 1
| #define HAVE_PTHREAD 1
| #define STDC_HEADERS 1
| #define HAVE_DIRENT_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_INLINE 1
| #define HAVE_CADDR_T 1
| #define SIZEOF_UNSIGNED_LONG 8
| #define SIZEOF_UNSIGNED_LONG_LONG 8
| #define SIZEOF_OFF_T 8
| #define HAVE_FSEEKO 1
| #define HAVE_MMAP_MAP_FILE 1
| #define HAVE_MMAP_MAP_SHARED 1
| #define HAVE_MMAP_MAP_PRIVATE 1
| #define HAVE_MADVISE_MADV_DONTNEED 1
| #define HAVE_MADVISE_MADV_WILLNEED 1
| #define HAVE_MADVISE_MADV_RANDOM 1
| #define HAVE_MADVISE_MADV_SEQUENTIAL 1
| #define HAVE_CEIL 1
| #define HAVE_FLOOR 1
| #define HAVE_INDEX 1
| #define HAVE_LOG 1
| #define HAVE_MADVISE 1
| #define HAVE_MEMCPY 1
| #define HAVE_MEMMOVE 1
| #define HAVE_MEMSET 1
| #define HAVE_MUNMAP 1
| #define HAVE_POW 1
| #define HAVE_RINT 1
| #define HAVE_STAT64 1
| #define HAVE_STRTOUL 1
| #define HAVE_SYSCONF 1
| #define HAVE_SYSCTL 1
| #define HAVE_SIGACTION 1
| #define HAVE_SHMGET 1
| #define HAVE_SHMCTL 1
| #define HAVE_SHMAT 1
| #define HAVE_SHMDT 1
| #define HAVE_SEMGET 1
| #define HAVE_SEMCTL 1
| #define HAVE_SEMOP 1
| #define PAGESIZE_VIA_SYSCONF 1
| #define PAGESIZE_VIA_SYSCTL 1
| #define USE_FOPEN_BINARY 1
| #define USE_FOPEN_TEXT 1
| #define DEFECTIVE_SSE2_COMPILER 1
| /* end confdefs.h. */
| #include <stdint.h>
| static void run_cpuid (uint32_t eax, uint32_t ecx, uint32_t *abcd) {
| uint32_t ebx, edx;
| __asm__ ("cpuid" : "+b" (ebx), "+a" (eax), "+c" (ecx), "=d" (edx));
| abcd[0] = eax; abcd[1] = ebx; abcd[2] = ecx; abcd[3] = edx;}
| int
| main ()
| {
| uint32_t abcd[4];
| uint32_t ssse3_mask = (1 << 9);
| run_cpuid(1, 0, abcd);
| return ((abcd[/*ECX*/2] & ssse3_mask) == ssse3_mask) ? 0 : 9;
| ;
| return 0;
| }
configure:9499: result: no
configure:9508: checking for sse4.1 support
configure:9534: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
conftest.c:76:22: error: invalid output constraint '+b' in asm
__asm__ ("cpuid" : "+b" (ebx), "+a" (eax), "+c" (ecx), "=d" (edx));
^
1 error generated.
configure:9534: $? = 1
configure: program exited with status 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gmap"
| #define PACKAGE_TARNAME "gmap"
| #define PACKAGE_VERSION "2021-12-17"
| #define PACKAGE_STRING "gmap 2021-12-17"
| #define PACKAGE_BUGREPORT "Thomas Wu <twu@gene.com>"
| #define PACKAGE_URL ""
| #define PACKAGE "gmap"
| #define VERSION "2021-12-17"
| #define HAVE_LIBM 1
| #define HAVE_PTHREAD 1
| #define STDC_HEADERS 1
| #define HAVE_DIRENT_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_INLINE 1
| #define HAVE_CADDR_T 1
| #define SIZEOF_UNSIGNED_LONG 8
| #define SIZEOF_UNSIGNED_LONG_LONG 8
| #define SIZEOF_OFF_T 8
| #define HAVE_FSEEKO 1
| #define HAVE_MMAP_MAP_FILE 1
| #define HAVE_MMAP_MAP_SHARED 1
| #define HAVE_MMAP_MAP_PRIVATE 1
| #define HAVE_MADVISE_MADV_DONTNEED 1
| #define HAVE_MADVISE_MADV_WILLNEED 1
| #define HAVE_MADVISE_MADV_RANDOM 1
| #define HAVE_MADVISE_MADV_SEQUENTIAL 1
| #define HAVE_CEIL 1
| #define HAVE_FLOOR 1
| #define HAVE_INDEX 1
| #define HAVE_LOG 1
| #define HAVE_MADVISE 1
| #define HAVE_MEMCPY 1
| #define HAVE_MEMMOVE 1
| #define HAVE_MEMSET 1
| #define HAVE_MUNMAP 1
| #define HAVE_POW 1
| #define HAVE_RINT 1
| #define HAVE_STAT64 1
| #define HAVE_STRTOUL 1
| #define HAVE_SYSCONF 1
| #define HAVE_SYSCTL 1
| #define HAVE_SIGACTION 1
| #define HAVE_SHMGET 1
| #define HAVE_SHMCTL 1
| #define HAVE_SHMAT 1
| #define HAVE_SHMDT 1
| #define HAVE_SEMGET 1
| #define HAVE_SEMCTL 1
| #define HAVE_SEMOP 1
| #define PAGESIZE_VIA_SYSCONF 1
| #define PAGESIZE_VIA_SYSCTL 1
| #define USE_FOPEN_BINARY 1
| #define USE_FOPEN_TEXT 1
| #define DEFECTIVE_SSE2_COMPILER 1
| /* end confdefs.h. */
| #include <stdint.h>
| static void run_cpuid (uint32_t eax, uint32_t ecx, uint32_t *abcd) {
| uint32_t ebx, edx;
| __asm__ ("cpuid" : "+b" (ebx), "+a" (eax), "+c" (ecx), "=d" (edx));
| abcd[0] = eax; abcd[1] = ebx; abcd[2] = ecx; abcd[3] = edx;}
| int
| main ()
| {
| uint32_t abcd[4];
| uint32_t sse4_1_mask = (1 << 19);
| run_cpuid(1, 0, abcd);
| return ((abcd[/*ECX*/2] & sse4_1_mask) == sse4_1_mask) ? 0 : 9;
| ;
| return 0;
| }
configure:9539: result: no
configure:9548: checking for sse4.2 support
configure:9574: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
conftest.c:76:22: error: invalid output constraint '+b' in asm
__asm__ ("cpuid" : "+b" (ebx), "+a" (eax), "+c" (ecx), "=d" (edx));
^
1 error generated.
