bioseqalign 0.0.2 → 0.0.3

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 0b96dd84832f04c18f665123a094d288a91c3030
+  data.tar.gz: 96d9c502f30a612eec662baeec5f0a275714e912
+SHA512:
+  metadata.gz: 792e24c7020440b3377f9c4f9218b21bdf5c986d582d2ffcf76f0292547d938353544fafe20b02fc2e0a9fe65e622736782e13ca8903807e2a5977c25e407206
+  data.tar.gz: fb8c79b054f34495d921307902e0554841e2771742065243912c4a8ff0bf332ede46b8ccbbdcd1cab60884a3575b61b8aa4df3bdf22242dc8a8fc2c027caf678

data/ext/bioseqalign/Makefile

@@ -5,37 +5,68 @@ SHELL = /bin/sh
 V = 0
 Q1 = $(V:1=)
 Q = $(Q1:0=@)
-n=$(NULLCMD)
-ECHO1 = $(V:1=@$n)
+ECHO1 = $(V:1=@:)
 ECHO = $(ECHO1:0=@echo)
+NULLCMD = :
 
 #### Start of system configuration section. ####
 
 srcdir = .
-topdir = /usr/include/ruby-1.9.1
-hdrdir = /usr/include/ruby-1.9.1
-arch_hdrdir = /usr/include/ruby-1.9.1/$(arch)
+topdir = /home/stef/.rvm/rubies/ruby-2.2.0/include/ruby-2.2.0
+hdrdir = $(topdir)
+arch_hdrdir = /home/stef/.rvm/rubies/ruby-2.2.0/include/ruby-2.2.0/x86_64-linux
+PATH_SEPARATOR = :
 VPATH = $(srcdir):$(arch_hdrdir)/ruby:$(hdrdir)/ruby
 
-prefix = $(DESTDIR)/usr
+prefix = $(DESTDIR)/home/stef/.rvm/rubies/ruby-2.2.0
+
+rubysitearchprefix = $(rubylibprefix)/$(sitearch)
+
+rubyarchprefix = $(rubylibprefix)/$(arch)
 
 rubylibprefix = $(libdir)/$(RUBY_BASE_NAME)
 
 exec_prefix = $(prefix)
 
+vendorarchhdrdir = $(vendorhdrdir)/$(sitearch)
+
+sitearchhdrdir = $(sitehdrdir)/$(sitearch)
+
+rubyarchhdrdir = $(rubyhdrdir)/$(arch)
+
 vendorhdrdir = $(rubyhdrdir)/vendor_ruby
 
 sitehdrdir = $(rubyhdrdir)/site_ruby
 
-rubyhdrdir = $(includedir)/$(RUBY_BASE_NAME)-$(ruby_version)
+rubyhdrdir = $(includedir)/$(RUBY_VERSION_NAME)
+
+vendorarchdir = $(vendorlibdir)/$(sitearch)
+
+vendorlibdir = $(vendordir)/$(ruby_version)
+
+vendordir = $(rubylibprefix)/vendor_ruby
+
+sitearchdir = $(sitelibdir)/$(sitearch)
+
+sitelibdir = $(sitedir)/$(ruby_version)
+
+sitedir = $(rubylibprefix)/site_ruby
+
+rubyarchdir = $(rubylibdir)/$(arch)
+
+rubylibdir = $(rubylibprefix)/$(ruby_version)
+
+sitearchincludedir = $(includedir)/$(sitearch)
+
+archincludedir = $(includedir)/$(arch)
 
-vendordir = $(DESTDIR)/usr/lib/ruby/vendor_ruby
+sitearchlibdir = $(libdir)/$(sitearch)
 
-sitedir = $(DESTDIR)/usr/local/lib/site_ruby
+archlibdir = $(libdir)/$(arch)
 
 ridir = $(datarootdir)/$(RI_BASE_NAME)
 
-mandir = $(prefix)/share/man
+mandir = $(datarootdir)/man
 
 localedir = $(datarootdir)/locale
 
@@ -49,7 +80,7 @@ dvidir = $(docdir)
 
 htmldir = $(docdir)
 
-infodir = $(prefix)/share/info
+infodir = $(datarootdir)/info
 
 docdir = $(datarootdir)/doc/$(PACKAGE)
 
