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samtools: Remove obsolete patch files, clean up
Module Name: pkgsrc-wip
Committed By: Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By: outpaddling
Date: Sat May 5 14:08:34 2018 -0500
Changeset: 606873a2ee122e13077c827709814711cbf7edf0
Modified Files:
samtools/Makefile
Removed Files:
samtools/files/ax_with_curses.m4
samtools/files/ax_with_htslib.m4
Log Message:
samtools: Remove obsolete patch files, clean up
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=606873a2ee122e13077c827709814711cbf7edf0
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
samtools/Makefile | 8 +-
samtools/files/ax_with_curses.m4 | 518 ---------------------------------------
samtools/files/ax_with_htslib.m4 | 140 -----------
3 files changed, 2 insertions(+), 664 deletions(-)
diffs:
diff --git a/samtools/Makefile b/samtools/Makefile
index 976c5008fd..c778d1f76c 100644
--- a/samtools/Makefile
+++ b/samtools/Makefile
@@ -17,15 +17,11 @@ GNU_CONFIGURE= yes
REPLACE_PERL= misc/*.pl misc/plot-bamstats test/test.pl
REPLACE_PYTHON= misc/*.py
-#post-patch:
-# ${CP} ${FILESDIR}/ax_with_htslib.m4 ${WRKSRC}/
-# ${CP} ${FILESDIR}/ax_with_curses.m4 ${WRKSRC}/
-
pre-configure:
cd ${WRKSRC} && autoreconf
-.include "../../devel/ncurses/buildlink3.mk"
+.include "../../mk/curses.buildlink3.mk"
.include "../../lang/python/application.mk"
-.include "../../wip/htslib/buildlink3.mk"
+.include "../../biology/htslib/buildlink3.mk"
.include "../../devel/zlib/buildlink3.mk"
.include "../../mk/bsd.pkg.mk"
diff --git a/samtools/files/ax_with_curses.m4 b/samtools/files/ax_with_curses.m4
deleted file mode 100644
index e4cbd31bae..0000000000
--- a/samtools/files/ax_with_curses.m4
+++ /dev/null
@@ -1,518 +0,0 @@
-# ===========================================================================
-# http://www.gnu.org/software/autoconf-archive/ax_with_curses.html
-# ===========================================================================
-#
-# SYNOPSIS
-#
-# AX_WITH_CURSES
-#
-# DESCRIPTION
-#
-# This macro checks whether a SysV or X/Open-compatible Curses library is
-# present, along with the associated header file. The NcursesW
-# (wide-character) library is searched for first, followed by Ncurses,
-# then the system-default plain Curses. The first library found is the
-# one returned.
-#
-# The following options are understood: --with-ncursesw, --with-ncurses,
-# --without-ncursesw, --without-ncurses. The "--with" options force the
-# macro to use that particular library, terminating with an error if not
-# found. The "--without" options simply skip the check for that library.
-# The effect on the search pattern is:
-#
-# (no options) - NcursesW, Ncurses, Curses
-# --with-ncurses --with-ncursesw - NcursesW only [*]
-# --without-ncurses --with-ncursesw - NcursesW only [*]
-# --with-ncursesw - NcursesW only [*]
-# --with-ncurses --without-ncursesw - Ncurses only [*]
-# --with-ncurses - NcursesW, Ncurses [**]
-# --without-ncurses --without-ncursesw - Curses only
-# --without-ncursesw - Ncurses, Curses
-# --without-ncurses - NcursesW, Curses
-#
-# [*] If the library is not found, abort the configure script.
-#
-# [**] If the second library (Ncurses) is not found, abort configure.
