debian/0000755000000000000000000000000012167042701007166 5ustar debian/mcl-doc.doc-base.mcxassemble0000644000000000000000000000057512101236635014413 0ustar Document: mcxassemble Title: mcxassemble - transform raw cooccurrence data to mcl matrix format Author: Stijn van Dongen Abstract: A document describing the mcxassemble command line tool. Section: Science/Mathematics Format: PostScript Files: /usr/share/doc/mcl/mcxassemble.ps.gz Format: HTML Index: /usr/share/doc/mcl/mcxassemble.html Files: /usr/share/doc/mcl/mcxassemble.html debian/mcl-doc.doc-base.mcxsubs0000644000000000000000000000063112101236635013565 0ustar Document: mcxsubs Title: mcxsubs - extract submatrices (subgraphs) of a matrix (graph) corresponding with index sets and sets of clusters Author: Stijn van Dongen Abstract: A document describing the mcxsubs command line tool. Section: Science/Mathematics Format: PostScript Files: /usr/share/doc/mcl/mcxsubs.ps.gz Format: HTML Index: /usr/share/doc/mcl/mcxsubs.html Files: /usr/share/doc/mcl/mcxsubs.html debian/README.Debian0000644000000000000000000000054512101236635011232 0ustar mcl for Debian -------------------------------------------------------------------------------- Install mcl-doc for documentation about how to use mcl. It provides a general introduction, input format specifications and more specific documentations as well as some examples. -- Philipp Benner , Mon, 14 Jan 2008 18:38:36 +0100 debian/rules0000755000000000000000000001256712167042363010265 0ustar #!/usr/bin/make -f # based upon sample debian/rules that uses debhelper. # GNU copyright 1997 to 1999 by Joey Hess. # Uncomment this to turn on verbose mode. # export DH_VERBOSE=1 DPKG_EXPORT_BUILDFLAGS = 1 include /usr/share/dpkg/buildflags.mk pkg=mcl # allow bashism's in commandlines SHELL = /bin/bash # Debian Policy 10.1 CFLAGS = -g -Wall ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS))) CFLAGS += -O0 else CFLAGS += -O2 endif INSTALL = install INSTALL_PROGRAM = $(INSTALL) -p -o root -g root -m 755 ifeq (,$(findstring nostrip,$(DEB_BUILD_OPTIONS))) INSTALL_PROGRAM += -s endif # variables to be used in configure invocation. see # autotools-dev/README.Debian.gz export DEB_HOST_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_HOST_GNU_TYPE) export DEB_BUILD_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE) # use autoconf 2.52 or newer ifeq ($(DEB_BUILD_GNU_TYPE), $(DEB_HOST_GNU_TYPE)) confflags += --build $(DEB_HOST_GNU_TYPE) else confflags += --build $(DEB_BUILD_GNU_TYPE) --host $(DEB_HOST_GNU_TYPE) endif ## Build BLAST parsing script mcxdeblast and the pipeline script mclblastline ## (sources in src/alien/oxygen). It encapsulates all the stages of parsing, ## matrix creation, running mcl, and formatting the result ## into a single application. confflags += --enable-blast ## add --enable-tribe to confflags to add the upstreams supplied tribe tools ## (protein clustering stuff). This builds and installs the tools ## ## tribe-families tribe-matrix tribemcl tribe-parse ## ## We're not doing it since tribe-matrix segfaults, and the tools lackproper ## manpages. Furthermore, the BLAST parsing scripts can be used in place of ## the tribe module. # confflags += --enable-tribe ## If you really want to suppress the citation reference printed by MCL (the ## one which looks like ## ## Please cite: ## Stijn van Dongen, Graph Clustering by Flow