@@ -57,7 +88,7 @@ oldincludedir = $(DESTDIR)/usr/include
 
 includedir = $(prefix)/include
 
-localstatedir = $(DESTDIR)/var
+localstatedir = $(prefix)/var
 
 sharedstatedir = $(prefix)/com
 
@@ -67,48 +98,39 @@ datadir = $(datarootdir)
 
 datarootdir = $(prefix)/share
 
-libexecdir = $(prefix)/lib/ruby1.9.1
+libexecdir = $(exec_prefix)/libexec
 
 sbindir = $(exec_prefix)/sbin
 
 bindir = $(exec_prefix)/bin
 
-rubylibdir = $(rubylibprefix)/$(ruby_version)
-
-archdir = $(rubylibdir)/$(arch)
-
-sitelibdir = $(sitedir)/$(ruby_version)
-
-sitearchdir = $(sitelibdir)/$(sitearch)
-
-vendorlibdir = $(vendordir)/$(ruby_version)
-
-vendorarchdir = $(vendorlibdir)/$(sitearch)
+archdir = $(rubyarchdir)
 
 
-NULLCMD = :
 
 CC = gcc
 CXX = g++
 LIBRUBY = $(LIBRUBY_SO)
 LIBRUBY_A = lib$(RUBY_SO_NAME)-static.a
-LIBRUBYARG_SHARED = -l$(RUBY_SO_NAME)
-LIBRUBYARG_STATIC = -lruby-1.9.1-static
-OUTFLAG = -o 
-COUTFLAG = -o 
+LIBRUBYARG_SHARED = -Wl,-rpath,'$${ORIGIN}/../lib' -Wl,-R'$${ORIGIN}/../lib' -l$(RUBY_SO_NAME)
+LIBRUBYARG_STATIC = -Wl,-rpath,'${ORIGIN}/../lib' -Wl,-R'${ORIGIN}/../lib' -lruby-static
+empty =
+OUTFLAG = -o $(empty)
+COUTFLAG = -o $(empty)
 
 RUBY_EXTCONF_H = 
 cflags   =  $(optflags) $(debugflags) $(warnflags)
-optflags = -O3
-debugflags = -ggdb
-warnflags = -Wextra -Wno-unused-parameter -Wno-parentheses -Wno-long-long -Wno-missing-field-initializers -Wpointer-arith -Wwrite-strings -Wdeclaration-after-statement -Wimplicit-function-declaration
-CFLAGS   = -fPIC -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fno-strict-aliasing -fPIC $(ARCH_FLAG)
+optflags = -O3 -fno-fast-math
+debugflags = -ggdb3
+warnflags = -Wall -Wextra -Wno-unused-parameter -Wno-parentheses -Wno-long-long -Wno-missing-field-initializers -Wunused-variable -Wpointer-arith -Wwrite-strings -Wdeclaration-after-statement -Wimplicit-function-declaration -Wdeprecated-declarations -Wno-packed-bitfield-compat
+CCDLFLAGS = -fPIC
+CFLAGS   = $(CCDLFLAGS) $(cflags)  -fPIC $(ARCH_FLAG)
 INCFLAGS = -I. -I$(arch_hdrdir) -I$(hdrdir)/ruby/backward -I$(hdrdir) -I$(srcdir)
 DEFS     = 
-CPPFLAGS =  -D_FORTIFY_SOURCE=2 $(DEFS) $(cppflags)  -I/home/stef/ruby_gems/gems/rice-1.6.2/ruby/lib/include
+CPPFLAGS =  -I/home/stef/git_repos/tilapia/ext/seqan-1.3.1/  $(DEFS) $(cppflags)  -I/home/stef/.rvm/gems/ruby-2.2.0/gems/rice-1.7.0/ruby/lib/include -std=c++11 -Wno-deprecated -Wno-unused-local-typedefs -Wimplicit-function-declaration -Wdeclaration-after-statement
 CXXFLAGS = $(CFLAGS)  -Wall -g
-ldflags  = -L. -Wl,-Bsymbolic-functions -Wl,-z,relro -rdynamic -Wl,-export-dynamic  -L/home/stef/ruby_gems/gems/rice-1.6.2/ruby/lib/lib -lrice
-dldflags = 
+ldflags  = -L. -fstack-protector -rdynamic -Wl,-export-dynamic  -L/home/stef/.rvm/gems/ruby-2.2.0/gems/rice-1.7.0/ruby/lib/lib -lrice
+dldflags =  
 ARCH_FLAG = 
 DLDFLAGS = $(ldflags) $(dldflags) $(ARCH_FLAG)
 LDSHARED = g++ -shared
@@ -116,22 +138,36 @@ LDSHAREDXX = $(CXX) -shared
 AR = ar
 EXEEXT = 
 
+
+RUBY_INSTALL_NAME = $(RUBY_BASE_NAME)
+
+RUBY_SO_NAME = ruby
+
+RUBYW_INSTALL_NAME = 
+
+RUBY_VERSION_NAME = $(RUBY_BASE_NAME)-$(ruby_version)
+
+RUBYW_BASE_NAME = rubyw
+
 RUBY_BASE_NAME = ruby
-RUBY_INSTALL_NAME = ruby1.9.1
-RUBY_SO_NAME = ruby-1.9.1
+
+
 arch = x86_64-linux
 sitearch = $(arch)
-ruby_version = 1.9.1
-ruby = /usr/bin/ruby1.9.1
+ruby_version = 2.2.0
+ruby = $(bindir)/$(RUBY_BASE_NAME)
 RUBY = $(ruby)
+ruby_headers = $(hdrdir)/ruby.h $(hdrdir)/ruby/ruby.h $(hdrdir)/ruby/defines.h $(hdrdir)/ruby/missing.h $(hdrdir)/ruby/intern.h $(hdrdir)/ruby/st.h $(hdrdir)/ruby/subst.h $(arch_hdrdir)/ruby/config.h
+
 RM = rm -f
 RM_RF = $(RUBY) -run -e rm -- -rf
 RMDIRS = rmdir --ignore-fail-on-non-empty -p
 MAKEDIRS = /bin/mkdir -p
-INSTALL = /usr/bin/install -c
+INSTALL = /usr/bin/install
 INSTALL_PROG = $(INSTALL) -m 0755
 INSTALL_DATA = $(INSTALL) -m 644
 COPY = cp
+TOUCH = exit >
 
 #### End of system configuration section. ####
 
@@ -141,7 +177,7 @@ preload =
 CXX = g++
 
 libpath = . $(libdir)
-LIBPATH =  -L. -L$(libdir)
+LIBPATH =  -L. -L$(libdir) -Wl,-R$(libdir)
 DEFFILE = 
 
 CLEANFILES = mkmf.log
@@ -152,14 +188,19 @@ extout =
 extout_prefix = 
 target_prefix = 
 LOCAL_LIBS = 
-LIBS = -lruby-1.9.1 -lpthread -lrt -ldl -lcrypt -lm   -lc
-SRCS = PrefixSuffixAlign.cpp PairwiseAlign.cpp LocalAlign.cpp fitalgntest.cpp GlobalAlign.cpp FitAlign.cpp
+LIBS = -Wl,-rpath,'${ORIGIN}/../lib' -Wl,-R'${ORIGIN}/../lib' -lruby -lpthread -ldl -lcrypt -lm   -lc
+ORIG_SRCS = PrefixSuffixAlign.cpp PairwiseAlign.cpp LocalAlign.cpp fitalgntest.cpp GlobalAlign.cpp FitAlign.cpp
+SRCS = $(ORIG_SRCS) 
 OBJS = PrefixSuffixAlign.o PairwiseAlign.o LocalAlign.o fitalgntest.o GlobalAlign.o FitAlign.o
+HDRS = $(srcdir)/FitAlign.hpp $(srcdir)/GlobalAlign.hpp $(srcdir)/PrefixSuffixAlign.hpp $(srcdir)/LocalAlign.hpp $(srcdir)/PairwiseAlign.hpp
 TARGET = SeqAlign
+TARGET_NAME = SeqAlign
+TARGET_ENTRY = Init_$(TARGET_NAME)
 DLLIB = $(TARGET).so
 EXTSTATIC = 
 STATIC_LIB = 
 
+TIMESTAMP_DIR = .
 BINDIR        = $(bindir)
 RUBYCOMMONDIR = $(sitedir)$(target_prefix)
 RUBYLIBDIR    = $(sitelibdir)$(target_prefix)
@@ -174,78 +215,100 @@ CLEANOBJS     = *.o  *.bak
 all:    $(DLLIB)
 static: $(STATIC_LIB)
 .PHONY: all install static install-so install-rb
-.PHONY: clean clean-so clean-rb
+.PHONY: clean clean-so clean-static clean-rb
 
