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  • med-team/gmap
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Commits on Source (2)
2019-09-12 twu
* concordance.c, concordance.h, distant-dna.c, distant-dna.h,
extension-search.c, extension-search.h, gsnap.c, junction.c, junction.h,
kmer-search.c, kmer-search.h, list.c, list.h, src, stage1hr.c, stage1hr.h,
stage3hr.c, stage3hr.h, stage3hrdef.h, substring.c, substring.h: Merged
revisions 220290 through 220325 from
branches/2019-09-11-zero-length-introns to handle cases where ambiguous
ends are resolved and where distant DNA alignments yield a zero-length
intron
* index.html: Updated for latest version
2019-08-09 twu
* inbuffer.c, inbuffer.h: Removed references to interleavedp from GMAP
* gsnap.c: Added --interleaved feature
* bzip2.c: Saving a file handle and closing it
* Makefile.gsnaptoo.am: Including bzip2.c and bzip2.h to relevant programs
* atoiindex.c: Initializing filenames to be NULL
* cmetindex.c: Initializing filenames to be NULL
2019-07-15 twu
* inbuffer.c, inbuffer.h: Added interleavedp parameter
* shortread.h: Added interleavedp parameter
* shortread.c: Implemented interleaved format for gzip- and bzip2-compressed
files.
* getline.c, getline.h: Implemented Getline_gzip and Getline_bzip2
* shortread.c: Implemented Shortread_read_interleaved_text
2019-06-11 twu
* stage1hr.c: Added debugging statements
* concordance.c: Limiting number of overlaps to avoid combinatorial
explosion in some cases
2019-05-21 twu
* index.html: Updated for latest version
* ax_ext.m4: Improved structure for AVX2 and AVX512
2019-05-12 twu
 
* gmap.c: Adding support for avx512bw
......
Installation Instructions
*************************
Copyright (C) 1994-1996, 1999-2002, 2004-2013 Free Software Foundation,
Inc.
Copying and distribution of this file, with or without modification,
are permitted in any medium without royalty provided the copyright
notice and this notice are preserved. This file is offered as-is,
without warranty of any kind.
Basic Installation
==================
Briefly, the shell command `./configure && make && make install'
should configure, build, and install this package. The following
more-detailed instructions are generic; see the `README' file for
instructions specific to this package. Some packages provide this
`INSTALL' file but do not implement all of the features documented
below. The lack of an optional feature in a given package is not
necessarily a bug. More recommendations for GNU packages can be found
in *note Makefile Conventions: (standards)Makefile Conventions.
The `configure' shell script attempts to guess correct values for
various system-dependent variables used during compilation. It uses
those values to create a `Makefile' in each directory of the package.
It may also create one or more `.h' files containing system-dependent
definitions. Finally, it creates a shell script `config.status' that
you can run in the future to recreate the current configuration, and a
file `config.log' containing compiler output (useful mainly for
debugging `configure').
It can also use an optional file (typically called `config.cache'
and enabled with `--cache-file=config.cache' or simply `-C') that saves
the results of its tests to speed up reconfiguring. Caching is
disabled by default to prevent problems with accidental use of stale
cache files.
If you need to do unusual things to compile the package, please try
to figure out how `configure' could check whether to do them, and mail
diffs or instructions to the address given in the `README' so they can
be considered for the next release. If you are using the cache, and at
some point `config.cache' contains results you don't want to keep, you
may remove or edit it.
The file `configure.ac' (or `configure.in') is used to create
`configure' by a program called `autoconf'. You need `configure.ac' if
you want to change it or regenerate `configure' using a newer version
of `autoconf'.
The simplest way to compile this package is:
1. `cd' to the directory containing the package's source code and type
`./configure' to configure the package for your system.
Running `configure' might take a while. While running, it prints
some messages telling which features it is checking for.
2. Type `make' to compile the package.
3. Optionally, type `make check' to run any self-tests that come with
the package, generally using the just-built uninstalled binaries.
4. Type `make install' to install the programs and any data files and
documentation. When installing into a prefix owned by root, it is
recommended that the package be configured and built as a regular
user, and only the `make install' phase executed with root
privileges.
5. Optionally, type `make installcheck' to repeat any self-tests, but
this time using the binaries in their final installed location.
This target does not install anything. Running this target as a
regular user, particularly if the prior `make install' required
root privileges, verifies that the installation completed
correctly.
6. You can remove the program binaries and object files from the
source code directory by typing `make clean'. To also remove the
files that `configure' created (so you can compile the package for
a different kind of computer), type `make distclean'. There is
also a `make maintainer-clean' target, but that is intended mainly
for the package's developers. If you use it, you may have to get
all sorts of other programs in order to regenerate files that came
with the distribution.
7. Often, you can also type `make uninstall' to remove the installed
files again. In practice, not all packages have tested that
uninstallation works correctly, even though it is required by the
GNU Coding Standards.
8. Some packages, particularly those that use Automake, provide `make
distcheck', which can by used by developers to test that all other
targets like `make install' and `make uninstall' work correctly.
This target is generally not run by end users.
Compilers and Options
=====================
Some systems require unusual options for compilation or linking that
the `configure' script does not know about. Run `./configure --help'
for details on some of the pertinent environment variables.
You can give `configure' initial values for configuration parameters
by setting variables in the command line or in the environment. Here
is an example:
./configure CC=c99 CFLAGS=-g LIBS=-lposix
*Note Defining Variables::, for more details.
Compiling For Multiple Architectures
====================================
You can compile the package for more than one kind of computer at the
same time, by placing the object files for each architecture in their
own directory. To do this, you can use GNU `make'. `cd' to the
directory where you want the object files and executables to go and run
the `configure' script. `configure' automatically checks for the
source code in the directory that `configure' is in and in `..'. This
is known as a "VPATH" build.
With a non-GNU `make', it is safer to compile the package for one
architecture at a time in the source code directory. After you have
installed the package for one architecture, use `make distclean' before
reconfiguring for another architecture.
On MacOS X 10.5 and later systems, you can create libraries and
executables that work on multiple system types--known as "fat" or
"universal" binaries--by specifying multiple `-arch' options to the
compiler but only a single `-arch' option to the preprocessor. Like
this:
./configure CC="gcc -arch i386 -arch x86_64 -arch ppc -arch ppc64" \
CXX="g++ -arch i386 -arch x86_64 -arch ppc -arch ppc64" \
CPP="gcc -E" CXXCPP="g++ -E"
This is not guaranteed to produce working output in all cases, you
may have to build one architecture at a time and combine the results
using the `lipo' tool if you have problems.
Installation Names
==================
By default, `make install' installs the package's commands under
`/usr/local/bin', include files under `/usr/local/include', etc. You
can specify an installation prefix other than `/usr/local' by giving
`configure' the option `--prefix=PREFIX', where PREFIX must be an
absolute file name.
You can specify separate installation prefixes for
architecture-specific files and architecture-independent files. If you
pass the option `--exec-prefix=PREFIX' to `configure', the package uses
PREFIX as the prefix for installing programs and libraries.
Documentation and other data files still use the regular prefix.
