JWS-117 Compiled all tools with ./compilebin.sh and some were missing related files.
[jabaws.git] / binaries / src / ViennaRNA / RNAforester / man / Makefile
diff --git a/binaries/src/ViennaRNA/RNAforester/man/Makefile b/binaries/src/ViennaRNA/RNAforester/man/Makefile
new file mode 100644 (file)
index 0000000..d6dc82d
--- /dev/null
@@ -0,0 +1,448 @@
+# Makefile.in generated by automake 1.11.6 from Makefile.am.
+# man/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 $$am__dry = yes; \
+  }
+pkgdatadir = $(datadir)/RNAforester
+pkgincludedir = $(includedir)/RNAforester
+pkglibdir = $(libdir)/RNAforester
+pkglibexecdir = $(libexecdir)/RNAforester
+am__cd = CDPATH="$${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 = :
+subdir = man
+DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+am__aclocal_m4_deps = $(top_srcdir)/configure.ac
+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
+       $(ACLOCAL_M4)
+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
+CONFIG_HEADER = $(top_builddir)/config.h
+CONFIG_CLEAN_FILES =
+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 = @
+SOURCES =
+DIST_SOURCES =
+am__can_run_installinfo = \
+  case $$AM_UPDATE_INFO_DIR in \
+    n|no|NO) false;; \
+    *) (install-info --version) >/dev/null 2>&1;; \
+  esac
+am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
+am__vpath_adj = case $$p in \
+    $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
+    *) f=$$p;; \
+  esac;
+am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`;
+am__install_max = 40
+am__nobase_strip_setup = \
+  srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'`
+am__nobase_strip = \
+  for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||"
+am__nobase_list = $(am__nobase_strip_setup); \
+  for p in $$list; do echo "$$p $$p"; done | \
+  sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \
+  $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \
+    if (++n[$$2] == $(am__install_max)) \
+      { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \
+    END { for (dir in files) print dir, files[dir] }'
+am__base_list = \
+  sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \
+  sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
+am__uninstall_files_from_dir = { \
+  test -z "$$files" \
+    || { test ! -d "$$dir" && test ! -f "$$dir" && test ! -r "$$dir"; } \
+    || { echo " ( cd '$$dir' && rm -f" $$files ")"; \
+         $(am__cd) "$$dir" && rm -f $$files; }; \
+  }
+man1dir = $(mandir)/man1
+am__installdirs = "$(DESTDIR)$(man1dir)"
+NROFF = nroff
+MANS = $(man_MANS)
+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
+ACLOCAL = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/RNAforester/missing --run aclocal-1.11
+AMTAR = $${TAR-tar}
+AM_DEFAULT_VERBOSITY = 0
+AUTOCONF = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/RNAforester/missing --run autoconf
+AUTOHEADER = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/RNAforester/missing --run autoheader
+AUTOMAKE = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/RNAforester/missing --run automake-1.11
+AWK = gawk
+CC = gcc
+CCDEPMODE = depmode=gcc3
+CFLAGS = -g -O2
+CPPFLAGS =  -I../g2-0.70/include/ 
+CXX = g++
+CXXCPP = g++ -E
+CXXDEPMODE = depmode=gcc3
+CXXFLAGS = -g -O2
+CYGPATH_W = echo
+DEFS = -DHAVE_CONFIG_H
+DEPDIR = .deps
+ECHO_C = 
+ECHO_N = -n
+ECHO_T = 
+EGREP = /bin/grep -E
+EXEEXT = 
+GREP = /bin/grep
+INSTALL = /usr/bin/install -c
+INSTALL_DATA = ${INSTALL} -m 644
+INSTALL_PROGRAM = ${INSTALL}
+INSTALL_SCRIPT = ${INSTALL}
+INSTALL_STRIP_PROGRAM = $(install_sh) -c -s
+LDFLAGS = -L../g2-0.70 -L../../lib -L../../ViennaRNA  -fopenmp
+LIBOBJS = 
+LIBS = -lg2 -lRNA 
+LTLIBOBJS = 
+MAKEINFO = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/RNAforester/missing --run makeinfo
+MKDIR_P = /bin/mkdir -p
+OBJEXT = o
+OPENMP_CXXFLAGS = -fopenmp
+PACKAGE = RNAforester
+PACKAGE_BUGREPORT = mhoechsm@techfak.uni-bielefeld.de
+PACKAGE_NAME = RNAforester
+PACKAGE_STRING = RNAforester 1.5
+PACKAGE_TARNAME = RNAforester
+PACKAGE_URL = 
+PACKAGE_VERSION = 1.5
+PATH_SEPARATOR = :
+SET_MAKE = 
+SHELL = /bin/sh
+STRIP = 
+VERSION = 1.5
+abs_builddir = /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/RNAforester/man
+abs_srcdir = /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/RNAforester/man
+abs_top_builddir = /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/RNAforester
+abs_top_srcdir = /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/RNAforester
+ac_ct_CC = gcc
+ac_ct_CXX = g++
+am__include = include
+am__leading_dot = .