+clean-static::
 clean-rb-default::
 clean-rb::
 clean-so::
-clean: clean-so clean-rb-default clean-rb
-		@-$(RM) $(CLEANLIBS) $(CLEANOBJS) $(CLEANFILES)
+clean: clean-so clean-static clean-rb-default clean-rb
+		-$(Q)$(RM) $(CLEANLIBS) $(CLEANOBJS) $(CLEANFILES) .*.time
 
 distclean-rb-default::
 distclean-rb::
 distclean-so::
-distclean: clean distclean-so distclean-rb-default distclean-rb
-		@-$(RM) Makefile $(RUBY_EXTCONF_H) conftest.* mkmf.log
-		@-$(RM) core ruby$(EXEEXT) *~ $(DISTCLEANFILES)
-		@-$(RMDIRS) $(DISTCLEANDIRS) 2> /dev/null || true
+distclean-static::
+distclean: clean distclean-so distclean-static distclean-rb-default distclean-rb
+		-$(Q)$(RM) Makefile $(RUBY_EXTCONF_H) conftest.* mkmf.log
+		-$(Q)$(RM) core ruby$(EXEEXT) *~ $(DISTCLEANFILES)
+		-$(Q)$(RMDIRS) $(DISTCLEANDIRS) 2> /dev/null || true
 
 realclean: distclean
 install: install-so install-rb
 
-install-so: $(RUBYARCHDIR)
-install-so: $(RUBYARCHDIR)/$(DLLIB)
-$(RUBYARCHDIR)/$(DLLIB): $(DLLIB)
-	@-$(MAKEDIRS) $(@D)
-	$(INSTALL_PROG) $(DLLIB) $(@D)
+install-so: $(DLLIB) $(TIMESTAMP_DIR)/.RUBYARCHDIR.time
+	$(INSTALL_PROG) $(DLLIB) $(RUBYARCHDIR)
+clean-static::
+	-$(Q)$(RM) $(STATIC_LIB)
 install-rb: pre-install-rb install-rb-default
 install-rb-default: pre-install-rb-default
 pre-install-rb: Makefile
 pre-install-rb-default: Makefile
 pre-install-rb-default:
-	$(ECHO) installing default SeqAlign libraries
-$(RUBYARCHDIR):
-	$(Q) $(MAKEDIRS) $@
+	@$(NULLCMD)
+$(TIMESTAMP_DIR)/.RUBYARCHDIR.time:
+	$(Q) $(MAKEDIRS) $(@D) $(RUBYARCHDIR)
+	$(Q) $(TOUCH) $@
 
 site-install: site-install-so site-install-rb
 site-install-so: install-so
 site-install-rb: install-rb
 
-.SUFFIXES: .c .m .cc .mm .cxx .cpp .C .o
+.SUFFIXES: .c .m .cc .mm .cxx .cpp .o .S
 
 .cc.o:
 	$(ECHO) compiling $(<)
 	$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
 
+.cc.S:
+	$(ECHO) translating $(<)
+	$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -S $<
+
 .mm.o:
 	$(ECHO) compiling $(<)
 	$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
 
+.mm.S:
+	$(ECHO) translating $(<)
+	$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -S $<
+
 .cxx.o:
 	$(ECHO) compiling $(<)
 	$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
 
+.cxx.S:
+	$(ECHO) translating $(<)
+	$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -S $<
+
 .cpp.o:
 	$(ECHO) compiling $(<)
 	$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
 
-.C.o:
-	$(ECHO) compiling $(<)
-	$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
+.cpp.S:
+	$(ECHO) translating $(<)
+	$(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -S $<
 
 .c.o:
 	$(ECHO) compiling $(<)
 	$(Q) $(CC) $(INCFLAGS) $(CPPFLAGS) $(CFLAGS) $(COUTFLAG)$@ -c $<
 
+.c.S:
+	$(ECHO) translating $(<)
+	$(Q) $(CC) $(INCFLAGS) $(CPPFLAGS) $(CFLAGS) $(COUTFLAG)$@ -S $<
+
 .m.o:
 	$(ECHO) compiling $(<)
 	$(Q) $(CC) $(INCFLAGS) $(CPPFLAGS) $(CFLAGS) $(COUTFLAG)$@ -c $<
 
+.m.S:
+	$(ECHO) translating $(<)
+	$(Q) $(CC) $(INCFLAGS) $(CPPFLAGS) $(CFLAGS) $(COUTFLAG)$@ -S $<
+
 $(DLLIB): $(OBJS) Makefile
 	$(ECHO) linking shared-object $(DLLIB)
-	@-$(RM) $(@)
+	-$(Q)$(RM) $(@)
 	$(Q) $(LDSHAREDXX) -o $@ $(OBJS) $(LIBPATH) $(DLDFLAGS) $(LOCAL_LIBS) $(LIBS)
 