In addition, if you use an unusual directory layout you can give
options like `--bindir=DIR' to specify different values for particular
kinds of files. Run `configure --help' for a list of the directories
you can set and what kinds of files go in them. In general, the
default for these options is expressed in terms of `${prefix}', so that
specifying just `--prefix' will affect all of the other directory
specifications that were not explicitly provided.
The most portable way to affect installation locations is to pass the
correct locations to `configure'; however, many packages provide one or
both of the following shortcuts of passing variable assignments to the
`make install' command line to change installation locations without
having to reconfigure or recompile.
The first method involves providing an override variable for each
affected directory. For example, `make install
prefix=/alternate/directory' will choose an alternate location for all
directory configuration variables that were expressed in terms of
`${prefix}'. Any directories that were specified during `configure',
but not in terms of `${prefix}', must each be overridden at install
time for the entire installation to be relocated. The approach of
makefile variable overrides for each directory variable is required by
the GNU Coding Standards, and ideally causes no recompilation.
However, some platforms have known limitations with the semantics of
shared libraries that end up requiring recompilation when using this
method, particularly noticeable in packages that use GNU Libtool.
The second method involves providing the `DESTDIR' variable. For
example, `make install DESTDIR=/alternate/directory' will prepend
`/alternate/directory' before all installation names. The approach of
`DESTDIR' overrides is not required by the GNU Coding Standards, and
does not work on platforms that have drive letters. On the other hand,
it does better at avoiding recompilation issues, and works well even
when some directory options were not specified in terms of `${prefix}'
at `configure' time.
Optional Features
=================
If the package supports it, you can cause programs to be installed
with an extra prefix or suffix on their names by giving `configure' the
option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'.
Some packages pay attention to `--enable-FEATURE' options to
`configure', where FEATURE indicates an optional part of the package.
They may also pay attention to `--with-PACKAGE' options, where PACKAGE
is something like `gnu-as' or `x' (for the X Window System). The
`README' should mention any `--enable-' and `--with-' options that the
package recognizes.
For packages that use the X Window System, `configure' can usually
find the X include and library files automatically, but if it doesn't,
you can use the `configure' options `--x-includes=DIR' and
`--x-libraries=DIR' to specify their locations.
Some packages offer the ability to configure how verbose the
execution of `make' will be. For these packages, running `./configure
--enable-silent-rules' sets the default to minimal output, which can be
overridden with `make V=1'; while running `./configure
--disable-silent-rules' sets the default to verbose, which can be
overridden with `make V=0'.
Particular systems
==================
On HP-UX, the default C compiler is not ANSI C compatible. If GNU
CC is not installed, it is recommended to use the following options in
order to use an ANSI C compiler:
./configure CC="cc -Ae -D_XOPEN_SOURCE=500"
and if that doesn't work, install pre-built binaries of GCC for HP-UX.
HP-UX `make' updates targets which have the same time stamps as
their prerequisites, which makes it generally unusable when shipped
generated files such as `configure' are involved. Use GNU `make'
instead.
On OSF/1 a.k.a. Tru64, some versions of the default C compiler cannot
parse its `<wchar.h>' header file. The option `-nodtk' can be used as
a workaround. If GNU CC is not installed, it is therefore recommended
to try
./configure CC="cc"
and if that doesn't work, try
./configure CC="cc -nodtk"
On Solaris, don't put `/usr/ucb' early in your `PATH'. This
directory contains several dysfunctional programs; working variants of
these programs are available in `/usr/bin'. So, if you need `/usr/ucb'
in your `PATH', put it _after_ `/usr/bin'.
On Haiku, software installed for all users goes in `/boot/common',
not `/usr/local'. It is recommended to use the following options:
./configure --prefix=/boot/common
Specifying the System Type
==========================
There may be some features `configure' cannot figure out
automatically, but needs to determine by the type of machine the package
will run on. Usually, assuming the package is built to be run on the
_same_ architectures, `configure' can figure that out, but if it prints
a message saying it cannot guess the machine type, give it the
`--build=TYPE' option. TYPE can either be a short name for the system
type, such as `sun4', or a canonical name which has the form:
CPU-COMPANY-SYSTEM
where SYSTEM can have one of these forms:
OS
KERNEL-OS
See the file `config.sub' for the possible values of each field. If
`config.sub' isn't included in this package, then this package doesn't
need to know the machine type.
If you are _building_ compiler tools for cross-compiling, you should
use the option `--target=TYPE' to select the type of system they will
produce code for.
If you want to _use_ a cross compiler, that generates code for a
platform different from the build platform, you should specify the
"host" platform (i.e., that on which the generated programs will
eventually be run) with `--host=TYPE'.
Sharing Defaults
================
If you want to set default values for `configure' scripts to share,
you can create a site shell script called `config.site' that gives
default values for variables like `CC', `cache_file', and `prefix'.
`configure' looks for `PREFIX/share/config.site' if it exists, then
`PREFIX/etc/config.site' if it exists. Or, you can set the
`CONFIG_SITE' environment variable to the location of the site script.
A warning: not all `configure' scripts look for a site script.
Defining Variables
==================
Variables not defined in a site shell script can be set in the
environment passed to `configure'. However, some packages may run
configure again during the build, and the customized values of these
variables may be lost. In order to avoid this problem, you should set
them in the `configure' command line, using `VAR=value'. For example:
./configure CC=/usr/local2/bin/gcc
causes the specified `gcc' to be used as the C compiler (unless it is
overridden in the site shell script).
Unfortunately, this technique does not work for `CONFIG_SHELL' due to
an Autoconf limitation. Until the limitation is lifted, you can use
this workaround:
CONFIG_SHELL=/bin/bash ./configure CONFIG_SHELL=/bin/bash
`configure' Invocation
======================
`configure' recognizes the following options to control how it
operates.
`--help'
`-h'
Print a summary of all of the options to `configure', and exit.
`--help=short'
`--help=recursive'
Print a summary of the options unique to this package's
`configure', and exit. The `short' variant lists options used
only in the top level, while the `recursive' variant lists options
also present in any nested packages.
`--version'
`-V'
Print the version of Autoconf used to generate the `configure'
script, and exit.
`--cache-file=FILE'
Enable the cache: use and save the results of the tests in FILE,
traditionally `config.cache'. FILE defaults to `/dev/null' to
disable caching.
`--config-cache'
`-C'
Alias for `--cache-file=config.cache'.
`--quiet'
`--silent'
`-q'
Do not print messages saying which checks are being made. To
suppress all normal output, redirect it to `/dev/null' (any error
messages will still be shown).
`--srcdir=DIR'
Look for the package's source code in directory DIR. Usually
`configure' can determine that directory automatically.
`--prefix=DIR'
Use DIR as the installation prefix. *note Installation Names::
for more details, including other options available for fine-tuning
the installation locations.
`--no-create'
`-n'
Run the configure checks, but stop before creating any output
files.
`configure' also accepts some other, not widely useful, options. Run
`configure --help' for more details.
This diff is collapsed.
2019-05-12
\ No newline at end of file
2019-09-12
\ No newline at end of file
This diff is collapsed.
......@@ -17,9 +17,13 @@
#
# AC_SUBST(SIMD_CFLAGS)
#
# And defines:
# And previously defined:
#
# HAVE_MMX / HAVE_SSE / HAVE_SSE2 / HAVE_SSE3 / HAVE_SSSE3 / HAVE_SSE4_1 / HAVE_SSE4_2 / HAVE_AVX
# HAVE_MMX / HAVE_SSE / HAVE_SSE2 / HAVE_SSE3 / HAVE_SSSE3 / HAVE_SSE4_1 / HAVE_SSE4_2
#
# But now defines:
#
# HAVE_MM_POPCNT / HAVE_POPCNT / HAVE_LZCNT / HAVE_TZCNT / HAVE_PEXT
#
#
# LICENSE
......@@ -65,6 +69,7 @@ AC_DEFUN([AX_EXT],
# AX_CHECK_COMPILE_FLAG tests CFLAGS EXTRA-FLAGS FLAG
if test x"$ax_cv_cpu_has_sse2_ext" = xyes; then
#AC_MSG_CHECKING(for sse2 compiler/linker support)
CFLAGS=
TEST_CFLAGS=-msse2
AX_CHECK_COMPILE_FLAG([$TEST_CFLAGS], [ax_cv_compile_sse2_ext=yes], [ax_cv_ext_compile_problem=yes])
......@@ -77,7 +82,6 @@ AC_DEFUN([AX_EXT],
[ax_cv_link_emmintrin_h=yes],
[ax_cv_ext_linker_problem=yes])
if test x"$ax_cv_link_emmintrin_h" != xyes; then
AC_MSG_RESULT([no])
AC_MSG_WARN([Your compiler supports SSE2 instructions but not your linker.])
else
AC_MSG_RESULT([yes])
......@@ -88,7 +92,9 @@ AC_DEFUN([AX_EXT],
fi
fi
if test x"$ax_cv_cpu_has_ssse3_ext" = xyes; then
#AC_MSG_CHECKING(for ssse3 compiler/linker support)
CFLAGS=
if test x"$ax_cv_c_compiler_vendor" = xintel; then
TEST_CFLAGS="-mssse3"
......@@ -105,7 +111,6 @@ AC_DEFUN([AX_EXT],
[ax_cv_link_tmmintrin_h=yes],
[ax_cv_ext_linker_problem=yes])
if test x"$ax_cv_link_tmmintrin_h" != xyes; then
AC_MSG_RESULT([no])
AC_MSG_WARN([Your compiler supports SSSE3 instructions but not your linker.])
else
AC_MSG_RESULT([yes])
......@@ -119,7 +124,9 @@ AC_DEFUN([AX_EXT],
fi
fi
if test x"$ax_cv_cpu_has_sse41_ext" = xyes; then
#AC_MSG_CHECKING(for sse41 compiler/linker support)
CFLAGS=
if test x"$ax_cv_c_compiler_vendor" = xintel; then
TEST_CFLAGS="-msse4.1"
......@@ -136,7 +143,6 @@ AC_DEFUN([AX_EXT],
[ax_cv_link_smmintrin_h=yes],
[ax_cv_ext_linker_problem=yes])
if test x"$ax_cv_link_smmintrin_h" != xyes; then
AC_MSG_RESULT([no])
AC_MSG_WARN([Your compiler supports SSE4.1 instructions but not your linker.])
else
AC_MSG_RESULT([yes])
......@@ -151,7 +157,9 @@ AC_DEFUN([AX_EXT],
fi
fi
if test x"$ax_cv_cpu_has_sse42_ext" = xyes; then
#AC_MSG_CHECKING(for sse42 compiler/linker support)
CFLAGS=
if test x"$ax_cv_c_compiler_vendor" = xintel; then
TEST_CFLAGS="-march=corei7"
......@@ -168,7 +176,6 @@ AC_DEFUN([AX_EXT],
[ax_cv_link_nmmintrin_h=yes],
[ax_cv_ext_linker_problem=yes])
if test x"$ax_cv_link_nmmintrin_h" != xyes; then
AC_MSG_RESULT([no])
AC_MSG_WARN([Your compiler supports SSE4.2 instructions but not your linker.])
else
AC_MSG_RESULT([yes])
......@@ -183,11 +190,13 @@ AC_DEFUN([AX_EXT],
fi
fi
# Extra options for SSE42
if test x"$ax_make_sse42" = xyes; then
AC_MSG_CHECKING(for mm_popcnt support)
if test x"$ax_cv_cpu_has_popcnt_ext" != xyes; then
AC_MSG_RESULT([no])
else
AC_MSG_CHECKING(for mm_popcnt run support)
AC_RUN_IFELSE(
[AC_LANG_PROGRAM([[#include <nmmintrin.h>]],
[[return (_mm_popcnt_u32(0xffffffffu) == 32) ? 0 : 9;]])],
......@@ -195,85 +204,96 @@ AC_DEFUN([AX_EXT],
AC_DEFINE(HAVE_MM_POPCNT,1,[Define to 1 if you support Intel intrinsic _mm_popcnt_u32/64 instructions])],
[AC_MSG_RESULT(no)])
fi
fi
if test x"$ax_cv_cpu_has_bmi1_ext" = xyes; then
CFLAGS=
if test x"$ax_cv_c_compiler_vendor" = xintel; then
TEST_CFLAGS="$SIMD_SSE4_2_CFLAGS"
else
TEST_CFLAGS="$SIMD_SSE4_2_CFLAGS -mabm"
fi
AX_CHECK_COMPILE_FLAG([$TEST_CFLAGS], [ax_cv_compile_abm_ext=yes], [ax_cv_ext_compile_problem=yes])
if test x"$ax_cv_compile_abm_ext" != xyes; then
AC_MSG_WARN([Your CPU supports BMI1 instructions but not your compiler. Can you try another compiler or update yours?])
else
CFLAGS=$TEST_CFLAGS
AC_LINK_IFELSE([AC_LANG_PROGRAM([])],
[ax_cv_link_abm=yes],
[ax_cv_ext_linker_problem=yes])
if test x"$ax_cv_link_abm" != xyes; then
AC_MSG_WARN([Your compiler supports -mabm but not your linker])
else
SIMD_SSE4_2_CFLAGS=$CFLAGS
# Test for functionality with the -mabm compiler flag
AC_MSG_CHECKING(for _popcnt32 support)
AC_RUN_IFELSE(
[AC_LANG_PROGRAM([[#include <immintrin.h>]],
[[return (_popcnt32(0xffffffffu) == 32) ? 0 : 9;]])],
[AC_MSG_RESULT(yes)
AC_DEFINE(HAVE_POPCNT,1,[Define to 1 if you support Intel intrinsic _popcnt instruction])],
[AC_MSG_RESULT(no)])
AC_MSG_CHECKING(for _lzcnt support)
AC_RUN_IFELSE(
[AC_LANG_PROGRAM([[#include <immintrin.h>]],
[[return (_lzcnt_u32(0x0fffffffu) == 4) ? 0 : 9;]])],
[AC_MSG_RESULT(yes)
AC_DEFINE(HAVE_LZCNT,1,[Define to 1 if you support Intel intrinsic _lzcnt instruction])],
[AC_MSG_RESULT(no)])
fi
fi
fi
if test x"$ax_cv_cpu_has_bmi1_ext" = xyes; then
CFLAGS=
if test x"$ax_cv_c_compiler_vendor" = xintel; then
TEST_CFLAGS="$SIMD_SSE4_2_CFLAGS"
else
TEST_CFLAGS="$SIMD_SSE4_2_CFLAGS -mabm"
fi
AX_CHECK_COMPILE_FLAG([$TEST_CFLAGS], [ax_cv_compile_abm_ext=yes], [ax_cv_ext_compile_problem=yes])
if test x"$ax_cv_compile_abm_ext" != xyes; then
AC_MSG_WARN([Your CPU supports BMI1 instructions but not your compiler. Can you try another compiler or update yours?])