+am__quote = 
+am__tar = $${TAR-tar} chof - "$$tardir"
+am__untar = $${TAR-tar} xf -
+bindir = ${exec_prefix}/bin
+build_alias = 
+builddir = .
+datadir = ${datarootdir}
+datarootdir = ${prefix}/share
+docdir = ${datarootdir}/doc/${PACKAGE_TARNAME}
+dvidir = ${docdir}
+exec_prefix = ${prefix}
+host_alias = 
+htmldir = ${docdir}
+includedir = ${prefix}/include
+infodir = ${datarootdir}/info
+install_sh = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/RNAforester/install-sh
+libdir = ${exec_prefix}/lib
+libexecdir = ${exec_prefix}/libexec
+localedir = ${datarootdir}/locale
+localstatedir = ${prefix}/var
+mandir = ${datarootdir}/man
+mkdir_p = /bin/mkdir -p
+oldincludedir = /usr/include
+pdfdir = ${docdir}
+prefix = /usr/local
+program_transform_name = s,x,x,
+psdir = ${docdir}
+sbindir = ${exec_prefix}/sbin
+sharedstatedir = ${prefix}/com
+srcdir = .
+subdirs =  g2-0.70
+sysconfdir = ${prefix}/etc
+target_alias = 
+top_build_prefix = ../
+top_builddir = ..
+top_srcdir = ..
+man_MANS = RNAforester.1
+EXTRA_DIST = $(man_MANS)
+all: all-am
+
+.SUFFIXES:
+$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
+       @for dep in $?; do \
+         case '$(am__configure_deps)' in \
+           *$$dep*) \
+             ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
+               && { if test -f $@; then exit 0; else break; fi; }; \
+             exit 1;; \
+         esac; \
+       done; \
+       echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu man/Makefile'; \
+       $(am__cd) $(top_srcdir) && \
+         $(AUTOMAKE) --gnu man/Makefile
+.PRECIOUS: Makefile
+Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+       @case '$?' in \
+         *config.status*) \
+           cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
+         *) \
+           echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
+           cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+       esac;
+
+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
+       cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+
+$(top_srcdir)/configure:  $(am__configure_deps)
+       cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
+       cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(am__aclocal_m4_deps):
+install-man1: $(man_MANS)
+       @$(NORMAL_INSTALL)
+       @list1=''; \
+       list2='$(man_MANS)'; \
+       test -n "$(man1dir)" \
+         && test -n "`echo $$list1$$list2`" \
+         || exit 0; \
+       echo " $(MKDIR_P) '$(DESTDIR)$(man1dir)'"; \
+       $(MKDIR_P) "$(DESTDIR)$(man1dir)" || exit 1; \
+       { for i in $$list1; do echo "$$i"; done;  \
+       if test -n "$$list2"; then \
+         for i in $$list2; do echo "$$i"; done \
+           | sed -n '/\.1[a-z]*$$/p'; \
+       fi; \
+       } | while read p; do \
+         if test -f $$p; then d=; else d="$(srcdir)/"; fi; \
+         echo "$$d$$p"; echo "$$p"; \
+       done | \
+       sed -e 'n;s,.*/,,;p;h;s,.*\.,,;s,^[^1][0-9a-z]*$$,1,;x' \
+             -e 's,\.[0-9a-z]*$$,,;$(transform);G;s,\n,.,' | \
+       sed 'N;N;s,\n, ,g' | { \
+       list=; while read file base inst; do \
+         if test "$$base" = "$$inst"; then list="$$list $$file"; else \
+           echo " $(INSTALL_DATA) '$$file' '$(DESTDIR)$(man1dir)/$$inst'"; \
