diff options
Diffstat (limited to 'academic/rbio')
| -rw-r--r-- | academic/rbio/patches/autoconfiscate.diff | 551 | ||||
| -rw-r--r-- | academic/rbio/patches/autotoolize.diff | 245 | ||||
| -rw-r--r-- | academic/rbio/rbio.SlackBuild | 12 | ||||
| -rw-r--r-- | academic/rbio/rbio.info | 4 |
4 files changed, 558 insertions, 254 deletions
diff --git a/academic/rbio/patches/autoconfiscate.diff b/academic/rbio/patches/autoconfiscate.diff new file mode 100644 index 0000000000..93b2e1bff9 --- /dev/null +++ b/academic/rbio/patches/autoconfiscate.diff @@ -0,0 +1,551 @@ +diff --git a/Demo/Makefile.am b/Demo/Makefile.am +new file mode 100644 +--- /dev/null ++++ b/Demo/Makefile.am +@@ -0,0 +1,94 @@ ++AM_CPPFLAGS = -I$(top_srcdir)/Include $(SUITESPARSECONFIG_CFLAGS) ++LDADD = $(top_builddir)/Source/librbio.la $(SUITESPARSECONFIG_LIBS) ++ ++EXTRA_DIST = \ ++ RBdemo.out ++ ++# Disable the .out implicit pattern rule. Prevents GNU make from ++# adding bogus dependencies for the .out files listed above. ++%.out: % ++ ++check_PROGRAMS = \ ++ RBdemo ++ ++RBdemo_SOURCES = \ ++ RBdemo.c ++ ++if !CODE_COVERAGE_ENABLED ++RB = \ ++ $(top_srcdir)/RBio/private/west0479.rua ++ ++check-local: $(check_PROGRAMS) $(RB) ++ ./RBdemo < $(top_srcdir)/RBio/private/west0479.rua ++ ++else ++TAR = tar -O -xvvzf ++ ++RB = \ ++ $(top_srcdir)/RBio/private/bcsstk01.rb \ ++ $(top_srcdir)/RBio/private/farm.rb \ ++ $(top_srcdir)/RBio/private/lap_25.pse \ ++ $(top_srcdir)/RBio/private/lap_25.rb \ ++ $(top_srcdir)/RBio/private/west0479.rb \ ++ $(top_srcdir)/RBio/private/west0479.rua \ ++ $(top_srcdir)/Tcov/matrices/dwg961a.tar.gz \ ++ $(top_srcdir)/Tcov/matrices/mhd1280a.tar.gz \ ++ $(top_srcdir)/Tcov/matrices/mhd1280b.tar.gz \ ++ $(top_srcdir)/Tcov/matrices/qc324.tar.gz \ ++ $(top_srcdir)/Tcov/matrices/plskz362.tar.gz \ ++ $(top_srcdir)/Tcov/matrices/west0067.tar.gz \ ++ $(top_srcdir)/Tcov/matrices/Tina_DisCog.tar.gz \ ++ $(top_srcdir)/Tcov/matrices/m4.rb \ ++ $(top_srcdir)/Tcov/matrices/s4.rb \ ++ $(top_srcdir)/Tcov/matrices/m4b.rb \ ++ $(top_srcdir)/Tcov/mangled/1.rb \ ++ $(top_srcdir)/Tcov/mangled/2.rb \ ++ $(top_srcdir)/Tcov/mangled/3.rb \ ++ $(top_srcdir)/Tcov/mangled/4.rb \ ++ $(top_srcdir)/Tcov/mangled/5.rb \ ++ $(top_srcdir)/Tcov/mangled/6.rb \ ++ $(top_srcdir)/Tcov/mangled/7.rb \ ++ $(top_srcdir)/Tcov/mangled/8.rb \ ++ $(top_srcdir)/Tcov/mangled/9.rb \ ++ $(top_srcdir)/Tcov/mangled/10.rb \ ++ $(top_srcdir)/Tcov/mangled/11.rb \ ++ $(top_srcdir)/Tcov/mangled/12.rb \ ++ $(top_srcdir)/Tcov/mangled/13.rb \ ++ $(top_srcdir)/Tcov/mangled/14.rb \ ++ $(top_srcdir)/Tcov/mangled/15.rb ++ ++check-local: $(check_PROGRAMS) $(RB) ++ -./RBdemo $(top_srcdir)/RBio/private/bcsstk01.rb ++ -./RBdemo $(top_srcdir)/RBio/private/farm.rb ++ -./RBdemo $(top_srcdir)/RBio/private/lap_25.pse ++ -./RBdemo $(top_srcdir)/RBio/private/lap_25.rb ++ -./RBdemo $(top_srcdir)/RBio/private/west0479.rb ++ -./RBdemo $(top_srcdir)/RBio/private/west0479.rua ++ -$(TAR) $(top_srcdir)/Tcov/matrices/dwg961a.tar.gz dwg961a/dwg961a.rb | ./RBdemo ++ -$(TAR) $(top_srcdir)/Tcov/matrices/mhd1280a.tar.gz mhd1280a/mhd1280a.rb | ./RBdemo ++ -$(TAR) $(top_srcdir)/Tcov/matrices/mhd1280b.tar.gz mhd1280b/mhd1280b.rb | ./RBdemo ++ -$(TAR) $(top_srcdir)/Tcov/matrices/qc324.tar.gz qc324/qc324.rb | ./RBdemo ++ -$(TAR) $(top_srcdir)/Tcov/matrices/plskz362.tar.gz plskz362/plskz362.rb | ./RBdemo ++ -$(TAR) $(top_srcdir)/Tcov/matrices/west0067.tar.gz west0067/west0067.rb | ./RBdemo ++ -$(TAR) $(top_srcdir)/Tcov/matrices/Tina_DisCog.tar.gz Tina_DisCog/Tina_DisCog.rb | ./RBdemo ++ -./RBdemo $(top_srcdir)/Tcov/matrices/m4.rb ++ -./RBdemo $(top_srcdir)/Tcov/matrices/s4.rb ++ -./RBdemo $(top_srcdir)/Tcov/matrices/m4b.rb ++ -./RBdemo $(top_srcdir)/Tcov/mangled/1.rb ++ -./RBdemo $(top_srcdir)/Tcov/mangled/2.rb ++ -./RBdemo $(top_srcdir)/Tcov/mangled/3.rb ++ -./RBdemo $(top_srcdir)/Tcov/mangled/4.rb ++ -./RBdemo $(top_srcdir)/Tcov/mangled/5.rb ++ -./RBdemo $(top_srcdir)/Tcov/mangled/6.rb ++ -./RBdemo $(top_srcdir)/Tcov/mangled/7.rb ++ -./RBdemo $(top_srcdir)/Tcov/mangled/8.rb ++ -./RBdemo $(top_srcdir)/Tcov/mangled/9.rb ++ -./RBdemo $(top_srcdir)/Tcov/mangled/10.rb ++ -./RBdemo $(top_srcdir)/Tcov/mangled/11.rb ++ -./RBdemo $(top_srcdir)/Tcov/mangled/12.rb ++ -./RBdemo $(top_srcdir)/Tcov/mangled/13.rb ++ -./RBdemo $(top_srcdir)/Tcov/mangled/14.rb ++ -./RBdemo $(top_srcdir)/Tcov/mangled/15.rb ++endif ++ ++CLEANFILES = temp.rb +diff --git a/Include/Makefile.am b/Include/Makefile.am +new file mode 100644 +--- /dev/null ++++ b/Include/Makefile.am +@@ -0,0 +1 @@ ++pkginclude_HEADERS = RBio.h +diff --git a/Makefile.am b/Makefile.am +new file mode 100644 +--- /dev/null ++++ b/Makefile.am +@@ -0,0 +1,9 @@ ++ACLOCAL_AMFLAGS = -I m4 ++ ++SUBDIRS = Include Source RBio Demo Tcov ++EXTRA_DIST = README.txt Doc/ChangeLog Doc/License.txt Doc/gpl.txt ++ ++pkgconfig_DATA = rbio.pc ++ ++CODE_COVERAGE_BRANCH_COVERAGE = 1 ++@CODE_COVERAGE_RULES@ +diff --git a/RBio/Makefile.am b/RBio/Makefile.am +new file mode 100644 +--- /dev/null ++++ b/RBio/Makefile.am +@@ -0,0 +1,3 @@ ++SUBDIRS = private ++dist_noinst_DATA = \ ++ mywest +diff --git a/RBio/private/Makefile.am b/RBio/private/Makefile.am +new file mode 100644 +--- /dev/null ++++ b/RBio/private/Makefile.am +@@ -0,0 +1,7 @@ ++dist_noinst_DATA = \ ++ bcsstk01.rb \ ++ farm.rb \ ++ lap_25.pse \ ++ lap_25.rb \ ++ west0479.rb \ ++ west0479.rua +diff --git a/Source/Makefile.am b/Source/Makefile.am +new file mode 100644 +--- /dev/null ++++ b/Source/Makefile.am +@@ -0,0 +1,21 @@ ++AM_CPPFLAGS = -I$(top_srcdir)/Include $(SUITESPARSECONFIG_CFLAGS) ++ ++RBIOSRC = \ ++ RBio.c ++ ++lib_LTLIBRARIES = librbio.la ++noinst_LTLIBRARIES = librbioi.la librbiol.la ++ ++librbioi_la_SOURCES = $(RBIOSRC) ++librbioi_la_LIBADD = $(SUITESPARSECONFIG_LIBS) ++librbioi_la_CPPFLAGS = $(AM_CPPFLAGS) -DINT ++librbioi_la_CFLAGS = $(AM_CFLAGS) ++ ++librbiol_la_SOURCES = $(RBIOSRC) ++librbiol_la_LIBADD = $(SUITESPARSECONFIG_LIBS) $(CODE_COVERAGE_LIBS) ++librbiol_la_CPPFLAGS = $(AM_CPPFLAGS) $(CODE_COVERAGE_CPPFLAGS) ++librbiol_la_CFLAGS = $(AM_CFLAGS) $(CODE_COVERAGE_CFLAGS) ++ ++librbio_la_SOURCES = ++librbio_la_LIBADD = librbioi.la librbiol.la ++librbio_la_LDFLAGS = -no-undefined -release $(PACKAGE_VERSION) +diff --git a/Tcov/Makefile.am b/Tcov/Makefile.am +new file mode 100644 +--- /dev/null ++++ b/Tcov/Makefile.am +@@ -0,0 +1,45 @@ ++AM_CPPFLAGS = -I$(top_srcdir)/Include $(SUITESPARSECONFIG_CFLAGS) ++LDADD = $(top_builddir)/Source/librbio.la $(SUITESPARSECONFIG_LIBS) ++ ++EXTRA_DIST = \ ++ README.txt ++ ++dist_noinst_DATA = \ ++ matrices/Tina_DisCog.tar.gz \ ++ matrices/dwg961a.tar.gz \ ++ matrices/m4.rb \ ++ matrices/m4b.rb \ ++ matrices/mhd1280a.tar.gz \ ++ matrices/mhd1280b.tar.gz \ ++ matrices/plskz362.tar.gz \ ++ matrices/qc324.tar.gz \ ++ matrices/s4.rb \ ++ matrices/west0067.tar.gz \ ++ mangled/1.rb \ ++ mangled/2.rb \ ++ mangled/3.rb \ ++ mangled/4.rb \ ++ mangled/5.rb \ ++ mangled/6.rb \ ++ mangled/7.rb \ ++ mangled/8.rb \ ++ mangled/9.rb \ ++ mangled/10.rb \ ++ mangled/11.rb \ ++ mangled/12.rb \ ++ mangled/13.rb \ ++ mangled/14.rb \ ++ mangled/15.rb ++ ++if CODE_COVERAGE_ENABLED ++check_PROGRAMS = \ ++ RBtest ++ ++RBtest_SOURCES = \ ++ RBtest.c ++ ++check-local: $(check_PROGRAMS) ++ -./RBtest ++endif ++ ++CLEANFILES = temp*.rb +diff --git a/configure.ac b/configure.ac +new file mode 100644 +--- /dev/null ++++ b/configure.ac +@@ -0,0 +1,45 @@ ++# -*- Autoconf -*- ++# Process this file with autoconf to produce a configure script. ++ ++AC_PREREQ([2.69]) ++AC_INIT([RBio],[2.2.6],[DrTimothyAldenDavis@gmail.com],[rbio],[http://www.suitesparse.com/]) ++AC_CONFIG_SRCDIR([Source/RBio.c]) ++AC_CONFIG_AUX_DIR([build-aux]) ++AC_CONFIG_MACRO_DIR([m4]) ++AC_CONFIG_HEADERS([config.h]) ++AM_INIT_AUTOMAKE([foreign]) ++AM_SILENT_RULES([yes]) ++LT_INIT([disable-static]) ++ ++# Checks for programs. ++PKG_PROG_PKG_CONFIG ++AC_PROG_INSTALL ++AC_PROG_CC ++AX_CODE_COVERAGE ++ ++AS_VAR_SET([LIBS_SAVED], [$LIBS]) ++ ++# Checks for libraries. ++PKG_CHECK_MODULES([SUITESPARSECONFIG], [suitesparseconfig]) ++ ++# Checks for header files. ++AC_CHECK_HEADERS([stddef.h stdlib.h string.h]) ++ ++# Checks for typedefs, structures, and compiler characteristics. ++ ++# Checks for library functions. ++ ++AS_VAR_SET([LIBS], [$LIBS_SAVED]) ++ ++PKG_INSTALLDIR ++AC_CONFIG_FILES([ ++ rbio.pc ++ Makefile ++ Demo/Makefile ++ Include/Makefile ++ RBio/Makefile ++ RBio/private/Makefile ++ Source/Makefile ++ Tcov/Makefile ++]) ++AC_OUTPUT +diff --git a/m4/ax_code_coverage.m4 b/m4/ax_code_coverage.m4 +new file mode 100644 +--- /dev/null ++++ b/m4/ax_code_coverage.m4 +@@ -0,0 +1,264 @@ ++# =========================================================================== ++# https://www.gnu.org/software/autoconf-archive/ax_code_coverage.html ++# =========================================================================== ++# ++# SYNOPSIS ++# ++# AX_CODE_COVERAGE() ++# ++# DESCRIPTION ++# ++# Defines CODE_COVERAGE_CPPFLAGS, CODE_COVERAGE_CFLAGS, ++# CODE_COVERAGE_CXXFLAGS and CODE_COVERAGE_LIBS which should be included ++# in the CPPFLAGS, CFLAGS CXXFLAGS and LIBS/LIBADD variables of every ++# build target (program or library) which should be built with code ++# coverage support. Also defines CODE_COVERAGE_RULES which should be ++# substituted in your Makefile; and $enable_code_coverage which can be ++# used in subsequent configure output. CODE_COVERAGE_ENABLED is defined ++# and substituted, and corresponds to the value of the ++# --enable-code-coverage option, which defaults to being disabled. ++# ++# Test also for gcov program and create GCOV variable that could be ++# substituted. ++# ++# Note that all optimization flags in CFLAGS must be disabled when code ++# coverage is enabled. ++# ++# Usage example: ++# ++# configure.ac: ++# ++# AX_CODE_COVERAGE ++# ++# Makefile.am: ++# ++# @CODE_COVERAGE_RULES@ ++# my_program_LIBS = ... $(CODE_COVERAGE_LIBS) ... ++# my_program_CPPFLAGS = ... $(CODE_COVERAGE_CPPFLAGS) ... ++# my_program_CFLAGS = ... $(CODE_COVERAGE_CFLAGS) ... ++# my_program_CXXFLAGS = ... $(CODE_COVERAGE_CXXFLAGS) ... ++# ++# This results in a "check-code-coverage" rule being added to any ++# Makefile.am which includes "@CODE_COVERAGE_RULES@" (assuming the module ++# has been configured with --enable-code-coverage). Running `make ++# check-code-coverage` in that directory will run the module's test suite ++# (`make check`) and build a code coverage report detailing the code which ++# was touched, then print the URI for the report. ++# ++# In earlier versions of this macro, CODE_COVERAGE_LDFLAGS was defined ++# instead of CODE_COVERAGE_LIBS. They are both still defined, but use of ++# CODE_COVERAGE_LIBS is preferred for clarity; CODE_COVERAGE_LDFLAGS is ++# deprecated. They have the same value. ++# ++# This code was derived from Makefile.decl in GLib, originally licenced ++# under LGPLv2.1+. ++# ++# LICENSE ++# ++# Copyright (c) 2012, 2016 Philip Withnall ++# Copyright (c) 2012 Xan Lopez ++# Copyright (c) 2012 Christian Persch ++# Copyright (c) 2012 Paolo Borelli ++# Copyright (c) 2012 Dan Winship ++# Copyright (c) 2015 Bastien ROUCARIES ++# ++# This library is free software; you can redistribute it and/or modify it ++# under the terms of the GNU Lesser General Public License as published by ++# the Free