else
CFLAGS=$TEST_CFLAGS
AC_MSG_CHECKING(for abm linker support)
AC_LINK_IFELSE([AC_LANG_PROGRAM([])],
[ax_cv_link_abm=yes],
[ax_cv_ext_linker_problem=yes])
if test x"$ax_cv_link_abm" != xyes; then
AC_MSG_WARN([Your compiler supports -mabm but not your linker])
else
AC_MSG_RESULT([yes])
SIMD_SSE4_2_CFLAGS=$CFLAGS
if test x"$ax_cv_cpu_has_bmi1_ext" = xyes; then
CFLAGS=
if test x"$ax_cv_c_compiler_vendor" = xintel; then
TEST_CFLAGS="$SIMD_SSE4_2_CFLAGS"
else
TEST_CFLAGS="$SIMD_SSE4_2_CFLAGS -mbmi"
fi
AX_CHECK_COMPILE_FLAG([$TEST_CFLAGS], [ax_cv_compile_bmi_ext=yes], [ax_cv_ext_compile_problem=yes])
if test x"$ax_cv_compile_bmi_ext" != xyes; then
AC_MSG_WARN([Your CPU supports BMI1 instructions but not your compiler. Can you try another compiler or update yours?])
else
CFLAGS=$TEST_CFLAGS
AC_LINK_IFELSE([AC_LANG_PROGRAM([])],
[ax_cv_link_bmi=yes],
[ax_cv_ext_linker_problem=yes])
if test x"$ax_cv_link_bmi" != xyes; then
AC_MSG_WARN([Your compiler supports -mbmi but not your linker])
else
SIMD_SSE4_2_CFLAGS=$CFLAGS
# Test for functionality with the -mbmi compiler flag
AC_MSG_CHECKING(for _tzcnt support)
AC_RUN_IFELSE(
[AC_LANG_PROGRAM([[#include <immintrin.h>]],
[[return (_tzcnt_u32(0xfffffff0u) == 4) ? 0 : 9;]])],
[AC_MSG_RESULT(yes)
AC_DEFINE(HAVE_TZCNT,1,[Define to 1 if you support Intel intrinsic _tzcnt instruction])],
[AC_MSG_RESULT(no)])
fi
fi
# Test for functionality with the -mabm compiler flag
AC_MSG_CHECKING(for _popcnt32 run support)
AC_RUN_IFELSE(
[AC_LANG_PROGRAM([[#include <immintrin.h>]],
[[return (_popcnt32(0xffffffffu) == 32) ? 0 : 9;]])],
[AC_MSG_RESULT(yes)
AC_DEFINE(HAVE_POPCNT,1,[Define to 1 if you support Intel intrinsic _popcnt instruction])],
[AC_MSG_RESULT(no)])
AC_MSG_CHECKING(for _lzcnt run support)
AC_RUN_IFELSE(
[AC_LANG_PROGRAM([[#include <immintrin.h>]],
[[return (_lzcnt_u32(0x0fffffffu) == 4) ? 0 : 9;]])],
[AC_MSG_RESULT(yes)
AC_DEFINE(HAVE_LZCNT,1,[Define to 1 if you support Intel intrinsic _lzcnt instruction])],
[AC_MSG_RESULT(no)])
fi
fi
fi
if test x"$ax_cv_cpu_has_bmi1_ext" = xyes; then
#AC_MSG_CHECKING(for bmi compiler/linker support)
CFLAGS=
if test x"$ax_cv_c_compiler_vendor" = xintel; then
TEST_CFLAGS="$SIMD_SSE4_2_CFLAGS"
else
TEST_CFLAGS="$SIMD_SSE4_2_CFLAGS -mbmi"
fi
AX_CHECK_COMPILE_FLAG([$TEST_CFLAGS], [ax_cv_compile_bmi_ext=yes], [ax_cv_ext_compile_problem=yes])
if test x"$ax_cv_compile_bmi_ext" != xyes; then
AC_MSG_WARN([Your CPU supports BMI1 instructions but not your compiler. Can you try another compiler or update yours?])
else
CFLAGS=$TEST_CFLAGS
AC_MSG_CHECKING(for bmi linker support)
AC_LINK_IFELSE([AC_LANG_PROGRAM([])],
[ax_cv_link_bmi=yes],
[ax_cv_ext_linker_problem=yes])
if test x"$ax_cv_link_bmi" != xyes; then
AC_MSG_WARN([Your compiler supports -mbmi but not your linker])
else
AC_MSG_RESULT([yes])
SIMD_SSE4_2_CFLAGS=$CFLAGS
# Test for functionality with the -mbmi compiler flag
AC_MSG_CHECKING(for _tzcnt run support)
AC_RUN_IFELSE(
[AC_LANG_PROGRAM([[#include <immintrin.h>]],
[[return (_tzcnt_u32(0xfffffff0u) == 4) ? 0 : 9;]])],
[AC_MSG_RESULT(yes)
AC_DEFINE(HAVE_TZCNT,1,[Define to 1 if you support Intel intrinsic _tzcnt instruction])],
[AC_MSG_RESULT(no)])
fi
fi
fi
fi
if test x"$ax_cv_cpu_has_avx2_ext" = xyes; then
#AC_MSG_CHECKING(for avx2 compiler/linker support)
CFLAGS=
if test x"$ax_cv_c_compiler_vendor" = xintel; then
TEST_CFLAGS="-march=core-avx2"
else
TEST_CFLAGS="$SIMD_SSE4_2_CFLAGS -mavx2 -mbmi2"
TEST_CFLAGS="$SIMD_SSE4_2_CFLAGS -mavx2"
fi
AX_CHECK_COMPILE_FLAG([$TEST_CFLAGS], [ax_cv_compile_avx2_ext=yes], [ax_cv_ext_compile_problem=yes])
if test x"$ax_cv_compile_avx2_ext" != xyes; then
......@@ -285,7 +305,6 @@ AC_DEFUN([AX_EXT],
[ax_cv_link_immintrin_h=yes],
[ax_cv_ext_linker_problem=yes])
if test x"$ax_cv_link_immintrin_h" != xyes; then
AC_MSG_RESULT([no])
AC_MSG_WARN([Your compiler supports AVX2 instructions but not your linker.])
