JWS-117 Compiled all tools with ./compilebin.sh and some were missing related files.
[jabaws.git] / binaries / src / ViennaRNA / interfaces / Perl / Makefile
diff --git a/binaries/src/ViennaRNA/interfaces/Perl/Makefile b/binaries/src/ViennaRNA/interfaces/Perl/Makefile
new file mode 100644 (file)
index 0000000..fda9b9d
--- /dev/null
@@ -0,0 +1,429 @@
+# Makefile.in generated by automake 1.11.6 from Makefile.am.
+# interfaces/Perl/Makefile.  Generated from Makefile.in by configure.
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 Free Software
+# Foundation, Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+
+
+am__make_dryrun = \
+  { \
+    am__dry=no; \
+    case $$MAKEFLAGS in \
+      *\\[\ \  ]*) \
+        echo 'am--echo: ; @echo "AM"  OK' | $(MAKE) -f - 2>/dev/null \
+          | grep '^AM OK$$' >/dev/null || am__dry=yes;; \
+      *) \
+        for am__flg in $$MAKEFLAGS; do \
+          case $$am__flg in \
+            *=*|--*) ;; \
+            *n*) am__dry=yes; break;; \
+          esac; \
+        done;; \
+    esac; \
+    test $$am__dry = yes; \
+  }
+pkgdatadir = $(datadir)/ViennaRNA
+pkgincludedir = $(includedir)/ViennaRNA
+pkglibdir = $(libdir)/ViennaRNA
+pkglibexecdir = $(libexecdir)/ViennaRNA
+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
+install_sh_DATA = $(install_sh) -c -m 644
+install_sh_PROGRAM = $(install_sh) -c
+install_sh_SCRIPT = $(install_sh) -c
+INSTALL_HEADER = $(INSTALL_DATA)
+transform = $(program_transform_name)
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+build_triplet = x86_64-unknown-linux-gnu
+host_triplet = x86_64-unknown-linux-gnu
+subdir = interfaces/Perl
+DIST_COMMON = $(srcdir)/Makefile.PL.in $(srcdir)/Makefile.am \
+       $(srcdir)/Makefile.in
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+am__aclocal_m4_deps = $(top_srcdir)/acinclude.m4 \
+       $(top_srcdir)/m4/package.m4 $(top_srcdir)/configure.ac
+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
+       $(ACLOCAL_M4)
+mkinstalldirs = $(install_sh) -d
+CONFIG_HEADER = $(top_builddir)/config.h
+CONFIG_CLEAN_FILES = Makefile.PL
+CONFIG_CLEAN_VPATH_FILES =
+AM_V_GEN = $(am__v_GEN_$(V))
+am__v_GEN_ = $(am__v_GEN_$(AM_DEFAULT_VERBOSITY))
+am__v_GEN_0 = @echo "  GEN   " $@;
+AM_V_at = $(am__v_at_$(V))
+am__v_at_ = $(am__v_at_$(AM_DEFAULT_VERBOSITY))
+am__v_at_0 = @
+DIST_SOURCES =
+am__can_run_installinfo = \
+  case $$AM_UPDATE_INFO_DIR in \
+    n|no|NO) false;; \
+    *) (install-info --version) >/dev/null 2>&1;; \
+  esac
+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
+ACLOCAL = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/config/missing --run aclocal-1.11
+AMTAR = $${TAR-tar}
+AM_DEFAULT_VERBOSITY = 0
+AUTOCONF = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/config/missing --run autoconf
+AUTOHEADER = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/config/missing --run autoheader
+AUTOMAKE = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/config/missing --run automake-1.11
+AWK = gawk
+CC = gcc
+CCDEPMODE = depmode=gcc3
+CFLAGS = -g -O2
+CLUSTER_DIR = 
+CPP = gcc -E
+CPPFLAGS = 
+CXX = g++
+CXXCPP = g++ -E
+CXXDEPMODE = depmode=gcc3
+CXXFLAGS = -g -O2
+CXXLD = g++
+CYGPATH_W = echo
+DEFS = -DHAVE_CONFIG_H
+DEPDIR = .deps
+DOXYGEN_CMD_LATEX = /usr/bin/latex
+DOXYGEN_CMD_MAKEINDEX = /usr/bin/makeindex
+DOXYGEN_CONF = doxygen.conf
+DOXYGEN_DOCDIR = doc
+DOXYGEN_GENERATE_HTML = YES
+DOXYGEN_GENERATE_LATEX = YES
+DOXYGEN_HAVE_DOT = YES
+DOXYGEN_PROJECT_NAME = RNAlib-2.1.2
+DOXYGEN_SRCDIR = .