configure:9574: $? = 1
configure: program exited with status 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gmap"
| #define PACKAGE_TARNAME "gmap"
| #define PACKAGE_VERSION "2021-12-17"
| #define PACKAGE_STRING "gmap 2021-12-17"
| #define PACKAGE_BUGREPORT "Thomas Wu <twu@gene.com>"
| #define PACKAGE_URL ""
| #define PACKAGE "gmap"
| #define VERSION "2021-12-17"
| #define HAVE_LIBM 1
| #define HAVE_PTHREAD 1
| #define STDC_HEADERS 1
| #define HAVE_DIRENT_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_INLINE 1
| #define HAVE_CADDR_T 1
| #define SIZEOF_UNSIGNED_LONG 8
| #define SIZEOF_UNSIGNED_LONG_LONG 8
| #define SIZEOF_OFF_T 8
| #define HAVE_FSEEKO 1
| #define HAVE_MMAP_MAP_FILE 1
| #define HAVE_MMAP_MAP_SHARED 1
| #define HAVE_MMAP_MAP_PRIVATE 1
| #define HAVE_MADVISE_MADV_DONTNEED 1
| #define HAVE_MADVISE_MADV_WILLNEED 1
| #define HAVE_MADVISE_MADV_RANDOM 1
| #define HAVE_MADVISE_MADV_SEQUENTIAL 1
| #define HAVE_CEIL 1
| #define HAVE_FLOOR 1
| #define HAVE_INDEX 1
| #define HAVE_LOG 1
| #define HAVE_MADVISE 1
| #define HAVE_MEMCPY 1
| #define HAVE_MEMMOVE 1
| #define HAVE_MEMSET 1
| #define HAVE_MUNMAP 1
| #define HAVE_POW 1
| #define HAVE_RINT 1
| #define HAVE_STAT64 1
| #define HAVE_STRTOUL 1
| #define HAVE_SYSCONF 1
| #define HAVE_SYSCTL 1
| #define HAVE_SIGACTION 1
| #define HAVE_SHMGET 1
| #define HAVE_SHMCTL 1
| #define HAVE_SHMAT 1
| #define HAVE_SHMDT 1
| #define HAVE_SEMGET 1
| #define HAVE_SEMCTL 1
| #define HAVE_SEMOP 1
| #define PAGESIZE_VIA_SYSCONF 1
| #define PAGESIZE_VIA_SYSCTL 1
| #define USE_FOPEN_BINARY 1
| #define USE_FOPEN_TEXT 1
| #define DEFECTIVE_SSE2_COMPILER 1
| /* end confdefs.h. */
| #include <stdint.h>
| static void run_cpuid (uint32_t eax, uint32_t ecx, uint32_t *abcd) {
| uint32_t ebx, edx;
| __asm__ ("cpuid" : "+b" (ebx), "+a" (eax), "+c" (ecx), "=d" (edx));
| abcd[0] = eax; abcd[1] = ebx; abcd[2] = ecx; abcd[3] = edx;}
| int
| main ()
| {
| uint32_t abcd[4];
| uint32_t sse4_2_mask = (1 << 20);
| run_cpuid(1, 0, abcd);
| return ((abcd[/*ECX*/2] & sse4_2_mask) == sse4_2_mask) ? 0 : 9;
| ;
| return 0;
| }
configure:9579: result: no
configure:9588: checking for popcnt support
configure:9614: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
conftest.c:76:22: error: invalid output constraint '+b' in asm
__asm__ ("cpuid" : "+b" (ebx), "+a" (eax), "+c" (ecx), "=d" (edx));
^
1 error generated.
configure:9614: $? = 1
configure: program exited with status 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gmap"
| #define PACKAGE_TARNAME "gmap"
| #define PACKAGE_VERSION "2021-12-17"
| #define PACKAGE_STRING "gmap 2021-12-17"
| #define PACKAGE_BUGREPORT "Thomas Wu <twu@gene.com>"
| #define PACKAGE_URL ""
| #define PACKAGE "gmap"
| #define VERSION "2021-12-17"
| #define HAVE_LIBM 1
| #define HAVE_PTHREAD 1
| #define STDC_HEADERS 1
| #define HAVE_DIRENT_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_INLINE 1
| #define HAVE_CADDR_T 1
| #define SIZEOF_UNSIGNED_LONG 8
| #define SIZEOF_UNSIGNED_LONG_LONG 8
| #define SIZEOF_OFF_T 8
| #define HAVE_FSEEKO 1
| #define HAVE_MMAP_MAP_FILE 1
| #define HAVE_MMAP_MAP_SHARED 1
| #define HAVE_MMAP_MAP_PRIVATE 1
| #define HAVE_MADVISE_MADV_DONTNEED 1
| #define HAVE_MADVISE_MADV_WILLNEED 1
| #define HAVE_MADVISE_MADV_RANDOM 1
| #define HAVE_MADVISE_MADV_SEQUENTIAL 1
| #define HAVE_CEIL 1
| #define HAVE_FLOOR 1
| #define HAVE_INDEX 1
| #define HAVE_LOG 1
| #define HAVE_MADVISE 1
| #define HAVE_MEMCPY 1
| #define HAVE_MEMMOVE 1
| #define HAVE_MEMSET 1
| #define HAVE_MUNMAP 1
| #define HAVE_POW 1
| #define HAVE_RINT 1
| #define HAVE_STAT64 1
| #define HAVE_STRTOUL 1
| #define HAVE_SYSCONF 1
| #define HAVE_SYSCTL 1
| #define HAVE_SIGACTION 1
| #define HAVE_SHMGET 1
| #define HAVE_SHMCTL 1
| #define HAVE_SHMAT 1
| #define HAVE_SHMDT 1
| #define HAVE_SEMGET 1
| #define HAVE_SEMCTL 1
| #define HAVE_SEMOP 1
| #define PAGESIZE_VIA_SYSCONF 1
| #define PAGESIZE_VIA_SYSCTL 1
| #define USE_FOPEN_BINARY 1
| #define USE_FOPEN_TEXT 1
| #define DEFECTIVE_SSE2_COMPILER 1
| /* end confdefs.h. */
| #include <stdint.h>
| static void run_cpuid (uint32_t eax, uint32_t ecx, uint32_t *abcd) {
| uint32_t ebx, edx;
| __asm__ ("cpuid" : "+b" (ebx), "+a" (eax), "+c" (ecx), "=d" (edx));
| abcd[0] = eax; abcd[1] = ebx; abcd[2] = ecx; abcd[3] = edx;}
| int
| main ()
| {
| uint32_t abcd[4];
| uint32_t popcnt_mask = (1 << 23);
| run_cpuid(1, 0, abcd);
| return ((abcd[/*ECX*/2] & popcnt_mask) == popcnt_mask) ? 0 : 9;
| ;
| return 0;
| }
configure:9619: result: no
configure:9628: checking for bmi1 support
configure:9654: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
conftest.c:76:22: error: invalid output constraint '+b' in asm
__asm__ ("cpuid" : "+b" (ebx), "+a" (eax), "+c" (ecx), "=d" (edx));
^
1 error generated.
configure:9654: $? = 1
configure: program exited with status 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gmap"
| #define PACKAGE_TARNAME "gmap"
| #define PACKAGE_VERSION "2021-12-17"
| #define PACKAGE_STRING "gmap 2021-12-17"
| #define PACKAGE_BUGREPORT "Thomas Wu <twu@gene.com>"
| #define PACKAGE_URL ""
| #define PACKAGE "gmap"
| #define VERSION "2021-12-17"
| #define HAVE_LIBM 1
| #define HAVE_PTHREAD 1
| #define STDC_HEADERS 1
| #define HAVE_DIRENT_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_INLINE 1
| #define HAVE_CADDR_T 1
| #define SIZEOF_UNSIGNED_LONG 8
| #define SIZEOF_UNSIGNED_LONG_LONG 8
| #define SIZEOF_OFF_T 8
| #define HAVE_FSEEKO 1
| #define HAVE_MMAP_MAP_FILE 1
| #define HAVE_MMAP_MAP_SHARED 1
| #define HAVE_MMAP_MAP_PRIVATE 1
| #define HAVE_MADVISE_MADV_DONTNEED 1
| #define HAVE_MADVISE_MADV_WILLNEED 1
| #define HAVE_MADVISE_MADV_RANDOM 1
| #define HAVE_MADVISE_MADV_SEQUENTIAL 1
| #define HAVE_CEIL 1
| #define HAVE_FLOOR 1
| #define HAVE_INDEX 1
| #define HAVE_LOG 1
| #define HAVE_MADVISE 1
| #define HAVE_MEMCPY 1
| #define HAVE_MEMMOVE 1
| #define HAVE_MEMSET 1
| #define HAVE_MUNMAP 1
| #define HAVE_POW 1
| #define HAVE_RINT 1
| #define HAVE_STAT64 1
| #define HAVE_STRTOUL 1
| #define HAVE_SYSCONF 1
| #define HAVE_SYSCTL 1
| #define HAVE_SIGACTION 1
| #define HAVE_SHMGET 1
| #define HAVE_SHMCTL 1
| #define HAVE_SHMAT 1
| #define HAVE_SHMDT 1
| #define HAVE_SEMGET 1
| #define HAVE_SEMCTL 1
| #define HAVE_SEMOP 1
| #define PAGESIZE_VIA_SYSCONF 1
| #define PAGESIZE_VIA_SYSCTL 1
| #define USE_FOPEN_BINARY 1
| #define USE_FOPEN_TEXT 1
| #define DEFECTIVE_SSE2_COMPILER 1
| /* end confdefs.h. */
| #include <stdint.h>
| static void run_cpuid (uint32_t eax, uint32_t ecx, uint32_t *abcd) {
| uint32_t ebx, edx;
| __asm__ ("cpuid" : "+b" (ebx), "+a" (eax), "+c" (ecx), "=d" (edx));
| abcd[0] = eax; abcd[1] = ebx; abcd[2] = ecx; abcd[3] = edx;}
| int
| main ()
| {
| uint32_t abcd[4];
| uint32_t bmi1_mask = (1 << 3);
| run_cpuid(1, 0, abcd);
| return ((abcd[/*EBX*/1] & bmi1_mask) == bmi1_mask) ? 0 : 9;
| ;
| return 0;
| }
configure:9659: result: no
configure:9668: checking for avx2 support
configure:9716: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
conftest.c:76:22: error: invalid output constraint '+b' in asm
__asm__ ("cpuid" : "+b" (ebx), "+a" (eax), "+c" (ecx), "=d" (edx));
^
conftest.c:80:23: error: invalid output constraint '=a' in asm
__asm__ ("xgetbv" : "=a" (xcr0) : "c" (0) : "%edx");
^
2 errors generated.
configure:9716: $? = 1
configure: program exited with status 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gmap"
| #define PACKAGE_TARNAME "gmap"
| #define PACKAGE_VERSION "2021-12-17"
| #define PACKAGE_STRING "gmap 2021-12-17"
| #define PACKAGE_BUGREPORT "Thomas Wu <twu@gene.com>"
| #define PACKAGE_URL ""
| #define PACKAGE "gmap"
| #define VERSION "2021-12-17"
| #define HAVE_LIBM 1
| #define HAVE_PTHREAD 1
| #define STDC_HEADERS 1
| #define HAVE_DIRENT_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_INLINE 1
| #define HAVE_CADDR_T 1
| #define SIZEOF_UNSIGNED_LONG 8
| #define SIZEOF_UNSIGNED_LONG_LONG 8
| #define SIZEOF_OFF_T 8
| #define HAVE_FSEEKO 1
| #define HAVE_MMAP_MAP_FILE 1
| #define HAVE_MMAP_MAP_SHARED 1
| #define HAVE_MMAP_MAP_PRIVATE 1
| #define HAVE_MADVISE_MADV_DONTNEED 1
| #define HAVE_MADVISE_MADV_WILLNEED 1
| #define HAVE_MADVISE_MADV_RANDOM 1
| #define HAVE_MADVISE_MADV_SEQUENTIAL 1
| #define HAVE_CEIL 1
| #define HAVE_FLOOR 1
| #define HAVE_INDEX 1
| #define HAVE_LOG 1
| #define HAVE_MADVISE 1
| #define HAVE_MEMCPY 1
| #define HAVE_MEMMOVE 1
| #define HAVE_MEMSET 1
| #define HAVE_MUNMAP 1
| #define HAVE_POW 1
| #define HAVE_RINT 1
| #define HAVE_STAT64 1
| #define HAVE_STRTOUL 1
| #define HAVE_SYSCONF 1
| #define HAVE_SYSCTL 1
| #define HAVE_SIGACTION 1
| #define HAVE_SHMGET 1
| #define HAVE_SHMCTL 1
| #define HAVE_SHMAT 1
| #define HAVE_SHMDT 1
| #define HAVE_SEMGET 1
| #define HAVE_SEMCTL 1
| #define HAVE_SEMOP 1
| #define PAGESIZE_VIA_SYSCONF 1
| #define PAGESIZE_VIA_SYSCTL 1
| #define USE_FOPEN_BINARY 1
| #define USE_FOPEN_TEXT 1
| #define DEFECTIVE_SSE2_COMPILER 1
| /* end confdefs.h. */
| #include <stdint.h>
| static void run_cpuid (uint32_t eax, uint32_t ecx, uint32_t *abcd) {
| uint32_t ebx, edx;
| __asm__ ("cpuid" : "+b" (ebx), "+a" (eax), "+c" (ecx), "=d" (edx));
| abcd[0] = eax; abcd[1] = ebx; abcd[2] = ecx; abcd[3] = edx;}
| static int check_xcr0_ymm () {
| uint32_t xcr0;
| __asm__ ("xgetbv" : "=a" (xcr0) : "c" (0) : "%edx");
| return ((xcr0 & 6) == 6);}
| int
| main ()
| {
| uint32_t abcd[4];
| uint32_t fma_movbe_osxsave_mask = ((1 << 12) | (1 << 22) | (1 << 27));
| uint32_t avx2_bmi12_mask = ((1 << 5) | (1 << 3) | (1 << 8));
| uint32_t lzcnt_mask = (1 << 5);
| run_cpuid(1, 0, abcd);
| if ((abcd[/*ECX*/2] & fma_movbe_osxsave_mask) != fma_movbe_osxsave_mask) {
| return 9;
| } else if (!check_xcr0_ymm()) {
| return 8;
| } else {
| run_cpuid(7, 0, abcd);
| if ((abcd[/*EBX*/1] & avx2_bmi12_mask) != avx2_bmi12_mask) {
| return 7;
| } else {
| run_cpuid(0x80000001, 0, abcd);
| if ((abcd[/*ECX*/2] & lzcnt_mask) != lzcnt_mask) {
| return 6;
| } else {
| return 0;
| }
| }
| }
| ;
| return 0;
| }
configure:9721: result: no
configure:9730: checking for bmi2 support
configure:9756: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
conftest.c:76:22: error: invalid output constraint '+b' in asm
__asm__ ("cpuid" : "+b" (ebx), "+a" (eax), "+c" (ecx), "=d" (edx));
^
1 error generated.