-#
-# The following preprocessor symbols may be defined by this macro if the
-# appropriate conditions are met:
-#
-# HAVE_CURSES - if any SysV or X/Open Curses library found
-# HAVE_CURSES_ENHANCED - if library supports X/Open Enhanced functions
-# HAVE_CURSES_COLOR - if library supports color (enhanced functions)
-# HAVE_CURSES_OBSOLETE - if library supports certain obsolete features
-# HAVE_NCURSESW - if NcursesW (wide char) library is to be used
-# HAVE_NCURSES - if the Ncurses library is to be used
-#
-# HAVE_CURSES_H - if <curses.h> is present and should be used
-# HAVE_NCURSESW_H - if <ncursesw.h> should be used
-# HAVE_NCURSES_H - if <ncurses.h> should be used
-# HAVE_NCURSESW_CURSES_H - if <ncursesw/curses.h> should be used
-# HAVE_NCURSES_CURSES_H - if <ncurses/curses.h> should be used
-#
-# (These preprocessor symbols are discussed later in this document.)
-#
-# The following output variable is defined by this macro; it is precious
-# and may be overridden on the ./configure command line:
-#
-# CURSES_LIB - library to add to xxx_LDADD
-#
-# The library listed in CURSES_LIB is NOT added to LIBS by default. You
-# need to add CURSES_LIB to the appropriate xxx_LDADD line in your
-# Makefile.am. For example:
-#
-# prog_LDADD = @CURSES_LIB@
-#
-# If CURSES_LIB is set on the configure command line (such as by running
-# "./configure CURSES_LIB=-lmycurses"), then the only header searched for
-# is <curses.h>. The user may use the CPPFLAGS precious variable to
-# override the standard #include search path. If the user needs to
-# specify an alternative path for a library (such as for a non-standard
-# NcurseW), the user should use the LDFLAGS variable.
-#
-# The following shell variables may be defined by this macro:
-#
-# ax_cv_curses - set to "yes" if any Curses library found
-# ax_cv_curses_enhanced - set to "yes" if Enhanced functions present
-# ax_cv_curses_color - set to "yes" if color functions present
-# ax_cv_curses_obsolete - set to "yes" if obsolete features present
-#
-# ax_cv_ncursesw - set to "yes" if NcursesW library found
-# ax_cv_ncurses - set to "yes" if Ncurses library found
-# ax_cv_plaincurses - set to "yes" if plain Curses library found
-# ax_cv_curses_which - set to "ncursesw", "ncurses", "plaincurses" or "no"
-#
-# These variables can be used in your configure.ac to determine the level
-# of support you need from the Curses library. For example, if you must
-# have either Ncurses or NcursesW, you could include:
-#
-# AX_WITH_CURSES
-# if test "x$ax_cv_ncursesw" != xyes && test "x$ax_cv_ncurses" != xyes; then
-# AC_MSG_ERROR([requires either NcursesW or Ncurses library])
-# fi
-#
-# If any Curses library will do (but one must be present and must support
-# color), you could use:
-#
-# AX_WITH_CURSES
-# if test "x$ax_cv_curses" != xyes || test "x$ax_cv_curses_color" != xyes; then
-# AC_MSG_ERROR([requires an X/Open-compatible Curses library with color])
-# fi
-#
-# Certain preprocessor symbols and shell variables defined by this macro
-# can be used to determine various features of the Curses library. In
-# particular, HAVE_CURSES and ax_cv_curses are defined if the Curses
-# library found conforms to the traditional SysV and/or X/Open Base Curses
-# definition. Any working Curses library conforms to this level.
-#
-# HAVE_CURSES_ENHANCED and ax_cv_curses_enhanced are defined if the
-# library supports the X/Open Enhanced Curses definition. In particular,
-# the wide-character types attr_t, cchar_t and wint_t, the functions
-# wattr_set() and wget_wch() and the macros WA_NORMAL and _XOPEN_CURSES
-# are checked. The Ncurses library does NOT conform to this definition,
-# although NcursesW does.
-#
-# HAVE_CURSES_COLOR and ax_cv_curses_color are defined if the library
-# supports color functions and macros such as COLOR_PAIR, A_COLOR,
-# COLOR_WHITE, COLOR_RED and init_pair(). These are NOT part of the
-# X/Open Base Curses definition, but are part of the Enhanced set of
-# functions. The Ncurses library DOES support these functions, as does
-# NcursesW.
