From 615d6e210e3321921c0ef102826b36d2d9bb3669 Mon Sep 17 00:00:00 2001 From: pizzamig Date: Wed, 25 Oct 2017 10:19:50 +0000 Subject: biology/htslib biology/bcftools biology/samtools: Update to 1.6 PR: 223094 Submitted by: mzaki@niid.go.jp Approved by: cartwright@asu.edu (maintainer) Approved by: olivier (mentor) Differential Revision: https://reviews.freebsd.org/D12768 --- biology/samtools/Makefile | 22 +- biology/samtools/distinfo | 6 +- biology/samtools/files/ax_with_curses.m4 | 518 ------------------------------ biology/samtools/files/ax_with_htslib.m4 | 140 -------- biology/samtools/files/patch-Makefile | 58 +--- biology/samtools/files/patch-configure.ac | 19 -- biology/samtools/files/patch-dict.c | 10 - biology/samtools/files/patch-errmod.c | 16 - biology/samtools/files/patch-test_test.pl | 15 +- biology/samtools/files/pkg-message.in | 2 +- 10 files changed, 29 insertions(+), 777 deletions(-) delete mode 100644 biology/samtools/files/ax_with_curses.m4 delete mode 100644 biology/samtools/files/ax_with_htslib.m4 delete mode 100644 biology/samtools/files/patch-configure.ac delete mode 100644 biology/samtools/files/patch-dict.c delete mode 100644 biology/samtools/files/patch-errmod.c (limited to 'biology/samtools') diff --git a/biology/samtools/Makefile b/biology/samtools/Makefile index 632d0a9c001e..da12548a1714 100644 --- a/biology/samtools/Makefile +++ b/biology/samtools/Makefile @@ -2,7 +2,7 @@ # $FreeBSD$ PORTNAME= samtools -PORTVERSION= 1.3.1 +PORTVERSION= 1.6 CATEGORIES= biology MAINTAINER= cartwright@asu.edu @@ -11,34 +11,22 @@ COMMENT= Tools for manipulating next-generation sequencing data LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE -BUILD_DEPENDS= htslib>=1.3:biology/htslib +BUILD_DEPENDS= htslib>=1.6:biology/htslib LIB_DEPENDS= libhts.so:biology/htslib TEST_DEPENDS= bash:shells/bash USE_GITHUB= yes -USES= autoreconf gmake ncurses perl5 shebangfix +USES= autoreconf gmake ncurses perl5 python shebangfix USE_PERL5= test +PYTHON_NO_DEPENDS= yes GNU_CONFIGURE= yes SUB_FILES= pkg-message -SHEBANG_FILES= misc/*.pl misc/plot-bamstats test/test.pl +SHEBANG_FILES= misc/*.pl misc/*.py misc/plot-bamstats test/test.pl CPPFLAGS+= -I${LOCALBASE}/include LDFLAGS+= -L${LOCALBASE}/lib -MAKE_ENV= INSTALL_LIB="${INSTALL_LIB}" \ - INSTALL_DATA="${INSTALL_DATA}" \ - INSTALL_PROGRAM="${INSTALL_PROGRAM}" \ - INSTALL_SCRIPT="${INSTALL_SCRIPT}" \ - INSTALL_DIR="${MKDIR}" - -PLIST_SUB= PORTVERSION="${PORTVERSION}" - TEST_TARGET= test -post-patch: - @${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' ${WRKSRC}/configure.ac - ${CP} ${FILESDIR}/ax_with_htslib.m4 ${WRKSRC}/ - ${CP} ${FILESDIR}/ax_with_curses.m4 ${WRKSRC}/ - .include diff --git a/biology/samtools/distinfo b/biology/samtools/distinfo index 439a947c14cb..a0736b452989 100644 --- a/biology/samtools/distinfo +++ b/biology/samtools/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1463691050 -SHA256 (samtools-samtools-1.3.1_GH0.tar.gz) = 30752c7b92cd9e146f4017983b2a41beb58c8966e93572cea76a14719f95a768 -SIZE (samtools-samtools-1.3.1_GH0.tar.gz) = 3757176 +TIMESTAMP = 1508304738 +SHA256 (samtools-samtools-1.6_GH0.tar.gz) = c0d1ffefe441297ee0eec0e032ac3131519f82fd1a11d38fbcec19e2d5822b28 +SIZE (samtools-samtools-1.6_GH0.tar.gz) = 4014195 diff --git a/biology/samtools/files/ax_with_curses.m4 b/biology/samtools/files/ax_with_curses.m4 deleted file mode 100644 index e4cbd31bae42..000000000000 --- a/biology/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 is present and should be used -# HAVE_NCURSESW_H - if should be used -# HAVE_NCURSES_H - if should be used -# HAVE_NCURSESW_CURSES_H - if should be used -# HAVE_NCURSES_CURSES_H - if 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 . 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 -# #elif defined HAVE_NCURSESW_H -# # include -# #elif defined HAVE_NCURSES_CURSES_H -# # include -# #elif defined HAVE_NCURSES_H -# # include -# #elif defined HAVE_CURSES_H -# # include -# #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 -# Copyright (c) 2009 Damian Pietras -# Copyright (c) 2012 Reuben Thomas -# Copyright (c) 2011 John Zaitseff -# -# 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 . -# -# 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 - ]], [[ - 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$ax_cv_header_ncursesw_curses_h" = xyes], [ - ax_cv_curses_enhanced=yes - ax_cv_curses_color=yes - ax_cv_curses_obsolete=yes - AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions]) - AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) - AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features]) - AC_DEFINE([HAVE_NCURSESW_CURSES_H], [1], [Define to 1 if is present]) - ]) - - AC_CACHE_CHECK([for working ncursesw.h], [ax_cv_header_ncursesw_h], [ - AC_LINK_IFELSE([AC_LANG_PROGRAM([[ - @%:@define _XOPEN_SOURCE_EXTENDED 1 - @%:@include - ]], [[ - chtype a = A_BOLD; - int b = KEY_LEFT; - chtype c = COLOR_PAIR(1) & A_COLOR; - attr_t d = WA_NORMAL; - cchar_t e; - wint_t f; - int g = getattrs(stdscr); - int h = getcurx(stdscr) + getmaxx(stdscr); - initscr(); - init_pair(1, COLOR_WHITE, COLOR_RED); - wattr_set(stdscr, d, 0, NULL); - wget_wch(stdscr, &f); - ]])], - [ax_cv_header_ncursesw_h=yes], - [ax_cv_header_ncursesw_h=no]) - ]) - AS_IF([test "x$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 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 - ]], [[ - 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$ax_cv_header_ncurses_h_with_ncursesw" = xyes], [ - ax_cv_curses_enhanced=yes - ax_cv_curses_color=yes - ax_cv_curses_obsolete=yes - AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions]) - AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) - AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features]) - AC_DEFINE([HAVE_NCURSES_H], [1], [Define to 1 if is present]) - ]) - - AS_IF([test "x$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$ax_cv_ncurses" = xyes], [ - ax_cv_curses=yes - ax_cv_curses_which=ncurses - CURSES_LIB="-lncurses" - AC_DEFINE([HAVE_NCURSES], [1], [Define to 1 if the Ncurses library is present]) - AC_DEFINE([HAVE_CURSES], [1], [Define to 1 if a SysV or X/Open compatible Curses library is present]) - - AC_CACHE_CHECK([for working ncurses/curses.h], [ax_cv_header_ncurses_curses_h], [ - AC_LINK_IFELSE([AC_LANG_PROGRAM([[ - @%:@include - ]], [[ - chtype a = A_BOLD; - int b = KEY_LEFT; - chtype c = COLOR_PAIR(1) & A_COLOR; - int g = getattrs(stdscr); - int h = getcurx(stdscr) + getmaxx(stdscr); - initscr(); - init_pair(1, COLOR_WHITE, COLOR_RED); - ]])], - [ax_cv_header_ncurses_curses_h=yes], - [ax_cv_header_ncurses_curses_h=no]) - ]) - AS_IF([test "x$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 is present]) - ]) - - AC_CACHE_CHECK([for working ncurses.h], [ax_cv_header_ncurses_h], [ - AC_LINK_IFELSE([AC_LANG_PROGRAM([[ - @%:@include - ]], [[ - 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$ax_cv_header_ncurses_h" = xyes], [ - ax_cv_curses_color=yes - ax_cv_curses_obsolete=yes - AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) - AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features]) - AC_DEFINE([HAVE_NCURSES_H], [1], [Define to 1 if is present]) - ]) - - AS_IF([test "x$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 - ]], [[ - 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$ax_cv_header_curses_h" = xyes], [ - AC_DEFINE([HAVE_CURSES_H], [1], [Define to 1 if is present]) - - # Check for X/Open Enhanced conformance - - AC_CACHE_CHECK([for X/Open Enhanced Curses conformance], [ax_cv_plaincurses_enhanced], [ - AC_LINK_IFELSE([AC_LANG_PROGRAM([[ - @%:@define _XOPEN_SOURCE_EXTENDED 1 - @%:@include - @%:@ifndef _XOPEN_CURSES - @%:@error "this Curses library is not enhanced" - "this Curses library is not enhanced" - @%:@endif - ]], [[ - chtype a = A_BOLD; - int b = KEY_LEFT; - chtype c = COLOR_PAIR(1) & A_COLOR; - attr_t d = WA_NORMAL; - cchar_t e; - wint_t f; - initscr(); - init_pair(1, COLOR_WHITE, COLOR_RED); - wattr_set(stdscr, d, 0, NULL); - wget_wch(stdscr, &f); - ]])], - [ax_cv_plaincurses_enhanced=yes], - [ax_cv_plaincurses_enhanced=no]) - ]) - AS_IF([test "x$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 - ]], [[ - 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$ax_cv_plaincurses_color" = xyes], [ - ax_cv_curses_color=yes - AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)]) - ]) - - # Check for obsolete functions - - AC_CACHE_CHECK([for obsolete Curses functions], [ax_cv_plaincurses_obsolete], [ - AC_LINK_IFELSE([AC_LANG_PROGRAM([[ - @%:@include - ]], [[ - chtype a = A_BOLD; - int b = KEY_LEFT; - int g = getattrs(stdscr); - int h = getcurx(stdscr) + getmaxx(stdscr); - initscr(); - ]])], - [ax_cv_plaincurses_obsolete=yes], - [ax_cv_plaincurses_obsolete=no]) - ]) - AS_IF([test "x$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/biology/samtools/files/ax_with_htslib.m4 b/biology/samtools/files/ax_with_htslib.m4 deleted file mode 100644 index f39e4eb1427b..000000000000 --- a/biology/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 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])]) diff --git a/biology/samtools/files/patch-Makefile b/biology/samtools/files/patch-Makefile index eaa977f79e05..afdbfd1ed1ab 100644 --- a/biology/samtools/files/patch-Makefile +++ b/biology/samtools/files/patch-Makefile @@ -1,11 +1,11 @@ ---- Makefile.orig 2016-04-22 09:22:44 UTC +--- Makefile.orig 2017-09-28 11:12:01 UTC +++ Makefile -@@ -38,18 +38,18 @@ AOBJS= bam_index.o bam_plcmd.o sam_ +@@ -40,23 +40,22 @@ AOBJS= bam_index.o bam_plcmd.o sam_ bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o \ - bam_quickcheck.o bam_addrprg.o + bam_quickcheck.o bam_addrprg.o bam_markdup.o -prefix = /usr/local -+prefix = ${STAGEDIR}${PREFIX} ++prefix = ${PREFIX} exec_prefix = $(prefix) bindir = $(exec_prefix)/bin datarootdir = $(prefix)/share @@ -13,46 +13,22 @@ +mandir = $(prefix)/man man1dir = $(mandir)/man1 --MKDIR_P = mkdir -p + # Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS) +-misc_bindir = $(bindir) ++misc_bindir = $(bindir)/samtools_misc + + MKDIR_P = mkdir -p -INSTALL = install -p --INSTALL_PROGRAM = $(INSTALL) -INSTALL_DATA = $(INSTALL) -m 644 -INSTALL_DIR = $(MKDIR_P) -m 755 -+#MKDIR_P = mkdir -p -+#INSTALL = install -p -+#INSTALL_PROGRAM = $(INSTALL) -+#INSTALL_DATA = $(INSTALL) -m 644 -+#INSTALL_DIR = $(MKDIR_P) -m 755 +-INSTALL_MAN = $(INSTALL_DATA) +-INSTALL_PROGRAM = $(INSTALL) +-INSTALL_SCRIPT = $(INSTALL_PROGRAM) ++INSTALL_DATA = ${BSD_INSTALL_DATA} ++INSTALL_DIR = $(MKDIR_P) ++INSTALL_MAN = ${BSD_INSTALL_MAN} ++INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM} ++INSTALL_SCRIPT = ${BSD_INSTALL_SCRIPT} PROGRAMS = samtools -@@ -59,7 +59,6 @@ BUILT_MISC_PROGRAMS = \ - misc/md5fa misc/md5sum-lite misc/wgsim - - MISC_PROGRAMS = \ -- $(BUILT_MISC_PROGRAMS) \ - misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl \ - misc/interpolate_sam.pl misc/novo2sam.pl \ - misc/plot-bamstats misc/psl2sam.pl \ -@@ -82,7 +81,7 @@ all: $(PROGRAMS) $(BUILT_MISC_PROGRAMS) - # TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally - ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) - ALL_LDFLAGS = -rdynamic $(HTSLIB_LDFLAGS) $(LDFLAGS) --ALL_LIBS = -lz -ldl $(LIBS) -+ALL_LIBS = -lz $(LIBS) - - # Usually config.mk and config.h are generated by running configure - # or config.status, but if those aren't used create defaults here. -@@ -280,8 +279,10 @@ misc/maq2sam-long.o: misc/maq2sam.c conf - - - install: $(PROGRAMS) $(BUILT_MISC_PROGRAMS) -- $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir) -- $(INSTALL_PROGRAM) $(PROGRAMS) $(MISC_PROGRAMS) $(DESTDIR)$(bindir) -+ $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(bindir)/samtools_misc $(DESTDIR)$(man1dir) -+ $(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir) -+ $(INSTALL_PROGRAM) $(BUILT_MISC_PROGRAMS) $(DESTDIR)$(bindir)/samtools_misc -+ $(INSTALL_SCRIPT) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)/samtools_misc - $(INSTALL_DATA) samtools.1 misc/wgsim.1 $(DESTDIR)$(man1dir) - - diff --git a/biology/samtools/files/patch-configure.ac b/biology/samtools/files/patch-configure.ac deleted file mode 100644 index 94264e9994f1..000000000000 --- a/biology/samtools/files/patch-configure.ac +++ /dev/null @@ -1,19 +0,0 @@ ---- configure.ac.orig 2015-12-15 21:26:20 UTC -+++ configure.ac -@@ -23,12 +23,15 @@ - # DEALINGS IN THE SOFTWARE. - - dnl Process this file with autoconf to produce a configure script --AC_INIT([Samtools], m4_esyscmd_s([make print-version]), -+AC_INIT([Samtools], [1.3], - [samtools-help@lists.sourceforge.net], [], [http://www.htslib.org/]) - AC_PREREQ([2.63]) dnl This version introduced 4-argument AC_CHECK_HEADER - AC_CONFIG_SRCDIR([bamtk.c]) - AC_CONFIG_HEADERS([config.h]) - -+m4_include([ax_with_htslib.m4]) -+m4_include([ax_with_curses.m4]) -+ - dnl Copyright notice to be copied into the generated configure script - AC_COPYRIGHT([Portions copyright (C) 2015 Genome Research Ltd. - diff --git a/biology/samtools/files/patch-dict.c b/biology/samtools/files/patch-dict.c deleted file mode 100644 index 5f00387a43c0..000000000000 --- a/biology/samtools/files/patch-dict.c +++ /dev/null @@ -1,10 +0,0 @@ ---- dict.c.orig 2015-12-15 21:26:20 UTC -+++ dict.c -@@ -25,6 +25,7 @@ DEALINGS IN THE SOFTWARE. */ - #include - #include - #include -+#include - #include "htslib/kseq.h" - #include "htslib/hts.h" - diff --git a/biology/samtools/files/patch-errmod.c b/biology/samtools/files/patch-errmod.c deleted file mode 100644 index 4473c96af530..000000000000 --- a/biology/samtools/files/patch-errmod.c +++ /dev/null @@ -1,16 +0,0 @@ ---- errmod.c.orig 2015-12-15 21:26:20 UTC -+++ errmod.c -@@ -24,6 +24,13 @@ FROM, OUT OF OR IN CONNECTION WITH THE S - DEALINGS IN THE SOFTWARE. */ - - #include -+ -+#include -+#if defined(__FreeBSD__) && (__FreeBSD_version < 1000034) -+# define logl(x) log(x) -+# define expl(x) exp(x) -+#endif -+ - #include "errmod.h" - #include "htslib/ksort.h" - KSORT_INIT_GENERIC(uint16_t) diff --git a/biology/samtools/files/patch-test_test.pl b/biology/samtools/files/patch-test_test.pl index 918afb8be324..c8450c500568 100644 --- a/biology/samtools/files/patch-test_test.pl +++ b/biology/samtools/files/patch-test_test.pl @@ -1,15 +1,6 @@ ---- test/test.pl.orig 2015-12-22 22:43:15 UTC +--- test/test.pl.orig 2017-10-18 06:08:39 UTC +++ test/test.pl -@@ -136,7 +136,7 @@ sub _cmd - else - { - # child -- exec('/bin/bash', '-o','pipefail','-c', "($cmd) 2> $err_filename") or error("Cannot execute the command [/bin/sh -o pipefail -c $cmd]: $!"); -+ exec('/usr/local/bin/bash', '-o','pipefail','-c', "($cmd) 2> $err_filename") or error("Cannot execute the command [/usr/local/bin/bash -o pipefail -c $cmd]: $!"); - } - } - sub cmd -@@ -560,7 +560,7 @@ sub test_usage +@@ -636,7 +636,7 @@ sub test_usage my $command = $args{cmd}; my $commandpath = $$opts{bin}."/".$command; my ($ret,$out,$err) = _cmd("$commandpath $args{redirection}"); @@ -18,7 +9,7 @@ my @sections = ($err =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)|\z)/msg); -@@ -615,7 +615,7 @@ sub test_usage_subcommand +@@ -694,7 +694,7 @@ sub test_usage_subcommand my $commandpath = $$opts{bin}."/".$command; my ($ret,$out,$err) = _cmd("$commandpath $subcommand $args{redirection}"); diff --git a/biology/samtools/files/pkg-message.in b/biology/samtools/files/pkg-message.in index e996d1340a7e..388a94893ec9 100644 --- a/biology/samtools/files/pkg-message.in +++ b/biology/samtools/files/pkg-message.in @@ -3,5 +3,5 @@ The miscellaneous tools included with Samtools have been installed to Add that directory to your path if you want to use these tools. -Some of these tools depend on Perl5, and it will need to be installed to +Some of these tools depend on Perl5/Python, and it will need to be installed to use them. -- cgit