else
AC_MSG_RESULT([yes])
......@@ -302,51 +321,57 @@ AC_DEFUN([AX_EXT],
fi
fi
if test x"$ax_cv_cpu_has_bmi2_ext" = xyes; then
CFLAGS=
if test x"$ax_cv_c_compiler_vendor" = xintel; then
TEST_CFLAGS="$SIMD_AVX2_CFLAGS"
else
TEST_CFLAGS="$SIMD_AVX2_CFLAGS -mbmi2"
fi
AX_CHECK_COMPILE_FLAG([$TEST_CFLAGS], [ax_cv_compile_bmi2_ext=yes], [ax_cv_ext_compile_problem=yes])
if test x"$ax_cv_compile_bmi2_ext" != xyes; then
AC_MSG_WARN([Your CPU supports BMI2 instructions but not your compiler. Can you try another compiler or update yours?])
else
CFLAGS=$TEST_CFLAGS
AC_LINK_IFELSE([AC_LANG_PROGRAM([])],
[ax_cv_link_bmi2=yes],
[ax_cv_ext_linker_problem=yes])
if test x"$ax_cv_link_bmi2" != xyes; then
AC_MSG_WARN([Your compiler supports -mbmi2 but not your linker. Can you try another linker or update yours?])
else
SIMD_AVX2_CFLAGS=$CFLAGS
if test x"$ax_cv_c_compiler_vendor" != xintel; then
SIMD_SSE2_CFLAGS="$SIMD_SSE2_CFLAGS -mno-bmi2"
SIMD_SSSE3_CFLAGS="$SIMD_SSSE3_CFLAGS -mno-bmi2"
SIMD_SSE4_1_CFLAGS="$SIMD_SSE4_1_CFLAGS -mno-bmi2"
SIMD_SSE4_2_CFLAGS="$SIMD_SSE4_2_CFLAGS -mno-bmi2"
# Extra option for AVX2
if test x"$ax_make_avx2" = xyes; then
if test x"$ax_cv_cpu_has_bmi2_ext" = xyes; then
CFLAGS=
if test x"$ax_cv_c_compiler_vendor" = xintel; then
TEST_CFLAGS="$SIMD_AVX2_CFLAGS"
else
TEST_CFLAGS="$SIMD_AVX2_CFLAGS -mbmi2"
fi
AX_CHECK_COMPILE_FLAG([$TEST_CFLAGS], [ax_cv_compile_bmi2_ext=yes], [ax_cv_ext_compile_problem=yes])
if test x"$ax_cv_compile_bmi2_ext" != xyes; then
AC_MSG_WARN([Your CPU supports BMI2 instructions but not your compiler. Can you try another compiler or update yours?])
else
CFLAGS=$TEST_CFLAGS
AC_MSG_CHECKING(for bmi2 linker support)
AC_LINK_IFELSE([AC_LANG_PROGRAM([])],
[ax_cv_link_bmi2=yes],
[ax_cv_ext_linker_problem=yes])
if test x"$ax_cv_link_bmi2" != xyes; then
AC_MSG_WARN([Your compiler supports -mbmi2 but not your linker. Can you try another linker or update yours?])
else
AC_MSG_RESULT([yes])
SIMD_AVX2_CFLAGS=$CFLAGS
if test x"$ax_cv_c_compiler_vendor" != xintel; then
SIMD_SSE2_CFLAGS="$SIMD_SSE2_CFLAGS -mno-bmi2"
SIMD_SSSE3_CFLAGS="$SIMD_SSSE3_CFLAGS -mno-bmi2"
SIMD_SSE4_1_CFLAGS="$SIMD_SSE4_1_CFLAGS -mno-bmi2"
SIMD_SSE4_2_CFLAGS="$SIMD_SSE4_2_CFLAGS -mno-bmi2"
fi
AC_MSG_CHECKING(for _pext run support)
AC_RUN_IFELSE(
[AC_LANG_PROGRAM([[#include <immintrin.h>]],
[[return (_pext_u32(0x01234567u,0x0f33aa55) == 0x00001b0b) ? 0 : 9;]])],
[AC_MSG_RESULT(yes)
AC_DEFINE(HAVE_PEXT,1,[Define to 1 if you support Intel intrinsic _pext instruction])],
[AC_MSG_RESULT(no)])
fi
AC_MSG_CHECKING(for _pext support)
AC_RUN_IFELSE(
[AC_LANG_PROGRAM([[#include <immintrin.h>]],
[[return (_pext_u32(0x01234567u,0x0f33aa55) == 0x00001b0b) ? 0 : 9;]])],
[AC_MSG_RESULT(yes)
AC_DEFINE(HAVE_PEXT,1,[Define to 1 if you support Intel intrinsic _pext instruction])],
[AC_MSG_RESULT(no)])
fi
fi
fi
fi
fi
if test x"$ax_cv_cpu_has_avx512_ext" = xyes; then
#AC_MSG_CHECKING(for avx512f and avx512cd support)
CFLAGS=
if test x"$ax_cv_c_compiler_vendor" = xintel; then
TEST_CFLAGS="-xCOMMON-AVX512"
elif test x"$ax_cv_cpu_has_avx512bw_ext" != xyes; then
TEST_CFLAGS="$SIMD_AVX2_CFLAGS -mavx512f -mavx512cd -mno-avx512bw -mno-avx512vl"
else
TEST_CFLAGS="$SIMD_AVX2_CFLAGS -mavx512f -mavx512cd -mavx512bw -mavx512vl"
TEST_CFLAGS="$SIMD_AVX2_CFLAGS -mavx512f -mavx512cd"
fi
AX_CHECK_COMPILE_FLAG([$TEST_CFLAGS], [ax_cv_compile_avx512_ext=yes], [ax_cv_ext_compile_problem=yes])
if test x"$ax_cv_compile_avx512_ext" != xyes; then
......@@ -358,8 +383,7 @@ AC_DEFUN([AX_EXT],
[ax_cv_link_nmmintrin_h=yes],
[ax_cv_ext_linker_problem=yes])
if test x"$ax_cv_link_nmmintrin_h" != xyes; then
AC_MSG_RESULT([no])
AC_MSG_WARN([Your compiler supports AVX512 instructions but not your linker.])