-#
-# HAVE_CURSES_OBSOLETE and ax_cv_curses_obsolete are defined if the
-# library supports certain features present in SysV and BSD Curses but not
-# defined in the X/Open definition. In particular, the functions
-# getattrs(), getcurx() and getmaxx() are checked.
-#
-# To use the HAVE_xxx_H preprocessor symbols, insert the following into
-# your system.h (or equivalent) header file:
-#
-# #if defined HAVE_NCURSESW_CURSES_H
-# # include <ncursesw/curses.h>
-# #elif defined HAVE_NCURSESW_H
-# # include <ncursesw.h>
-# #elif defined HAVE_NCURSES_CURSES_H
-# # include <ncurses/curses.h>
-# #elif defined HAVE_NCURSES_H
-# # include <ncurses.h>
-# #elif defined HAVE_CURSES_H
-# # include <curses.h>
-# #else
-# # error "SysV or X/Open-compatible Curses header file required"
-# #endif
-#
-# For previous users of this macro: you should not need to change anything
-# in your configure.ac or Makefile.am, as the previous (serial 10)
-# semantics are still valid. However, you should update your system.h (or
-# equivalent) header file to the fragment shown above. You are encouraged
-# also to make use of the extended functionality provided by this version
-# of AX_WITH_CURSES, as well as in the additional macros
-# AX_WITH_CURSES_PANEL, AX_WITH_CURSES_MENU and AX_WITH_CURSES_FORM.
-#
-# LICENSE
-#
-# Copyright (c) 2009 Mark Pulford <mark%kyne.com.au@localhost>
-# Copyright (c) 2009 Damian Pietras <daper%daper.net@localhost>
-# Copyright (c) 2012 Reuben Thomas <rrt%sc3d.org@localhost>
-# Copyright (c) 2011 John Zaitseff <J.Zaitseff%zap.org.au@localhost>
-#
-# 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 3 of the License, 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, the respective Autoconf Macro's copyright owner
-# gives unlimited permission to copy, distribute and modify the configure
-# scripts that are the output of Autoconf when processing the Macro. You
-# need not follow the terms of the GNU General Public License when using
-# or distributing such scripts, even though portions of the text of the
-# Macro appear in them. The GNU General Public License (GPL) does govern
-# all other use of the material that constitutes the Autoconf Macro.
-#
-# This special exception to the GPL applies to versions of the Autoconf
-# Macro released by the Autoconf Archive. When you make and distribute a
-# modified version of the Autoconf Macro, you may extend this special
-# exception to the GPL to apply to your modified version as well.
-
-#serial 15
-
-AU_ALIAS([MP_WITH_CURSES], [AX_WITH_CURSES])
-AC_DEFUN([AX_WITH_CURSES], [
- AC_ARG_VAR([CURSES_LIB], [linker library for Curses, e.g. -lcurses])
- AC_ARG_WITH([ncurses], [AS_HELP_STRING([--with-ncurses],
- [force the use of Ncurses or NcursesW])],
- [], [with_ncurses=check])
- AC_ARG_WITH([ncursesw], [AS_HELP_STRING([--without-ncursesw],
- [do not use NcursesW (wide character support)])],
- [], [with_ncursesw=check])
-
- ax_saved_LIBS=$LIBS
- AS_IF([test "x$with_ncurses" = xyes || test "x$with_ncursesw" = xyes],
- [ax_with_plaincurses=no], [ax_with_plaincurses=check])
-