+           $(INSTALL_DATA) "$$file" "$(DESTDIR)$(man1dir)/$$inst" || exit $$?; \
+         fi; \
+       done; \
+       for i in $$list; do echo "$$i"; done | $(am__base_list) | \
+       while read files; do \
+         test -z "$$files" || { \
+           echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(man1dir)'"; \
+           $(INSTALL_DATA) $$files "$(DESTDIR)$(man1dir)" || exit $$?; }; \
+       done; }
+
+uninstall-man1:
+       @$(NORMAL_UNINSTALL)
+       @list=''; test -n "$(man1dir)" || exit 0; \
+       files=`{ for i in $$list; do echo "$$i"; done; \
+       l2='$(man_MANS)'; for i in $$l2; do echo "$$i"; done | \
+         sed -n '/\.1[a-z]*$$/p'; \
+       } | sed -e 's,.*/,,;h;s,.*\.,,;s,^[^1][0-9a-z]*$$,1,;x' \
+             -e 's,\.[0-9a-z]*$$,,;$(transform);G;s,\n,.,'`; \
+       dir='$(DESTDIR)$(man1dir)'; $(am__uninstall_files_from_dir)
+tags: TAGS
+TAGS:
+
+ctags: CTAGS
+CTAGS:
+
+
+distdir: $(DISTFILES)
+       @list='$(MANS)'; if test -n "$$list"; then \
+         list=`for p in $$list; do \
+           if test -f $$p; then d=; else d="$(srcdir)/"; fi; \
+           if test -f "$$d$$p"; then echo "$$d$$p"; else :; fi; done`; \
+         if test -n "$$list" && \
+           grep 'ab help2man is required to generate this page' $$list >/dev/null; then \
+           echo "error: found man pages containing the \`missing help2man' replacement text:" >&2; \
+           grep -l 'ab help2man is required to generate this page' $$list | sed 's/^/         /' >&2; \
+           echo "       to fix them, install help2man, remove and regenerate the man pages;" >&2; \
+           echo "       typically \`make maintainer-clean' will remove them" >&2; \
+           exit 1; \
+         else :; fi; \
+       else :; fi
+       @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/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)/$$file" \
+           || exit 1; \
+         fi; \
+       done
+check-am: all-am
+check: check-am
+all-am: Makefile $(MANS)
+installdirs:
+       for dir in "$(DESTDIR)$(man1dir)"; do \
+         test -z "$$dir" || $(MKDIR_P) "$$dir"; \
+       done
+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-man
+
+install-dvi: install-dvi-am
+
+install-dvi-am:
+
+install-exec-am:
+
+install-html: install-html-am
+
+install-html-am:
+
+install-info: install-info-am
+
+install-info-am:
+
+install-man: install-man1
+
+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
+
+mostlyclean: mostlyclean-am
+
+mostlyclean-am: mostlyclean-generic
+
+pdf: pdf-am
+
+pdf-am:
+
+ps: ps-am
+
+ps-am:
+
+uninstall-am: uninstall-man
+
+uninstall-man: uninstall-man1
+
+.MAKE: install-am install-strip
+
+.PHONY: all all-am check check-am 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-html \
+       install-html-am install-info install-info-am install-man \
+       install-man1 install-pdf install-pdf-am install-ps \
+       install-ps-am install-strip installcheck installcheck-am \
+       installdirs maintainer-clean maintainer-clean-generic \
+       mostlyclean mostlyclean-generic pdf pdf-am ps ps-am uninstall \
+       uninstall-am uninstall-man uninstall-man1
+
+
+# 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: