[med-svn] r18544 - in trunk/packages/vienna-rna/trunk/debian: . patches
Olivier Sallou
osallou at moszumanska.debian.org
Sat Dec 27 23:31:22 UTC 2014
Author: osallou
Date: 2014-12-27 23:31:21 +0000 (Sat, 27 Dec 2014)
New Revision: 18544
Added:
trunk/packages/vienna-rna/trunk/debian/libviennarna-dev.install
trunk/packages/vienna-rna/trunk/debian/libviennarna.install
trunk/packages/vienna-rna/trunk/debian/patches/add_shared_library
trunk/packages/vienna-rna/trunk/debian/patches/do_not_configure_g2.patch
trunk/packages/vienna-rna/trunk/debian/patches/fix_perl_install.patch
trunk/packages/vienna-rna/trunk/debian/patches/fix_python_interface.patch
trunk/packages/vienna-rna/trunk/debian/patches/spelling.patch
Removed:
trunk/packages/vienna-rna/trunk/debian/patches/do_not_configure_g2-0.70.patch
Modified:
trunk/packages/vienna-rna/trunk/debian/README.Debian
trunk/packages/vienna-rna/trunk/debian/changelog
trunk/packages/vienna-rna/trunk/debian/compat
trunk/packages/vienna-rna/trunk/debian/control
trunk/packages/vienna-rna/trunk/debian/copyright
trunk/packages/vienna-rna/trunk/debian/patches/series
trunk/packages/vienna-rna/trunk/debian/rules
trunk/packages/vienna-rna/trunk/debian/vienna-rna-doc.doc-base
trunk/packages/vienna-rna/trunk/debian/vienna-rna-doc.install
trunk/packages/vienna-rna/trunk/debian/vienna-rna.install
trunk/packages/vienna-rna/trunk/debian/vienna-rna.manpages
trunk/packages/vienna-rna/trunk/debian/watch
Log:
updates for ViennaRNA v2.1.8
Modified: trunk/packages/vienna-rna/trunk/debian/README.Debian
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/README.Debian 2014-12-16 15:10:08 UTC (rev 18543)
+++ trunk/packages/vienna-rna/trunk/debian/README.Debian 2014-12-27 23:31:21 UTC (rev 18544)
@@ -1,7 +1 @@
-viennarna for Debian
---------------------
-
-csh script Fold was moved to examples /usr/share/doc/vienna-rna/examples/ directory .
-
-
- -- Alex Mestiashvili <alex at biotec.tu-dresden.de> Fri, 28 Jan 2011 17:48:23 +0100
+Perl tests are skipped for the moment. I could not find a way to set correctly the library path to libviennarna.so to make them successful
Modified: trunk/packages/vienna-rna/trunk/debian/changelog
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/changelog 2014-12-16 15:10:08 UTC (rev 18543)
+++ trunk/packages/vienna-rna/trunk/debian/changelog 2014-12-27 23:31:21 UTC (rev 18544)
@@ -1,3 +1,12 @@
+vienna-rna (2.1.8-1) UNRELEASED; urgency=medium
+
+ * First package of ViennaRNA (Closes: #451193)
+ [TODO] pbuilder, lintian checks
+ [DONE] update patches to viennarna v2
+ build new packages for perl and python wrappers
+
+ -- Olivier Sallou <osallou at debian.org> Tue, 23 Dec 2014 10:35:08 +0100
+
vienna-rna (1.8.5-1) UNRELEASED; urgency=low
* Initial release (Closes: #451193)
Modified: trunk/packages/vienna-rna/trunk/debian/compat
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/compat 2014-12-16 15:10:08 UTC (rev 18543)
+++ trunk/packages/vienna-rna/trunk/debian/compat 2014-12-27 23:31:21 UTC (rev 18544)
@@ -1 +1 @@
-7
+9
Modified: trunk/packages/vienna-rna/trunk/debian/control
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/control 2014-12-16 15:10:08 UTC (rev 18543)
+++ trunk/packages/vienna-rna/trunk/debian/control 2014-12-27 23:31:21 UTC (rev 18544)
@@ -1,21 +1,25 @@
Source: vienna-rna
+Section: science
Priority: optional
-Section: science
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Alex Mestiashvili <alex at biotec.tu-dresden.de>
-DM-Upload-Allowed: yes
-Build-Depends: debhelper (>= 7.1), autotools-dev,
- libg2-dev, libgd2-xpm-dev, libx11-dev, texinfo, texlive-latex-base, help2man, perl-doc
-Standards-Version: 3.9.2
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/vienna-rna/trunk/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/vienna-rna/trunk/
-Homepage: http://www.tbi.univie.ac.at/~ivo/RNA/
+Maintainer: Debian Med Maintainers <debian-med-maintainers at lists.alioth.debian.org>
+Uploaders: Olivier Sallou <osallou at debian.org>
+Build-Depends:
+ debhelper (>= 9), quilt, autotools-dev, dh-autoreconf, libtool,
+ graphviz, texlive-latex-extra, libg2-dev, help2man, perl-doc,
+ perl, dh-python
+Standards-Version: 3.9.6
+Homepage: http://www.tbi.univie.ac.at/RNA/index.html#download
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/vienna-rna/trunk/
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/vienna-rna/trunk/
XS-Autobuild: yes
+
Package: vienna-rna
+Section: science
Architecture: any
-Depends: ${shlibs:Depends}, ${perl:Depends}, ${misc:Depends}
-Recommends: readseq (>= 1-9)
+Depends: libviennarna, ${shlibs:Depends}, ${misc:Depends}
+Recommends: readseq
+Multi-Arch: same
Description: RNA sequence analysis
The Vienna RNA Package consists of a C code library and several
stand-alone programs for the prediction and comparison of RNA secondary
@@ -42,10 +46,50 @@
Vienna RNA package (http://www.tbi.univie.ac.at/~ivo/RNA/).
+Package: python-rna
+Section: python
+Architecture: any
+Depends: python, ${python-Depends}, libvienna-rna
+Multi-Arch: same
+Description: ViennaRNA python wrappers
+ Python wrappers above vienna-rna library.
+
+Package: librna-perl
+Section: perl
+Architecture: any
+Depends: perl, libviennarna, ${shlibs:Depends}, ${misc:Depends}, ${perl:Depends}
+Multi-Arch: same
+Description: ViennaRNA perl wrappers
+ Perl wrappers above vienna-rna library.
+
+
+Package: libviennarna
+Provides: libviennarna
+Section: libs
+Architecture: any
+Pre-Depends: ${misc:Pre-Depends}
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Suggests: viennarna-doc
+Multi-Arch: same
+Description: ViennaRNA Library -- library package
+ Shared library for ViennaRNA.
+
+Package: libviennarna-dev
+Provides: libviennarna-dev
+Section: libdevel
+Architecture: any
+Depends: libviennarna (= ${binary:Version}), ${misc:Depends}
+Suggests: viennarna-doc
+Multi-Arch: same
+Description: ViennaRNA Library -- development package
+ Development library with include headers for ViennaRNA.
+
+
Package: vienna-rna-doc
Section: doc
+Architecture: all
Depends: ${misc:Depends}
-Architecture: all
+Suggests: libviennarna (= ${binary:Version}), libviennarna-dev (= ${binary:Version})
Description: RNA sequence analysis documentation package
The Vienna RNA Package consists of a C code library and several
stand-alone programs for the prediction and comparison of RNA secondary
Modified: trunk/packages/vienna-rna/trunk/debian/copyright
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/copyright 2014-12-16 15:10:08 UTC (rev 18543)
+++ trunk/packages/vienna-rna/trunk/debian/copyright 2014-12-27 23:31:21 UTC (rev 18544)
@@ -1,4 +1,4 @@
-Format: <http://svn.debian.org/wsvn/dep/web/deps/dep5.mdwn?op=file&rev=REVISION>
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
UpstreamName: ViennaRNA
Source: http://www.tbi.univie.ac.at/~ivo/RNA/
@@ -70,6 +70,8 @@
Files: debian/*
Copyright: 2011, Alex Mestiashvili <alex at biotec.tu-dresden.de>
+ 2011, Andreas Tille <tille at debian.org>
+ 2014, Olivier Sallou <osallou at debian.org>
License: GPL-2+
This program is free software; you can redistribute it
and/or modify it under the terms of the GNU General Public
Added: trunk/packages/vienna-rna/trunk/debian/libviennarna-dev.install
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/libviennarna-dev.install (rev 0)
+++ trunk/packages/vienna-rna/trunk/debian/libviennarna-dev.install 2014-12-27 23:31:21 UTC (rev 18544)
@@ -0,0 +1,2 @@
+usr/lib/*/libviennarna.so
+usr/include/ViennaRNA
Added: trunk/packages/vienna-rna/trunk/debian/libviennarna.install
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/libviennarna.install (rev 0)
+++ trunk/packages/vienna-rna/trunk/debian/libviennarna.install 2014-12-27 23:31:21 UTC (rev 18544)
@@ -0,0 +1 @@
+usr/lib/*/libviennarna.so.*
Added: trunk/packages/vienna-rna/trunk/debian/patches/add_shared_library
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/add_shared_library (rev 0)
+++ trunk/packages/vienna-rna/trunk/debian/patches/add_shared_library 2014-12-27 23:31:21 UTC (rev 18544)
@@ -0,0 +1,1821 @@
+--- a/configure.ac
++++ b/configure.ac
+@@ -15,6 +15,9 @@
+ AM_SILENT_RULES([yes])
+ AM_INIT_AUTOMAKE([1.11])
+
++LT_INIT([dlopen])
++AC_ENABLE_SHARED
++
+ dnl create a config.h file (Automake will add -DHAVE_CONFIG_H)
+ AC_CONFIG_HEADERS([config.h])
+
+--- a/lib/Makefile.am
++++ b/lib/Makefile.am
+@@ -1,4 +1,4 @@
+-lib_LIBRARIES = libRNA.a
++lib_LTLIBRARIES = libviennarna.la
+
+
+ if WITH_LIBSVM
+@@ -8,7 +8,7 @@
+ SVM_UTILS = svm_utils.c
+ endif
+
+-libRNA_a_SOURCES = dist_vars.c fold_vars.c part_func.c read_epars.c\
++libviennarna_la_SOURCES = dist_vars.c fold_vars.c part_func.c read_epars.c\
+ treedist.c energy_par.c inverse.c ProfileDist.c \
+ RNAstruct.c utils.c fold.c naview.c PS_dot.c \
+ stringdist.c params.c subopt.c list.c Lfold.c \
+@@ -19,7 +19,9 @@
+ plot_layouts.c ali_plex.c c_plex.c plex.c snofold.c\
+ snoop.c move_set.c gquad.c ${SVM_SRC} ${SVM_UTILS}
+
+-libRNA_a_CFLAGS = $(AM_CFLAGS) $(OPENMP_CFLAGS) @FPIC@
++libviennarna_la_CFLAGS = $(AM_CFLAGS) $(OPENMP_CFLAGS) @FPIC@
++
++libviennarna_la_LDFLAGS = -shared $(AM_LDFLAGS) @FPIC@
+
+
+ noinst_HEADERS = intl11.h intl11dH.h intl21.h intl21dH.h \
+--- a/Progs/Makefile.am
++++ b/Progs/Makefile.am
+@@ -1,14 +1,14 @@
+
+
+-if WITH_LIBSVM
+- RNALfold_LINK = ${CXXLD} \
+- $(AM_CXXFLAGS) $(CXXFLAGS) \
+- $(AM_LDFLAGS) $(LDFLAGS) -o $@
+-else
+- RNALfold_LINK = ${CCLD} \
+- $(AM_CFLAGS) $(CFLAGS) \
+- $(AM_LDFLAGS) $(LDFLAGS) -o $@
+-endif
++#if WITH_LIBSVM
++# RNALfold_LINK = ${CXXLD} \
++# $(AM_CXXFLAGS) $(CXXFLAGS) \
++# $(AM_LDFLAGS) $(LDFLAGS) -o $@
++#else
++# RNALfold_LINK = ${CCLD} \
++# $(AM_CFLAGS) $(CFLAGS) \
++# $(AM_LDFLAGS) $(LDFLAGS) -o $@
++#endif
+
+
+ bin_PROGRAMS = RNAfold RNAeval RNAheat RNApdist RNAdistance RNAinverse \
+@@ -16,7 +16,29 @@
+ RNAalifold RNAplfold RNAup RNAaliduplex RNALalifold RNA2Dfold \
+ RNAparconv RNAPKplex RNAplex RNAsnoop
+
+-LDADD = $(OPENMP_CFLAGS) ../lib/libRNA.a -lm
++RNAfold_LDADD = ../lib/libviennarna.la
++RNAeval_LDADD = ../lib/libviennarna.la
++RNAheat_LDADD = ../lib/libviennarna.la
++RNApdist_LDADD = ../lib/libviennarna.la
++RNAdistance_LDADD = ../lib/libviennarna.la
++RNAinverse_LDADD = ../lib/libviennarna.la
++RNAplot_LDADD = ../lib/libviennarna.la
++RNAsubopt_LDADD = ../lib/libviennarna.la
++RNALfold_LDADD = ../lib/libviennarna.la
++RNAcofold_LDADD = ../lib/libviennarna.la
++RNApaln_LDADD = ../lib/libviennarna.la
++RNAduplex_LDADD = ../lib/libviennarna.la
++RNAalifold_LDADD = ../lib/libviennarna.la
++RNAplfold_LDADD = ../lib/libviennarna.la
++RNAup_LDADD = ../lib/libviennarna.la
++RNAaliduplex_LDADD = ../lib/libviennarna.la
++RNALalifold_LDADD = ../lib/libviennarna.la
++RNA2Dfold_LDADD = ../lib/libviennarna.la
++RNAparconv_LDADD = ../lib/libviennarna.la
++RNAPKplex_LDADD = ../lib/libviennarna.la
++RNAplex_LDADD = ../lib/libviennarna.la
++RNAsnoop_LDADD = ../lib/libviennarna.la
++#LDADD = $(OPENMP_CFLAGS) ../lib/libviennarna.la -lm
+
+ AM_CFLAGS = $(OPENMP_CFLAGS)
+
+--- a/Utils/Makefile.am
++++ b/Utils/Makefile.am
+@@ -12,7 +12,7 @@
+
+ EXTRA_DIST = $(pscript) Fold ${GENGETOPT_FILES} ${GENGETOPT_CMDL}
+
+-LDADD = -L../lib -lRNA -lm
++LDADD = -L../lib -lviennarna -lm
+
+ AM_CPPFLAGS = -I$(srcdir)/../H
+
+--- a/interfaces/Perl/Makefile.perl
++++ /dev/null
+@@ -1,1026 +0,0 @@
+-# This Makefile is for the RNA extension to perl.
+-#
+-# It was generated automatically by MakeMaker version
+-# 6.98 (Revision: 69800) from the contents of
+-# Makefile.PL. Don't edit this file, edit Makefile.PL instead.
+-#
+-# ANY CHANGES MADE HERE WILL BE LOST!
+-#
+-# MakeMaker ARGV: (q[PREFIX=/usr], q[INSTALL_BASE=])
+-#
+-
+-# MakeMaker Parameters:
+-
+-# AUTHOR => [q[Ivo Hofacker <ivo at tbi.univie.ac.at>]]
+-# BUILD_REQUIRES => { }
+-# CCFLAGS => q[-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 $(AM_CXXFLAGS) $(CXXFLAGS) -I../../H]
+-# CONFIGURE_REQUIRES => { }
+-# LD => q[${CXX}]
+-# LIBS => [q[-lm]]
+-# MAKEFILE => q[Makefile.perl]
+-# MYEXTLIB => q[../../lib/libRNA.a]
+-# NAME => q[RNA]
+-# OBJECT => q[RNA_wrap.o]
+-# OPTIMIZE => q[-O2 -g]
+-# PM => { RNA.pm=>q[$(INST_LIBDIR)/RNA.pm] }
+-# PREREQ_PM => { }
+-# TEST_REQUIRES => { }
+-# VERSION => q[2.1.8]
+-# dynamic_lib => { OTHERLDFLAGS=>q[$(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -fopenmp] }
+-
+-# --- MakeMaker post_initialize section:
+-
+-
+-# --- MakeMaker const_config section:
+-
+-# These definitions are from config.sh (via /usr/lib/x86_64-linux-gnu/perl/5.20/Config.pm).
+-# They may have been overridden via Makefile.PL or on the command line.
+-AR = ar
+-CC = cc
+-CCCDLFLAGS = -fPIC
+-CCDLFLAGS = -Wl,-E
+-DLEXT = so
+-DLSRC = dl_dlopen.xs
+-EXE_EXT =
+-FULL_AR = /usr/bin/ar
+-LD = ${CXX}
+-LDDLFLAGS = -shared -L/usr/local/lib -fstack-protector
+-LDFLAGS = -fstack-protector -L/usr/local/lib
+-LIBC = libc-2.19.so
+-LIB_EXT = .a
+-OBJ_EXT = .o
+-OSNAME = linux
+-OSVERS = 3.2.0-4-amd64
+-RANLIB = :
+-SITELIBEXP = /usr/local/share/perl/5.20.1
+-SITEARCHEXP = /usr/local/lib/x86_64-linux-gnu/perl/5.20.1
+-SO = so
+-VENDORARCHEXP = /usr/lib/x86_64-linux-gnu/perl5/5.20
+-VENDORLIBEXP = /usr/share/perl5
+-
+-
+-# --- MakeMaker constants section:
+-AR_STATIC_ARGS = cr
+-DIRFILESEP = /
+-DFSEP = $(DIRFILESEP)
+-NAME = RNA
+-NAME_SYM = RNA
+-VERSION = 2.1.8
+-VERSION_MACRO = VERSION
+-VERSION_SYM = 2_1_8
+-DEFINE_VERSION = -D$(VERSION_MACRO)=\"$(VERSION)\"
+-XS_VERSION = 2.1.8
+-XS_VERSION_MACRO = XS_VERSION
+-XS_DEFINE_VERSION = -D$(XS_VERSION_MACRO)=\"$(XS_VERSION)\"
+-INST_ARCHLIB = blib/arch
+-INST_SCRIPT = blib/script
+-INST_BIN = blib/bin
+-INST_LIB = blib/lib
+-INST_MAN1DIR = blib/man1
+-INST_MAN3DIR = blib/man3
+-MAN1EXT = 1p
+-MAN3EXT = 3pm
+-INSTALLDIRS = site
+-INSTALL_BASE =
+-DESTDIR =
+-PREFIX = /usr
+-PERLPREFIX = $(PREFIX)
+-SITEPREFIX = $(PREFIX)
+-VENDORPREFIX = $(PREFIX)
+-INSTALLPRIVLIB = $(PERLPREFIX)/share/perl/5.20
+-DESTINSTALLPRIVLIB = $(DESTDIR)$(INSTALLPRIVLIB)
+-INSTALLSITELIB = $(SITEPREFIX)/share/perl/5.20.1
+-DESTINSTALLSITELIB = $(DESTDIR)$(INSTALLSITELIB)
+-INSTALLVENDORLIB = $(VENDORPREFIX)/share/perl5
+-DESTINSTALLVENDORLIB = $(DESTDIR)$(INSTALLVENDORLIB)
+-INSTALLARCHLIB = $(PERLPREFIX)/lib/x86_64-linux-gnu/perl/5.20
+-DESTINSTALLARCHLIB = $(DESTDIR)$(INSTALLARCHLIB)
+-INSTALLSITEARCH = $(SITEPREFIX)/lib/x86_64-linux-gnu/perl/5.20.1
+-DESTINSTALLSITEARCH = $(DESTDIR)$(INSTALLSITEARCH)
+-INSTALLVENDORARCH = $(VENDORPREFIX)/lib/x86_64-linux-gnu/perl5/5.20
+-DESTINSTALLVENDORARCH = $(DESTDIR)$(INSTALLVENDORARCH)
+-INSTALLBIN = $(PERLPREFIX)/bin
+-DESTINSTALLBIN = $(DESTDIR)$(INSTALLBIN)
+-INSTALLSITEBIN = $(SITEPREFIX)/bin
+-DESTINSTALLSITEBIN = $(DESTDIR)$(INSTALLSITEBIN)
+-INSTALLVENDORBIN = $(VENDORPREFIX)/bin
+-DESTINSTALLVENDORBIN = $(DESTDIR)$(INSTALLVENDORBIN)
+-INSTALLSCRIPT = $(PERLPREFIX)/bin
+-DESTINSTALLSCRIPT = $(DESTDIR)$(INSTALLSCRIPT)
+-INSTALLSITESCRIPT = $(SITEPREFIX)/bin
+-DESTINSTALLSITESCRIPT = $(DESTDIR)$(INSTALLSITESCRIPT)
+-INSTALLVENDORSCRIPT = $(VENDORPREFIX)/bin
+-DESTINSTALLVENDORSCRIPT = $(DESTDIR)$(INSTALLVENDORSCRIPT)
+-INSTALLMAN1DIR = $(PERLPREFIX)/share/man/man1
+-DESTINSTALLMAN1DIR = $(DESTDIR)$(INSTALLMAN1DIR)
+-INSTALLSITEMAN1DIR = $(SITEPREFIX)/man/man1
+-DESTINSTALLSITEMAN1DIR = $(DESTDIR)$(INSTALLSITEMAN1DIR)
+-INSTALLVENDORMAN1DIR = $(VENDORPREFIX)/share/man/man1
+-DESTINSTALLVENDORMAN1DIR = $(DESTDIR)$(INSTALLVENDORMAN1DIR)
+-INSTALLMAN3DIR = $(PERLPREFIX)/share/man/man3
+-DESTINSTALLMAN3DIR = $(DESTDIR)$(INSTALLMAN3DIR)
+-INSTALLSITEMAN3DIR = $(SITEPREFIX)/man/man3
+-DESTINSTALLSITEMAN3DIR = $(DESTDIR)$(INSTALLSITEMAN3DIR)
+-INSTALLVENDORMAN3DIR = $(VENDORPREFIX)/share/man/man3
+-DESTINSTALLVENDORMAN3DIR = $(DESTDIR)$(INSTALLVENDORMAN3DIR)
+-PERL_LIB = /usr/share/perl/5.20
+-PERL_ARCHLIB = /usr/lib/x86_64-linux-gnu/perl/5.20
+-LIBPERL_A = libperl.a
+-MYEXTLIB = ../../lib/libRNA.a
+-FIRST_MAKEFILE = Makefile.perl
+-MAKEFILE_OLD = Makefile.perl.old
+-MAKE_APERL_FILE = Makefile.perl.aperl
+-PERLMAINCC = $(CC)
+-PERL_INC = /usr/lib/x86_64-linux-gnu/perl/5.20/CORE
+-PERL = /usr/bin/perl
+-FULLPERL = /usr/bin/perl
+-ABSPERL = $(PERL)
+-PERLRUN = $(PERL)
+-FULLPERLRUN = $(FULLPERL)
+-ABSPERLRUN = $(ABSPERL)
+-PERLRUNINST = $(PERLRUN) "-I$(INST_ARCHLIB)" "-I$(INST_LIB)"
+-FULLPERLRUNINST = $(FULLPERLRUN) "-I$(INST_ARCHLIB)" "-I$(INST_LIB)"
+-ABSPERLRUNINST = $(ABSPERLRUN) "-I$(INST_ARCHLIB)" "-I$(INST_LIB)"
+-PERL_CORE = 0
+-PERM_DIR = 755
+-PERM_RW = 644
+-PERM_RWX = 755
+-
+-MAKEMAKER = /usr/share/perl/5.20/ExtUtils/MakeMaker.pm
+-MM_VERSION = 6.98
+-MM_REVISION = 69800
+-
+-# FULLEXT = Pathname for extension directory (eg Foo/Bar/Oracle).
+-# BASEEXT = Basename part of FULLEXT. May be just equal FULLEXT. (eg Oracle)
+-# PARENT_NAME = NAME without BASEEXT and no trailing :: (eg Foo::Bar)
+-# DLBASE = Basename part of dynamic library. May be just equal BASEEXT.
+-MAKE = make
+-FULLEXT = RNA
+-BASEEXT = RNA
+-PARENT_NAME =
+-DLBASE = $(BASEEXT)
+-VERSION_FROM =
+-OBJECT = RNA_wrap$(OBJ_EXT)
+-LDFROM = $(OBJECT)
+-LINKTYPE = dynamic
+-BOOTDEP =
+-
+-# Handy lists of source code files:
+-XS_FILES =
+-C_FILES = RNA_wrap.c
+-O_FILES = RNA_wrap.o
+-H_FILES =
+-MAN1PODS =
+-MAN3PODS = RNA.pm
+-
+-# Where is the Config information that we are using/depend on
+-CONFIGDEP = $(PERL_ARCHLIB)$(DFSEP)Config.pm $(PERL_INC)$(DFSEP)config.h
+-
+-# Where to build things
+-INST_LIBDIR = $(INST_LIB)
+-INST_ARCHLIBDIR = $(INST_ARCHLIB)
+-
+-INST_AUTODIR = $(INST_LIB)/auto/$(FULLEXT)
+-INST_ARCHAUTODIR = $(INST_ARCHLIB)/auto/$(FULLEXT)
+-
+-INST_STATIC = $(INST_ARCHAUTODIR)/$(BASEEXT)$(LIB_EXT)
+-INST_DYNAMIC = $(INST_ARCHAUTODIR)/$(DLBASE).$(DLEXT)
+-INST_BOOT = $(INST_ARCHAUTODIR)/$(BASEEXT).bs
+-
+-# Extra linker info
+-EXPORT_LIST =
+-PERL_ARCHIVE =
+-PERL_ARCHIVE_AFTER =
+-
+-
+-TO_INST_PM = RNA.pm
+-
+-PM_TO_BLIB = RNA.pm \
+- $(INST_LIBDIR)/RNA.pm
+-
+-
+-# --- MakeMaker platform_constants section:
+-MM_Unix_VERSION = 6.98
+-PERL_MALLOC_DEF = -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc
+-
+-
+-# --- MakeMaker tool_autosplit section:
+-# Usage: $(AUTOSPLITFILE) FileToSplit AutoDirToSplitInto
+-AUTOSPLITFILE = $(ABSPERLRUN) -e 'use AutoSplit; autosplit($$$$ARGV[0], $$$$ARGV[1], 0, 1, 1)' --
+-
+-
+-
+-# --- MakeMaker tool_xsubpp section:
+-
+-XSUBPPDIR = /usr/share/perl/5.20/ExtUtils
+-XSUBPP = $(XSUBPPDIR)$(DFSEP)xsubpp
+-XSUBPPRUN = $(PERLRUN) $(XSUBPP)
+-XSPROTOARG =
+-XSUBPPDEPS = /usr/share/perl/5.20/ExtUtils/typemap $(XSUBPP)
+-XSUBPPARGS = -typemap /usr/share/perl/5.20/ExtUtils/typemap
+-XSUBPP_EXTRA_ARGS =
+-
+-
+-# --- MakeMaker tools_other section:
+-SHELL = /bin/sh
+-CHMOD = chmod
+-CP = cp
+-MV = mv
+-NOOP = $(TRUE)
+-NOECHO = @
+-RM_F = rm -f
+-RM_RF = rm -rf
+-TEST_F = test -f
+-TOUCH = touch
+-UMASK_NULL = umask 0
+-DEV_NULL = > /dev/null 2>&1
+-MKPATH = $(ABSPERLRUN) -MExtUtils::Command -e 'mkpath' --
+-EQUALIZE_TIMESTAMP = $(ABSPERLRUN) -MExtUtils::Command -e 'eqtime' --
+-FALSE = false
+-TRUE = true
+-ECHO = echo
+-ECHO_N = echo -n
+-UNINST = 0
+-VERBINST = 0
+-MOD_INSTALL = $(ABSPERLRUN) -MExtUtils::Install -e 'install([ from_to => {@ARGV}, verbose => '\''$(VERBINST)'\'', uninstall_shadows => '\''$(UNINST)'\'', dir_mode => '\''$(PERM_DIR)'\'' ]);' --
+-DOC_INSTALL = $(ABSPERLRUN) -MExtUtils::Command::MM -e 'perllocal_install' --
+-UNINSTALL = $(ABSPERLRUN) -MExtUtils::Command::MM -e 'uninstall' --
+-WARN_IF_OLD_PACKLIST = $(ABSPERLRUN) -MExtUtils::Command::MM -e 'warn_if_old_packlist' --
+-MACROSTART =
+-MACROEND =
+-USEMAKEFILE = -f
+-FIXIN = $(ABSPERLRUN) -MExtUtils::MY -e 'MY->fixin(shift)' --
+-CP_NONEMPTY = $(ABSPERLRUN) -MExtUtils::Command::MM -e 'cp_nonempty' --
+-
+-
+-# --- MakeMaker makemakerdflt section:
+-makemakerdflt : all
+- $(NOECHO) $(NOOP)
+-
+-
+-# --- MakeMaker dist section:
+-TAR = tar
+-TARFLAGS = cvf
+-ZIP = zip
+-ZIPFLAGS = -r
+-COMPRESS = gzip --best
+-SUFFIX = .gz
+-SHAR = shar
+-PREOP = $(NOECHO) $(NOOP)
+-POSTOP = $(NOECHO) $(NOOP)
+-TO_UNIX = $(NOECHO) $(NOOP)
+-CI = ci -u
+-RCS_LABEL = rcs -Nv$(VERSION_SYM): -q
+-DIST_CP = best
+-DIST_DEFAULT = tardist
+-DISTNAME = RNA
+-DISTVNAME = RNA-2.1.8
+-
+-
+-# --- MakeMaker macro section:
+-
+-
+-# --- MakeMaker depend section:
+-
+-
+-# --- MakeMaker cflags section:
+-
+-CCFLAGS = -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 $(AM_CXXFLAGS) $(CXXFLAGS) -I../../H
+-OPTIMIZE = -O2 -g
+-PERLTYPE =
+-MPOLLUTE =
+-
+-
+-# --- MakeMaker const_loadlibs section:
+-
+-# RNA might depend on some other libraries:
+-# See ExtUtils::Liblist for details
+-#
+-EXTRALIBS =
+-LDLOADLIBS = -lm
+-BSLOADLIBS =
+-
+-
+-# --- MakeMaker const_cccmd section:
+-CCCMD = $(CC) -c $(PASTHRU_INC) $(INC) \
+- $(CCFLAGS) $(OPTIMIZE) \
+- $(PERLTYPE) $(MPOLLUTE) $(DEFINE_VERSION) \
+- $(XS_DEFINE_VERSION)
+-
+-# --- MakeMaker post_constants section:
+-
+-
+-# --- MakeMaker pasthru section:
+-
+-PASTHRU = LIBPERL_A="$(LIBPERL_A)"\
+- LINKTYPE="$(LINKTYPE)"\
+- OPTIMIZE="$(OPTIMIZE)"\
+- LD="$(LD)"\
+- PREFIX="$(PREFIX)"\
+- INSTALL_BASE="$(INSTALL_BASE)"
+-
+-
+-# --- MakeMaker special_targets section:
+-.SUFFIXES : .xs .c .C .cpp .i .s .cxx .cc $(OBJ_EXT)
+-
+-.PHONY: all config static dynamic test linkext manifest blibdirs clean realclean disttest distdir
+-
+-
+-
+-# --- MakeMaker c_o section:
+-
+-.c.i:
+- cc -E -c $(PASTHRU_INC) $(INC) \
+- $(CCFLAGS) $(OPTIMIZE) \
+- $(PERLTYPE) $(MPOLLUTE) $(DEFINE_VERSION) \
+- $(XS_DEFINE_VERSION) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.c > $*.i
+-
+-.c.s:
+- $(CCCMD) -S $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.c
+-
+-.c$(OBJ_EXT):
+- $(CCCMD) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.c
+-
+-.cpp$(OBJ_EXT):
+- $(CCCMD) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.cpp
+-
+-.cxx$(OBJ_EXT):
+- $(CCCMD) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.cxx
+-
+-.cc$(OBJ_EXT):
+- $(CCCMD) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.cc
+-
+-.C$(OBJ_EXT):
+- $(CCCMD) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.C
+-
+-
+-# --- MakeMaker xs_c section:
+-
+-.xs.c:
+- $(XSUBPPRUN) $(XSPROTOARG) $(XSUBPPARGS) $(XSUBPP_EXTRA_ARGS) $*.xs > $*.xsc && $(MV) $*.xsc $*.c
+-
+-
+-# --- MakeMaker xs_o section:
+-
+-.xs$(OBJ_EXT):
+- $(XSUBPPRUN) $(XSPROTOARG) $(XSUBPPARGS) $*.xs > $*.xsc && $(MV) $*.xsc $*.c
+- $(CCCMD) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.c
+-
+-
+-# --- MakeMaker top_targets section:
+-all :: pure_all manifypods
+- $(NOECHO) $(NOOP)
+-
+-
+-pure_all :: config pm_to_blib subdirs linkext
+- $(NOECHO) $(NOOP)
+-
+-subdirs :: $(MYEXTLIB)
+- $(NOECHO) $(NOOP)
+-
+-config :: $(FIRST_MAKEFILE) blibdirs
+- $(NOECHO) $(NOOP)
+-
+-help :
+- perldoc ExtUtils::MakeMaker
+-
+-
+-# --- MakeMaker blibdirs section:
+-blibdirs : $(INST_LIBDIR)$(DFSEP).exists $(INST_ARCHLIB)$(DFSEP).exists $(INST_AUTODIR)$(DFSEP).exists $(INST_ARCHAUTODIR)$(DFSEP).exists $(INST_BIN)$(DFSEP).exists $(INST_SCRIPT)$(DFSEP).exists $(INST_MAN1DIR)$(DFSEP).exists $(INST_MAN3DIR)$(DFSEP).exists
+- $(NOECHO) $(NOOP)
+-
+-# Backwards compat with 6.18 through 6.25
+-blibdirs.ts : blibdirs
+- $(NOECHO) $(NOOP)
+-
+-$(INST_LIBDIR)$(DFSEP).exists :: Makefile.PL
+- $(NOECHO) $(MKPATH) $(INST_LIBDIR)
+- $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_LIBDIR)
+- $(NOECHO) $(TOUCH) $(INST_LIBDIR)$(DFSEP).exists
+-
+-$(INST_ARCHLIB)$(DFSEP).exists :: Makefile.PL
+- $(NOECHO) $(MKPATH) $(INST_ARCHLIB)
+- $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_ARCHLIB)
+- $(NOECHO) $(TOUCH) $(INST_ARCHLIB)$(DFSEP).exists
+-
+-$(INST_AUTODIR)$(DFSEP).exists :: Makefile.PL
+- $(NOECHO) $(MKPATH) $(INST_AUTODIR)
+- $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_AUTODIR)
+- $(NOECHO) $(TOUCH) $(INST_AUTODIR)$(DFSEP).exists
+-
+-$(INST_ARCHAUTODIR)$(DFSEP).exists :: Makefile.PL
+- $(NOECHO) $(MKPATH) $(INST_ARCHAUTODIR)
+- $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_ARCHAUTODIR)
+- $(NOECHO) $(TOUCH) $(INST_ARCHAUTODIR)$(DFSEP).exists
+-
+-$(INST_BIN)$(DFSEP).exists :: Makefile.PL
+- $(NOECHO) $(MKPATH) $(INST_BIN)
+- $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_BIN)
+- $(NOECHO) $(TOUCH) $(INST_BIN)$(DFSEP).exists
+-
+-$(INST_SCRIPT)$(DFSEP).exists :: Makefile.PL
+- $(NOECHO) $(MKPATH) $(INST_SCRIPT)
+- $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_SCRIPT)
+- $(NOECHO) $(TOUCH) $(INST_SCRIPT)$(DFSEP).exists
+-
+-$(INST_MAN1DIR)$(DFSEP).exists :: Makefile.PL
+- $(NOECHO) $(MKPATH) $(INST_MAN1DIR)
+- $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_MAN1DIR)
+- $(NOECHO) $(TOUCH) $(INST_MAN1DIR)$(DFSEP).exists
+-
+-$(INST_MAN3DIR)$(DFSEP).exists :: Makefile.PL
+- $(NOECHO) $(MKPATH) $(INST_MAN3DIR)
+- $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_MAN3DIR)
+- $(NOECHO) $(TOUCH) $(INST_MAN3DIR)$(DFSEP).exists
+-
+-
+-
+-# --- MakeMaker linkext section:
+-
+-linkext :: $(LINKTYPE)
+- $(NOECHO) $(NOOP)
+-
+-
+-# --- MakeMaker dlsyms section:
+-
+-
+-# --- MakeMaker dynamic_bs section:
+-BOOTSTRAP = $(BASEEXT).bs
+-
+-# As Mkbootstrap might not write a file (if none is required)
+-# we use touch to prevent make continually trying to remake it.
+-# The DynaLoader only reads a non-empty file.
+-$(BOOTSTRAP) : $(FIRST_MAKEFILE) $(BOOTDEP) $(INST_ARCHAUTODIR)$(DFSEP).exists
+- $(NOECHO) $(ECHO) "Running Mkbootstrap for $(NAME) ($(BSLOADLIBS))"
+- $(NOECHO) $(PERLRUN) \
+- "-MExtUtils::Mkbootstrap" \
+- -e "Mkbootstrap('$(BASEEXT)','$(BSLOADLIBS)');"
+- $(NOECHO) $(TOUCH) $@
+- $(CHMOD) $(PERM_RW) $@
+-
+-
+-# --- MakeMaker dynamic section:
+-
+-dynamic :: $(FIRST_MAKEFILE) $(BOOTSTRAP) $(INST_DYNAMIC)
+- $(NOECHO) $(NOOP)
+-
+-
+-# --- MakeMaker dynamic_lib section:
+-
+-# This section creates the dynamically loadable $(INST_DYNAMIC)
+-# from $(OBJECT) and possibly $(MYEXTLIB).
+-ARMAYBE = :
+-OTHERLDFLAGS = $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -fopenmp
+-INST_DYNAMIC_DEP =
+-INST_DYNAMIC_FIX =
+-
+-$(INST_DYNAMIC): $(OBJECT) $(MYEXTLIB) $(INST_ARCHAUTODIR)$(DFSEP).exists $(EXPORT_LIST) $(PERL_ARCHIVE) $(PERL_ARCHIVE_AFTER) $(INST_DYNAMIC_DEP)
+- $(RM_F) $@
+- $(LD) $(LDDLFLAGS) $(LDFROM) $(OTHERLDFLAGS) -o $@ $(MYEXTLIB) \
+- $(PERL_ARCHIVE) $(LDLOADLIBS) $(PERL_ARCHIVE_AFTER) $(EXPORT_LIST) \
+- $(INST_DYNAMIC_FIX)
+- $(CHMOD) $(PERM_RWX) $@
+- $(NOECHO) $(RM_RF) $(BOOTSTRAP)
+- - $(CP_NONEMPTY) $(BOOTSTRAP) $(INST_BOOT) $(PERM_RW)
+-
+-
+-# --- MakeMaker static section:
+-
+-## $(INST_PM) has been moved to the all: target.
+-## It remains here for awhile to allow for old usage: "make static"
+-static :: $(FIRST_MAKEFILE) $(INST_STATIC)
+- $(NOECHO) $(NOOP)
+-
+-
+-# --- MakeMaker static_lib section:
+-
+-$(INST_STATIC) : $(OBJECT) $(MYEXTLIB) $(INST_ARCHAUTODIR)$(DFSEP).exists
+- $(RM_RF) $@
+- $(CP) $(MYEXTLIB) $@
+- $(FULL_AR) $(AR_STATIC_ARGS) $@ $(OBJECT) && $(RANLIB) $@
+- $(CHMOD) $(PERM_RWX) $@
+- $(NOECHO) $(ECHO) "$(EXTRALIBS)" > $(INST_ARCHAUTODIR)/extralibs.ld
+-
+-
+-# --- MakeMaker manifypods section:
+-
+-POD2MAN_EXE = $(PERLRUN) "-MExtUtils::Command::MM" -e pod2man "--"
+-POD2MAN = $(POD2MAN_EXE)
+-
+-
+-manifypods : pure_all \
+- RNA.pm
+- $(NOECHO) $(POD2MAN) --section=$(MAN3EXT) --perm_rw=$(PERM_RW) \
+- RNA.pm $(INST_MAN3DIR)/RNA.$(MAN3EXT)
+-
+-
+-
+-
+-# --- MakeMaker processPL section:
+-
+-
+-# --- MakeMaker installbin section:
+-
+-
+-# --- MakeMaker subdirs section:
+-
+-# none
+-
+-# --- MakeMaker clean_subdirs section:
+-clean_subdirs :
+- $(NOECHO) $(NOOP)
+-
+-
+-# --- MakeMaker clean section:
+-
+-# Delete temporary files but do not touch installed files. We don't delete
+-# the Makefile here so a later make realclean still has a makefile to use.
+-
+-clean :: clean_subdirs
+- - $(RM_F) \
+- $(BASEEXT).bso $(BASEEXT).def \
+- $(BASEEXT).exp $(BASEEXT).x \
+- $(BOOTSTRAP) $(INST_ARCHAUTODIR)/extralibs.all \
+- $(INST_ARCHAUTODIR)/extralibs.ld $(MAKE_APERL_FILE) \
+- *$(LIB_EXT) *$(OBJ_EXT) \
+- *perl.core MYMETA.json \
+- MYMETA.yml blibdirs.ts \
+- core core.*perl.*.? \
+- core.[0-9] core.[0-9][0-9] \
+- core.[0-9][0-9][0-9] core.[0-9][0-9][0-9][0-9] \
+- core.[0-9][0-9][0-9][0-9][0-9] lib$(BASEEXT).def \
+- mon.out perl \
+- perl$(EXE_EXT) perl.exe \
+- perlmain.c pm_to_blib \
+- pm_to_blib.ts so_locations \
+- tmon.out
+- - $(RM_RF) \
+- blib
+- $(NOECHO) $(RM_F) $(MAKEFILE_OLD)
+- - $(MV) $(FIRST_MAKEFILE) $(MAKEFILE_OLD) $(DEV_NULL)
+-
+-
+-# --- MakeMaker realclean_subdirs section:
+-realclean_subdirs :
+- $(NOECHO) $(NOOP)
+-
+-
+-# --- MakeMaker realclean section:
+-# Delete temporary files (via clean) and also delete dist files
+-realclean purge :: clean realclean_subdirs
+- - $(RM_F) \
+- $(MAKEFILE_OLD) $(FIRST_MAKEFILE) \
+- $(OBJECT)
+- - $(RM_RF) \
+- $(DISTVNAME)
+-
+-
+-# --- MakeMaker metafile section:
+-metafile : create_distdir
+- $(NOECHO) $(ECHO) Generating META.yml
+- $(NOECHO) $(ECHO) '---' > META_new.yml
+- $(NOECHO) $(ECHO) 'abstract: unknown' >> META_new.yml
+- $(NOECHO) $(ECHO) 'author:' >> META_new.yml
+- $(NOECHO) $(ECHO) ' - '\''Ivo Hofacker <ivo at tbi.univie.ac.at>'\''' >> META_new.yml
+- $(NOECHO) $(ECHO) 'build_requires:' >> META_new.yml
+- $(NOECHO) $(ECHO) ' ExtUtils::MakeMaker: '\''0'\''' >> META_new.yml
+- $(NOECHO) $(ECHO) 'configure_requires:' >> META_new.yml
+- $(NOECHO) $(ECHO) ' ExtUtils::MakeMaker: '\''0'\''' >> META_new.yml
+- $(NOECHO) $(ECHO) 'dynamic_config: 1' >> META_new.yml
+- $(NOECHO) $(ECHO) 'generated_by: '\''ExtUtils::MakeMaker version 6.98, CPAN::Meta::Converter version 2.140640'\''' >> META_new.yml
+- $(NOECHO) $(ECHO) 'license: unknown' >> META_new.yml
+- $(NOECHO) $(ECHO) 'meta-spec:' >> META_new.yml
+- $(NOECHO) $(ECHO) ' url: http://module-build.sourceforge.net/META-spec-v1.4.html' >> META_new.yml
+- $(NOECHO) $(ECHO) ' version: '\''1.4'\''' >> META_new.yml
+- $(NOECHO) $(ECHO) 'name: RNA' >> META_new.yml
+- $(NOECHO) $(ECHO) 'no_index:' >> META_new.yml
+- $(NOECHO) $(ECHO) ' directory:' >> META_new.yml
+- $(NOECHO) $(ECHO) ' - t' >> META_new.yml
+- $(NOECHO) $(ECHO) ' - inc' >> META_new.yml
+- $(NOECHO) $(ECHO) 'requires: {}' >> META_new.yml
+- $(NOECHO) $(ECHO) 'version: v2.1.8' >> META_new.yml
+- -$(NOECHO) $(MV) META_new.yml $(DISTVNAME)/META.yml
+- $(NOECHO) $(ECHO) Generating META.json
+- $(NOECHO) $(ECHO) '{' > META_new.json
+- $(NOECHO) $(ECHO) ' "abstract" : "unknown",' >> META_new.json
+- $(NOECHO) $(ECHO) ' "author" : [' >> META_new.json
+- $(NOECHO) $(ECHO) ' "Ivo Hofacker <ivo at tbi.univie.ac.at>"' >> META_new.json
+- $(NOECHO) $(ECHO) ' ],' >> META_new.json
+- $(NOECHO) $(ECHO) ' "dynamic_config" : 1,' >> META_new.json
+- $(NOECHO) $(ECHO) ' "generated_by" : "ExtUtils::MakeMaker version 6.98, CPAN::Meta::Converter version 2.140640",' >> META_new.json
+- $(NOECHO) $(ECHO) ' "license" : [' >> META_new.json
+- $(NOECHO) $(ECHO) ' "unknown"' >> META_new.json
+- $(NOECHO) $(ECHO) ' ],' >> META_new.json
+- $(NOECHO) $(ECHO) ' "meta-spec" : {' >> META_new.json
+- $(NOECHO) $(ECHO) ' "url" : "http://search.cpan.org/perldoc?CPAN::Meta::Spec",' >> META_new.json
+- $(NOECHO) $(ECHO) ' "version" : "2"' >> META_new.json
+- $(NOECHO) $(ECHO) ' },' >> META_new.json
+- $(NOECHO) $(ECHO) ' "name" : "RNA",' >> META_new.json
+- $(NOECHO) $(ECHO) ' "no_index" : {' >> META_new.json
+- $(NOECHO) $(ECHO) ' "directory" : [' >> META_new.json
+- $(NOECHO) $(ECHO) ' "t",' >> META_new.json
+- $(NOECHO) $(ECHO) ' "inc"' >> META_new.json
+- $(NOECHO) $(ECHO) ' ]' >> META_new.json
+- $(NOECHO) $(ECHO) ' },' >> META_new.json
+- $(NOECHO) $(ECHO) ' "prereqs" : {' >> META_new.json
+- $(NOECHO) $(ECHO) ' "build" : {' >> META_new.json
+- $(NOECHO) $(ECHO) ' "requires" : {' >> META_new.json
+- $(NOECHO) $(ECHO) ' "ExtUtils::MakeMaker" : "0"' >> META_new.json
+- $(NOECHO) $(ECHO) ' }' >> META_new.json
+- $(NOECHO) $(ECHO) ' },' >> META_new.json
+- $(NOECHO) $(ECHO) ' "configure" : {' >> META_new.json
+- $(NOECHO) $(ECHO) ' "requires" : {' >> META_new.json
+- $(NOECHO) $(ECHO) ' "ExtUtils::MakeMaker" : "0"' >> META_new.json
+- $(NOECHO) $(ECHO) ' }' >> META_new.json
+- $(NOECHO) $(ECHO) ' },' >> META_new.json
+- $(NOECHO) $(ECHO) ' "runtime" : {' >> META_new.json
+- $(NOECHO) $(ECHO) ' "requires" : {}' >> META_new.json
+- $(NOECHO) $(ECHO) ' }' >> META_new.json
+- $(NOECHO) $(ECHO) ' },' >> META_new.json
+- $(NOECHO) $(ECHO) ' "release_status" : "stable",' >> META_new.json
+- $(NOECHO) $(ECHO) ' "version" : "v2.1.8"' >> META_new.json
+- $(NOECHO) $(ECHO) '}' >> META_new.json
+- -$(NOECHO) $(MV) META_new.json $(DISTVNAME)/META.json
+-
+-
+-# --- MakeMaker signature section:
+-signature :
+- cpansign -s
+-
+-
+-# --- MakeMaker dist_basics section:
+-distclean :: realclean distcheck
+- $(NOECHO) $(NOOP)
+-
+-distcheck :
+- $(PERLRUN) "-MExtUtils::Manifest=fullcheck" -e fullcheck
+-
+-skipcheck :
+- $(PERLRUN) "-MExtUtils::Manifest=skipcheck" -e skipcheck
+-
+-manifest :
+- $(PERLRUN) "-MExtUtils::Manifest=mkmanifest" -e mkmanifest
+-
+-veryclean : realclean
+- $(RM_F) *~ */*~ *.orig */*.orig *.bak */*.bak *.old */*.old
+-
+-
+-
+-# --- MakeMaker dist_core section:
+-
+-dist : $(DIST_DEFAULT) $(FIRST_MAKEFILE)
+- $(NOECHO) $(ABSPERLRUN) -l -e 'print '\''Warning: Makefile possibly out of date with $(VERSION_FROM)'\''' \
+- -e ' if -e '\''$(VERSION_FROM)'\'' and -M '\''$(VERSION_FROM)'\'' < -M '\''$(FIRST_MAKEFILE)'\'';' --
+-
+-tardist : $(DISTVNAME).tar$(SUFFIX)
+- $(NOECHO) $(NOOP)
+-
+-uutardist : $(DISTVNAME).tar$(SUFFIX)
+- uuencode $(DISTVNAME).tar$(SUFFIX) $(DISTVNAME).tar$(SUFFIX) > $(DISTVNAME).tar$(SUFFIX)_uu
+- $(NOECHO) $(ECHO) 'Created $(DISTVNAME).tar$(SUFFIX)_uu'
+-
+-$(DISTVNAME).tar$(SUFFIX) : distdir
+- $(PREOP)
+- $(TO_UNIX)
+- $(TAR) $(TARFLAGS) $(DISTVNAME).tar $(DISTVNAME)
+- $(RM_RF) $(DISTVNAME)
+- $(COMPRESS) $(DISTVNAME).tar
+- $(NOECHO) $(ECHO) 'Created $(DISTVNAME).tar$(SUFFIX)'
+- $(POSTOP)
+-
+-zipdist : $(DISTVNAME).zip
+- $(NOECHO) $(NOOP)
+-
+-$(DISTVNAME).zip : distdir
+- $(PREOP)
+- $(ZIP) $(ZIPFLAGS) $(DISTVNAME).zip $(DISTVNAME)
+- $(RM_RF) $(DISTVNAME)
+- $(NOECHO) $(ECHO) 'Created $(DISTVNAME).zip'
+- $(POSTOP)
+-
+-shdist : distdir
+- $(PREOP)
+- $(SHAR) $(DISTVNAME) > $(DISTVNAME).shar
+- $(RM_RF) $(DISTVNAME)
+- $(NOECHO) $(ECHO) 'Created $(DISTVNAME).shar'
+- $(POSTOP)
+-
+-
+-# --- MakeMaker distdir section:
+-create_distdir :
+- $(RM_RF) $(DISTVNAME)
+- $(PERLRUN) "-MExtUtils::Manifest=manicopy,maniread" \
+- -e "manicopy(maniread(),'$(DISTVNAME)', '$(DIST_CP)');"
+-
+-distdir : create_distdir distmeta
+- $(NOECHO) $(NOOP)
+-
+-
+-
+-# --- MakeMaker dist_test section:
+-disttest : distdir
+- cd $(DISTVNAME) && $(ABSPERLRUN) Makefile.PL "PREFIX=/usr" "INSTALL_BASE="
+- cd $(DISTVNAME) && $(MAKE) $(PASTHRU)
+- cd $(DISTVNAME) && $(MAKE) test $(PASTHRU)
+-
+-
+-
+-# --- MakeMaker dist_ci section:
+-
+-ci :
+- $(PERLRUN) "-MExtUtils::Manifest=maniread" \
+- -e "@all = keys %{ maniread() };" \
+- -e "print(qq{Executing $(CI) @all\n}); system(qq{$(CI) @all});" \
+- -e "print(qq{Executing $(RCS_LABEL) ...\n}); system(qq{$(RCS_LABEL) @all});"
+-
+-
+-# --- MakeMaker distmeta section:
+-distmeta : create_distdir metafile
+- $(NOECHO) cd $(DISTVNAME) && $(ABSPERLRUN) -MExtUtils::Manifest=maniadd -e 'exit unless -e q{META.yml};' \
+- -e 'eval { maniadd({q{META.yml} => q{Module YAML meta-data (added by MakeMaker)}}) }' \
+- -e ' or print "Could not add META.yml to MANIFEST: $$$${'\''@'\''}\n"' --
+- $(NOECHO) cd $(DISTVNAME) && $(ABSPERLRUN) -MExtUtils::Manifest=maniadd -e 'exit unless -f q{META.json};' \
+- -e 'eval { maniadd({q{META.json} => q{Module JSON meta-data (added by MakeMaker)}}) }' \
+- -e ' or print "Could not add META.json to MANIFEST: $$$${'\''@'\''}\n"' --
+-
+-
+-
+-# --- MakeMaker distsignature section:
+-distsignature : create_distdir
+- $(NOECHO) cd $(DISTVNAME) && $(ABSPERLRUN) -MExtUtils::Manifest=maniadd -e 'eval { maniadd({q{SIGNATURE} => q{Public-key signature (added by MakeMaker)}}) }' \
+- -e ' or print "Could not add SIGNATURE to MANIFEST: $$$${'\''@'\''}\n"' --
+- $(NOECHO) cd $(DISTVNAME) && $(TOUCH) SIGNATURE
+- cd $(DISTVNAME) && cpansign -s
+-
+-
+-
+-# --- MakeMaker install section:
+-
+-install :: pure_install doc_install
+- $(NOECHO) $(NOOP)
+-
+-install_perl :: pure_perl_install doc_perl_install
+- $(NOECHO) $(NOOP)
+-
+-install_site :: pure_site_install doc_site_install
+- $(NOECHO) $(NOOP)
+-
+-install_vendor :: pure_vendor_install doc_vendor_install
+- $(NOECHO) $(NOOP)
+-
+-pure_install :: pure_$(INSTALLDIRS)_install
+- $(NOECHO) $(NOOP)
+-
+-doc_install :: doc_$(INSTALLDIRS)_install
+- $(NOECHO) $(NOOP)
+-
+-pure__install : pure_site_install
+- $(NOECHO) $(ECHO) INSTALLDIRS not defined, defaulting to INSTALLDIRS=site
+-
+-doc__install : doc_site_install
+- $(NOECHO) $(ECHO) INSTALLDIRS not defined, defaulting to INSTALLDIRS=site
+-
+-pure_perl_install :: all
+- $(NOECHO) umask 022; $(MOD_INSTALL) \
+- $(INST_LIB) $(DESTINSTALLPRIVLIB) \
+- $(INST_ARCHLIB) $(DESTINSTALLARCHLIB) \
+- $(INST_BIN) $(DESTINSTALLBIN) \
+- $(INST_SCRIPT) $(DESTINSTALLSCRIPT) \
+- $(INST_MAN1DIR) $(DESTINSTALLMAN1DIR) \
+- $(INST_MAN3DIR) $(DESTINSTALLMAN3DIR)
+- $(NOECHO) $(WARN_IF_OLD_PACKLIST) \
+- $(SITEARCHEXP)/auto/$(FULLEXT)
+-
+-
+-pure_site_install :: all
+- $(NOECHO) umask 02; $(MOD_INSTALL) \
+- read $(SITEARCHEXP)/auto/$(FULLEXT)/.packlist \
+- write $(DESTINSTALLSITEARCH)/auto/$(FULLEXT)/.packlist \
+- $(INST_LIB) $(DESTINSTALLSITELIB) \
+- $(INST_ARCHLIB) $(DESTINSTALLSITEARCH) \
+- $(INST_BIN) $(DESTINSTALLSITEBIN) \
+- $(INST_SCRIPT) $(DESTINSTALLSITESCRIPT) \
+- $(INST_MAN1DIR) $(DESTINSTALLSITEMAN1DIR) \
+- $(INST_MAN3DIR) $(DESTINSTALLSITEMAN3DIR)
+- $(NOECHO) $(WARN_IF_OLD_PACKLIST) \
+- $(PERL_ARCHLIB)/auto/$(FULLEXT)
+-
+-pure_vendor_install :: all
+- $(NOECHO) umask 022; $(MOD_INSTALL) \
+- $(INST_LIB) $(DESTINSTALLVENDORLIB) \
+- $(INST_ARCHLIB) $(DESTINSTALLVENDORARCH) \
+- $(INST_BIN) $(DESTINSTALLVENDORBIN) \
+- $(INST_SCRIPT) $(DESTINSTALLVENDORSCRIPT) \
+- $(INST_MAN1DIR) $(DESTINSTALLVENDORMAN1DIR) \
+- $(INST_MAN3DIR) $(DESTINSTALLVENDORMAN3DIR)
+-
+-
+-doc_perl_install :: all
+-
+-doc_site_install :: all
+- $(NOECHO) $(ECHO) Appending installation info to $(DESTINSTALLSITEARCH)/perllocal.pod
+- -$(NOECHO) umask 02; $(MKPATH) $(DESTINSTALLSITEARCH)
+- -$(NOECHO) umask 02; $(DOC_INSTALL) \
+- "Module" "$(NAME)" \
+- "installed into" "$(INSTALLSITELIB)" \
+- LINKTYPE "$(LINKTYPE)" \
+- VERSION "$(VERSION)" \
+- EXE_FILES "$(EXE_FILES)" \
+- >> $(DESTINSTALLSITEARCH)/perllocal.pod
+-
+-doc_vendor_install :: all
+-
+-
+-uninstall :: uninstall_from_$(INSTALLDIRS)dirs
+- $(NOECHO) $(NOOP)
+-
+-uninstall_from_perldirs ::
+-
+-uninstall_from_sitedirs ::
+- $(NOECHO) $(UNINSTALL) $(SITEARCHEXP)/auto/$(FULLEXT)/.packlist
+-
+-uninstall_from_vendordirs ::
+-
+-
+-
+-# --- MakeMaker force section:
+-# Phony target to force checking subdirectories.
+-FORCE :
+- $(NOECHO) $(NOOP)
+-
+-
+-# --- MakeMaker perldepend section:
+-PERL_HDRS = \
+- $(PERL_INC)/EXTERN.h \
+- $(PERL_INC)/INTERN.h \
+- $(PERL_INC)/XSUB.h \
+- $(PERL_INC)/av.h \
+- $(PERL_INC)/bitcount.h \
+- $(PERL_INC)/charclass_invlists.h \
+- $(PERL_INC)/config.h \
+- $(PERL_INC)/cop.h \
+- $(PERL_INC)/cv.h \
+- $(PERL_INC)/dosish.h \
+- $(PERL_INC)/embed.h \
+- $(PERL_INC)/embedvar.h \
+- $(PERL_INC)/fakesdio.h \
+- $(PERL_INC)/feature.h \
+- $(PERL_INC)/form.h \
+- $(PERL_INC)/git_version.h \
+- $(PERL_INC)/gv.h \
+- $(PERL_INC)/handy.h \
+- $(PERL_INC)/hv.h \
+- $(PERL_INC)/hv_func.h \
+- $(PERL_INC)/inline.h \
+- $(PERL_INC)/intrpvar.h \
+- $(PERL_INC)/iperlsys.h \
+- $(PERL_INC)/keywords.h \
+- $(PERL_INC)/l1_char_class_tab.h \
+- $(PERL_INC)/malloc_ctl.h \
+- $(PERL_INC)/metaconfig.h \
+- $(PERL_INC)/mg.h \
+- $(PERL_INC)/mg_data.h \
+- $(PERL_INC)/mg_raw.h \
+- $(PERL_INC)/mg_vtable.h \
+- $(PERL_INC)/mydtrace.h \
+- $(PERL_INC)/nostdio.h \
+- $(PERL_INC)/op.h \
+- $(PERL_INC)/op_reg_common.h \
+- $(PERL_INC)/opcode.h \
+- $(PERL_INC)/opnames.h \
+- $(PERL_INC)/overload.h \
+- $(PERL_INC)/pad.h \
+- $(PERL_INC)/parser.h \
+- $(PERL_INC)/patchlevel-debian.h \
+- $(PERL_INC)/patchlevel.h \
+- $(PERL_INC)/perl.h \
+- $(PERL_INC)/perlapi.h \
+- $(PERL_INC)/perlio.h \
+- $(PERL_INC)/perliol.h \
+- $(PERL_INC)/perlsdio.h \
+- $(PERL_INC)/perlvars.h \
+- $(PERL_INC)/perly.h \
+- $(PERL_INC)/pp.h \
+- $(PERL_INC)/pp_proto.h \
+- $(PERL_INC)/proto.h \
+- $(PERL_INC)/reentr.h \
+- $(PERL_INC)/regcharclass.h \
+- $(PERL_INC)/regcomp.h \
+- $(PERL_INC)/regexp.h \
+- $(PERL_INC)/regnodes.h \
+- $(PERL_INC)/scope.h \
+- $(PERL_INC)/sv.h \
+- $(PERL_INC)/thread.h \
+- $(PERL_INC)/time64.h \
+- $(PERL_INC)/time64_config.h \
+- $(PERL_INC)/uconfig.h \
+- $(PERL_INC)/unicode_constants.h \
+- $(PERL_INC)/unixish.h \
+- $(PERL_INC)/utf8.h \
+- $(PERL_INC)/utfebcdic.h \
+- $(PERL_INC)/util.h \
+- $(PERL_INC)/uudmap.h \
+- $(PERL_INC)/vutil.h \
+- $(PERL_INC)/warnings.h
+-
+-$(OBJECT) : $(PERL_HDRS)
+-
+-
+-# --- MakeMaker makefile section:
+-
+-$(OBJECT) : $(FIRST_MAKEFILE)
+-
+-# We take a very conservative approach here, but it's worth it.
+-# We move Makefile to Makefile.old here to avoid gnu make looping.
+-$(FIRST_MAKEFILE) : Makefile.PL $(CONFIGDEP)
+- $(NOECHO) $(ECHO) "Makefile out-of-date with respect to $?"
+- $(NOECHO) $(ECHO) "Cleaning current config before rebuilding Makefile..."
+- -$(NOECHO) $(RM_F) $(MAKEFILE_OLD)
+- -$(NOECHO) $(MV) $(FIRST_MAKEFILE) $(MAKEFILE_OLD)
+- - $(MAKE) $(USEMAKEFILE) $(MAKEFILE_OLD) clean $(DEV_NULL)
+- $(PERLRUN) Makefile.PL "PREFIX=/usr" "INSTALL_BASE="
+- $(NOECHO) $(ECHO) "==> Your Makefile has been rebuilt. <=="
+- $(NOECHO) $(ECHO) "==> Please rerun the $(MAKE) command. <=="
+- $(FALSE)
+-
+-
+-
+-# --- MakeMaker staticmake section:
+-
+-# --- MakeMaker makeaperl section ---
+-MAP_TARGET = perl
+-FULLPERL = /usr/bin/perl
+-
+-$(MAP_TARGET) :: static $(MAKE_APERL_FILE)
+- $(MAKE) $(USEMAKEFILE) $(MAKE_APERL_FILE) $@
+-
+-$(MAKE_APERL_FILE) : $(FIRST_MAKEFILE) pm_to_blib
+- $(NOECHO) $(ECHO) Writing \"$(MAKE_APERL_FILE)\" for this $(MAP_TARGET)
+- $(NOECHO) $(PERLRUNINST) \
+- Makefile.PL DIR= \
+- MAKEFILE=$(MAKE_APERL_FILE) LINKTYPE=static \
+- MAKEAPERL=1 NORECURS=1 CCCDLFLAGS= \
+- PREFIX=/usr \
+- INSTALL_BASE=
+-
+-
+-# --- MakeMaker test section:
+-
+-TEST_VERBOSE=0
+-TEST_TYPE=test_$(LINKTYPE)
+-TEST_FILE = test.pl
+-TEST_FILES =
+-TESTDB_SW = -d
+-
+-testdb :: testdb_$(LINKTYPE)
+-
+-test :: $(TEST_TYPE) subdirs-test
+-
+-subdirs-test ::
+- $(NOECHO) $(NOOP)
+-
+-
+-test_dynamic :: pure_all
+- PERL_DL_NONLAZY=1 $(FULLPERLRUN) "-I$(INST_LIB)" "-I$(INST_ARCHLIB)" $(TEST_FILE)
+-
+-testdb_dynamic :: pure_all
+- PERL_DL_NONLAZY=1 $(FULLPERLRUN) $(TESTDB_SW) "-I$(INST_LIB)" "-I$(INST_ARCHLIB)" $(TEST_FILE)
+-
+-test_ : test_dynamic
+-
+-test_static :: pure_all $(MAP_TARGET)
+- PERL_DL_NONLAZY=1 ./$(MAP_TARGET) "-I$(INST_LIB)" "-I$(INST_ARCHLIB)" $(TEST_FILE)
+-
+-testdb_static :: pure_all $(MAP_TARGET)
+- PERL_DL_NONLAZY=1 ./$(MAP_TARGET) $(TESTDB_SW) "-I$(INST_LIB)" "-I$(INST_ARCHLIB)" $(TEST_FILE)
+-
+-
+-
+-# --- MakeMaker ppd section:
+-# Creates a PPD (Perl Package Description) for a binary distribution.
+-ppd :
+- $(NOECHO) $(ECHO) '<SOFTPKG NAME="$(DISTNAME)" VERSION="$(VERSION)">' > $(DISTNAME).ppd
+- $(NOECHO) $(ECHO) ' <ABSTRACT></ABSTRACT>' >> $(DISTNAME).ppd
+- $(NOECHO) $(ECHO) ' <AUTHOR>Ivo Hofacker <ivo at tbi.univie.ac.at></AUTHOR>' >> $(DISTNAME).ppd
+- $(NOECHO) $(ECHO) ' <IMPLEMENTATION>' >> $(DISTNAME).ppd
+- $(NOECHO) $(ECHO) ' <ARCHITECTURE NAME="x86_64-linux-gnu-thread-multi-5.20" />' >> $(DISTNAME).ppd
+- $(NOECHO) $(ECHO) ' <CODEBASE HREF="" />' >> $(DISTNAME).ppd
+- $(NOECHO) $(ECHO) ' </IMPLEMENTATION>' >> $(DISTNAME).ppd
+- $(NOECHO) $(ECHO) '</SOFTPKG>' >> $(DISTNAME).ppd
+-
+-
+-# --- MakeMaker pm_to_blib section:
+-
+-pm_to_blib : $(FIRST_MAKEFILE) $(TO_INST_PM)
+- $(NOECHO) $(ABSPERLRUN) -MExtUtils::Install -e 'pm_to_blib({@ARGV}, '\''$(INST_LIB)/auto'\'', q[$(PM_FILTER)], '\''$(PERM_DIR)'\'')' -- \
+- RNA.pm $(INST_LIBDIR)/RNA.pm
+- $(NOECHO) $(TOUCH) pm_to_blib
+-
+-
+-# --- MakeMaker selfdocument section:
+-
+-
+-# --- MakeMaker postamble section:
+-
+-
+-# End.
+--- a/Kinfold/configure.ac
++++ b/Kinfold/configure.ac
+@@ -55,7 +55,7 @@
+
+ dnl checking for -lRNA will fail if both are built simultaneously
+ dnl AC_CHECK_LIB(RNA, fold)
+-LIBS=["-lRNA ${LIBS}"]
++LIBS=["-lviennarna -L../lib/.libs ${LIBS}"]
+
+ dnl Checks for typedefs, structures, and compiler characteristics.
+ AC_C_CONST
+--- a/interfaces/Perl/Makefile.PL.in
++++ b/interfaces/Perl/Makefile.PL.in
+@@ -41,11 +41,11 @@
+ LIBS => ["-lm"],
+ CCFLAGS => $CCFLAGS,
+ OPTIMIZE => $OPTIMIZE,
+- MYEXTLIB => "../../lib/libRNA.a",
++ #MYEXTLIB => "../../lib/libRNA.a",
+ LD => '${CXX}',
+ PM => {"RNA.pm", '$(INST_LIBDIR)/RNA.pm'},
+ OBJECT => "RNA_wrap.o",
+- dynamic_lib => {OTHERLDFLAGS => '$(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) @OPENMP_CFLAGS@'},
++ dynamic_lib => {OTHERLDFLAGS => '$(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) @OPENMP_CFLAGS@ -lviennarna -L../../lib/.libs'},
+ AUTHOR => 'Ivo Hofacker <ivo at tbi.univie.ac.at>',
+ VERSION => '@VERSION@'
+ );
+--- a/interfaces/Perl/Makefile.PL
++++ /dev/null
+@@ -1,51 +0,0 @@
+-# File : Makefile.PL
+-use ExtUtils::MakeMaker;
+-use Config;
+-
+-# unfortunately MakeMaker thinks it is clever
+-# with forcing several compiler and/or linker flags
+-# However, this behavior is a real pain in the a**
+-# when crosscompiling and therefore we need to adjust
+-# some things prior to the call of WriteMakefile()
+-
+-my $CCFLAGS = $Config{'ccflags'};
+-my $OPTIMIZE = $Config{'optimize'};
+-
+-# Perl is built with -Wdeclaration-after-statement on RHEL5 - this isn't
+-# meaningful for C++ - it only emits a warning but it's easy to fix.
+-$CCFLAGS =~ s/(?:^|\s+)-Wdeclaration-after-statement(?:\s+|$)/ /;
+-
+-# The generated code causes "variable may be used uninitialized" warnings
+-# if Perl was built with -Wall.
+-$CCFLAGS =~ s/(^|\s+)-Wall(\s+|$)/$1-Wall -Wno-uninitialized$2/;
+-
+-# add CPP/CXX flags if they exist
+-$CCFLAGS .= ' ' . $var{CPPFLAGS} if exists $var{CPPFLAGS};
+-$CCFLAGS .= ' ' . $var{CXXFLAGS} if exists $var{CXXFLAGS};
+-
+-# add CXXFLAGS and AM_CXXFLAGS as shell variables
+-$CCFLAGS .= ' $(AM_CXXFLAGS) $(CXXFLAGS) -I../../H';
+-
+-# we also need to strip some compiler flags from 'optimize'
+-# since architecture features of the host system may interfere
+-# with the target architecture when crooscompiling
+-$OPTIMIZE =~ s/-march=[a-zA-Z0-9_\-]+//g;
+-$OPTIMIZE =~ s/-mtune=[a-zA-Z0-9_\-]+//g;
+-
+-# print "CCFLAGS:\t", $CCFLAGS, "\n";
+-# print "OPTIMIZE:\t", $OPTIMIZE, "\n";
+-
+-WriteMakefile(
+- MAKEFILE => "Makefile.perl",
+- NAME => "RNA",
+- LIBS => ["-lm"],
+- CCFLAGS => $CCFLAGS,
+- OPTIMIZE => $OPTIMIZE,
+- MYEXTLIB => "../../lib/libRNA.a",
+- LD => '${CXX}',
+- PM => {"RNA.pm", '$(INST_LIBDIR)/RNA.pm'},
+- OBJECT => "RNA_wrap.o",
+- dynamic_lib => {OTHERLDFLAGS => '$(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -fopenmp'},
+- AUTHOR => 'Ivo Hofacker <ivo at tbi.univie.ac.at>',
+- VERSION => '2.1.8'
+-);
+--- a/RNAforester/configure.ac
++++ b/RNAforester/configure.ac
+@@ -26,12 +26,12 @@
+ LDFLAGS="-L../../lib -L../../ViennaRNA ${LDFLAGS} ${OPENMP_CXXFLAGS}"
+ if test -r "../lib/fold.c"; then
+ AC_DEFINE(HAVE_LIBRNA)
+- LIBS=["-lviennarna ${LIBS}"]
++ LIBS=["-lviennarna -L../../lib/.libs ${LIBS}"]
+ AC_MSG_RESULT([using (to be built) libviennarna.so in ../lib])
+ else
+ if test -r "../ViennaRNA/fold.c"; then
+ AC_DEFINE(HAVE_LIBRNA)
+- LIBS=["-lviennarna ${LIBS}"]
++ LIBS=["-lviennarna -L../../lib/.libs ${LIBS}"]
+ AC_MSG_RESULT([using (to be built) libviennarna.so in ../ViennaRNA])
+ fi
+ fi
+--- a/interfaces/Perl/test.pl
++++ b/interfaces/Perl/test.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl -Iblib/arch -Iblib/lib
++#!/usr/bin/perl -Iblib/arch -Iblib/lib -I../../lib/.libs
+
+ # Last changed Time-stamp: <2007-09-27 17:21:23 ivo>
+
+@@ -6,7 +6,7 @@
+ # (It may become useful if the test is moved to ./t subdirectory.)
+ use strict;
+ use Test;
+-use lib qw|blib/arch blib/lib|;
++use lib qw|blib/arch blib/lib ../../lib/.libs|;
+
+ BEGIN { plan tests => 24; }
+
+--- a/interfaces/Perl/Makefile.am
++++ b/interfaces/Perl/Makefile.am
+@@ -22,7 +22,7 @@
+ $(MAKE) -f Makefile.perl install
+
+ check-local: all-local
+- $(MAKE) -f Makefile.perl test
++# $(MAKE) -f Makefile.perl test
+
+ mostlyclean-local: Makefile.perl
+ $(MAKE) -f Makefile.perl clean
+--- a/interfaces/Perl/Makefile.in
++++ /dev/null
+@@ -1,555 +0,0 @@
+-# Makefile.in generated by automake 1.14.1 from Makefile.am.
+-# @configure_input@
+-
+-# Copyright (C) 1994-2013 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.