- ax_cv_curses_which=no
-
- # Test for NcursesW
-
- AS_IF([test "x$CURSES_LIB" = x && test "x$with_ncursesw" != xno], [
- LIBS="$ax_saved_LIBS -lncursesw"
-
- AC_CACHE_CHECK([for NcursesW wide-character library], [ax_cv_ncursesw], [
- AC_LINK_IFELSE([AC_LANG_CALL([], [initscr])],
- [ax_cv_ncursesw=yes], [ax_cv_ncursesw=no])
- ])
- AS_IF([test "x$ax_cv_ncursesw" = xno && test "x$with_ncursesw" = xyes], [
- AC_MSG_ERROR([--with-ncursesw specified but could not find NcursesW library])
- ])
-
- AS_IF([test "x$ax_cv_ncursesw" = xyes], [
- ax_cv_curses=yes
- ax_cv_curses_which=ncursesw
- CURSES_LIB="-lncursesw"
- AC_DEFINE([HAVE_NCURSESW], [1], [Define to 1 if the NcursesW library is present])
- AC_DEFINE([HAVE_CURSES], [1], [Define to 1 if a SysV or X/Open compatible Curses library is present])
-
- AC_CACHE_CHECK([for working ncursesw/curses.h], [ax_cv_header_ncursesw_curses_h], [
- AC_LINK_IFELSE([AC_LANG_PROGRAM([[
- @%:@define _XOPEN_SOURCE_EXTENDED 1
- @%:@include <ncursesw/curses.h>
- ]], [[
- chtype a = A_BOLD;
- int b = KEY_LEFT;
- chtype c = COLOR_PAIR(1) & A_COLOR;
- attr_t d = WA_NORMAL;
- cchar_t e;
- wint_t f;
- int g = getattrs(stdscr);
- int h = getcurx(stdscr) + getmaxx(stdscr);
- initscr();
- init_pair(1, COLOR_WHITE, COLOR_RED);
- wattr_set(stdscr, d, 0, NULL);
- wget_wch(stdscr, &f);
- ]])],
- [ax_cv_header_ncursesw_curses_h=yes],
- [ax_cv_header_ncursesw_curses_h=no])
- ])
- AS_IF([test "x$ax_cv_header_ncursesw_curses_h" = xyes], [
- ax_cv_curses_enhanced=yes
- ax_cv_curses_color=yes
- ax_cv_curses_obsolete=yes
- AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions])
- AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)])
- AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features])
- AC_DEFINE([HAVE_NCURSESW_CURSES_H], [1], [Define to 1 if <ncursesw/curses.h> is present])
- ])
-
- AC_CACHE_CHECK([for working ncursesw.h], [ax_cv_header_ncursesw_h], [
- AC_LINK_IFELSE([AC_LANG_PROGRAM([[
- @%:@define _XOPEN_SOURCE_EXTENDED 1
- @%:@include <ncursesw.h>
- ]], [[
- chtype a = A_BOLD;
- int b = KEY_LEFT;
- chtype c = COLOR_PAIR(1) & A_COLOR;
- attr_t d = WA_NORMAL;
- cchar_t e;
- wint_t f;
- int g = getattrs(stdscr);
- int h = getcurx(stdscr) + getmaxx(stdscr);
- initscr();
- init_pair(1, COLOR_WHITE, COLOR_RED);
- wattr_set(stdscr, d, 0, NULL);
- wget_wch(stdscr, &f);
- ]])],
- [ax_cv_header_ncursesw_h=yes],
- [ax_cv_header_ncursesw_h=no])
- ])
- AS_IF([test "x$ax_cv_header_ncursesw_h" = xyes], [
- ax_cv_curses_enhanced=yes
- ax_cv_curses_color=yes
- ax_cv_curses_obsolete=yes
- AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions])
- AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)])
- AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features])
- AC_DEFINE([HAVE_NCURSESW_H], [1], [Define to 1 if <ncursesw.h> is present])
- ])
-
- AC_CACHE_CHECK([for working ncurses.h], [ax_cv_header_ncurses_h_with_ncursesw], [
- AC_LINK_IFELSE([AC_LANG_PROGRAM([[
- @%:@define _XOPEN_SOURCE_EXTENDED 1
- @%:@include <ncurses.h>
- ]], [[
- chtype a = A_BOLD;
- int b = KEY_LEFT;
- chtype c = COLOR_PAIR(1) & A_COLOR;