Simulation. PhD thesis, ## University of Utrecht, May 2000. ## ( http://www.library.uu.nl/digiarchief/dip/diss/1895620/full.pdf ## or http://micans.org/mcl/lit/svdthesis.pdf.gz) ## OR ## Stijn van Dongen, A cluster algorithm for graphs. Technical ## Report INS-R0010, National Research Institute for Mathematics ## and Computer Science in the Netherlands, Amsterdam, May 2000. ## ( http://www.cwi.nl/ftp/CWIreports/INS/INS-R0010.ps.Z ## or http://micans.org/mcl/lit/INS-R0010.ps.Z) ## ## ), then this is the place to do it. Of course we honor the choice of ## upstream here, and build as suggested by upsteam. # confflags += --disable-helpful-reminder config: config-stamp config-stamp: dh_testdir # # Make sure we have fresh config.{sub,guess}, in order to make life # # more easy for porters to new architectures. See # # autotools-dev/README.Debian.gz if [ -r /usr/share/misc/config.sub ] && [ ! -f autofoo/config.sub.backup ]; then \ mv -v autofoo/config.sub autofoo/config.sub.backup; \ cp -f /usr/share/misc/config.sub autofoo/config.sub; \ fi if [ -r /usr/share/misc/config.guess ] && [ ! -f autofoo/config.guess.backup ]; then \ mv -v autofoo/config.guess autofoo/config.guess.backup; \ cp -f /usr/share/misc/config.guess autofoo/config.guess; \ fi touch $@ config-clean: dh_testdir dh_testroot if [ -f autofoo/config.sub.backup ]; then \ mv -fv autofoo/config.sub.backup autofoo/config.sub; \ fi if [ -f autofoo/config.guess.backup ]; then \ mv -fv autofoo/config.guess.backup autofoo/config.guess; \ fi $(RM) config-stamp configure: config configure-stamp configure-stamp: dh_testdir ./configure \ $(confflags) \ --prefix=/usr \ --mandir=\$${prefix}/share/man \ --infodir=\$${prefix}/share/info touch configure-stamp build: build-arch build-indep build-arch: build-stamp build-indep: build-stamp build-stamp: configure $(QUILT_STAMPFN) dh_testdir $(MAKE) touch build-stamp clean: config-clean dh_testdir dh_testroot $(RM) -f build-stamp configure-stamp [ ! -f Makefile ] || $(MAKE) distclean dh_clean install: build dh_testdir dh_testroot dh_clean -k dh_installdirs $(MAKE) install DESTDIR=$(CURDIR)/debian/mcl # # install some extra stuff not installed by upstream install -c -m 644 $(CURDIR)/{AUTHORS,README,THANKS} $(CURDIR)/debian/mcl/usr/share/doc/mcl/ mkdir $(CURDIR)/debian/mcl/usr/share/doc/mcl/scripts install -c -m 644 $(CURDIR)/scripts/clx* $(CURDIR)/debian/mcl/usr/share/doc/mcl/scripts/ # # clean up unneeded docs $(RM) $(CURDIR)/debian/mcl/usr/share/doc/mcl/*txt # # process mcl-doc.install dh_install --sourcedir=debian/mcl dh_installdocs # # clean up files just copied to mcl-doc $(RM) $(CURDIR)/debian/mcl/usr/share/doc/mcl/{AUTHORS,README,THANKS} $(RM) $(CURDIR)/debian/mcl/usr/share/doc/mcl/*{html,ps,minimcl} $(RM) -r $(CURDIR)/debian/mcl/usr/share/doc/mcl/examples $(RM) -r $(CURDIR)/debian/mcl/usr/share/man/man[5,7] binary-indep: build install dh_installman dh_installchangelogs ChangeLog dh_compress dh_fixperms dh_installdeb dh_shlibdeps dh_gencontrol dh_md5sums dh_builddeb -pmcl-doc binary-arch: build install # no need to call dh_installexamples: upstream takes care of # this in 'make install' dh_installman dh_installchangelogs ChangeLog dh_strip dh_compress dh_fixperms dh_installdeb dh_shlibdeps dh_gencontrol dh_md5sums dh_builddeb -pmcl binary: binary-indep binary-arch .PHONY: build clean binary-indep binary-arch binary install configure config config-clean debian/mcl-doc.doc-base.mcxload0000644000000000000000000000053612101236635013534 0ustar Document: mcxload Title: mcxload - load matrices and tab files from label format Author: Stijn van Dongen Abstract: A document describing the mcxload command line tool. Section: Science/Mathematics Format: PostScript Files: /usr/share/doc/mcl/mcxload.ps.gz Format: HTML Index: /usr/share/doc/mcl/mcxload.html Files: /usr/share/doc/mcl/mcxload.html debian/mcl-doc.doc-base.clmformat0000644000000000000000000000054512101236635014071 0ustar Document: clmformat Title: clmformat - display cluster results in readable form Author: Stijn van Dongen Abstract: A document describing the clmformat command line tool. Section: Science/Mathematics Format: PostScript Files: /usr/share/doc/mcl/clmformat.ps.gz Format: HTML Index: /usr/share/doc/mcl/clmformat.html Files: /usr/share/doc/mcl/clmformat.html debian/mcl-doc.doc-base.mclpipeline0000644000000000000000000000062512101236635014405 0ustar Document: mclpipeline Title: mclpipeline - a generic pipeline for generating and scrutinizing mcl clusterings Author: Stijn van Dongen Abstract: A document describing the mclpipeline command line tool. Section: Science/Mathematics Format: PostScript Files: /usr/share/doc/mcl/mclpipeline.ps.gz Format: HTML Index: /usr/share/doc/mcl/mclpipeline.html Files: /usr/share/doc/mcl/mclpipeline.html debian/upstream0000644000000000000000000000056712101236635010760 0ustar Reference: Author: Stijn van Dongen and Cei Abreu-Goodger Title: Using MCL to extract clusters from networks Journal: Methods Mol Biol. Year: 2012 Volume: 804 Pages: 281-95 DOI: 10.1007/978-1-61779-361-5_15 PMID: 22144159 URL: http://www.springerlink.com/content/u5380k70754v8017 eprint: http://www.springerlink.com/content/u5380k70754v8017/fulltext.pdf debian/docs0000644000000000000000000000002612101236635010036 0ustar AUTHORS README THANKS debian/source/0000755000000000000000000000000012167042701010466 5ustar debian/source/format0000644000000000000000000000001412101236635011673 0ustar 3.0 (quilt) debian/mcl-doc.install0000644000000000000000000000032712101236635012075 0ustar usr/share/doc/mcl/AUTHORS usr/share/doc/mcl/README usr/share/doc/mcl/THANKS usr/share/doc/mcl/*.html usr/share/doc/mcl/*.ps usr/share/doc/mcl/minimcl usr/share/doc/mcl/examples usr/share/man/man5 usr/share/man/man7 debian/mcl-doc.doc-base.mclfaq0000644000000000000000000000072012101236635013343 0ustar Document: mclfaq Title: mclfaq - MCL and mcl quick faqs, facts, and terminology Author: Stijn van Dongen Abstract: A FAQ answering questions related to both the generic MCL algorithm and the MCL process on which the algorithm is based, as well as those related to the implementation. Section: Science/Mathematics Format: PostScript Files: /usr/share/doc/mcl/mclfaq.ps.gz Format: HTML Index: /usr/share/doc/mcl/mclfaq.html Files: /usr/share/doc/mcl/mclfaq.html debian/mcl-doc.doc-base.clmdist0000644000000000000000000000056612101236635013547 0ustar Document: clmdist Title: clmdist - compute the split/join distance between two partitions (clusterings) Author: Stijn van Dongen Abstract: A document describing the clmdist command line tool. Section: Science/Mathematics Format: PostScript Files: /usr/share/doc/mcl/clmdist.ps.gz Format: HTML Index: /usr/share/doc/mcl/clmdist.html Files: /usr/share/doc/mcl/clmdist.html debian/copyright0000644000000000000000000000535512101236635011130 0ustar This package was downloaded from http://micans.org/mcl/src/ Files: * Copyright: © 1999-2007 Stijn van Dongen License: GPL-2 This program is free software; you can redistribute it and/or modify it under the terms of version 2 of the GNU General Public License as published by the Free Software Foundation. It should be shipped with MCL in the top level directory as the file COPYING. . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . If you use MCL software in your scientific research, please cite it appropriately as you would cite a journal or a book. This includes papers published in regular or electronic journals, usage of MCL as a back-end to a database that is accessible via a web interface, or inclusion of MCL in a larger framework of software that is distributed for other people for scientific use. Include one of the following citations: . Stijn van Dongen, Graph Clustering by Flow Simulation. PhD thesis, University of Utrecht, May 2000. ( http://www.library.uu.nl/digiarchief/dip/diss/1895620/inhoud.htm ) . Stijn van Dongen. A cluster algorithm for graphs. Technical Report INS-R0010, National Research Institute for Mathematics and Computer Science in the Netherlands, Amsterdam, May 2000. ( http://www.cwi.nl/ftp/CWIreports/INS/INS-R0010.ps.Z ) . and proper attributions to mcl's home http://micans.org/mcl/ and its author, Stijn van Dongen. The publications listed above can be retrieved from the preceding URL. . If you are using some wrapper around mcl such as the blast module or the tribe module, you are asked to act likewise. . For biological applications, it is appropriate to cite, additionally, the reference article for the first application of mcl to biological data: . Enright A.J., Van Dongen S., Ouzounis C.A. An efficient algorithm for large-scale detection of protein families, Nucleic Acids Research 30(7):1575-1584 (2002). Files: src/alien/oxygen/src/mcxdeblast Copyright: © 2002-2005 Stijn van Dongen, © 2004 Jason Stajich License: GPL-2 Files: src/contrib/tribe/* Copyright: © 2002 EMBL-EBI Anton Enright License: GPL-2 Files: debian/* Copyright: © 2001-2007 Joost van Baal , © 2007-2009 Philipp Benner License: GPL-2+ The Debian packaging information is under the GPL, version 2 or later. On Debian GNU/Linux systems, the complete text of the GNU General Public License can be found in `/usr/share/common-licenses/GPL' and the complete text of the GNU Lesser General Public License can be found in `/usr/share/common-licenses/LGPL'. debian/mcl-doc.doc-base.mcx0000644000000000000000000000055412101236635012674 0ustar Document: mcx Title: mcx - a stack language interpreter for interaction with the mcl libraries Author: Stijn van Dongen Abstract: A document describing the mcx command line and interactive tool. Section: Science/Mathematics Format: PostScript Files: /usr/share/doc/mcl/mcx.ps.gz Format: HTML Index: /usr/share/doc/mcl/mcx.html Files: /usr/share/doc/mcl/mcx.html debian/control0000644000000000000000000000265112167041457010604 0ustar Source: mcl Section: math Priority: optional Maintainer: Debian Med Packaging Team Uploaders: Philipp Benner , Andreas Tille Build-Depends: debhelper (>= 7), dpkg-dev (>= 1.16.1~), autotools-dev, quilt, zoem, tidy, aephea Standards-Version: 3.9.4 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mcl/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mcl/ Homepage: http://micans.org/mcl/ Package: mcl Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: mcl-doc Enhances: blast2, ncbi-tools-bin, bioperl-run Description: Markov Cluster algorithm The MCL package is an implementation of the MCL algorithm, and offers utilities for manipulating sparse matrices (the essential data structure in the MCL algorithm) and conducting cluster experiments. . MCL is currently being used in sciences like biology (protein family detection, genomics), computer science (node clustering in Peer-to-Peer networks), and linguistics (text analysis). Package: mcl-doc Architecture: all Depends: ${misc:Depends} Section: doc Suggests: mcl Description: documentation for mcl The MCL package is an implementation of the Markov Cluster algorithm, for manipulating sparse matricess and conducting cluster experiments. . This is documention for mcl: the MCL FAQ, some examples as well as manpages in HTML and PostScript format. debian/compat0000644000000000000000000000000212101236635010363 0ustar 5 debian/mcl-doc.doc-base.mcxio0000644000000000000000000000066612101236635013230 0ustar Document: mcxio Title: mcxio - format spec for matrix input and output in mcl family Author: Stijn van Dongen Abstract: A document describing the generic matrix format used in the mcl libraries. It also describes the raw intermediate format used by mcxassemble. Section: Science/Mathematics Format: PostScript Files: /usr/share/doc/mcl/mcxio.ps.gz Format: HTML Index: /usr/share/doc/mcl/mcxio.html Files: /usr/share/doc/mcl/mcxio.html debian/mcl-doc.doc-base.mcl0000644000000000000000000000054412101236635012657 0ustar Document: mcl Title: MCL - the Amsterdam implementation of the Markov Cluster Algorithm Author: Stijn van Dongen Abstract: Description of the mcl command line tool and the MCL algorithm. Section: Science/Mathematics Format: PostScript Files: /usr/share/doc/mcl/mcl.ps.gz Format: HTML Index: /usr/share/doc/mcl/mcl.html Files: /usr/share/doc/mcl/mcl.html debian/patches/0000755000000000000000000000000012167042701010615 5ustar debian/patches/03-mayhem-io.patch0000644000000000000000000000222112167035421013741 0ustar --- a/src/impala/io.c +++ b/src/impala/io.c @@ -380,6 +380,7 @@ ) { unsigned char format = '0' ; mclxIOinfo* info = mclxIOinfofy(xf) + ; mclp ivp ; if (!info || mcxIOtestOpen(xf, RETURN_ON_FAIL) != STATUS_OK) { if (!info) @@ -395,9 +396,23 @@ if (mcxIOtryCookie(xf, mclxCookie)) { format = 'b' - ; fread(pn_cols, sizeof(long), 1, xf->fp) - ; fread(pn_rows, sizeof(long), 1, xf->fp) - ; info->n_read += 2 * sizeof(long) + ; if + ( 1 != fread(pn_cols, sizeof(long), 1, xf->fp) + || 1 != fread(pn_rows, sizeof(long), 1, xf->fp) + || pn_cols[0] < 0 + || DIM_MAX / sizeof ivp < pn_cols[0] + || pn_rows[0] < 0 + || DIM_MAX / sizeof ivp < pn_rows[0] + ) + { mcxErr + ( "mclxReadDimensions" + , "dimensions corrupt or too large (have %ld %ld)" + , (long) pn_cols[0] + , (long) pn_rows[0] + ) + ; return STATUS_FAIL + ; } + info->n_read += 2 * sizeof(long) ; } else if (mclxa_read_dimpart(xf, pn_cols, pn_rows) == STATUS_OK) format = 'a' debian/patches/01-restrict-variables.patch0000644000000000000000000000203312101241513015645 0ustar --- a/src/impala/matrix.c +++ b/src/impala/matrix.c @@ -1855,18 +1855,18 @@ mclv* mclgUnionv ( mclx* mx , const mclv* coldom -, const mclv* restrict +, const mclv* restrict_var , mcxenum