+-
+- at SET_MAKE@
+-VPATH = @srcdir@
+-am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
+-am__make_running_with_option = \
+- case $${target_option-} in \
+- ?) ;; \
+- *) echo "am__make_running_with_option: internal error: invalid" \
+- "target option '$${target_option-}' specified" >&2; \
+- exit 1;; \
+- esac; \
+- has_opt=no; \
+- sane_makeflags=$$MAKEFLAGS; \
+- if $(am__is_gnu_make); then \
+- sane_makeflags=$$MFLAGS; \
+- else \
+- case $$MAKEFLAGS in \
+- *\\[\ \ ]*) \
+- bs=\\; \
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+- | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \
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+- fi; \
+- skip_next=no; \
+- strip_trailopt () \
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+- }; \
+- for flg in $$sane_makeflags; do \
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+- *$$target_option*) has_opt=yes; break;; \
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+-am__make_dryrun = (target_option=n; $(am__make_running_with_option))
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+-PACKAGE = @PACKAGE@
+-PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
+-PACKAGE_NAME = @PACKAGE_NAME@
+-PACKAGE_STRING = @PACKAGE_STRING@
+-PACKAGE_TARNAME = @PACKAGE_TARNAME@
+-PACKAGE_URL = @PACKAGE_URL@
+-PACKAGE_VERSION = @PACKAGE_VERSION@
+-PATH_SEPARATOR = @PATH_SEPARATOR@
+-PERLPREFIX = @PERLPREFIX@
+-PERL_INTERFACE = @PERL_INTERFACE@
+-POW_LIB = @POW_LIB@
+-PYTHON_INTERFACE = @PYTHON_INTERFACE@
+-PerlCmd = @PerlCmd@
+-PythonCmd = @PythonCmd@
+-RANLIB = @RANLIB@
+-REFERENCE_MANUAL_PDF_NAME = @REFERENCE_MANUAL_PDF_NAME@
+-REFERENCE_MANUAL_TAGFILE = @REFERENCE_MANUAL_TAGFILE@
+-SED = @SED@
+-SET_MAKE = @SET_MAKE@
+-SHELL = @SHELL@
+-STRIP = @STRIP@
+-VERSION = @VERSION@
+-abs_builddir = @abs_builddir@
+-abs_srcdir = @abs_srcdir@
+-abs_top_builddir = @abs_top_builddir@
+-abs_top_srcdir = @abs_top_srcdir@
+-ac_ct_AR = @ac_ct_AR@
+-ac_ct_CC = @ac_ct_CC@
+-ac_ct_CXX = @ac_ct_CXX@
+-ac_ct_DUMPBIN = @ac_ct_DUMPBIN@
+-am__include = @am__include@
+-am__leading_dot = @am__leading_dot@
+-am__quote = @am__quote@
+-am__tar = @am__tar@
+-am__untar = @am__untar@
+-bindir = @bindir@
+-build = @build@
+-build_alias = @build_alias@
+-build_cpu = @build_cpu@
+-build_os = @build_os@
+-build_vendor = @build_vendor@
+-builddir = @builddir@
+-datadir = @datadir@
+-datarootdir = @datarootdir@
+-docdir = @docdir@
+-dot = @dot@
+-doxygen = @doxygen@
+-dvidir = @dvidir@
+-egrep = @egrep@
+-exec_prefix = @exec_prefix@
+-host = @host@
+-host_alias = @host_alias@
+-host_cpu = @host_cpu@
+-host_os = @host_os@
+-host_vendor = @host_vendor@
+-htmldir = @htmldir@
+-includedir = @includedir@
+-infodir = @infodir@
+-install_sh = @install_sh@
+-latex = @latex@
+-libdir = @libdir@
+-libexecdir = @libexecdir@
+-localedir = @localedir@
+-localstatedir = @localstatedir@
+-makeindex = @makeindex@
+-mandir = @mandir@
+-mkdir_p = @mkdir_p@
+-oldincludedir = @oldincludedir@
+-pdfdir = @pdfdir@
+-pdflatex = @pdflatex@
+-perl = @perl@
+-prefix = @prefix@
+-program_transform_name = @program_transform_name@
+-psdir = @psdir@
+-sbindir = @sbindir@
+-sharedstatedir = @sharedstatedir@
+-srcdir = @srcdir@
+-subdirs = @subdirs@
+-sysconfdir = @sysconfdir@
+-target_alias = @target_alias@
+-top_build_prefix = @top_build_prefix@
+-top_builddir = @top_builddir@
+-top_srcdir = @top_srcdir@
+- at WITH_LARGE_PF_FALSE@USE_LARGE_PF =
+- at WITH_LARGE_PF_TRUE@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 \
+- *$$dep*) \
+- ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
+- && { if test -f $@; then exit 0; else break; fi; }; \
+- exit 1;; \
+- esac; \
+- done; \
+- echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu interfaces/Perl/Makefile'; \
+- $(am__cd) $(top_srcdir) && \
+- $(AUTOMAKE) --gnu interfaces/Perl/Makefile
+-.PRECIOUS: Makefile
+-Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+- @case '$?' in \
+- *config.status*) \
+- cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
+- *) \
+- echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
+- cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+- esac;
+-
+-$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
+- cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+-
+-$(top_srcdir)/configure: $(am__configure_deps)
+- cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+-$(ACLOCAL_M4): $(am__aclocal_m4_deps)
+- cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+-$(am__aclocal_m4_deps):
+-Makefile.PL: $(top_builddir)/config.status $(srcdir)/Makefile.PL.in
+- cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@
+-
+-mostlyclean-libtool:
+- -rm -f *.lo
+-
+-clean-libtool:
+- -rm -rf .libs _libs
+-
+-ID: $(am__tagged_files)
+- $(am__define_uniq_tagged_files); mkid -fID $$unique
+-tags: tags-am
+-TAGS: tags
+-
+-tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+- set x; \
+- here=`pwd`; \
+- $(am__define_uniq_tagged_files); \
+- shift; \
+- if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
+- test -n "$$unique" || unique=$$empty_fix; \
+- if test $$# -gt 0; then \
+- $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+- "$$@" $$unique; \
+- else \
+- $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+- $$unique; \
+- fi; \
+- fi
+-ctags: ctags-am
+-
+-CTAGS: ctags
+-ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
+- $(am__define_uniq_tagged_files); \
+- test -z "$(CTAGS_ARGS)$$unique" \
+- || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
+- $$unique
+-
+-GTAGS:
+- here=`$(am__cd) $(top_builddir) && pwd` \
+- && $(am__cd) $(top_srcdir) \
+- && gtags -i $(GTAGS_ARGS) "$$here"
+-cscopelist: cscopelist-am
+-
+-cscopelist-am: $(am__tagged_files)
+- list='$(am__tagged_files)'; \
+- case "$(srcdir)" in \
+- [\\/]* | ?:[\\/]*) sdir="$(srcdir)" ;; \
+- *) sdir=$(subdir)/$(srcdir) ;; \
+- esac; \
+- for i in $$list; do \
+- if test -f "$$i"; then \
+- echo "$(subdir)/$$i"; \
+- else \
+- echo "$$sdir/$$i"; \
+- fi; \
+- done >> $(top_builddir)/cscope.files
+-
+-distclean-tags:
+- -rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
+-
+-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 clean-libtool mostlyclean-am
+-
+-distclean: distclean-am
+- -rm -f Makefile
+-distclean-am: clean-am distclean-generic distclean-tags
+-
+-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-libtool \
+- mostlyclean-local
+-
+-pdf: pdf-am
+-
+-pdf-am:
+-
+-ps: ps-am
+-
+-ps-am:
+-
+-uninstall-am:
+-
+-.MAKE: check-am install-am install-strip
+-
+-.PHONY: CTAGS GTAGS TAGS all all-am all-local check check-am \
+- check-local clean clean-generic clean-libtool cscopelist-am \
+- ctags ctags-am distclean distclean-generic distclean-libtool \
+- distclean-tags 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-libtool mostlyclean-local pdf pdf-am ps ps-am tags \
+- tags-am uninstall uninstall-am
+-
+-
+-Makefile.perl: Makefile.PL Makefile
+- @PerlCmd@ Makefile.PL PREFIX=$(prefix) INSTALL_BASE=
+-
+-# 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
+- $(MAKE) -f Makefile.perl clean
+-
+-# remove all generated content
+-maintainer-clean-local:
+- -rm -f RNA_wrap.c Makefile.perl.old RNA.pm
+-
+-# Tell versions [3.59,3.63) of GNU make to not export all variables.
+-# Otherwise a system limit (for SysV at least) may be exceeded.
+-.NOEXPORT:
Deleted: trunk/packages/vienna-rna/trunk/debian/patches/do_not_configure_g2-0.70.patch
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/do_not_configure_g2-0.70.patch 2014-12-16 15:10:08 UTC (rev 18543)
+++ trunk/packages/vienna-rna/trunk/debian/patches/do_not_configure_g2-0.70.patch 2014-12-27 23:31:21 UTC (rev 18544)
@@ -1,57 +0,0 @@
-Description: The g2 library is just packaged for Debian and because we link
- against this there is no need to even configure in this directory.
-Author: Andreas Tille <tille at debian.org>
-Applied-Upstream: 1.8.5 .
-Last-Update: 2011-01-31
-
---- ViennaRNA-1.8.4.orig/RNAforester/configure
-+++ ViennaRNA-1.8.4/RNAforester/configure
-@@ -748,7 +748,7 @@
- CC
- CFLAGS
- CXXCPP'
--ac_subdirs_all='g2-0.70'
-+#ac_subdirs_all='g2-0.70'
-
- # Initialize some variables set by options.
- ac_init_help=
-@@ -4193,7 +4193,7 @@
-
-
- save_CPPFLAGS=$CPPFLAGS
--CPPFLAGS="-Ig2-0.70/src/ ${CPPFLAGS}"
-+CPPFLAGS="${CPPFLAGS}"
-
-
- { $as_echo "$as_me:$LINENO: checking for main in -lgd" >&5
-@@ -5310,8 +5310,8 @@
- fi
-
-
--CPPFLAGS="$save_CPPFLAGS -I../g2-0.70/include/ "
--LDFLAGS="-L../g2-0.70 ${LDFLAGS}"
-+CPPFLAGS="$save_CPPFLAGS"
-+LDFLAGS="${LDFLAGS}"
-
- if ${HAVE_LIBG2}; then
- LIBS="-lg2 ${LIBS}"
-@@ -5325,7 +5325,7 @@
-
-
-
--subdirs="$subdirs g2-0.70"
-+subdirs="$subdirs"
-
- ac_config_files="$ac_config_files Makefile src/Makefile man/Makefile"
-
---- ViennaRNA-1.8.4.orig/RNAforester/Makefile.in
-+++ ViennaRNA-1.8.4/RNAforester/Makefile.in
-@@ -189,7 +189,7 @@
- top_build_prefix = @top_build_prefix@
- top_builddir = @top_builddir@
- top_srcdir = @top_srcdir@
--SUBDIRS = g2-0.70 src man
-+SUBDIRS = src man
- all: config.h
- $(MAKE) $(AM_MAKEFLAGS) all-recursive
-
Added: trunk/packages/vienna-rna/trunk/debian/patches/do_not_configure_g2.patch
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/do_not_configure_g2.patch (rev 0)
+++ trunk/packages/vienna-rna/trunk/debian/patches/do_not_configure_g2.patch 2014-12-27 23:31:21 UTC (rev 18544)
@@ -0,0 +1,42 @@
+Description: The g2 library is just packaged for Debian and because we link
+ against this there is no need to even configure in this directory.
+Author: Andreas Tille <tille at debian.org>
+Last-Update: 2014-12-28
+Forwarded: No
+--- a/RNAforester/Makefile.am
++++ b/RNAforester/Makefile.am
+@@ -1,2 +1,2 @@
+-SUBDIRS = g2-0.70 src man
++SUBDIRS = src man
+
+--- a/RNAforester/configure.ac
++++ b/RNAforester/configure.ac
+@@ -55,7 +55,7 @@
+ [])
+
+ save_CPPFLAGS=$CPPFLAGS
+-CPPFLAGS=["-Ig2-0.70/src/ ${CPPFLAGS}"]
++CPPFLAGS=["${CPPFLAGS}"]
+
+ dnl AC_CHECK_LIB(gd,main,,)
+
+@@ -69,8 +69,8 @@
+ AC_C_INLINE
+ AC_TYPE_SIZE_T
+
+-CPPFLAGS="$save_CPPFLAGS -I../g2-0.70/include/ "
+-LDFLAGS=["-L../g2-0.70 ${LDFLAGS}"]
++CPPFLAGS="$save_CPPFLAGS "
++LDFLAGS=["${LDFLAGS}"]
+
+ if ${HAVE_LIBG2}; then
+ LIBS=["-lg2 ${LIBS}"]
+@@ -83,7 +83,7 @@
+
+ dnl Checks for library functions.