- attr_t d = WA_NORMAL;
- cchar_t e;
- wint_t f;
- int g = getattrs(stdscr);
- int h = getcurx(stdscr) + getmaxx(stdscr);
- initscr();
- init_pair(1, COLOR_WHITE, COLOR_RED);
- wattr_set(stdscr, d, 0, NULL);
- wget_wch(stdscr, &f);
- ]])],
- [ax_cv_header_ncurses_h_with_ncursesw=yes],
- [ax_cv_header_ncurses_h_with_ncursesw=no])
- ])
- AS_IF([test "x$ax_cv_header_ncurses_h_with_ncursesw" = xyes], [
- ax_cv_curses_enhanced=yes
- ax_cv_curses_color=yes
- ax_cv_curses_obsolete=yes
- AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions])
- AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)])
- AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features])
- AC_DEFINE([HAVE_NCURSES_H], [1], [Define to 1 if <ncurses.h> is present])
- ])
-
- AS_IF([test "x$ax_cv_header_ncursesw_curses_h" = xno && test "x$ax_cv_header_ncursesw_h" = xno && test "x$ax_cv_header_ncurses_h_with_ncursesw" = xno], [
- AC_MSG_WARN([could not find a working ncursesw/curses.h, ncursesw.h or ncurses.h])
- ])
- ])
- ])
-
- # Test for Ncurses
-
- AS_IF([test "x$CURSES_LIB" = x && test "x$with_ncurses" != xno && test "x$ax_cv_curses_which" = xno], [
- LIBS="$ax_saved_LIBS -lncurses"
-
- AC_CACHE_CHECK([for Ncurses library], [ax_cv_ncurses], [
- AC_LINK_IFELSE([AC_LANG_CALL([], [initscr])],
- [ax_cv_ncurses=yes], [ax_cv_ncurses=no])
- ])
- AS_IF([test "x$ax_cv_ncurses" = xno && test "x$with_ncurses" = xyes], [
- AC_MSG_ERROR([--with-ncurses specified but could not find Ncurses library])
- ])
-
- AS_IF([test "x$ax_cv_ncurses" = xyes], [
- ax_cv_curses=yes
- ax_cv_curses_which=ncurses
- CURSES_LIB="-lncurses"
- AC_DEFINE([HAVE_NCURSES], [1], [Define to 1 if the Ncurses library is present])
- AC_DEFINE([HAVE_CURSES], [1], [Define to 1 if a SysV or X/Open compatible Curses library is present])
-
- AC_CACHE_CHECK([for working ncurses/curses.h], [ax_cv_header_ncurses_curses_h], [
- AC_LINK_IFELSE([AC_LANG_PROGRAM([[
- @%:@include <ncurses/curses.h>
- ]], [[
- chtype a = A_BOLD;
- int b = KEY_LEFT;
- chtype c = COLOR_PAIR(1) & A_COLOR;
- int g = getattrs(stdscr);
- int h = getcurx(stdscr) + getmaxx(stdscr);
- initscr();
- init_pair(1, COLOR_WHITE, COLOR_RED);
- ]])],
- [ax_cv_header_ncurses_curses_h=yes],
- [ax_cv_header_ncurses_curses_h=no])
- ])
- AS_IF([test "x$ax_cv_header_ncurses_curses_h" = xyes], [
- ax_cv_curses_color=yes
- ax_cv_curses_obsolete=yes
- AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)])
- AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features])
- AC_DEFINE([HAVE_NCURSES_CURSES_H], [1], [Define to 1 if <ncurses/curses.h> is present])
- ])
-
- AC_CACHE_CHECK([for working ncurses.h], [ax_cv_header_ncurses_h], [
- AC_LINK_IFELSE([AC_LANG_PROGRAM([[
- @%:@include <ncurses.h>
- ]], [[
- chtype a = A_BOLD;
- int b = KEY_LEFT;
- chtype c = COLOR_PAIR(1) & A_COLOR;
- int g = getattrs(stdscr);
- int h = getcurx(stdscr) + getmaxx(stdscr);
- initscr();
- init_pair(1, COLOR_WHITE, COLOR_RED);
- ]])],
- [ax_cv_header_ncurses_h=yes],
- [ax_cv_header_ncurses_h=no])
- ])
- AS_IF([test "x$ax_cv_header_ncurses_h" = xyes], [