configure:9756: $? = 1
configure: program exited with status 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gmap"
| #define PACKAGE_TARNAME "gmap"
| #define PACKAGE_VERSION "2021-12-17"
| #define PACKAGE_STRING "gmap 2021-12-17"
| #define PACKAGE_BUGREPORT "Thomas Wu <twu@gene.com>"
| #define PACKAGE_URL ""
| #define PACKAGE "gmap"
| #define VERSION "2021-12-17"
| #define HAVE_LIBM 1
| #define HAVE_PTHREAD 1
| #define STDC_HEADERS 1
| #define HAVE_DIRENT_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_INLINE 1
| #define HAVE_CADDR_T 1
| #define SIZEOF_UNSIGNED_LONG 8
| #define SIZEOF_UNSIGNED_LONG_LONG 8
| #define SIZEOF_OFF_T 8
| #define HAVE_FSEEKO 1
| #define HAVE_MMAP_MAP_FILE 1
| #define HAVE_MMAP_MAP_SHARED 1
| #define HAVE_MMAP_MAP_PRIVATE 1
| #define HAVE_MADVISE_MADV_DONTNEED 1
| #define HAVE_MADVISE_MADV_WILLNEED 1
| #define HAVE_MADVISE_MADV_RANDOM 1
| #define HAVE_MADVISE_MADV_SEQUENTIAL 1
| #define HAVE_CEIL 1
| #define HAVE_FLOOR 1
| #define HAVE_INDEX 1
| #define HAVE_LOG 1
| #define HAVE_MADVISE 1
| #define HAVE_MEMCPY 1
| #define HAVE_MEMMOVE 1
| #define HAVE_MEMSET 1
| #define HAVE_MUNMAP 1
| #define HAVE_POW 1
| #define HAVE_RINT 1
| #define HAVE_STAT64 1
| #define HAVE_STRTOUL 1
| #define HAVE_SYSCONF 1
| #define HAVE_SYSCTL 1
| #define HAVE_SIGACTION 1
| #define HAVE_SHMGET 1
| #define HAVE_SHMCTL 1
| #define HAVE_SHMAT 1
| #define HAVE_SHMDT 1
| #define HAVE_SEMGET 1
| #define HAVE_SEMCTL 1
| #define HAVE_SEMOP 1
| #define PAGESIZE_VIA_SYSCONF 1
| #define PAGESIZE_VIA_SYSCTL 1
| #define USE_FOPEN_BINARY 1
| #define USE_FOPEN_TEXT 1
| #define DEFECTIVE_SSE2_COMPILER 1
| /* end confdefs.h. */
| #include <stdint.h>
| static void run_cpuid (uint32_t eax, uint32_t ecx, uint32_t *abcd) {
| uint32_t ebx, edx;
| __asm__ ("cpuid" : "+b" (ebx), "+a" (eax), "+c" (ecx), "=d" (edx));
| abcd[0] = eax; abcd[1] = ebx; abcd[2] = ecx; abcd[3] = edx;}
| int
| main ()
| {
| uint32_t abcd[4];
| uint32_t bmi2_mask = (1 << 8);
| run_cpuid(1, 0, abcd);
| return ((abcd[/*EBX*/1] & bmi2_mask) == bmi2_mask) ? 0 : 9;
| ;
| return 0;
| }
configure:9761: result: no
configure:9771: checking for avx512 support
configure:9811: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
conftest.c:76:22: error: invalid output constraint '+b' in asm
__asm__ ("cpuid" : "+b" (ebx), "+a" (eax), "+c" (ecx), "=d" (edx));
^
conftest.c:81:23: error: invalid output constraint '=a' in asm
__asm__ ("xgetbv" : "=a" (xcr0) : "c" (0) : "%edx");
^
2 errors generated.