+
+-AC_CONFIG_SUBDIRS(g2-0.70)
++#AC_CONFIG_SUBDIRS(g2-0.70)
+ AC_OUTPUT(Makefile src/Makefile man/Makefile)
+
+
Added: trunk/packages/vienna-rna/trunk/debian/patches/fix_perl_install.patch
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/fix_perl_install.patch (rev 0)
+++ trunk/packages/vienna-rna/trunk/debian/patches/fix_perl_install.patch 2014-12-27 23:31:21 UTC (rev 18544)
@@ -0,0 +1,25 @@
+Subject: install for Debian
+Description: Install in Debian perl directories
+Author: Olivier Sallou <osallou at debian.org>
+Last-Update: 2014-12-28
+Forwarded: No
+--- a/interfaces/Perl/Makefile.am
++++ b/interfaces/Perl/Makefile.am
+@@ -9,7 +9,7 @@
+ EXTRA_DIST = RNA.pm RNA_wrap.c RNAfold.pl test.pl RNAfold.cgi Makefile.PL
+
+ Makefile.perl: Makefile.PL Makefile
+- @PerlCmd@ Makefile.PL PREFIX=$(prefix) INSTALL_BASE=
++ @PerlCmd@ Makefile.PL INSTALLDIRS=vendor PREFIX=$(prefix) INSTALL_BASE=
+
+ # the perl command repairs some errors in the SWIG CVS version
+ RNA_wrap.c: ../RNA.i ../tmaps.i
+@@ -19,7 +19,7 @@
+ $(MAKE) -f Makefile.perl
+
+ install-exec-local: all-local
+- $(MAKE) -f Makefile.perl install
++ $(MAKE) -f Makefile.perl install DESTDIR=../../debian/librna-perl
+
+ check-local: all-local
+ # $(MAKE) -f Makefile.perl test
Added: trunk/packages/vienna-rna/trunk/debian/patches/fix_python_interface.patch
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/fix_python_interface.patch (rev 0)
+++ trunk/packages/vienna-rna/trunk/debian/patches/fix_python_interface.patch 2014-12-27 23:31:21 UTC (rev 18544)
@@ -0,0 +1,29 @@
+Subject: install for Debian
+Description: Install in Debian python directories
+Author: Olivier Sallou <osallou at debian.org>
+Last-Update: 2014-12-28
+Forwarded: No
+--- a/interfaces/Python/setup.py.in
++++ b/interfaces/Python/setup.py.in
+@@ -18,8 +18,8 @@
+ extension = Extension("_RNA",
+ ["RNA_wrap.c"],
+ include_dirs=['../../H'],
+- libraries=['RNA'],
+- library_dirs=['../../lib'],
++ libraries=['viennarna'],
++ library_dirs=['../../lib/.libs'],
+ extra_compile_args=extra_compile_args,
+ extra_link_args=extra_link_args
+ )
+--- a/interfaces/Python/Makefile.am
++++ b/interfaces/Python/Makefile.am
+@@ -15,7 +15,7 @@
+ @PythonCmd@ setup.py build
+
+ install-exec-local: all-local
+- @PythonCmd@ setup.py install --prefix=$(prefix) --record install.record
++ @PythonCmd@ setup.py install --prefix=../../debian/python-rna/usr --record install.record
+
+ #check-local: all-local
+ # $(MAKE) -f Makefile.perl test
Modified: trunk/packages/vienna-rna/trunk/debian/patches/series
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/series 2014-12-16 15:10:08 UTC (rev 18543)
+++ trunk/packages/vienna-rna/trunk/debian/patches/series 2014-12-27 23:31:21 UTC (rev 18544)
@@ -1,9 +1,5 @@
-fix_utils_make_install.patch
-readseq_exclude.patch
-fix_manpages.patch
-debian_perl_modules_path.patch
-02_RNAforester_missing_libs.patch
-do_not_configure_g2-0.70.patch
-fix_RNAlib_info.patch
-naview_copyright.patch
-fix_syntax.patch
+add_shared_library
+do_not_configure_g2.patch
+fix_perl_install.patch
+fix_python_interface.patch
+spelling.patch
Added: trunk/packages/vienna-rna/trunk/debian/patches/spelling.patch
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/spelling.patch (rev 0)
+++ trunk/packages/vienna-rna/trunk/debian/patches/spelling.patch 2014-12-27 23:31:21 UTC (rev 18544)
@@ -0,0 +1,27 @@
+Description: lintian findout spelling-error .
+Author: Alex Mestiashvili <alex at biotec.tu-dresden.de>
+Applied-Upstream: version 1.8.5
+Last-Update: 2014-12-28
+Forwarded: No
+--- a/Cluster/AnalyseDists.1
++++ b/Cluster/AnalyseDists.1
+@@ -18,7 +18,7 @@
+ This matches the output format of, e.g., RNAdistance.
+ The input data file may contain arbitrary lines before and after the
+ distance matrix. All lines beginning with '> ' that are not of the
+-above form are written to stdout. The programm continues reading
++above form are written to stdout. The program continues reading
+ until it encounters an EOF condition or the terminator character '@'.
+ .br
+ A list of taxa names can be specified in the input stream. The list
+--- a/lib/utils.c
++++ b/lib/utils.c
+@@ -500,7 +500,7 @@
+ case ')':
+ p += 2;
+ break;
+- default: nrerror("pack_structure: illegal charcter in structure");
++ default: nrerror("pack_structure: illegal character in structure");
+ }
+ if (i<l) i++;
+ }
Modified: trunk/packages/vienna-rna/trunk/debian/rules
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/rules 2014-12-16 15:10:08 UTC (rev 18543)
+++ trunk/packages/vienna-rna/trunk/debian/rules 2014-12-27 23:31:21 UTC (rev 18544)
@@ -1,56 +1,36 @@
#!/usr/bin/make -f
-# debian/rules for vienna-rna
-# Andreas Tille <tille at debian.org>
-# GPL
-# Uncomment this to turn on verbose mode.
-#export DH_VERBOSE=1
-pkg=vienna-rna
-DEB_COMPRESS_EXCLUDE := .pdf
-
%:
- dh --with autotools_dev $@
+ dh $@ --with python2 --with autoreconf --parallel
+
override_dh_auto_configure:
- dh_auto_configure -- --with-cluster
+ dh_auto_configure -- --with-cluster --with-python
-override_dh_auto_clean:
- echo "Do not run dh_auto_clean because it forces removal of man pages"
-
-override_dh_clean:
- # upstream seems to have forgotten a make distclean and the manpages remained - so we try hard to keep them alive
- mkdir -p man_tmp; mv man/*.1 man_tmp || true
- # do not try to clean up where nothing was done
- [ ! -f Makefile ] || $(MAKE) distclean
- dh_clean --exclude=Readseq --exclude=RNAforester/g2-0.70/autom4te.cache
- # Reinstall manpages where they were before
- mv man_tmp/* man/ || true; rmdir man_tmp
- # Clean up in Perl directory
- cd Perl; [ ! -f Makefile ] || $(MAKE) distclean; rm -f *.old *.ps test.coord test.par
-
override_dh_auto_install:
# rename perl scripts to remove the *.pl extension and create manpage via perldoc
+ mkdir -p $(CURDIR)/debian/tmp/usr/bin
+ mkdir -p $(CURDIR)/debian/tmp/usr/share/man/man1
for script in `ls Utils/*.pl` ; do \
- newscript=`basename $${script} .pl` ; \
- cp -a $${script} $(CURDIR)/debian/$(pkg)/usr/bin/$${newscript} ; \
- perldoc -onroff -F $${script} | \
- sed -e "s/$${newscript}\.pl/$${newscript}/g" \
- > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/$${newscript}.1 ; \
- if [ ! -s $(CURDIR)/debian/$(pkg)/usr/share/man/man1/$${newscript}.1 ] ; then \
- rm -f $(CURDIR)/debian/$(pkg)/usr/share/man/man1/$${newscript}.1 ; \
- fi ; \
+ newscript=`basename $${script} .pl` ; \
+ cp -a $${script} $(CURDIR)/debian/tmp/usr/bin/$${newscript} ; \
+ perldoc -onroff -F $${script} | \
+ sed -e "s/$${newscript}\.pl/$${newscript}/g" \
+ > $(CURDIR)/debian/tmp/usr/share/man/man1/$${newscript}.1 ; \
+ if [ ! -s $(CURDIR)/debian/tmp/usr/share/man/man1/$${newscript}.1 ] ; then \
+ rm -f $(CURDIR)/debian/tmp/usr/share/man/man1/$${newscript}.1 ; \
+ fi ; \
done
+ cp doc/RNAlib*.pdf doc/RNAlib.pdf
+ dh_auto_install
+ # Clean packlist for perl
+ find debian/librna-perl -type f -name .packlist -delete
- # Create manpages which we need to provide proper name strings for individual manpages
- help2man --name="aligning RNA secondary structures" --no-info \
- $(CURDIR)/RNAforester/src/RNAforester > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/RNAforester.1
- help2man --name="Kinetic Folding Program for Nucleic Acids" --no-info \
- $(CURDIR)/Kinfold/Kinfold > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/Kinfold.1
- #copy manual pages from cluster dir
- cp $(CURDIR)/Cluster/*.1 $(CURDIR)/debian/$(pkg)/usr/share/man/man1/
-
- cd man; $(MAKE) pdf; $(MAKE) html
+override_dh_auto_clean:
+ dh_auto_clean
+ rm -f doc/RNAlib.pdf
override_dh_compress:
dh_compress --exclude=.pdf
+
Modified: trunk/packages/vienna-rna/trunk/debian/vienna-rna-doc.doc-base
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/vienna-rna-doc.doc-base 2014-12-16 15:10:08 UTC (rev 18543)
+++ trunk/packages/vienna-rna/trunk/debian/vienna-rna-doc.doc-base 2014-12-27 23:31:21 UTC (rev 18544)
@@ -22,4 +22,3 @@
Format:pdf
Files: /usr/share/doc/vienna-rna/RNAlib.pdf
-
Modified: trunk/packages/vienna-rna/trunk/debian/vienna-rna-doc.install
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/vienna-rna-doc.install 2014-12-16 15:10:08 UTC (rev 18543)
+++ trunk/packages/vienna-rna/trunk/debian/vienna-rna-doc.install 2014-12-27 23:31:21 UTC (rev 18544)
@@ -1,3 +1,4 @@
-man/RNAlib.html/* usr/share/doc/vienna-rna/html
-man/*.pdf usr/share/doc/vienna-rna
-Utils/Fold usr/share/doc/vienna-rna/examples
+doc/RNAlib.pdf usr/share/doc/vienna-rna
+doc/html/* usr/share/doc/vienna-rna/html
+Utils/Fold usr/share/doc/vieenna-rna/examples
+
Modified: trunk/packages/vienna-rna/trunk/debian/vienna-rna.install
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/vienna-rna.install 2014-12-16 15:10:08 UTC (rev 18543)
+++ trunk/packages/vienna-rna/trunk/debian/vienna-rna.install 2014-12-27 23:31:21 UTC (rev 18544)
@@ -1,22 +1,2 @@
-Cluster/AnalyseDists usr/bin
-Cluster/AnalyseSeqs usr/bin
-Kinfold/Kinfold usr/bin
-Progs/RNAaliduplex usr/bin
-Progs/RNAalifold usr/bin
-Progs/RNAcofold usr/bin
-Progs/RNAdistance usr/bin
-Progs/RNAduplex usr/bin
-Progs/RNAeval usr/bin
-Progs/RNAfold usr/bin
-Progs/RNAheat usr/bin
-Progs/RNAinverse usr/bin
-Progs/RNALfold usr/bin
-Progs/RNApaln usr/bin
-Progs/RNApdist usr/bin
-Progs/RNAplfold usr/bin
-Progs/RNAplot usr/bin
-Progs/RNAsubopt usr/bin
-Progs/RNAup usr/bin
-RNAforester/src/RNAforester usr/bin
-Utils/b2ct usr/bin
-Utils/popt usr/bin
+usr/bin/*
+usr/share/man/man1
Modified: trunk/packages/vienna-rna/trunk/debian/vienna-rna.manpages
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/vienna-rna.manpages 2014-12-16 15:10:08 UTC (rev 18543)
+++ trunk/packages/vienna-rna/trunk/debian/vienna-rna.manpages 2014-12-27 23:31:21 UTC (rev 18544)
@@ -1,2 +1 @@
-man/*.1
debian/*.1
Modified: trunk/packages/vienna-rna/trunk/debian/watch
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/watch 2014-12-16 15:10:08 UTC (rev 18543)
+++ trunk/packages/vienna-rna/trunk/debian/watch 2014-12-27 23:31:21 UTC (rev 18544)
@@ -1,3 +1,3 @@
version=3
-http://www.tbi.univie.ac.at/~ivo/RNA/ViennaRNA-(.*)\.tar\.gz
+http://www.tbi.univie.ac.at/RNA/ download.php?id=viennarna-(\d[\d.-]+)
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