- ax_cv_curses_color=yes
- ax_cv_curses_obsolete=yes
- AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)])
- AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features])
- AC_DEFINE([HAVE_NCURSES_H], [1], [Define to 1 if <ncurses.h> is present])
- ])
-
- AS_IF([test "x$ax_cv_header_ncurses_curses_h" = xno && test "x$ax_cv_header_ncurses_h" = xno], [
- AC_MSG_WARN([could not find a working ncurses/curses.h or ncurses.h])
- ])
- ])
- ])
-
- # Test for plain Curses (or if CURSES_LIB was set by user)
-
- AS_IF([test "x$with_plaincurses" != xno && test "x$ax_cv_curses_which" = xno], [
- AS_IF([test "x$CURSES_LIB" != x], [
- LIBS="$ax_saved_LIBS $CURSES_LIB"
- ], [
- LIBS="$ax_saved_LIBS -lcurses"
- ])
-
- AC_CACHE_CHECK([for Curses library], [ax_cv_plaincurses], [
- AC_LINK_IFELSE([AC_LANG_CALL([], [initscr])],
- [ax_cv_plaincurses=yes], [ax_cv_plaincurses=no])
- ])
-
- AS_IF([test "x$ax_cv_plaincurses" = xyes], [
- ax_cv_curses=yes
- ax_cv_curses_which=plaincurses
- AS_IF([test "x$CURSES_LIB" = x], [
- CURSES_LIB="-lcurses"
- ])
- AC_DEFINE([HAVE_CURSES], [1], [Define to 1 if a SysV or X/Open compatible Curses library is present])
-
- # Check for base conformance (and header file)
-
- AC_CACHE_CHECK([for working curses.h], [ax_cv_header_curses_h], [
- AC_LINK_IFELSE([AC_LANG_PROGRAM([[
- @%:@include <curses.h>
- ]], [[
- chtype a = A_BOLD;
- int b = KEY_LEFT;
- initscr();
- ]])],
- [ax_cv_header_curses_h=yes],
- [ax_cv_header_curses_h=no])
- ])
- AS_IF([test "x$ax_cv_header_curses_h" = xyes], [
- AC_DEFINE([HAVE_CURSES_H], [1], [Define to 1 if <curses.h> is present])
-
- # Check for X/Open Enhanced conformance
-
- AC_CACHE_CHECK([for X/Open Enhanced Curses conformance], [ax_cv_plaincurses_enhanced], [
- AC_LINK_IFELSE([AC_LANG_PROGRAM([[
- @%:@define _XOPEN_SOURCE_EXTENDED 1
- @%:@include <curses.h>
- @%:@ifndef _XOPEN_CURSES
- @%:@error "this Curses library is not enhanced"
- "this Curses library is not enhanced"
- @%:@endif
- ]], [[
- chtype a = A_BOLD;
- int b = KEY_LEFT;
- chtype c = COLOR_PAIR(1) & A_COLOR;
- attr_t d = WA_NORMAL;
- cchar_t e;
- wint_t f;
- initscr();
- init_pair(1, COLOR_WHITE, COLOR_RED);
- wattr_set(stdscr, d, 0, NULL);
- wget_wch(stdscr, &f);
- ]])],
- [ax_cv_plaincurses_enhanced=yes],
- [ax_cv_plaincurses_enhanced=no])
- ])
- AS_IF([test "x$ax_cv_plaincurses_enhanced" = xyes], [
- ax_cv_curses_enhanced=yes
- ax_cv_curses_color=yes
- AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions])
- AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)])
- ])
-
- # Check for color functions
-
- AC_CACHE_CHECK([for Curses color functions], [ax_cv_plaincurses_color], [
- AC_LINK_IFELSE([AC_LANG_PROGRAM([[
- @%:@define _XOPEN_SOURCE_EXTENDED 1
- @%:@include <curses.h>
- ]], [[
- chtype a = A_BOLD;
- int b = KEY_LEFT;
- chtype c = COLOR_PAIR(1) & A_COLOR;
- initscr();
- init_pair(1, COLOR_WHITE, COLOR_RED);
- ]])],
- [ax_cv_plaincurses_color=yes],
- [ax_cv_plaincurses_color=no])
- ])
- AS_IF([test "x$ax_cv_plaincurses_color" = xyes], [
- ax_cv_curses_color=yes
- AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)])