 
 
-$(OBJS): $(hdrdir)/ruby.h $(hdrdir)/ruby/defines.h $(arch_hdrdir)/ruby/config.h
+$(OBJS): $(HDRS) $(ruby_headers)

data/ext/bioseqalign/extconf.rb

@@ -1,2 +1,3 @@
 require 'mkmf-rice'
+dir_config('seqan')
 create_makefile('SeqAlign')

data/lib/bioseqalign/version.rb

@@ -0,0 +1,6 @@
+
+module BioSeqAlign
+
+  VERSION='0.0.3'
+  
+end

metadata

@@ -1,8 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bioseqalign
 version: !ruby/object:Gem::Version
-  version: 0.0.2
-  prerelease: 
+  version: 0.0.3
 platform: ruby
 authors:
 - Stefano R.B.
@@ -14,17 +13,15 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: rice
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
 description: A simple gem to perform fast pairwise sequence alignment using seqan
@@ -34,58 +31,58 @@ extensions:
 - ext/bioseqalign/extconf.rb
 extra_rdoc_files: []
 files:
-- lib/bioseqalign.rb
+- ext/bioseqalign/FitAlign.cpp
+- ext/bioseqalign/FitAlign.cpp~
 - ext/bioseqalign/FitAlign.hpp
-- ext/bioseqalign/extconf.rb
-- ext/bioseqalign/PrefixSuffixAlign.hpp~
+- ext/bioseqalign/FitAlign.hpp~
+- ext/bioseqalign/GlobalAlign.cpp
+- ext/bioseqalign/GlobalAlign.cpp~
 - ext/bioseqalign/GlobalAlign.hpp
-- ext/bioseqalign/PrefixSuffixAlign.hpp
-- ext/bioseqalign/LocalAlign.cpp~
-- ext/bioseqalign/PrefixSuffixAlign.cpp~
-- ext/bioseqalign/runTest.rb
-- ext/bioseqalign/PrefixSuffixAlign.cpp
-- ext/bioseqalign/LocalAlign.hpp
 - ext/bioseqalign/GlobalAlign.hpp~
-- ext/bioseqalign/PairwiseAlign.cpp
-- ext/bioseqalign/runTest.rb~
-- ext/bioseqalign/FitAlign.cpp~
 - ext/bioseqalign/LocalAlign.cpp
+- ext/bioseqalign/LocalAlign.cpp~
+- ext/bioseqalign/LocalAlign.hpp
+- ext/bioseqalign/LocalAlign.hpp~
 - ext/bioseqalign/Makefile
-- ext/bioseqalign/fitalgntest.cpp~
-- ext/bioseqalign/PairwiseAlign.hpp
+- ext/bioseqalign/PairwiseAlign.cpp
 - ext/bioseqalign/PairwiseAlign.cpp~
-- ext/bioseqalign/LocalAlign.hpp~
-- ext/bioseqalign/GlobalAlign.cpp~
+- ext/bioseqalign/PairwiseAlign.hpp
 - ext/bioseqalign/PairwiseAlign.hpp~
+- ext/bioseqalign/PrefixSuffixAlign.cpp
+- ext/bioseqalign/PrefixSuffixAlign.cpp~
+- ext/bioseqalign/PrefixSuffixAlign.hpp
+- ext/bioseqalign/PrefixSuffixAlign.hpp~
+- ext/bioseqalign/extconf.rb
 - ext/bioseqalign/extconf.rb~
-- ext/bioseqalign/FitAlign.hpp~
 - ext/bioseqalign/fitalgntest.cpp
-- ext/bioseqalign/GlobalAlign.cpp
-- ext/bioseqalign/FitAlign.cpp
+- ext/bioseqalign/fitalgntest.cpp~
+- ext/bioseqalign/runTest.rb
+- ext/bioseqalign/runTest.rb~
+- lib/bioseqalign.rb
+- lib/bioseqalign/version.rb
 homepage: https://github.com/stefrb/bioseqalign
 licenses:
 - MIT
+metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 - ext
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - '>='
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - '>='
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.23
+rubygems_version: 2.4.3
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: Pairwise sequence alignment using seqan
 test_files: []