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 <[email protected]> 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 <[email protected]> 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 <[email protected]> -Uploaders: Alex Mestiashvili <[email protected]> -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 <[email protected]> +Uploaders: Olivier Sallou <[email protected]> +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 <[email protected]> + 2011, Andreas Tille <[email protected]> + 2014, Olivier Sallou <[email protected]> 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 <[email protected]>]] +-# 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 <[email protected]>'\''' >> 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 <[email protected]>"' >> 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) : 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"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 :: +- 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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 <[email protected]></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 <[email protected]>', + 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 <[email protected]>', +- 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 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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 <[email protected]> +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 <[email protected]> +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 <[email protected]> +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 <[email protected]> +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 <[email protected]> -# 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.-]+) _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