scratch_STATUS , mclv* dst ) - { return mclgUnionv2(mx, coldom, restrict, scratch_STATUS, dst, mx->dom_rows) + { return mclgUnionv2(mx, coldom, restrict_var, scratch_STATUS, dst, mx->dom_rows) ; } mclv* mclgUnionv2 ( const mclx* mx , const mclv* coldom -, const mclv* restrict +, const mclv* restrict_var , mcxenum scratch_STATUS , mclv* dst , mclv* scratch @@ -1911,8 +1911,8 @@ ) continue /* SNH if coldom is subset of mx->dom_cols */ ; if - ( restrict - && 0 > (o_restrict = mclvGetIvpOffset(restrict, idx, o_restrict)) + ( restrict_var + && 0 > (o_restrict = mclvGetIvpOffset(restrict_var, idx, o_restrict)) ) continue /* not found in restriction domain */ debian/patches/02-wrong-interpreter-path.patch0000644000000000000000000000042112101236635016500 0ustar Author: Philipp Benner Purpose: Fix wrong path of perl interpreter --- mcl-10-201.orig/src/alien/oxygen/src/mcxdeblast +++ mcl-10-201/src/alien/oxygen/src/mcxdeblast @@ -1,4 +1,4 @@ -#!/usr/local/bin/perl -w +#!/usr/bin/perl -w use Getopt::Long; debian/patches/series0000644000000000000000000000017612167042374012044 0ustar 01-restrict-variables.patch 02-wrong-interpreter-path.patch 03-mayhem-io.patch 04-mayhem-vector.patch 05-manual-what-is.patch debian/patches/05-manual-what-is.patch0000644000000000000000000001015212167040366014713 0ustar --- a/doc/clmclose.azm +++ b/doc/clmclose.azm @@ -15,7 +15,7 @@ \${html}{\"pud::man::maketoc"} \sec{name}{NAME} -\NAME{clm close}{Fetch connected components from graphs or subgraphs} +\NAME{clm_close}{Fetch connected components from graphs or subgraphs} \disclaim_clm{close} --- a/doc/clmdist.azm +++ b/doc/clmdist.azm @@ -23,7 +23,7 @@ \def{sjd}{\bf{sjd}} \sec{name}{NAME} -\NAME{clm dist}{compute the distance between two or more partitions\ +\NAME{clm_dist}{compute the distance between two or more partitions\ (clusterings).} \par{ --- a/doc/clmformat.azm +++ b/doc/clmformat.azm @@ -15,7 +15,7 @@ \${html}{\"pud::man::maketoc"} \sec{*}{name}{NAME} -\NAME{clm format}{display cluster results in readable form} +\NAME{clm_format}{display cluster results in readable form} \par{ (optionally with labels and/or cohesion and stickiness measures --- a/doc/clmimac.azm +++ b/doc/clmimac.azm @@ -15,7 +15,7 @@ \${html}{\"pud::man::maketoc"} \sec{name}{NAME} -\NAME{clm imac}{Interpret Matrices (c.q. MCL iterands output by \mcl)\ +\NAME{clm_imac}{Interpret Matrices (c.q. MCL iterands output by \mcl)\ As Clusterings.} \disclaim_clm{imac} --- a/doc/clminfo.azm +++ b/doc/clminfo.azm @@ -15,7 +15,7 @@ \${html}{\"pud::man::maketoc"} \sec{name}{NAME} -\NAME{clm info}{compute performance measures for graphs and clusterings.} +\NAME{clm_info}{compute performance measures for graphs and clusterings.} \disclaim_clm{info} --- a/doc/clmmate.azm +++ b/doc/clmmate.azm @@ -15,7 +15,7 @@ \${html}{\"pud::man::maketoc"} \sec{name}{NAME} -\NAME{clm mate}{compute best matches between two clusterings} +\NAME{clm_mate}{compute best matches between two clusterings} \disclaim_clm{mate} --- a/doc/clmmeet.azm +++ b/doc/clmmeet.azm @@ -15,7 +15,7 @@ \${html}{\"pud::man::maketoc"} \sec{name}{NAME} -\NAME{clm meet}{compute the intersection of a set of clusterings.} +\NAME{clm_meet}{compute the intersection of a set of clusterings.