AC_MSG_WARN([Your compiler supports AVX512 instructions but not your linker. Can you try another linker or update yours?])
else
AC_MSG_RESULT([yes])
ax_make_avx512=yes
......@@ -372,6 +396,41 @@ AC_DEFUN([AX_EXT],
SIMD_AVX2_CFLAGS="$SIMD_AVX2_CFLAGS -mno-avx512f -mno-avx512cd"
fi
# AC_DEFINE(HAVE_AVX512,1,[Define to 1 if you support AVX512 (Advanced Vector Extensions 512) instructions]) -- Defines run-type
# AC_DEFINE(HAVE_AVX512BW,1,[Define to 1 if you support AVX512BW (Advanced Vector Extensions 512) BW instructions]) -- Defines run-type
fi
fi
fi
# Extra options for AVX512
if test x"$ax_make_avx512" = xyes; then
CFLAGS=
if test x"$ax_cv_c_compiler_vendor" = xintel; then
TEST_CFLAGS="$SIMD_AVX512_CFLAGS"
else
TEST_CFLAGS="$SIMD_AVX512_CFLAGS -mavx512vl -mavx512bw"
fi
AX_CHECK_COMPILE_FLAG([$TEST_CFLAGS], [ax_cv_compile_avx512bw_ext=yes], [ax_cv_ext_compile_problem=yes])
if test x"$ax_cv_compile_avx512bw_ext" != xyes; then
AC_MSG_WARN([Your CPU supports AVX512BW instructions but not your compiler. Can you try another compiler or update yours?])
else
CFLAGS=$TEST_CFLAGS
AC_MSG_CHECKING(for avx512vl and avx512bw linker support)
AC_LINK_IFELSE([AC_LANG_PROGRAM([])],
[ax_cv_link_avx512bw=yes],
[ax_cv_ext_linker_problem=yes])
if test x"$ax_cv_link_avx512bw" != xyes; then
AC_MSG_WARN([Your compiler supports AVX512BW instructions but not your linker.])
else
AC_MSG_RESULT([yes])
SIMD_AVX512_CFLAGS=$CFLAGS
if test x"$ax_cv_c_compiler_vendor" != xintel; then
SIMD_SSE2_CFLAGS="$SIMD_SSE2_CFLAGS -mno-avx512vl -mno-avx512bw"
SIMD_SSSE3_CFLAGS="$SIMD_SSSE3_CFLAGS -mno-avx512vl -mno-avx512bw"
SIMD_SSE4_1_CFLAGS="$SIMD_SSE4_1_CFLAGS -mno-avx512vl -mno-avx512bw"
SIMD_SSE4_2_CFLAGS="$SIMD_SSE4_2_CFLAGS -mno-avx512vl -mno-avx512bw"
SIMD_AVX2_CFLAGS="$SIMD_AVX2_CFLAGS -mno-avx512vl -mno-avx512bw"
fi
# AC_DEFINE(HAVE_AVX512,1,[Define to 1 if you support AVX512 (Advanced Vector Extensions 512) instructions]) -- Defines run-type
# AC_DEFINE(HAVE_AVX512BW,1,[Define to 1 if you support AVX512BW (Advanced Vector Extensions 512) BW instructions]) -- Defines run-type
fi
fi
......
#! /bin/sh
# Wrapper for compilers which do not understand '-c -o'.
scriptversion=2012-10-14.11; # UTC
# Copyright (C) 1999-2014 Free Software Foundation, Inc.
# Written by Tom Tromey <tromey@cygnus.com>.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2, or (at your option)
# any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
# As a special exception to the GNU General Public License, if you
# distribute this file as part of a program that contains a
# configuration script generated by Autoconf, you may include it under
# the same distribution terms that you use for the rest of that program.
# This file is maintained in Automake, please report
# bugs to <bug-automake@gnu.org> or send patches to
# <automake-patches@gnu.org>.
nl='
'
# We need space, tab and new line, in precisely that order. Quoting is
# there to prevent tools from complaining about whitespace usage.
IFS=" "" $nl"
file_conv=
# func_file_conv build_file lazy
# Convert a $build file to $host form and store it in $file
# Currently only supports Windows hosts. If the determined conversion
# type is listed in (the comma separated) LAZY, no conversion will
# take place.
func_file_conv ()
{
file=$1
case $file in
/ | /[!/]*) # absolute file, and not a UNC file
if test -z "$file_conv"; then
# lazily determine how to convert abs files
case `uname -s` in
MINGW*)
file_conv=mingw
;;
CYGWIN*)
file_conv=cygwin
;;
*)
file_conv=wine
;;
esac
fi
case $file_conv/,$2, in
*,$file_conv,*)
;;
mingw/*)
file=`cmd //C echo "$file " | sed -e 's/"\(.*\) " *$/\1/'`
;;
cygwin/*)
file=`cygpath -m "$file" || echo "$file"`
;;
wine/*)
file=`winepath -w "$file" || echo "$file"`
;;
esac
;;
esac
}
# func_cl_dashL linkdir
# Make cl look for libraries in LINKDIR
func_cl_dashL ()
{
func_file_conv "$1"
if test -z "$lib_path"; then
lib_path=$file
else
lib_path="$lib_path;$file"
fi
linker_opts="$linker_opts -LIBPATH:$file"
}
# func_cl_dashl library
# Do a library search-path lookup for cl
func_cl_dashl ()
{
lib=$1
found=no
save_IFS=$IFS
IFS=';'
for dir in $lib_path $LIB
do
IFS=$save_IFS
if $shared && test -f "$dir/$lib.dll.lib"; then
found=yes
lib=$dir/$lib.dll.lib
break
fi
if test -f "$dir/$lib.lib"; then
found=yes
lib=$dir/$lib.lib
break
fi
if test -f "$dir/lib$lib.a"; then
found=yes
lib=$dir/lib$lib.a
break
fi
done
IFS=$save_IFS
if test "$found" != yes; then
lib=$lib.lib
fi
}
# func_cl_wrapper cl arg...
# Adjust compile command to suit cl
func_cl_wrapper ()
{
# Assume a capable shell
lib_path=
shared=:
linker_opts=
for arg
do
if test -n "$eat"; then
eat=
else
case $1 in
-o)
# configure might choose to run compile as 'compile cc -o foo foo.c'.
eat=1
case $2 in
*.o | *.[oO][bB][jJ])
func_file_conv "$2"
set x "$@" -Fo"$file"
shift
;;
*)
func_file_conv "$2"
set x "$@" -Fe"$file"
shift
;;
esac
;;
-I)
eat=1
func_file_conv "$2" mingw
set x "$@" -I"$file"
shift
;;
-I*)
func_file_conv "${1#-I}" mingw
set x "$@" -I"$file"
shift
;;
-l)
eat=1
func_cl_dashl "$2"
set x "$@" "$lib"
shift
;;
-l*)
func_cl_dashl "${1#-l}"
set x "$@" "$lib"
shift
;;
-L)
eat=1
func_cl_dashL "$2"
;;
-L*)
func_cl_dashL "${1#-L}"
;;
-static)
shared=false
;;
-Wl,*)
arg=${1#-Wl,}
save_ifs="$IFS"; IFS=','
for flag in $arg; do
IFS="$save_ifs"
linker_opts="$linker_opts $flag"
done
IFS="$save_ifs"
;;
-Xlinker)
eat=1
linker_opts="$linker_opts $2"
;;
-*)
set x "$@" "$1"
shift
;;
*.cc | *.CC | *.cxx | *.CXX | *.[cC]++)
func_file_conv "$1"
set x "$@" -Tp"$file"
shift
;;
*.c | *.cpp | *.CPP | *.lib | *.LIB | *.Lib | *.OBJ | *.obj | *.[oO])
func_file_conv "$1" mingw
set x "$@" "$file"
shift
;;
*)
set x "$@" "$1"
shift
;;
esac
fi
shift
done
if test -n "$linker_opts"; then
linker_opts="-link$linker_opts"
fi
exec "$@" $linker_opts
exit 1
}
eat=
case $1 in
'')
echo "$0: No command. Try '$0 --help' for more information." 1>&2
exit 1;
;;
-h | --h*)
cat <<\EOF
Usage: compile [--help] [--version] PROGRAM [ARGS]
Wrapper for compilers which do not understand '-c -o'.