+DOXYGEN_WITH_PDFLATEX = YES
+ECHO_C = 
+ECHO_N = -n
+ECHO_T = 
+EGREP = /bin/grep -E
+EXEEXT = 
+FPIC = -fpic
+GREP = /bin/grep
+INSTALL = /usr/bin/install -c
+INSTALL_DATA = ${INSTALL} -m 644
+INSTALL_PROGRAM = ${INSTALL}
+INSTALL_SCRIPT = ${INSTALL}
+INSTALL_STRIP_PROGRAM = $(install_sh) -c -s
+ISODATE = 2017-04-11
+LDFLAGS = 
+LIBOBJS = 
+LIBS = -lm 
+LIBSVM_DIR = libsvm-2.91
+LTLIBOBJS = 
+MAKEINFO = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/config/missing --run makeinfo
+MKDIR_P = /bin/mkdir -p
+OBJEXT = o
+OPENMP_CFLAGS = -fopenmp
+PACKAGE = ViennaRNA
+PACKAGE_BUGREPORT = rna@tbi.univie.ac.at
+PACKAGE_NAME = ViennaRNA
+PACKAGE_STRING = ViennaRNA 2.1.2
+PACKAGE_TARNAME = ViennaRNA
+PACKAGE_URL = http://www.tbi.univie.ac.a/~ivo/RNA
+PACKAGE_VERSION = 2.1.2
+PATH_SEPARATOR = :
+PERLPREFIX = 
+PERL_INTERFACE = Perl
+POW_LIB = 
+PYTHON_INTERFACE = 
+PerlCmd = /usr/bin/perl
+PythonCmd = /homes/fmmarquesmadeira/.local/anaconda/envs/python3/bin/python
+RANLIB = ranlib
+REFERENCE_MANUAL_PDF_NAME = RNAlib-2.1.2.pdf
+REFERENCE_MANUAL_TAGFILE = RNAlib-2.1.2.tag
+SET_MAKE = 
+SHELL = /bin/sh
+STRIP = 
+VERSION = 2.1.2
+abs_builddir = /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/interfaces/Perl
+abs_srcdir = /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/interfaces/Perl
+abs_top_builddir = /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA
+abs_top_srcdir = /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA
+ac_ct_CC = gcc
+ac_ct_CXX = g++
+am__include = include
+am__leading_dot = .
+am__quote = 
+am__tar = $${TAR-tar} chof - "$$tardir"
+am__untar = $${TAR-tar} xf -
+bindir = ${exec_prefix}/bin
+build = x86_64-unknown-linux-gnu
+build_alias = 
+build_cpu = x86_64
+build_os = linux-gnu
+build_vendor = unknown
+builddir = .
+datadir = ${datarootdir}
+datarootdir = ${prefix}/share
+docdir = ${datarootdir}/doc/${PACKAGE_TARNAME}
+dot = /usr/bin/dot
+doxygen = /usr/bin/doxygen
+dvidir = ${docdir}
+egrep = /bin/egrep
+exec_prefix = ${prefix}
+host = x86_64-unknown-linux-gnu
+host_alias = 
+host_cpu = x86_64
+host_os = linux-gnu
+host_vendor = unknown
+htmldir = ${docdir}
+includedir = ${prefix}/include
+infodir = ${datarootdir}/info
+install_sh = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/config/install-sh
+latex = /usr/bin/latex
+libdir = ${exec_prefix}/lib
+libexecdir = ${exec_prefix}/libexec
+localedir = ${datarootdir}/locale
+localstatedir = ${prefix}/var
+makeindex = /usr/bin/makeindex
+mandir = ${datarootdir}/man
+mkdir_p = /bin/mkdir -p
+oldincludedir = /usr/include
+pdfdir = ${docdir}
+pdflatex = no
+perl = /usr/bin/perl
+prefix = /usr/local
+program_transform_name = s,x,x,
+psdir = ${docdir}
+sbindir = ${exec_prefix}/sbin
+sharedstatedir = ${prefix}/com
+srcdir = .
+subdirs =  Kinfold RNAforester
+sysconfdir = ${prefix}/etc
+target_alias = 
+top_build_prefix = ../../
+top_builddir = ../..
+top_srcdir = ../..