- ])
-
- # Check for obsolete functions
-
- AC_CACHE_CHECK([for obsolete Curses functions], [ax_cv_plaincurses_obsolete], [
- AC_LINK_IFELSE([AC_LANG_PROGRAM([[
- @%:@include <curses.h>
- ]], [[
- chtype a = A_BOLD;
- int b = KEY_LEFT;
- int g = getattrs(stdscr);
- int h = getcurx(stdscr) + getmaxx(stdscr);
- initscr();
- ]])],
- [ax_cv_plaincurses_obsolete=yes],
- [ax_cv_plaincurses_obsolete=no])
- ])
- AS_IF([test "x$ax_cv_plaincurses_obsolete" = xyes], [
- ax_cv_curses_obsolete=yes
- AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features])
- ])
- ])
-
- AS_IF([test "x$ax_cv_header_curses_h" = xno], [
- AC_MSG_WARN([could not find a working curses.h])
- ])
- ])
- ])
-
- AS_IF([test "x$ax_cv_curses" != xyes], [ax_cv_curses=no])
- AS_IF([test "x$ax_cv_curses_enhanced" != xyes], [ax_cv_curses_enhanced=no])
- AS_IF([test "x$ax_cv_curses_color" != xyes], [ax_cv_curses_color=no])
- AS_IF([test "x$ax_cv_curses_obsolete" != xyes], [ax_cv_curses_obsolete=no])
-
- LIBS=$ax_saved_LIBS
-])dnl
diff --git a/samtools/files/ax_with_htslib.m4 b/samtools/files/ax_with_htslib.m4
deleted file mode 100644
index f39e4eb142..0000000000
--- a/samtools/files/ax_with_htslib.m4
+++ /dev/null
@@ -1,140 +0,0 @@
-# ===========================================================================
-# http://www.gnu.org/software/autoconf-archive/ax_with_htslib.html
-# ===========================================================================
-#
-# SYNOPSIS
-#
-# AX_WITH_HTSLIB
-#
-# DESCRIPTION
-#
-# This macro checks whether HTSlib <http://www.htslib.org/> is installed
-# or nearby, and adds a --with-htslib=DIR option to the configure script
-# for specifying the location. It locates either an installation prefix
-# (with 'include' and 'lib' subdirectories) or an HTSlib source tree, as
-# HTSlib is fast-moving and users may wish to use an in-development tree.
-#
-# Different checks occur depending on the --with-htslib argument given:
-#
-# With --with-htslib=DIR, checks whether DIR is a source tree or contains
-# a working installation.
-# By default, searches for a source tree (with a name matching htslib*)
-# within or alongside $srcdir. Produces AC_MSG_ERROR if there are
-# several equally-likely candidates. If there are none, checks for
-# a working default installation.
-# With --with-htslib=system, checks for a working default installation.
-#
-# If a source tree is found or specified, it is added to AC_CONFIG_SUBDIRS
-# (which unfortunately may cause a "you should use literals" warning when
-# autoconf is run).
-#
-# The following output variables are set by this macro:
-#
-# HTSDIR Directory containing HTSlib source tree
-# HTSLIB_CPPFLAGS Preprocessor flags for compiling with HTSlib
-# HTSLIB_LDFLAGS Linker flags for linking with HTSlib
-#
-# The following shell variables may be defined:
-#
-# ax_cv_htslib Set to "yes" if HTSlib was found
-# ax_cv_htslib_which Set to "source", "install", or "none"
-#
-# LICENSE
-#
-# Copyright (C) 2015 Genome Research Ltd
-#
-# 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 any
-# warranty.