Remove '-o dest.o' from ARGS, run PROGRAM with the remaining
arguments, and rename the output as expected.
If you are trying to build a whole package this is not the
right script to run: please start by reading the file 'INSTALL'.
Report bugs to <bug-automake@gnu.org>.
EOF
exit $?
;;
-v | --v*)
echo "compile $scriptversion"
exit $?
;;
cl | *[/\\]cl | cl.exe | *[/\\]cl.exe )
func_cl_wrapper "$@" # Doesn't return...
;;
esac
ofile=
cfile=
for arg
do
if test -n "$eat"; then
eat=
else
case $1 in
-o)
# configure might choose to run compile as 'compile cc -o foo foo.c'.
# So we strip '-o arg' only if arg is an object.
eat=1
case $2 in
*.o | *.obj)
ofile=$2
;;
*)
set x "$@" -o "$2"
shift
;;
esac
;;
*.c)
cfile=$1
set x "$@" "$1"
shift
;;
*)
set x "$@" "$1"
shift
;;
esac
fi
shift
done
if test -z "$ofile" || test -z "$cfile"; then
# If no '-o' option was seen then we might have been invoked from a
# pattern rule where we don't need one. That is ok -- this is a
# normal compilation that the losing compiler can handle. If no
# '.c' file was seen then we are probably linking. That is also
# ok.
exec "$@"
fi
# Name of file we expect compiler to create.
cofile=`echo "$cfile" | sed 's|^.*[\\/]||; s|^[a-zA-Z]:||; s/\.c$/.o/'`
# Create the lock directory.
# Note: use '[/\\:.-]' here to ensure that we don't use the same name
# that we are using for the .o file. Also, base the name on the expected
# object file name, since that is what matters with a parallel build.
lockdir=`echo "$cofile" | sed -e 's|[/\\:.-]|_|g'`.d
while true; do
if mkdir "$lockdir" >/dev/null 2>&1; then
break
fi
sleep 1
done
# FIXME: race condition here if user kills between mkdir and trap.
trap "rmdir '$lockdir'; exit 1" 1 2 15
# Run the compile.
"$@"
ret=$?
if test -f "$cofile"; then
test "$cofile" = "$ofile" || mv "$cofile" "$ofile"
elif test -f "${cofile}bj"; then
test "${cofile}bj" = "$ofile" || mv "${cofile}bj" "$ofile"
fi
rmdir "$lockdir"
exit $ret
# Local Variables:
# mode: shell-script
# sh-indentation: 2
# eval: (add-hook 'write-file-hooks 'time-stamp)
# time-stamp-start: "scriptversion="
# time-stamp-format: "%:y-%02m-%02d.%02H"
# time-stamp-time-zone: "UTC"
# time-stamp-end: "; # UTC"
# End:
This diff is collapsed.
This diff is collapsed.
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This diff is collapsed.
This diff is collapsed.
#! /bin/sh
# Common wrapper for a few potentially missing GNU programs.
scriptversion=2013-10-28.13; # UTC
# Copyright (C) 1996-2014 Free Software Foundation, Inc.
# Originally written by Fran,cois Pinard <pinard@iro.umontreal.ca>, 1996.
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2, or (at your option)
# any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
# As a special exception to the GNU General Public License, if you
# distribute this file as part of a program that contains a
# configuration script generated by Autoconf, you may include it under
# the same distribution terms that you use for the rest of that program.
if test $# -eq 0; then
echo 1>&2 "Try '$0 --help' for more information"
exit 1
fi
case $1 in
--is-lightweight)
# Used by our autoconf macros to check whether the available missing
# script is modern enough.
exit 0
;;
--run)
# Back-compat with the calling convention used by older automake.
shift
;;
-h|--h|--he|--hel|--help)
echo "\
$0 [OPTION]... PROGRAM [ARGUMENT]...
Run 'PROGRAM [ARGUMENT]...', returning a proper advice when this fails due
to PROGRAM being missing or too old.
Options:
-h, --help display this help and exit
-v, --version output version information and exit
Supported PROGRAM values:
aclocal autoconf autoheader autom4te automake makeinfo
bison yacc flex lex help2man
Version suffixes to PROGRAM as well as the prefixes 'gnu-', 'gnu', and
'g' are ignored when checking the name.
Send bug reports to <bug-automake@gnu.org>."
exit $?
;;
-v|--v|--ve|--ver|--vers|--versi|--versio|--version)
echo "missing $scriptversion (GNU Automake)"
exit $?
;;
-*)
echo 1>&2 "$0: unknown '$1' option"
echo 1>&2 "Try '$0 --help' for more information"
exit 1
;;
esac
# Run the given program, remember its exit status.
"$@"; st=$?
# If it succeeded, we are done.
test $st -eq 0 && exit 0
# Also exit now if we it failed (or wasn't found), and '--version' was
# passed; such an option is passed most likely to detect whether the
# program is present and works.
case $2 in --version|--help) exit $st;; esac
# Exit code 63 means version mismatch. This often happens when the user
# tries to use an ancient version of a tool on a file that requires a
# minimum version.
if test $st -eq 63; then
msg="probably too old"
elif test $st -eq 127; then
# Program was missing.
msg="missing on your system"
else
# Program was found and executed, but failed. Give up.
exit $st
fi
perl_URL=http://www.perl.org/
flex_URL=http://flex.sourceforge.net/
gnu_software_URL=http://www.gnu.org/software
program_details ()
{
case $1 in
aclocal|automake)
echo "The '$1' program is part of the GNU Automake package:"
echo "<$gnu_software_URL/automake>"
echo "It also requires GNU Autoconf, GNU m4 and Perl in order to run:"
echo "<$gnu_software_URL/autoconf>"
echo "<$gnu_software_URL/m4/>"
echo "<$perl_URL>"
;;
autoconf|autom4te|autoheader)
echo "The '$1' program is part of the GNU Autoconf package:"
echo "<$gnu_software_URL/autoconf/>"
echo "It also requires GNU m4 and Perl in order to run:"
echo "<$gnu_software_URL/m4/>"
echo "<$perl_URL>"
;;
esac
}
give_advice ()
{
# Normalize program name to check for.
normalized_program=`echo "$1" | sed '
s/^gnu-//; t
s/^gnu//; t
s/^g//; t'`
printf '%s\n' "'$1' is $msg."
configure_deps="'configure.ac' or m4 files included by 'configure.ac'"
case $normalized_program in
autoconf*)
echo "You should only need it if you modified 'configure.ac',"
echo "or m4 files included by it."