Software Foundation; either version 2.1 of the License, or (at ++# your option) any later version. ++# ++# This library 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 Lesser ++# General Public License for more details. ++# ++# You should have received a copy of the GNU Lesser General Public License ++# along with this program. If not, see <https://www.gnu.org/licenses/>. ++ ++#serial 24 ++ ++AC_DEFUN([AX_CODE_COVERAGE],[ ++ dnl Check for --enable-code-coverage ++ AC_REQUIRE([AC_PROG_SED]) ++ ++ # allow to override gcov location ++ AC_ARG_WITH([gcov], ++ [AS_HELP_STRING([--with-gcov[=GCOV]], [use given GCOV for coverage (GCOV=gcov).])], ++ [_AX_CODE_COVERAGE_GCOV_PROG_WITH=$with_gcov], ++ [_AX_CODE_COVERAGE_GCOV_PROG_WITH=gcov]) ++ ++ AC_MSG_CHECKING([whether to build with code coverage support]) ++ AC_ARG_ENABLE([code-coverage], ++ AS_HELP_STRING([--enable-code-coverage], ++ [Whether to enable code coverage support]),, ++ enable_code_coverage=no) ++ ++ AM_CONDITIONAL([CODE_COVERAGE_ENABLED], [test x$enable_code_coverage = xyes]) ++ AC_SUBST([CODE_COVERAGE_ENABLED], [$enable_code_coverage]) ++ AC_MSG_RESULT($enable_code_coverage) ++ ++ AS_IF([ test "$enable_code_coverage" = "yes" ], [ ++ # check for gcov ++ AC_CHECK_TOOL([GCOV], ++ [$_AX_CODE_COVERAGE_GCOV_PROG_WITH], ++ [:]) ++ AS_IF([test "X$GCOV" = "X:"], ++ [AC_MSG_ERROR([gcov is needed to do coverage])]) ++ AC_SUBST([GCOV]) ++ ++ dnl Check if gcc is being used ++ AS_IF([ test "$GCC" = "no" ], [ ++ AC_MSG_ERROR([not compiling with gcc, which is required for gcov code coverage]) ++ ]) ++ ++ AC_CHECK_PROG([LCOV], [lcov], [lcov]) ++ AC_CHECK_PROG([GENHTML], [genhtml], [genhtml]) ++ ++ AS_IF([ test -z "$LCOV" ], [ ++ AC_MSG_ERROR([To enable code coverage reporting you must have lcov installed]) ++ ]) ++ ++ AS_IF([ test -z "$GENHTML" ], [ ++ AC_MSG_ERROR([Could not find genhtml from the lcov package]) ++ ]) ++ ++ dnl Build the code coverage flags ++ dnl Define CODE_COVERAGE_LDFLAGS for backwards compatibility ++ CODE_COVERAGE_CPPFLAGS="-DNDEBUG" ++ CODE_COVERAGE_CFLAGS="-O0 -g -fprofile-arcs -ftest-coverage" ++ CODE_COVERAGE_CXXFLAGS="-O0 -g -fprofile-arcs -ftest-coverage" ++ CODE_COVERAGE_LIBS="-lgcov" ++ CODE_COVERAGE_LDFLAGS="$CODE_COVERAGE_LIBS" ++ ++ AC_SUBST([CODE_COVERAGE_CPPFLAGS]) ++ AC_SUBST([CODE_COVERAGE_CFLAGS]) ++ AC_SUBST([CODE_COVERAGE_CXXFLAGS]) ++ AC_SUBST([CODE_COVERAGE_LIBS]) ++ AC_SUBST([CODE_COVERAGE_LDFLAGS]) ++ ++ [CODE_COVERAGE_RULES_CHECK=' ++ -$(A''M_V_at)$(MAKE) $(AM_MAKEFLAGS) -k check ++ $(A''M_V_at)$(MAKE) $(AM_MAKEFLAGS) code-coverage-capture ++'] ++ [CODE_COVERAGE_RULES_CAPTURE=' ++ $(code_coverage_v_lcov_cap)$(LCOV) $(code_coverage_quiet) $(addprefix --directory ,$(CODE_COVERAGE_DIRECTORY)) --capture --output-file "$(CODE_COVERAGE_OUTPUT_FILE).tmp" --test-name "$(call code_coverage_sanitize,$(PACKAGE_NAME)-$(PACKAGE_VERSION))" --no-checksum --compat-libtool $(CODE_COVERAGE_LCOV_SHOPTS) $(CODE_COVERAGE_LCOV_OPTIONS) ++ $(code_coverage_v_lcov_ign)$(LCOV) $(code_coverage_quiet) $(addprefix --directory ,$(CODE_COVERAGE_DIRECTORY)) --remove "$(CODE_COVERAGE_OUTPUT_FILE).tmp" "/tmp/*" $(CODE_COVERAGE_IGNORE_PATTERN) --output-file "$(CODE_COVERAGE_OUTPUT_FILE)" $(CODE_COVERAGE_LCOV_SHOPTS) $(CODE_COVERAGE_LCOV_RMOPTS) ++ -@rm -f $(CODE_COVERAGE_OUTPUT_FILE).tmp ++ $(code_coverage_v_genhtml)LANG=C $(GENHTML) $(code_coverage_quiet) $(addprefix --prefix ,$(CODE_COVERAGE_DIRECTORY)) --output-directory "$(CODE_COVERAGE_OUTPUT_DIRECTORY)" --title "$(PACKAGE_NAME)-$(PACKAGE_VERSION) Code Coverage" --legend --show-details "$(CODE_COVERAGE_OUTPUT_FILE)" $(CODE_COVERAGE_GENHTML_OPTIONS) ++ @echo "file://$(abs_builddir)/$(CODE_COVERAGE_OUTPUT_DIRECTORY)/index.html" ++'] ++ [CODE_COVERAGE_RULES_CLEAN=' ++clean: code-coverage-clean ++distclean: code-coverage-clean ++code-coverage-clean: ++ -$(LCOV) --directory $(top_builddir) -z ++ -rm -rf $(CODE_COVERAGE_OUTPUT_FILE) $(CODE_COVERAGE_OUTPUT_FILE).tmp $(CODE_COVERAGE_OUTPUT_DIRECTORY) ++ -find . \( -name "*.gcda" -o -name "*.gcno" -o -name "*.gcov" \) -delete ++'] ++ ], [ ++ [CODE_COVERAGE_RULES_CHECK=' ++ @echo "Need to reconfigure with --enable-code-coverage" ++'] ++ CODE_COVERAGE_RULES_CAPTURE="$CODE_COVERAGE_RULES_CHECK" ++ CODE_COVERAGE_RULES_CLEAN='' ++ ]) ++ ++[CODE_COVERAGE_RULES=' ++# Code coverage ++# ++# Optional: ++# - CODE_COVERAGE_DIRECTORY: Top-level directory for code coverage reporting. ++# Multiple directories may be specified, separated by whitespace. ++# (Default: $(top_builddir)) ++# - CODE_COVERAGE_OUTPUT_FILE: Filename and path for the .info file generated ++# by lcov for code coverage. (Default: ++# $(PACKAGE_NAME)-$(PACKAGE_VERSION)-coverage.info) ++# - CODE_COVERAGE_OUTPUT_DIRECTORY: Directory for generated code coverage ++# reports to be created. (Default: ++# $(PACKAGE_NAME)-$(PACKAGE_VERSION)-coverage) ++# - CODE_COVERAGE_BRANCH_COVERAGE: Set to 1 to enforce branch coverage, ++# set to 0 to disable it and leave empty to stay with the default. ++# (Default: empty) ++# - CODE_COVERAGE_LCOV_SHOPTS_DEFAULT: Extra options shared between both lcov ++# instances. (Default: based on $CODE_COVERAGE_BRANCH_COVERAGE) ++# - CODE_COVERAGE_LCOV_SHOPTS: Extra options to shared between both lcov ++# instances. (Default: $CODE_COVERAGE_LCOV_SHOPTS_DEFAULT) ++# - CODE_COVERAGE_LCOV_OPTIONS_GCOVPATH: --gcov-tool pathtogcov ++# - CODE_COVERAGE_LCOV_OPTIONS_DEFAULT: Extra options to pass to the ++# collecting lcov instance. (Default: $CODE_COVERAGE_LCOV_OPTIONS_GCOVPATH) ++# - CODE_COVERAGE_LCOV_OPTIONS: Extra options to pass to the collecting lcov ++# instance. (Default: $CODE_COVERAGE_LCOV_OPTIONS_DEFAULT) ++# - CODE_COVERAGE_LCOV_RMOPTS_DEFAULT: Extra options to pass to the filtering ++# lcov instance. (Default: empty) ++# - CODE_COVERAGE_LCOV_RMOPTS: Extra options to pass to the filtering lcov ++# instance. (Default: $CODE_COVERAGE_LCOV_RMOPTS_DEFAULT) ++# - CODE_COVERAGE_GENHTML_OPTIONS_DEFAULT: Extra options to pass to the ++# genhtml instance. (Default: based on $CODE_COVERAGE_BRANCH_COVERAGE) ++# - CODE_COVERAGE_GENHTML_OPTIONS: Extra options to pass to the genhtml ++# instance. (Default: $CODE_COVERAGE_GENHTML_OPTIONS_DEFAULT) ++# - CODE_COVERAGE_IGNORE_PATTERN: Extra glob pattern of files to ignore ++# ++# The generated report will be titled using the $(PACKAGE_NAME) and ++# $(PACKAGE_VERSION). In order to add the current git hash to the title, ++# use the git-version-gen script, available online. ++ ++# Optional variables ++CODE_COVERAGE_DIRECTORY ?= $(top_builddir) ++CODE_COVERAGE_OUTPUT_FILE ?= $(PACKAGE_NAME)-$(PACKAGE_VERSION)-coverage.info ++CODE_COVERAGE_OUTPUT_DIRECTORY ?= $(PACKAGE_NAME)-$(PACKAGE_VERSION)-coverage ++CODE_COVERAGE_BRANCH_COVERAGE ?= ++CODE_COVERAGE_LCOV_SHOPTS_DEFAULT ?= $(if $(CODE_COVERAGE_BRANCH_COVERAGE),\ ++--rc lcov_branch_coverage=$(CODE_COVERAGE_BRANCH_COVERAGE)) ++CODE_COVERAGE_LCOV_SHOPTS ?= $(CODE_COVERAGE_LCOV_SHOPTS_DEFAULT) ++CODE_COVERAGE_LCOV_OPTIONS_GCOVPATH ?= --gcov-tool "$(GCOV)" ++CODE_COVERAGE_LCOV_OPTIONS_DEFAULT ?= $(CODE_COVERAGE_LCOV_OPTIONS_GCOVPATH) ++CODE_COVERAGE_LCOV_OPTIONS ?= $(CODE_COVERAGE_LCOV_OPTIONS_DEFAULT) ++CODE_COVERAGE_LCOV_RMOPTS_DEFAULT ?= ++CODE_COVERAGE_LCOV_RMOPTS ?= $(CODE_COVERAGE_LCOV_RMOPTS_DEFAULT) ++CODE_COVERAGE_GENHTML_OPTIONS_DEFAULT ?=\ ++$(if $(CODE_COVERAGE_BRANCH_COVERAGE),\ ++--rc genhtml_branch_coverage=$(CODE_COVERAGE_BRANCH_COVERAGE)) ++CODE_COVERAGE_GENHTML_OPTIONS ?= $(CODE_COVERAGE_GENHTML_OPTIONS_DEFAULT) ++CODE_COVERAGE_IGNORE_PATTERN ?= ++ ++code_coverage_v_lcov_cap = $(code_coverage_v_lcov_cap_$(V)) ++code_coverage_v_lcov_cap_ = $(code_coverage_v_lcov_cap_$(AM_DEFAULT_VERBOSITY)) ++code_coverage_v_lcov_cap_0 = @echo " LCOV --capture"\ ++ $(CODE_COVERAGE_OUTPUT_FILE); ++code_coverage_v_lcov_ign = $(code_coverage_v_lcov_ign_$(V)) ++code_coverage_v_lcov_ign_ = $(code_coverage_v_lcov_ign_$(AM_DEFAULT_VERBOSITY)) ++code_coverage_v_lcov_ign_0 = @echo " LCOV --remove /tmp/*"\ ++ $(CODE_COVERAGE_IGNORE_PATTERN); ++code_coverage_v_genhtml = $(code_coverage_v_genhtml_$(V)) ++code_coverage_v_genhtml_ = $(code_coverage_v_genhtml_$(AM_DEFAULT_VERBOSITY)) ++code_coverage_v_genhtml_0 = @echo " GEN " $(CODE_COVERAGE_OUTPUT_DIRECTORY); ++code_coverage_quiet = $(code_coverage_quiet_$(V)) ++code_coverage_quiet_ = $(code_coverage_quiet_$(AM_DEFAULT_VERBOSITY)) ++code_coverage_quiet_0 = --quiet ++ ++# sanitizes the test-name: replaces with underscores: dashes and dots ++code_coverage_sanitize = $(subst -,_,$(subst .,_,$(1))) ++ ++# Use recursive makes in order to ignore errors during check ++check-code-coverage:'"$CODE_COVERAGE_RULES_CHECK"' ++ ++# Capture code coverage data ++code-coverage-capture: code-coverage-capture-hook'"$CODE_COVERAGE_RULES_CAPTURE"' ++ ++# Hook rule executed before code-coverage-capture, overridable by the user ++code-coverage-capture-hook: ++ ++'"$CODE_COVERAGE_RULES_CLEAN"' ++ ++GITIGNOREFILES ?= ++GITIGNOREFILES += $(CODE_COVERAGE_OUTPUT_FILE) $(CODE_COVERAGE_OUTPUT_DIRECTORY) ++ ++A''M_DISTCHECK_CONFIGURE_FLAGS ?= ++A''M_DISTCHECK_CONFIGURE_FLAGS += --disable-code-coverage ++ ++.PHONY: check-code-coverage code-coverage-capture code-coverage-capture-hook code-coverage-clean ++'] ++ ++ AC_SUBST([CODE_COVERAGE_RULES]) ++ m4_ifdef([_AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE([CODE_COVERAGE_RULES])]) ++]) +diff --git a/rbio.pc.in b/rbio.pc.in +new file mode 100644 +--- /dev/null ++++ b/rbio.pc.in +@@ -0,0 +1,12 @@ ++prefix=@prefix@ ++exec_prefix=@exec_prefix@ ++libdir=@libdir@ ++includedir=@includedir@ ++ ++Name: @PACKAGE_NAME@ ++Description: Toolbox for reading/writing sparse matrices in Rutherford/Boeing format ++Version: @PACKAGE_VERSION@ ++URL: @PACKAGE_URL@ ++Requires.private: suitesparseconfig ++Libs: -L${libdir} -lrbio ++Cflags: -I${includedir}/rbio diff --git a/academic/rbio/patches/autotoolize.diff b/academic/rbio/patches/autotoolize.diff deleted file mode 100644 index b20e1a88e5..0000000000 --- a/academic/rbio/patches/autotoolize.diff +++ /dev/null @@ -1,245 +0,0 @@ -diff --git a/Demo/Makefile.am b/Demo/Makefile.am -new file mode 100644 ---- /dev/null -+++ b/Demo/Makefile.am -@@ -0,0 +1,22 @@ -+AM_CPPFLAGS = -I$(top_srcdir)/Include $(SUITESPARSECONFIG_CFLAGS) -+LDADD = $(top_builddir)/Source/librbio.la $(SUITESPARSECONFIG_LIBS) -+ -+EXTRA_DIST = \ -+ RBdemo.out -+ -+# Disable the .out implicit pattern rule. Prevents GNU make from -+# adding bogus dependencies for the .out files listed above. -+%.out: % -+ -+check_PROGRAMS = \ -+ RBdemo -+ -+RBdemo_SOURCES = RBdemo.c -+ -+RB = \ -+ $(top_srcdir)/RBio/private/west0479.rua -+ -+check-local: $(check_PROGRAMS) $(RB) -+ ./RBdemo < $(top_srcdir)/RBio/private/west0479.rua -+ -+CLEANFILES = temp.rb -diff --git a/Include/Makefile.am b/Include/Makefile.am -new file mode 100644 ---- /dev/null -+++ b/Include/Makefile.am -@@ -0,0 +1 @@ -+pkginclude_HEADERS = RBio.h -diff --git a/Makefile.am b/Makefile.am -new file mode 100644 ---- /dev/null -+++ b/Makefile.am -@@ -0,0 +1,4 @@ -+SUBDIRS = Include Source RBio Demo Tcov -+EXTRA_DIST = README.txt Doc/ChangeLog Doc/License.txt Doc/gpl.txt -+ -+pkgconfig_DATA = rbio.pc -diff --git a/RBio/Makefile.am b/RBio/Makefile.am -new file mode 100644 ---- /dev/null -+++ b/RBio/Makefile.am -@@ -0,0 +1,3 @@ -+SUBDIRS = private -+dist_noinst_DATA = \ -+ mywest -diff --git a/RBio/private/Makefile.am b/RBio/private/Makefile.am -new file mode 100644 ---- /dev/null -+++ b/RBio/private/Makefile.am -@@ -0,0 +1,7 @@ -+dist_noinst_DATA = \ -+ bcsstk01.rb \ -+ farm.rb \ -+ lap_25.pse \ -+ lap_25.rb \ -+ west0479.rb \ -+ west0479.rua -diff --git a/Source/Makefile.am b/Source/Makefile.am -new file mode 100644 ---- /dev/null -+++ b/Source/Makefile.am -@@ -0,0 +1,18 @@ -+AM_CPPFLAGS = -I$(top_srcdir)/Include $(SUITESPARSECONFIG_CFLAGS) -+ -+RBIOSRC = \ -+ RBio.c -+ -+lib_LTLIBRARIES = librbio.la -+noinst_LTLIBRARIES = librbioi.la librbiol.la -+ -+librbioi_la_SOURCES = $(RBIOSRC) -+librbioi_la_LIBADD = $(SUITESPARSECONFIG_LIBS) -+librbioi_la_CPPFLAGS = $(AM_CPPFLAGS) -DINT -+ -+librbiol_la_SOURCES = $(RBIOSRC) -+librbiol_la_LIBADD = $(SUITESPARSECONFIG_LIBS) -+ -+librbio_la_SOURCES = -+librbio_la_LIBADD = librbioi.la librbiol.la -+librbio_la_LDFLAGS = -no-undefined -release $(PACKAGE_VERSION) -diff --git a/Tcov/Makefile.am b/Tcov/Makefile.am -new file mode 100644 ---- /dev/null -+++ b/Tcov/Makefile.am -@@ -0,0 +1,92 @@ -+AM_CC = gcc -+AM_CFLAGS = -O0 -g --coverage -+AM_CPPFLAGS = -I$(top_srcdir)/Include $(SUITESPARSECONFIG_CFLAGS) -+LDADD = $(SUITESPARSECONFIG_LIBS) -+ -+dist_noinst_DATA = \ -+ matrices/Tina_DisCog.tar.gz \ -+ matrices/dwg961a.tar.gz \ -+ matrices/m4.rb \ -+ matrices/m4b.rb \ -+ matrices/mhd1280a.tar.gz \ -+ matrices/mhd1280b.tar.gz \ -+ matrices/plskz362.tar.gz \ -+ matrices/qc324.tar.gz \ -+ matrices/s4.rb \ -+ matrices/west0067.tar.gz \ -+ mangled/1.rb \ -+ mangled/2.rb \ -+ mangled/3.rb \ -+ mangled/4.rb \ -+ mangled/5.rb \ -+ mangled/6.rb \ -+ mangled/7.rb \ -+ mangled/8.rb \ -+ mangled/9.rb \ -+ mangled/10.rb \ -+ mangled/11.rb \ -+ mangled/12.rb \ -+ mangled/13.rb \ -+ mangled/14.rb \ -+ mangled/15.rb -+ -+check_PROGRAMS = \ -+ RBdemo \ -+ RBtest -+ -+RBdemo_SOURCES = $(top_srcdir)/Source/RBio.c $(top_srcdir)/Demo/RBdemo.c -+RBtest_SOURCES = $(top_srcdir)/Source/RBio.c RBtest.c -+ -+TAR = tar -O -xvvzf -+ -+RB = \ -+ $(top_srcdir)/RBio/private/bcsstk01.rb \ -+ $(top_srcdir)/RBio/private/farm.rb \ -+ $(top_srcdir)/RBio/private/lap_25.pse \ -+ $(top_srcdir)/RBio/private/lap_25.rb \ -+ $(top_srcdir)/RBio/private/west0479.rb \ -+ $(top_srcdir)/RBio/private/west0479.rua \ -+ $(addprefix $(srcdir)/,$(dist_noinst_DATA)) -+ -+COV = \ -+ $(top_srcdir)/Source/RBio.c \ -+ $(top_srcdir)/Demo/RBdemo.c \ -+ $(srcdir)/RBtest.c -+ -+check-local: $(check_PROGRAMS) $(RB) $(COV) -+ -./RBdemo $(top_srcdir)/RBio/private/bcsstk01.rb -+ -./RBdemo $(top_srcdir)/RBio/private/farm.rb -+ -./RBdemo $(top_srcdir)/RBio/private/lap_25.pse -+ -./RBdemo $(top_srcdir)/RBio/private/lap_25.rb -+ -./RBdemo $(top_srcdir)/RBio/private/west0479.rb -+ -./RBdemo $(top_srcdir)/RBio/private/west0479.rua -+ -$(TAR) $(srcdir)/matrices/dwg961a.tar.gz dwg961a/dwg961a.rb | ./RBdemo -+ -$(TAR) $(srcdir)/matrices/mhd1280a.tar.gz mhd1280a/mhd1280a.rb | ./RBdemo -+ -$(TAR) $(srcdir)/matrices/mhd1280b.tar.gz mhd1280b/mhd1280b.rb | ./RBdemo -+ -$(TAR) $(srcdir)/matrices/qc324.tar.gz qc324/qc324.rb | ./RBdemo -+ -$(TAR) $(srcdir)/matrices/plskz362.tar.gz plskz362/plskz362.rb | ./RBdemo -+ -$(TAR) $(srcdir)/matrices/west0067.tar.gz west0067/west0067.rb | ./RBdemo -+ -$(TAR) $(srcdir)/matrices/Tina_DisCog.tar.gz Tina_DisCog/Tina_DisCog.rb | ./RBdemo -+ -./RBdemo $(srcdir)/matrices/m4.rb -+ -./RBdemo $(srcdir)/matrices/s4.rb -+ -./RBdemo $(srcdir)/matrices/m4b.rb -+ -./RBdemo $(srcdir)/mangled/1.rb -+ -./RBdemo $(srcdir)/mangled/2.rb -+ -./RBdemo $(srcdir)/mangled/3.rb -+ -./RBdemo $(srcdir)/mangled/4.rb -+ -./RBdemo $(srcdir)/mangled/5.rb -+ -./RBdemo $(srcdir)/mangled/6.rb -+ -./RBdemo $(srcdir)/mangled/7.rb -+ -./RBdemo $(srcdir)/mangled/8.rb -+ -./RBdemo $(srcdir)/mangled/9.rb -+ -./RBdemo $(srcdir)/mangled/10.rb -+ -./RBdemo $(srcdir)/mangled/11.rb -+ -./RBdemo $(srcdir)/mangled/12.rb -+ -./RBdemo $(srcdir)/mangled/13.rb -+ -./RBdemo $(srcdir)/mangled/14.rb -+ -./RBdemo $(srcdir)/mangled/15.rb -+ -./RBtest -+ -gcov -o $(builddir) $(COV) > gcov.out -+ -grep -c "#####" RBio.c.gcov -+ -+CLEANFILES = gcov.out *.gcov *.gcda *.gcno temp*.rb -diff --git a/configure.ac b/configure.ac -new file mode 100644 ---- /dev/null -+++ b/configure.ac -@@ -0,0 +1,41 @@ -+# -*- Autoconf -*- -+# Process this file with autoconf to produce a configure script. -+ -+AC_PREREQ([2.69]) -+AC_INIT([RBio],[2.2.6],[DrTimothyAldenDavis@gmail.com],[rbio],[http://www.suitesparse.com/]) -+AC_CONFIG_SRCDIR([Source/RBio.c]) -+AC_CONFIG_HEADERS([config.h]) -+AM_INIT_AUTOMAKE([foreign]) -+LT_INIT -+ -+# Checks for programs. -+PKG_PROG_PKG_CONFIG -+AC_PROG_INSTALL -+AC_PROG_CC -+ -+AS_VAR_SET([LIBS_SAVED], [$LIBS]) -+ -+# Checks for libraries. -+PKG_CHECK_MODULES([SUITESPARSECONFIG], [suitesparseconfig]) -+ -+# Checks for header files. -+AC_CHECK_HEADERS([stddef.h stdlib.h string.h]) -+ -+# Checks for typedefs, structures, and compiler characteristics. -+ -+# Checks for library functions. -+ -+AS_VAR_SET([LIBS], [$LIBS_SAVED]) -+ -+PKG_INSTALLDIR -+AC_CONFIG_FILES([ -+ rbio.pc -+ Makefile -+ Demo/Makefile -+ Include/Makefile -+ RBio/Makefile -+ RBio/private/Makefile -+ Source/Makefile -+ Tcov/Makefile -+]) -+AC_OUTPUT -diff --git a/rbio.pc.in b/rbio.pc.in -new file mode 100644 ---- /dev/null -+++ b/rbio.pc.in -@@ -0,0 +1,12 @@ -+prefix=@prefix@ -+exec_prefix=@exec_prefix@ -+libdir=@libdir@ -+includedir=@includedir@ -+ -+Name: @PACKAGE_NAME@ -+Description: Toolbox for reading/writing sparse matrices in Rutherford/Boeing format -+Version: @PACKAGE_VERSION@ -+URL: @PACKAGE_URL@ -+Requires.private: suitesparseconfig -+Libs: -L${libdir} -lrbio -+Cflags: -I${includedir}/rbio diff --git a/academic/rbio/rbio.SlackBuild b/academic/rbio/rbio.SlackBuild index 51a0110fee..65ff84a50c 100644 --- a/academic/rbio/rbio.SlackBuild +++ b/academic/rbio/rbio.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for RBio -# Copyright 2013-2016 Kyle Guinn <elyk03@gmail.com>, USA +# Copyright 2013-2017 Kyle Guinn <elyk03@gmail.com>, USA # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -26,8 +26,8 @@ PRGNAM=rbio SRCNAM=SuiteSparse SUBDIR=RBio VERSION=${VERSION:-2.2.6} -SRCVER=${SRCVER:-4.5.3} -BUILD=${BUILD:-1} +SRCVER=${SRCVER:-4.5.5} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then @@ -40,7 +40,7 @@ fi CWD=$(pwd) TMP=${TMP:-/tmp/SBo} -PKG=$TMP/package-$PRGNAM +PKG=$TMP/package-$PRGNAM-$VERSION OUTPUT=${OUTPUT:-/tmp} DOCS="README.txt Doc/ChangeLog Doc/License.txt Doc/gpl.txt" @@ -76,7 +76,7 @@ cd $SRCNAM/$SUBDIR chown -R root:root . chmod -R u+w,go-w,a+rX-st . -patch -p1 < $CWD/patches/autotoolize.diff +patch -p1 < $CWD/patches/autoconfiscate.diff autoreconf -vif ./configure \ @@ -87,8 +87,6 @@ autoreconf -vif --mandir=/usr/man \ --infodir=/usr/info \ --docdir=/usr/doc/$PRGNAM-$VERSION \ - --enable-shared \ - --disable-static \ --disable-dependency-tracking \ --build=$ARCH-slackware-linux \ CFLAGS="$SLKCFLAGS" \ diff --git a/academic/rbio/rbio.info b/academic/rbio/rbio.info index 5e3c163a6c..f0e0d17f1a 100644 --- a/academic/rbio/rbio.info +++ b/academic/rbio/rbio.info @@ -1,8 +1,8 @@ PRGNAM="rbio" VERSION="2.2.6" HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html" -DOWNLOAD="http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.5.3.tar.gz" -MD5SUM="8ec57324585df3c6483ad7f556afccbd" +DOWNLOAD="http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.5.5.tar.gz" +MD5SUM="0a5b38af0016f009409a9606d2f1b555" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="suitesparseconfig" |