configure:9811: $? = 1
configure: program exited with status 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gmap"
| #define PACKAGE_TARNAME "gmap"
| #define PACKAGE_VERSION "2021-12-17"
| #define PACKAGE_STRING "gmap 2021-12-17"
| #define PACKAGE_BUGREPORT "Thomas Wu <twu@gene.com>"
| #define PACKAGE_URL ""
| #define PACKAGE "gmap"
| #define VERSION "2021-12-17"
| #define HAVE_LIBM 1
| #define HAVE_PTHREAD 1
| #define STDC_HEADERS 1
| #define HAVE_DIRENT_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_INLINE 1
| #define HAVE_CADDR_T 1
| #define SIZEOF_UNSIGNED_LONG 8
| #define SIZEOF_UNSIGNED_LONG_LONG 8
| #define SIZEOF_OFF_T 8
| #define HAVE_FSEEKO 1
| #define HAVE_MMAP_MAP_FILE 1
| #define HAVE_MMAP_MAP_SHARED 1
| #define HAVE_MMAP_MAP_PRIVATE 1
| #define HAVE_MADVISE_MADV_DONTNEED 1
| #define HAVE_MADVISE_MADV_WILLNEED 1
| #define HAVE_MADVISE_MADV_RANDOM 1
| #define HAVE_MADVISE_MADV_SEQUENTIAL 1
| #define HAVE_CEIL 1
| #define HAVE_FLOOR 1
| #define HAVE_INDEX 1
| #define HAVE_LOG 1
| #define HAVE_MADVISE 1
| #define HAVE_MEMCPY 1
| #define HAVE_MEMMOVE 1
| #define HAVE_MEMSET 1
| #define HAVE_MUNMAP 1
| #define HAVE_POW 1
| #define HAVE_RINT 1
| #define HAVE_STAT64 1
| #define HAVE_STRTOUL 1
| #define HAVE_SYSCONF 1
| #define HAVE_SYSCTL 1
| #define HAVE_SIGACTION 1
| #define HAVE_SHMGET 1
| #define HAVE_SHMCTL 1
| #define HAVE_SHMAT 1
| #define HAVE_SHMDT 1
| #define HAVE_SEMGET 1
| #define HAVE_SEMCTL 1
| #define HAVE_SEMOP 1
| #define PAGESIZE_VIA_SYSCONF 1
| #define PAGESIZE_VIA_SYSCTL 1
| #define USE_FOPEN_BINARY 1
| #define USE_FOPEN_TEXT 1
| #define DEFECTIVE_SSE2_COMPILER 1
| /* end confdefs.h. */
| #include <stdint.h>
| static void run_cpuid (uint32_t eax, uint32_t ecx, uint32_t *abcd) {
| uint32_t ebx, edx;
| __asm__ ("cpuid" : "+b" (ebx), "+a" (eax), "+c" (ecx), "=d" (edx));
| abcd[0] = eax; abcd[1] = ebx; abcd[2] = ecx; abcd[3] = edx;}
| static int check_xcr0_zmm () {
| uint32_t xcr0;
| uint32_t zmm_ymm_xmm = ((7 << 5) | (1 << 2) | (1 << 1));
| __asm__ ("xgetbv" : "=a" (xcr0) : "c" (0) : "%edx");
| return ((xcr0 & zmm_ymm_xmm) == zmm_ymm_xmm);}
| int
| main ()
| {
| uint32_t abcd[4];
| uint32_t osxsave_mask = (1 << 27);
| uint32_t avx512_mask = (/*512F*/(1 << 16) | /*512CD*/(1 << 28));
| run_cpuid(1, 0, abcd);
| if ((abcd[/*ECX*/2] & osxsave_mask) != osxsave_mask) {
| return 9;
| } else if (!check_xcr0_zmm()) {
| return 8;
| } else if ((abcd[/*EBX*/1] & avx512_mask) != avx512_mask) {
| return 0; /* Should be false here, but book/Web examples skip this test */
| } else {
| return 0;
| }
| ;
| return 0;
| }
configure:9816: result: no
configure:9826: checking for avx512bw and avx512vl support
configure:9866: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lm >&5
conftest.c:76:22: error: invalid output constraint '+b' in asm
__asm__ ("cpuid" : "+b" (ebx), "+a" (eax), "+c" (ecx), "=d" (edx));
^
conftest.c:81:23: error: invalid output constraint '=a' in asm
__asm__ ("xgetbv" : "=a" (xcr0) : "c" (0) : "%edx");
^
2 errors generated.
configure:9866: $? = 1
configure: program exited with status 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gmap"
| #define PACKAGE_TARNAME "gmap"
| #define PACKAGE_VERSION "2021-12-17"
| #define PACKAGE_STRING "gmap 2021-12-17"
| #define PACKAGE_BUGREPORT "Thomas Wu <twu@gene.com>"
| #define PACKAGE_URL ""
| #define PACKAGE "gmap"
| #define VERSION "2021-12-17"
| #define HAVE_LIBM 1
| #define HAVE_PTHREAD 1
| #define STDC_HEADERS 1
| #define HAVE_DIRENT_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_LIMITS_H 1
| #define HAVE_STDDEF_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_INLINE 1
| #define HAVE_CADDR_T 1
| #define SIZEOF_UNSIGNED_LONG 8
| #define SIZEOF_UNSIGNED_LONG_LONG 8
| #define SIZEOF_OFF_T 8
| #define HAVE_FSEEKO 1
| #define HAVE_MMAP_MAP_FILE 1
| #define HAVE_MMAP_MAP_SHARED 1
| #define HAVE_MMAP_MAP_PRIVATE 1
| #define HAVE_MADVISE_MADV_DONTNEED 1
| #define HAVE_MADVISE_MADV_WILLNEED 1
| #define HAVE_MADVISE_MADV_RANDOM 1
| #define HAVE_MADVISE_MADV_SEQUENTIAL 1
| #define HAVE_CEIL 1
| #define HAVE_FLOOR 1
| #define HAVE_INDEX 1
| #define HAVE_LOG 1
| #define HAVE_MADVISE 1
| #define HAVE_MEMCPY 1
| #define HAVE_MEMMOVE 1
| #define HAVE_MEMSET 1
| #define HAVE_MUNMAP 1
| #define HAVE_POW 1
| #define HAVE_RINT 1
| #define HAVE_STAT64 1
| #define HAVE_STRTOUL 1
| #define HAVE_SYSCONF 1
| #define HAVE_SYSCTL 1
| #define HAVE_SIGACTION 1
| #define HAVE_SHMGET 1
| #define HAVE_SHMCTL 1
| #define HAVE_SHMAT 1
| #define HAVE_SHMDT 1
| #define HAVE_SEMGET 1
| #define HAVE_SEMCTL 1
| #define HAVE_SEMOP 1
| #define PAGESIZE_VIA_SYSCONF 1
| #define PAGESIZE_VIA_SYSCTL 1
| #define USE_FOPEN_BINARY 1
| #define USE_FOPEN_TEXT 1
| #define DEFECTIVE_SSE2_COMPILER 1
| /* end confdefs.h. */
| #include <stdint.h>
| static void run_cpuid (uint32_t eax, uint32_t ecx, uint32_t *abcd) {
| uint32_t ebx, edx;
| __asm__ ("cpuid" : "+b" (ebx), "+a" (eax), "+c" (ecx), "=d" (edx));
| abcd[0] = eax; abcd[1] = ebx; abcd[2] = ecx; abcd[3] = edx;}
| static int check_xcr0_zmm () {
| uint32_t xcr0;
| uint32_t zmm_ymm_xmm = ((7 << 5) | (1 << 2) | (1 << 1));
| __asm__ ("xgetbv" : "=a" (xcr0) : "c" (0) : "%edx");
| return ((xcr0 & zmm_ymm_xmm) == zmm_ymm_xmm);}
| int
| main ()
| {
| uint32_t abcd[4];
| uint32_t osxsave_mask = (1 << 27);
| uint32_t avx512bw_vl_mask = (/*512BW*/(1 << 30) | /*512VL*/(1 << 31));
| run_cpuid(1, 0, abcd);
| if ((abcd[/*ECX*/2] & osxsave_mask) != osxsave_mask) {
| return 9;
| } else if (!check_xcr0_zmm()) {
| return 8;
| } else if ((abcd[/*EBX*/1] & avx512bw_vl_mask) != avx512bw_vl_mask) {
| return 9;
| } else {