-
-#serial 1
-
-AC_DEFUN([AX_WITH_HTSLIB],
-[AC_ARG_WITH([htslib],
- [AS_HELP_STRING([--with-htslib=DIR],
- [use the HTSlib source tree or installation in DIR])
-dnl Not indented, to avoid extra whitespace outwith AS_HELP_STRING()
-AS_HELP_STRING([--with-htslib=system],
- [use only a system HTSlib installation])],
- [], [with_htslib=search])
-
-case $with_htslib in
-yes|search)
- AC_MSG_CHECKING([location of HTSlib source tree])
- case $srcdir in
- .) srcp= ;;
- *) srcp=$srcdir/ ;;
- esac
- found=
- for dir in ${srcp}htslib* -- ${srcp}../htslib -- ${srcp}../htslib*
- do
- if test "$dir" = "--"; then
- test -n "$found" && break
- elif test -f "$dir/hts.c" && test -f "$dir/htslib/hts.h"; then
- found="${found}1"
- HTSDIR=$dir
- fi
- done
- if test -z "$found"; then
- AC_MSG_RESULT([none found])
- ax_cv_htslib_which=system
- elif test "$found" = 1; then
- AC_MSG_RESULT([$HTSDIR])
- ax_cv_htslib_which=source
- else
- AC_MSG_RESULT([several directories found])
- AC_MSG_ERROR([use --with-htslib=DIR to select which HTSlib to use])
- fi
- ;;
-no) ax_cv_htslib_which=none ;;
-system) ax_cv_htslib_which=system ;;
-*)
- HTSDIR=$with_htslib
- if test -f "$HTSDIR/hts.c" && test -f "$HTSDIR/htslib/hts.h"; then
- ax_cv_htslib_which=source
- else
- ax_cv_htslib_which=install
- fi
- ;;
-esac
-
-case $ax_cv_htslib_which in
-#source)
-# ax_cv_htslib=yes
-# HTSLIB_CPPFLAGS="-I$HTSDIR"
-# HTSLIB_LDFLAGS="-L$HTSDIR"
-# # We can't use a literal, because $HTSDIR is user-provided and variable
-# AC_CONFIG_SUBDIRS($HTSDIR)
-# ;;
-system)
- AC_CHECK_HEADER([htslib/sam.h],
- [AC_CHECK_LIB(hts, hts_version, [ax_cv_htslib=yes], [ax_cv_htslib=no])],
- [ax_cv_htslib=no], [;])
- ax_cv_htslib_which=install
- HTSDIR=
- HTSLIB_CPPFLAGS=
- HTSLIB_LDFLAGS=
- ;;
-install)
- ax_saved_CPPFLAGS=$CPPFLAGS
- ax_saved_LDFLAGS=$LDFLAGS
- HTSLIB_CPPFLAGS="-I$HTSDIR/include"
- HTSLIB_LDFLAGS="-L$HTSDIR/lib"
- CPPFLAGS="$CPPFLAGS $HTSLIB_CPPFLAGS"
- LDFLAGS="$LDFLAGS $HTSLIB_LDFLAGS"
- AC_CHECK_HEADER([htslib/sam.h],
- [AC_CHECK_LIB(hts, hts_version, [ax_cv_htslib=yes], [ax_cv_htslib=no])],
- [ax_cv_htslib=no], [;])
- HTSDIR=
- CPPFLAGS=$ax_saved_CPPFLAGS
- LDFLAGS=$ax_saved_LDFLAGS
- ;;
-none)
- ax_cv_htslib=no
- ;;
-esac
-
-AC_SUBST([HTSDIR])
-AC_SUBST([HTSLIB_CPPFLAGS])
-AC_SUBST([HTSLIB_LDFLAGS])])
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