program_details 'autoconf'
;;
autoheader*)
echo "You should only need it if you modified 'acconfig.h' or"
echo "$configure_deps."
program_details 'autoheader'
;;
automake*)
echo "You should only need it if you modified 'Makefile.am' or"
echo "$configure_deps."
program_details 'automake'
;;
aclocal*)
echo "You should only need it if you modified 'acinclude.m4' or"
echo "$configure_deps."
program_details 'aclocal'
;;
autom4te*)
echo "You might have modified some maintainer files that require"
echo "the 'autom4te' program to be rebuilt."
program_details 'autom4te'
;;
bison*|yacc*)
echo "You should only need it if you modified a '.y' file."
echo "You may want to install the GNU Bison package:"
echo "<$gnu_software_URL/bison/>"
;;
lex*|flex*)
echo "You should only need it if you modified a '.l' file."
echo "You may want to install the Fast Lexical Analyzer package:"
echo "<$flex_URL>"
;;
help2man*)
echo "You should only need it if you modified a dependency" \
"of a man page."
echo "You may want to install the GNU Help2man package:"
echo "<$gnu_software_URL/help2man/>"
;;
makeinfo*)
echo "You should only need it if you modified a '.texi' file, or"
echo "any other file indirectly affecting the aspect of the manual."
echo "You might want to install the Texinfo package:"
echo "<$gnu_software_URL/texinfo/>"
echo "The spurious makeinfo call might also be the consequence of"
echo "using a buggy 'make' (AIX, DU, IRIX), in which case you might"
echo "want to install GNU make:"
echo "<$gnu_software_URL/make/>"
;;
*)
echo "You might have modified some files without having the proper"
echo "tools for further handling them. Check the 'README' file, it"
echo "often tells you about the needed prerequisites for installing"
echo "this package. You may also peek at any GNU archive site, in"
echo "case some other package contains this missing '$1' program."
;;
esac
}
give_advice "$1" | sed -e '1s/^/WARNING: /' \
-e '2,$s/^/ /' >&2
# Propagate the correct exit status (expected to be 127 for a program
# not found, 63 for a program that failed due to version mismatch).
exit $st
# Local variables:
# eval: (add-hook 'write-file-hooks 'time-stamp)
# time-stamp-start: "scriptversion="
# time-stamp-format: "%:y-%02m-%02d.%02H"
# time-stamp-time-zone: "UTC"
# time-stamp-end: "; # UTC"
# End:
This diff is collapsed.
This diff is collapsed.
......@@ -778,7 +778,8 @@ TRINDEX_FILES = fopen.h bool.h types.h univcoord.h \
bitpack64-access.c bitpack64-access.h bitpack64-write.c bitpack64-write.h \
uintlist.c uintlist.h intlist.c intlist.h \
list.c list.h datadir.c datadir.h \
getline.c getline.h getopt.c getopt1.c getopt.h trindex.c
bzip2.c bzip2.h getline.c getline.h \
getopt.c getopt1.c getopt.h trindex.c
trindex_CC = $(PTHREAD_CC)
trindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
......@@ -821,13 +822,13 @@ IIT_STORE_FILES = fopen.h bool.h types.h univcoord.h \
doublelist.c doublelist.h \
iit-write-univ.c iit-write-univ.h iitdef.h iit-write.c iit-write.h \
tableint.c tableint.h table.c table.h chrom.c chrom.h \
getline.c getline.h \
bzip2.c bzip2.h getline.c getline.h \
getopt.c getopt1.c getopt.h iit_store.c
iit_store_CC = $(PTHREAD_CC)
iit_store_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DUTILITYP=1
iit_store_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
iit_store_LDADD = $(PTHREAD_LIBS)
iit_store_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_iit_store_SOURCES = $(IIT_STORE_FILES)
......@@ -841,13 +842,13 @@ IIT_GET_FILES = fopen.h bool.h types.h univcoord.h \
filestring.c filestring.h \
iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
complement.h parserange.c parserange.h \
getline.c getline.h \
bzip2.c bzip2.h getline.c getline.h \
getopt.c getopt1.c getopt.h iit_get.c
iit_get_CC = $(PTHREAD_CC)
iit_get_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DUTILITYP=1
iit_get_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
iit_get_LDADD = $(PTHREAD_LIBS)
iit_get_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_iit_get_SOURCES = $(IIT_GET_FILES)
IIT_DUMP_FILES = fopen.h bool.h types.h univcoord.h \
......@@ -895,13 +896,13 @@ SAM_SORT_FILES = bool.h types.h univcoord.h \
filestring.c filestring.h \
parserange.c parserange.h iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
samflags.h samheader.c samheader.h samread.c samread.h \
getline.c getline.h datadir.c datadir.h \
bzip2.c bzip2.h getline.c getline.h datadir.c datadir.h \
getopt.c getopt1.c getopt.h sam_sort.c
sam_sort_CC = $(PTHREAD_CC)
sam_sort_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
sam_sort_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
sam_sort_LDADD = $(PTHREAD_LIBS)
sam_sort_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_sam_sort_SOURCES = $(SAM_SORT_FILES)
......
This diff is collapsed.
static char rcsid[] = "$Id: atoiindex.c 218151 2019-01-17 05:36:54Z twu $";
static char rcsid[] = "$Id: atoiindex.c 219865 2019-08-09 19:56:50Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
......@@ -1469,8 +1469,8 @@ main (int argc, char *argv[]) {
char *sourcedir = NULL, *destdir = NULL, *filename, *fileroot;
Indexdb_filenames_T ifilenames;
Localdb_filenames_T lfilenames;
char *new_region_filename, *new_pointers_filename, *new_offsets_filename,
*new_positions_high_filename, *new_positions_filename;
char *new_region_filename = NULL, *new_pointers_filename = NULL, *new_offsets_filename = NULL,
*new_positions_high_filename = NULL, *new_positions_filename = NULL;
Univ_IIT_T chromosome_iit;
Univcoord_T genomelength;
......
static char rcsid[] = "$Id: bzip2.c 83593 2013-01-16 22:59:40Z twu $";
static char rcsid[] = "$Id: bzip2.c 219867 2019-08-09 20:06:43Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
......@@ -19,6 +19,7 @@ static char rcsid[] = "$Id: bzip2.c 83593 2013-01-16 22:59:40Z twu $";
#define T Bzip2_T
struct T {
FILE *fp;
#ifdef HAVE_BZLIB
BZFILE *bzfile;
#endif
......@@ -46,6 +47,8 @@ Bzip2_new (char *filename) {
if (fp == NULL) {
fprintf(stderr,"Unable to open bzip2 file %s\n",filename);
exit(9);
} else {
new->fp = fp;
}
new->bzfile = BZ2_bzReadOpen(&error,fp,/*small*/0,/*verbosity*/0,/*unused*/NULL,/*nunused*/0);
......@@ -73,6 +76,7 @@ Bzip2_free (T *old) {
fprintf(stderr,"BZ2_bzReadClose gave error %d\n",error);
exit(9);
}
fclose((*old)->fp);
#endif
FREE((*old)->buffer);
......