| return 0;
| }
| ;
| return 0;
| }
configure:9871: result: no
configure:11050: checking for user-selected SIMD level
configure:11053: result: sse42
configure:11146: checking gmapdb
configure:11189: result: /opt/homebrew/Cellar/gmap-gsnap/2021-12-17/share
configure:11194: checking MAX_STACK_READLENGTH
configure:11227: result: 300
configure:11233: checking for zlib support
configure:11251: result: enabled
configure:11255: checking zlib.h usability
configure:11255: clang -c -O3 -fomit-frame-pointer conftest.c >&5
configure:11255: $? = 0
configure:11255: result: yes
configure:11255: checking zlib.h presence
configure:11255: clang -E conftest.c
configure:11255: $? = 0
configure:11255: result: yes
configure:11255: checking for zlib.h
configure:11255: result: yes
configure:11263: checking for gzopen in -lz
configure:11288: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lz -lm >&5
configure:11288: $? = 0
configure:11297: result: yes
configure:11305: checking for gzeof in -lz
configure:11330: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lz -lm >&5
configure:11330: $? = 0
configure:11339: result: yes
configure:11347: checking for gzgetc in -lz
configure:11372: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lz -lm >&5
configure:11372: $? = 0
configure:11381: result: yes
configure:11389: checking for gzgets in -lz
configure:11414: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lz -lm >&5
configure:11414: $? = 0
configure:11423: result: yes
configure:11431: checking for gzclose in -lz
configure:11456: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lz -lm >&5
configure:11456: $? = 0
configure:11465: result: yes
configure:11473: checking if zlib package is complete
configure:11482: result: working
configure:11490: checking for gzbuffer in -lz
configure:11515: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lz -lm >&5
configure:11515: $? = 0
configure:11524: result: yes
configure:11547: checking for bzlib support
configure:11565: result: enabled
configure:11569: checking bzlib.h usability
configure:11569: clang -c -O3 -fomit-frame-pointer conftest.c >&5
configure:11569: $? = 0
configure:11569: result: yes
configure:11569: checking bzlib.h presence
configure:11569: clang -E conftest.c
configure:11569: $? = 0
configure:11569: result: yes
configure:11569: checking for bzlib.h
configure:11569: result: yes
configure:11577: checking for BZ2_bzReadOpen in -lbz2
configure:11602: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lbz2 -lm >&5
configure:11602: $? = 0
configure:11611: result: yes
configure:11619: checking for BZ2_bzRead in -lbz2
configure:11644: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lbz2 -lm >&5
configure:11644: $? = 0
configure:11653: result: yes
configure:11661: checking for BZ2_bzReadClose in -lbz2
configure:11686: clang -o conftest -O3 -fomit-frame-pointer conftest.c -lbz2 -lm >&5
configure:11686: $? = 0
configure:11695: result: yes
configure:11703: checking if bzlib package is complete
configure:11712: result: working
configure:11891: checking that generated files are newer than configure
configure:11897: result: done
configure:11961: creating ./config.status
## ---------------------- ##
## Running config.status. ##
## ---------------------- ##
This file was extended by gmap config.status 2021-12-17, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES =
CONFIG_HEADERS =
CONFIG_LINKS =
CONFIG_COMMANDS =
$ ./config.status
on Alex-MacBook.fibertel.com.ar
config.status:986: creating Makefile
config.status:986: creating src/Makefile
config.status:986: creating util/Makefile
config.status:986: creating util/gmap_process.pl
config.status:986: creating util/gmap_build.pl
config.status:986: creating util/gmap_cat.pl
config.status:986: creating util/md_coords.pl
config.status:986: creating util/fa_coords.pl
config.status:986: creating util/psl_splicesites.pl
config.status:986: creating util/psl_introns.pl
config.status:986: creating util/psl_genes.pl
config.status:986: creating util/ensembl_genes.pl
config.status:986: creating util/gtf_splicesites.pl
config.status:986: creating util/gtf_transcript_splicesites.pl
config.status:986: creating util/gtf_introns.pl
config.status:986: creating util/gtf_genes.pl
config.status:986: creating util/gff3_splicesites.pl
config.status:986: creating util/gff3_introns.pl
config.status:986: creating util/gff3_genes.pl
config.status:986: creating util/dbsnp_iit.pl
config.status:986: creating util/gvf_iit.pl
config.status:986: creating util/vcf_iit.pl
config.status:986: creating tests/Makefile
config.status:986: creating tests/align.test
config.status:986: creating tests/coords1.test
config.status:986: creating tests/setup1.test
config.status:986: creating tests/iit.test
config.status:986: creating src/config.h
config.status:1215: executing depfiles commands
configure:13358: WARNING:
WARNING: You don't seem to have memory mapping. GMAP will work
without this, but the program can run faster if memory mapping is
available. If you wish to enable memory mapping, please specify the
appropriate values for CC, PTHREAD_CFLAGS, and PTHREAD_LIBS in the
config.site file and run configure again. Otherwise, you may proceed
with the rest of the installation.
configure:13380: WARNING:
WARNING: Your C compiler does not know how to handle a particular
form of the SSE2 shift commands, and must be somewhat old (probably
gcc 4.1 or gcc 4.2). The configure script has therefore substituted
alternate C code that your compiler can handle. However, for
optimal performance, you may want to obtain a more recent C compiler
and build the code with that.
configure:13436: checking standard compiler and flags to be used
configure:13438: result: clang -O3 -fomit-frame-pointer
configure:13440: checking standard linker flags to be used
configure:13442: result:
configure:13445: checking pthread compiler flags to be used
configure:13447: result: -D_THREAD_SAFE
configure:13450: checking popcnt flags to be used
configure:13452: result: -mpopcnt
configure:13455: checking compile level
configure:13457: result: sse42
configure:13484: checking SSE4.2 compiler flags to be used
configure:13486: result:
## ---------------- ##
## Cache variables. ##
## ---------------- ##
ac_cv_build=arm-apple-darwin21.6.0
ac_cv_c_bigendian=no
ac_cv_c_compiler_gnu=yes
ac_cv_c_const=yes
ac_cv_c_inline=inline
ac_cv_c_volatile=yes
ac_cv_env_CC_set=set
ac_cv_env_CC_value=clang
ac_cv_env_CFLAGS_set=
ac_cv_env_CFLAGS_value=
ac_cv_env_CPPFLAGS_set=
ac_cv_env_CPPFLAGS_value=
ac_cv_env_CPP_set=
ac_cv_env_CPP_value=
ac_cv_env_LDFLAGS_set=
ac_cv_env_LDFLAGS_value=
ac_cv_env_LIBS_set=
ac_cv_env_LIBS_value=
ac_cv_env_MAX_STACK_READLENGTH_set=
ac_cv_env_MAX_STACK_READLENGTH_value=
ac_cv_env_build_alias_set=
ac_cv_env_build_alias_value=
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_func_ceil=yes
ac_cv_func_floor=yes
ac_cv_func_index=yes
ac_cv_func_log=yes
ac_cv_func_madvise=yes
ac_cv_func_memcpy=yes
ac_cv_func_memmove=yes
ac_cv_func_memset=yes
ac_cv_func_munmap=yes
ac_cv_func_pow=yes
ac_cv_func_rint=yes
ac_cv_func_semctl=yes
ac_cv_func_semget=yes
ac_cv_func_semop=yes
ac_cv_func_shmat=yes
ac_cv_func_shmctl=yes
ac_cv_func_shmdt=yes
ac_cv_func_shmget=yes
ac_cv_func_sigaction=yes
ac_cv_func_stat64=yes
ac_cv_func_strtoul=yes
ac_cv_func_sysconf=yes
ac_cv_func_sysctl=yes
ac_cv_have_decl___builtin_clz=no
ac_cv_have_decl___builtin_ctz=no
ac_cv_have_decl___builtin_popcount=no
ac_cv_header_bzlib_h=yes
ac_cv_header_dirent_dirent_h=yes
ac_cv_header_fcntl_h=yes
ac_cv_header_inttypes_h=yes
ac_cv_header_limits_h=yes
ac_cv_header_memory_h=yes
ac_cv_header_stdc=yes
ac_cv_header_stddef_h=yes
ac_cv_header_stdint_h=yes
ac_cv_header_stdlib_h=yes
ac_cv_header_string_h=yes
ac_cv_header_strings_h=yes
ac_cv_header_sys_stat_h=yes
ac_cv_header_sys_types_h=yes
ac_cv_header_unistd_h=yes
ac_cv_header_zlib_h=yes
ac_cv_host=arm-apple-darwin21.6.0
ac_cv_lib_bz2_BZ2_bzRead=yes
ac_cv_lib_bz2_BZ2_bzReadClose=yes
ac_cv_lib_bz2_BZ2_bzReadOpen=yes
ac_cv_lib_m_rint=yes
ac_cv_lib_z_gzbuffer=yes
ac_cv_lib_z_gzclose=yes
ac_cv_lib_z_gzeof=yes
ac_cv_lib_z_gzgetc=yes
ac_cv_lib_z_gzgets=yes
ac_cv_lib_z_gzopen=yes
ac_cv_objext=o
ac_cv_path_EGREP='/usr/bin/grep -E'
ac_cv_path_GREP=/usr/bin/grep
ac_cv_path_PERL=/usr/bin/perl
ac_cv_path_install='/usr/bin/install -c'
ac_cv_prog_AWK=awk
ac_cv_prog_CPP='clang -E'
ac_cv_prog_PTHREAD_CC=clang
ac_cv_prog_ac_ct_CC=clang
ac_cv_prog_cc_c89=
ac_cv_prog_cc_clang_c_o=yes
ac_cv_prog_cc_g=yes
ac_cv_prog_make_make_set=yes
ac_cv_search_opendir='none required'
ac_cv_sizeof_off_t=8
ac_cv_sizeof_unsigned_long=8
ac_cv_sizeof_unsigned_long_long=8
ac_cv_sys_file_offset_bits=no
ac_cv_sys_largefile_CC=no
ac_cv_sys_largefile_source=no
ac_cv_target=arm-apple-darwin21.6.0
ac_cv_type_caddr_t=yes
ac_cv_type_off_t=yes
ac_cv_type_size_t=yes
am_cv_CC_dependencies_compiler_type=gcc3
am_cv_make_support_nested_variables=yes
ax_cv_c_compiler_vendor=clang
ax_cv_check_cflags___O3__fomit_frame_pointer__mpopcnt=yes
ax_cv_compile_popcnt_ext=yes
ax_cv_link_popcnt=yes
ax_cv_sse2_shift_defect=yes
ax_cv_want_simd=yes
cvx_cv_func_fopen_b=yes
cvx_cv_func_fopen_t=yes
## ----------------- ##
## Output variables. ##
## ----------------- ##
ACLOCAL='${SHELL} /private/tmp/gmap-gsnap-20220927-65980-i46hu0/gmap-2021-12-17/config/missing aclocal-1.13'
ALLOCA=''
AMDEPBACKSLASH='\'
AMDEP_FALSE='#'
AMDEP_TRUE=''
AMTAR='$${TAR-tar}'
AM_BACKSLASH='\'
AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)'
AM_DEFAULT_VERBOSITY='1'
AM_V='$(V)'
AUTOCONF='${SHELL} /private/tmp/gmap-gsnap-20220927-65980-i46hu0/gmap-2021-12-17/config/missing autoconf'
AUTOHEADER='${SHELL} /private/tmp/gmap-gsnap-20220927-65980-i46hu0/gmap-2021-12-17/config/missing autoheader'
AUTOMAKE='${SHELL} /private/tmp/gmap-gsnap-20220927-65980-i46hu0/gmap-2021-12-17/config/missing automake-1.13'
AWK='awk'
BINDIR='/opt/homebrew/Cellar/gmap-gsnap/2021-12-17/bin'
BZLIB_LIBS='-lbz2'
CC='clang'
CCDEPMODE='depmode=gcc3'
CFLAGS='-O3 -fomit-frame-pointer'
CPP='clang -E'
CPPFLAGS=''
CYGPATH_W='echo'
DEFS='-DHAVE_CONFIG_H'
DEPDIR='.deps'
ECHO_C='\c'
ECHO_N=''
ECHO_T=''
EGREP='/usr/bin/grep -E'
EXEEXT=''
FULLDIST_FALSE=''
FULLDIST_TRUE='#'
GMAPDB='/opt/homebrew/Cellar/gmap-gsnap/2021-12-17/share'
GREP='/usr/bin/grep'
HAVE_INLINE=''
INSTALL_DATA='${INSTALL} -m 644'