+#USE_LARGE_PF = 
+USE_LARGE_PF = -DLARGE_PF
+SOURCES = Makefile.PL RNA.pod
+EXTRA_DIST = RNA.pm RNA_wrap.c RNAfold.pl test.pl RNAfold.cgi Makefile.PL
+all: all-am
+
+.SUFFIXES:
+$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
+       @for dep in $?; do \
+         case '$(am__configure_deps)' in \
+           *$$dep*) \
+             ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
+               && { if test -f $@; then exit 0; else break; fi; }; \
+             exit 1;; \
+         esac; \
+       done; \
+       echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu interfaces/Perl/Makefile'; \
+       $(am__cd) $(top_srcdir) && \
+         $(AUTOMAKE) --gnu interfaces/Perl/Makefile
+.PRECIOUS: Makefile
+Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+       @case '$?' in \
+         *config.status*) \
+           cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
+         *) \
+           echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
+           cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+       esac;
+
+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
+       cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+
+$(top_srcdir)/configure:  $(am__configure_deps)
+       cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
+       cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(am__aclocal_m4_deps):
+Makefile.PL: $(top_builddir)/config.status $(srcdir)/Makefile.PL.in
+       cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@
+tags: TAGS
+TAGS:
+
+ctags: CTAGS
+CTAGS:
+
+
+distdir: $(DISTFILES)
+       @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+       topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
+       list='$(DISTFILES)'; \
+         dist_files=`for file in $$list; do echo $$file; done | \
+         sed -e "s|^$$srcdirstrip/||;t" \
+             -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
+       case $$dist_files in \
+         */*) $(MKDIR_P) `echo "$$dist_files" | \
+                          sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
+                          sort -u` ;; \
+       esac; \
+       for file in $$dist_files; do \
+         if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
+         if test -d $$d/$$file; then \
+           dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
+           if test -d "$(distdir)/$$file"; then \
+             find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+           fi; \
+           if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
+             cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
+             find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+           fi; \
+           cp -fpR $$d/$$file "$(distdir)$$dir" || exit 1; \
+         else \
+           test -f "$(distdir)/$$file" \
+           || cp -p $$d/$$file "$(distdir)/$$file" \
+           || exit 1; \
+         fi; \
+       done
+check-am: all-am
+       $(MAKE) $(AM_MAKEFLAGS) check-local
+check: check-am
+all-am: Makefile all-local
+installdirs:
+install: install-am
+install-exec: install-exec-am
+install-data: install-data-am
+uninstall: uninstall-am
+
+install-am: all-am
+       @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+
+installcheck: installcheck-am
+install-strip:
+       if test -z '$(STRIP)'; then \
+         $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+           install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+             install; \
+       else \
+         $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+           install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+           "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'" install; \
+       fi
+mostlyclean-generic:
+
+clean-generic:
+
+distclean-generic:
+       -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+       -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
+
+maintainer-clean-generic:
+       @echo "This command is intended for maintainers to use"
+       @echo "it deletes files that may require special tools to rebuild."
+clean: clean-am
+
+clean-am: clean-generic mostlyclean-am
+
+distclean: distclean-am
+       -rm -f Makefile
+distclean-am: clean-am distclean-generic
+
+dvi: dvi-am
+
+dvi-am:
+
+html: html-am
+
+html-am:
+
+info: info-am
+
+info-am:
+
+install-data-am:
+
+install-dvi: install-dvi-am
+
+install-dvi-am:
+
+install-exec-am: install-exec-local
+
+install-html: install-html-am
+
+install-html-am:
+
+install-info: install-info-am
+
+install-info-am:
+
+install-man:
+
+install-pdf: install-pdf-am
+
+install-pdf-am:
+
+install-ps: install-ps-am
+
+install-ps-am:
+
+installcheck-am:
+
+maintainer-clean: maintainer-clean-am
+       -rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic \
+       maintainer-clean-local
+
+mostlyclean: mostlyclean-am
+
+mostlyclean-am: mostlyclean-generic mostlyclean-local
+
+pdf: pdf-am
+
+pdf-am:
+
+ps: ps-am
+
+ps-am:
+
+uninstall-am:
+
+.MAKE: check-am install-am install-strip
+
+.PHONY: all all-am all-local check check-am check-local clean \
+       clean-generic distclean distclean-generic distdir dvi dvi-am \
+       html html-am info info-am install install-am install-data \
+       install-data-am install-dvi install-dvi-am install-exec \
+       install-exec-am install-exec-local install-html \
+       install-html-am install-info install-info-am install-man \
+       install-pdf install-pdf-am install-ps install-ps-am \
+       install-strip installcheck installcheck-am installdirs \
+       maintainer-clean maintainer-clean-generic \
+       maintainer-clean-local mostlyclean mostlyclean-generic \
+       mostlyclean-local pdf pdf-am ps ps-am uninstall uninstall-am
+
+
+Makefile.perl: Makefile.PL Makefile
+       /usr/bin/perl Makefile.PL PREFIX=$(prefix) LDDLFLAGS="${LDFLAGS} -shared"
+
+# the perl command repairs some errors in the SWIG CVS version
+RNA_wrap.c: ../RNA.i ../tmaps.i
+       swig -perl5 -shadow $(USE_LARGE_PF) -I../ RNA.i
+
+all-local: RNA_wrap.c Makefile.perl
+       $(MAKE) -f Makefile.perl
+
+install-exec-local: all-local
+       $(MAKE) -f Makefile.perl install
+
+check-local: all-local
+       $(MAKE) -f Makefile.perl test
+
+mostlyclean-local: Makefile.perl
+       $(MAKE) -f Makefile.perl clean
+
+# remove all generated content
+maintainer-clean-local:
+       -rm -f RNA_wrap.c Makefile.perl.old RNA.pm
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT: