[med-svn] r18545 - in trunk/packages/vienna-rna/trunk/debian: . patches
Olivier Sallou
osallou at moszumanska.debian.org
Sun Dec 28 00:17:09 UTC 2014
Author: osallou
Date: 2014-12-28 00:17:07 +0000 (Sun, 28 Dec 2014)
New Revision: 18545
Added:
trunk/packages/vienna-rna/trunk/debian/libviennarna0.install
Removed:
trunk/packages/vienna-rna/trunk/debian/libviennarna.install
Modified:
trunk/packages/vienna-rna/trunk/debian/changelog
trunk/packages/vienna-rna/trunk/debian/control
trunk/packages/vienna-rna/trunk/debian/patches/add_shared_library
Log:
update status, fix multi-arch
Modified: trunk/packages/vienna-rna/trunk/debian/changelog
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/changelog 2014-12-27 23:31:21 UTC (rev 18544)
+++ trunk/packages/vienna-rna/trunk/debian/changelog 2014-12-28 00:17:07 UTC (rev 18545)
@@ -2,6 +2,8 @@
* First package of ViennaRNA (Closes: #451193)
[TODO] pbuilder, lintian checks
+ replace jquery by debian jquery for doc
+ [ISSUES] watch file
[DONE] update patches to viennarna v2
build new packages for perl and python wrappers
Modified: trunk/packages/vienna-rna/trunk/debian/control
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/control 2014-12-27 23:31:21 UTC (rev 18544)
+++ trunk/packages/vienna-rna/trunk/debian/control 2014-12-28 00:17:07 UTC (rev 18545)
@@ -6,7 +6,7 @@
Build-Depends:
debhelper (>= 9), quilt, autotools-dev, dh-autoreconf, libtool,
graphviz, texlive-latex-extra, libg2-dev, help2man, perl-doc,
- perl, dh-python
+ perl, dh-python, 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/
@@ -15,11 +15,10 @@
Package: vienna-rna
-Section: science
Architecture: any
-Depends: libviennarna, ${shlibs:Depends}, ${misc:Depends}
+Depends: libviennarna0, ${shlibs:Depends}, ${misc:Depends}
Recommends: readseq
-Multi-Arch: same
+Multi-Arch: no
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
@@ -49,28 +48,25 @@
Package: python-rna
Section: python
Architecture: any
-Depends: python, ${python-Depends}, libvienna-rna
-Multi-Arch: same
-Description: ViennaRNA python wrappers
+Depends: python, ${python:Depends}, ${shlibs:Depends}, ${misc:Depends}, libvienna-rna
+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
+Depends: perl, libviennarna0, ${shlibs:Depends}, ${misc:Depends}, ${perl:Depends}
Description: ViennaRNA perl wrappers
Perl wrappers above vienna-rna library.
-Package: libviennarna
-Provides: libviennarna
+Package: libviennarna0
+Provides: libviennarna0
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.
@@ -78,9 +74,8 @@
Provides: libviennarna-dev
Section: libdevel
Architecture: any
-Depends: libviennarna (= ${binary:Version}), ${misc:Depends}
+Depends: libviennarna0 (= ${binary:Version}), ${misc:Depends}
Suggests: viennarna-doc
-Multi-Arch: same
Description: ViennaRNA Library -- development package
Development library with include headers for ViennaRNA.
@@ -89,7 +84,7 @@
Section: doc
Architecture: all
Depends: ${misc:Depends}
-Suggests: libviennarna (= ${binary:Version}), libviennarna-dev (= ${binary:Version})
+Suggests: libviennarna0 (= ${binary:Version}), libviennarna-dev (= ${binary:Version})
Description: RNA sequence analysis documentation package
The Vienna RNA Package consists of a C code library and several
stand-alone programs for the prediction and comparison of RNA secondary
Deleted: trunk/packages/vienna-rna/trunk/debian/libviennarna.install
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/libviennarna.install 2014-12-27 23:31:21 UTC (rev 18544)
+++ trunk/packages/vienna-rna/trunk/debian/libviennarna.install 2014-12-28 00:17:07 UTC (rev 18545)
@@ -1 +0,0 @@
-usr/lib/*/libviennarna.so.*
Copied: trunk/packages/vienna-rna/trunk/debian/libviennarna0.install (from rev 18544, trunk/packages/vienna-rna/trunk/debian/libviennarna.install)
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/libviennarna0.install (rev 0)
+++ trunk/packages/vienna-rna/trunk/debian/libviennarna0.install 2014-12-28 00:17:07 UTC (rev 18545)
@@ -0,0 +1 @@
+usr/lib/*/libviennarna.so.*
Modified: trunk/packages/vienna-rna/trunk/debian/patches/add_shared_library
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/add_shared_library 2014-12-27 23:31:21 UTC (rev 18544)
+++ trunk/packages/vienna-rna/trunk/debian/patches/add_shared_library 2014-12-28 00:17:07 UTC (rev 18545)
@@ -1,3 +1,8 @@
+Subject: use shared library
+Description: generate shared library instead of static library
+Author: Olivier Sallou <osallou at debian.org>
+Forwarded: no
+Last-Updated: 2014-12-28
--- a/configure.ac
+++ b/configure.ac
@@ -15,6 +15,9 @@
@@ -106,1035 +111,6 @@
AM_CPPFLAGS = -I$(srcdir)/../H
---- a/interfaces/Perl/Makefile.perl
-+++ /dev/null
-@@ -1,1026 +0,0 @@
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--#
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--# 6.98 (Revision: 69800) from the contents of
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--# MakeMaker ARGV: (q[PREFIX=/usr], q[INSTALL_BASE=])
--#
--
--# MakeMaker Parameters:
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--# AUTHOR => [q[Ivo Hofacker <ivo at tbi.univie.ac.at>]]
--# BUILD_REQUIRES => { }
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--# 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]
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-- $(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 @@
@@ -1162,77 +138,6 @@
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 @@
@@ -1261,561 +166,20 @@
mostlyclean-local: Makefile.perl
$(MAKE) -f Makefile.perl clean
---- a/interfaces/Perl/Makefile.in
-+++ /dev/null
-@@ -1,555 +0,0 @@
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--
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--# gives unlimited permission to copy and/or distribute it,
--# with or without modifications, as long as this notice is preserved.
--
--# This program is distributed in the hope that it will be useful,
--# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
--# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
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--
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--VPATH = @srcdir@
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--distclean-generic:
-- -test -z "$(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:
+--- 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=["-lRNA ${LIBS}"]
++ LIBS=["-lviennarna -L../../lib/.libs ${LIBS}"]
+ AC_MSG_RESULT([using (to be built) libRNA.a in ../lib])
+ else
+ if test -r "../ViennaRNA/fold.c"; then
+ AC_DEFINE(HAVE_LIBRNA)
+- LIBS=["-lRNA ${LIBS}"]
++ LIBS=["-lviennarna -L../../lib/.libs ${LIBS}"]
+ AC_MSG_RESULT([using (to be built) libRNA.a in ../ViennaRNA])
+ fi
+ fi
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