INSTALL_PROGRAM='${INSTALL}'
INSTALL_SCRIPT='${INSTALL}'
INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
LDFLAGS=''
LIBGMAP_SO_VERSION='1:0:0'
LIBOBJS=''
LIBS='-lm '
LTLIBOBJS=''
MAINT='#'
MAINTAINER_FALSE=''
MAINTAINER_MODE_FALSE=''
MAINTAINER_MODE_TRUE='#'
MAINTAINER_TRUE='#'
MAKEINFO='${SHELL} /private/tmp/gmap-gsnap-20220927-65980-i46hu0/gmap-2021-12-17/config/missing makeinfo'
MAKE_AVX2_FALSE=''
MAKE_AVX2_TRUE='#'
MAKE_AVX512BW_FALSE=''
MAKE_AVX512BW_TRUE='#'
MAKE_AVX512_FALSE=''
MAKE_AVX512_TRUE='#'
MAKE_SSE2_FALSE=''
MAKE_SSE2_TRUE='#'
MAKE_SSE4_1_FALSE=''
MAKE_SSE4_1_TRUE='#'
MAKE_SSE4_2_FALSE='#'
MAKE_SSE4_2_TRUE=''
MAKE_SSSE3_FALSE=''
MAKE_SSSE3_TRUE='#'
MAX_STACK_READLENGTH='300'
MKDIR_P='config/install-sh -c -d'
OBJEXT='o'
PACKAGE='gmap'
PACKAGE_BUGREPORT='Thomas Wu <twu@gene.com>'
PACKAGE_NAME='gmap'
PACKAGE_STRING='gmap 2021-12-17'
PACKAGE_TARNAME='gmap'
PACKAGE_URL=''
PACKAGE_VERSION='2021-12-17'
PATH_SEPARATOR=':'
PERL='/usr/bin/perl'
POPCNT_CFLAGS='-mpopcnt'
PTHREAD_CC='clang'
PTHREAD_CFLAGS='-D_THREAD_SAFE '
PTHREAD_LIBS=''
SET_MAKE=''
SHELL='/bin/sh'
SIMD_AVX2_CFLAGS=''
SIMD_AVX512_CFLAGS=''
SIMD_SSE2_CFLAGS=''
SIMD_SSE4_1_CFLAGS=''
SIMD_SSE4_2_CFLAGS=''
SIMD_SSSE3_CFLAGS=''
STRIP=''
VERSION='2021-12-17'
ZLIB_LIBS='-lz'
ac_ct_CC='clang'
acx_pthread_config=''
am__EXEEXT_FALSE=''
am__EXEEXT_TRUE='#'
am__fastdepCC_FALSE='#'
am__fastdepCC_TRUE=''
am__include='include'
am__isrc=''
am__leading_dot='.'
am__nodep='_no'
am__quote=''
am__tar='$${TAR-tar} chof - "$$tardir"'
am__untar='$${TAR-tar} xf -'
bindir='${exec_prefix}/bin'
build='arm-apple-darwin21.6.0'
build_alias=''
build_cpu='arm'
build_os='darwin21.6.0'
build_vendor='apple'
datadir='${datarootdir}'
datarootdir='${prefix}/share'
docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
dvidir='${docdir}'
exec_prefix='${prefix}'
host='arm-apple-darwin21.6.0'
host_alias=''
host_cpu='arm'
host_os='darwin21.6.0'
host_vendor='apple'
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${datarootdir}/info'
install_sh='${SHELL} /private/tmp/gmap-gsnap-20220927-65980-i46hu0/gmap-2021-12-17/config/install-sh'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localedir='${datarootdir}/locale'
localstatedir='${prefix}/var'
mandir='${datarootdir}/man'
mkdir_p='$(MKDIR_P)'
oldincludedir='/usr/include'
pdfdir='${docdir}'
prefix='/opt/homebrew/Cellar/gmap-gsnap/2021-12-17'
program_transform_name='s,x,x,'
psdir='${docdir}'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='${prefix}/etc'
target='arm-apple-darwin21.6.0'
target_alias=''
target_cpu='arm'
target_os='darwin21.6.0'
target_vendor='apple'
## ----------- ##
## confdefs.h. ##
## ----------- ##
/* confdefs.h */
#define PACKAGE_NAME "gmap"
#define PACKAGE_TARNAME "gmap"
#define PACKAGE_VERSION "2021-12-17"
#define PACKAGE_STRING "gmap 2021-12-17"
#define PACKAGE_BUGREPORT "Thomas Wu <twu@gene.com>"
#define PACKAGE_URL ""
#define PACKAGE "gmap"
#define VERSION "2021-12-17"
#define HAVE_LIBM 1
#define HAVE_PTHREAD 1
#define STDC_HEADERS 1
#define HAVE_DIRENT_H 1
#define HAVE_SYS_TYPES_H 1
#define HAVE_SYS_STAT_H 1
#define HAVE_STDLIB_H 1
#define HAVE_STRING_H 1
#define HAVE_MEMORY_H 1
#define HAVE_STRINGS_H 1
#define HAVE_INTTYPES_H 1
#define HAVE_STDINT_H 1
#define HAVE_UNISTD_H 1
#define HAVE_FCNTL_H 1
#define HAVE_LIMITS_H 1
#define HAVE_STDDEF_H 1
#define HAVE_STDLIB_H 1
#define HAVE_STRING_H 1
#define HAVE_STRINGS_H 1
#define HAVE_UNISTD_H 1
#define HAVE_SYS_TYPES_H 1
#define HAVE_INLINE 1
#define HAVE_CADDR_T 1
#define SIZEOF_UNSIGNED_LONG 8
#define SIZEOF_UNSIGNED_LONG_LONG 8
#define SIZEOF_OFF_T 8
#define HAVE_FSEEKO 1
#define HAVE_MMAP_MAP_FILE 1
#define HAVE_MMAP_MAP_SHARED 1
#define HAVE_MMAP_MAP_PRIVATE 1
#define HAVE_MADVISE_MADV_DONTNEED 1
#define HAVE_MADVISE_MADV_WILLNEED 1
#define HAVE_MADVISE_MADV_RANDOM 1
#define HAVE_MADVISE_MADV_SEQUENTIAL 1
#define HAVE_CEIL 1
#define HAVE_FLOOR 1
#define HAVE_INDEX 1
#define HAVE_LOG 1
#define HAVE_MADVISE 1
#define HAVE_MEMCPY 1
#define HAVE_MEMMOVE 1
#define HAVE_MEMSET 1
#define HAVE_MUNMAP 1
#define HAVE_POW 1
#define HAVE_RINT 1
#define HAVE_STAT64 1
#define HAVE_STRTOUL 1
#define HAVE_SYSCONF 1
#define HAVE_SYSCTL 1
#define HAVE_SIGACTION 1
#define HAVE_SHMGET 1
#define HAVE_SHMCTL 1
#define HAVE_SHMAT 1
#define HAVE_SHMDT 1
#define HAVE_SEMGET 1
#define HAVE_SEMCTL 1
#define HAVE_SEMOP 1
#define PAGESIZE_VIA_SYSCONF 1
#define PAGESIZE_VIA_SYSCTL 1
#define USE_FOPEN_BINARY 1
#define USE_FOPEN_TEXT 1
#define DEFECTIVE_SSE2_COMPILER 1
#define HAVE_ZLIB 1
#define HAVE_ZLIB_GZBUFFER 1
#define HAVE_BZLIB 1
configure: exit 0
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