} \disclaim_clm{meet} --- a/doc/clmorder.azm +++ b/doc/clmorder.azm @@ -15,7 +15,7 @@ \${html}{\"pud::man::maketoc"} \sec{name}{NAME} -\NAME{clm order}{reorder clusterings conformal to inclusion structure} +\NAME{clm_order}{reorder clusterings conformal to inclusion structure} \disclaim_clm{order} --- a/doc/clmresidue.azm +++ b/doc/clmresidue.azm @@ -15,7 +15,7 @@ \${html}{\"pud::man::maketoc"} \sec{name}{NAME} -\NAME{clm residue}{extend clustering of subgraph to clustering of graph.} +\NAME{clm_residue}{extend clustering of subgraph to clustering of graph.} \disclaim_clm{residue} --- a/doc/clmvol.azm +++ b/doc/clmvol.azm @@ -15,7 +15,7 @@ \${html}{\"pud::man::maketoc"} \sec{name}{NAME} -\NAME{clm vol}{compute volatile nodes from a set of clusterings} +\NAME{clm_vol}{compute volatile nodes from a set of clusterings} \disclaim_clm{vol} --- a/doc/mcxclcf.azm +++ b/doc/mcxclcf.azm @@ -15,7 +15,7 @@ \${html}{\"pud::man::maketoc"} \sec{name}{NAME} -\NAME{mcx clcf}{compute the clustering coefficient of a graph} +\NAME{mcx_clcf}{compute the clustering coefficient of a graph} \sec{synopsis}{SYNOPSIS} \par{ --- a/doc/mcxconvert.azm +++ b/doc/mcxconvert.azm @@ -15,7 +15,7 @@ \${html}{\"pud::man::maketoc"} \sec{name}{NAME} -\NAME{mcx convert}{convert between mcx storage types} +\NAME{mcx_convert}{convert between mcx storage types} \sec{synopsis}{SYNOPSIS} \par{ --- a/doc/mcxctty.azm +++ b/doc/mcxctty.azm @@ -15,7 +15,7 @@ \${html}{\"pud::man::maketoc"} \sec{name}{NAME} -\NAME{mcx ctty}{compute betweenness centrality for network nodes} +\NAME{mcx_ctty}{compute betweenness centrality for network nodes} \sec{synopsis}{SYNOPSIS} \par{ --- a/doc/mcxdiameter.azm +++ b/doc/mcxdiameter.azm @@ -15,7 +15,7 @@ \${html}{\"pud::man::maketoc"} \sec{name}{NAME} -\NAME{mcx diameter}{compute the diameter of a graph} +\NAME{mcx_diameter}{compute the diameter of a graph} \sec{synopsis}{SYNOPSIS} \par{ --- a/doc/mcxerdos.azm +++ b/doc/mcxerdos.azm @@ -15,7 +15,7 @@ \${html}{\"pud::man::maketoc"} \sec{name}{NAME} -\NAME{mcx erdos}{compute shortest paths in a graph} +\NAME{mcx_erdos}{compute shortest paths in a graph} \sec{synopsis}{SYNOPSIS} \par{ debian/patches/04-mayhem-vector.patch0000644000000000000000000000133212167032005014632 0ustar --- a/src/impala/vector.c 2013-07-09 11:05:22.084990745 +0100 +++ b/src/impala/vector.c 2013-07-09 11:05:51.940525340 +0100 @@ -139,7 +139,9 @@ /* I've had a suspicion that some reallocs might be too lazy * to reuse shrunk array space. */ - ; if (old_n_ivps / 2 > new_n_ivps) + ; if (DIM_MAX / sizeof new_ivps[0] < new_n_ivps) + /* DO NOTHING, enter mcxMemDenied below */ + ; else if (old_n_ivps / 2 > new_n_ivps) { new_ivps = mcxAlloc(new_n_ivps * sizeof new_ivps[0], ENQUIRE_ON_FAIL) ; if (new_ivps && !src_ivps) memcpy(new_ivps, dst_vec->ivps, new_n_ivps * sizeof new_ivps[0]) debian/changelog0000644000000000000000000003347312167033275011060 0ustar mcl (1:12-135-2) unstable; urgency=low * Added mayhem bugfixes. * Standards version 3.9.4. -- Philipp Benner Sun, 07 Jul 2013 15:01:08 +0200 mcl (1:12-135-1) unstable; urgency=low [ Andreas Tille ] * debian/upstream: Add citation information [ Philipp Benner ] * New upstream release * Hardening flags * Renamed variables with name 'restricted' in src/impala/matrix.c (Closes: #688655) -- Philipp Benner Sun, 27 Jan 2013 15:49:50 +0100 mcl (1:12-068-1) unstable; urgency=low * New upstream version * debian/control: Standards version 3.9.2 -- Philipp Benner Fri, 09 Mar 2012 15:15:48 +0000 mcl (1:11-294-1) unstable; urgency=low * New upstream version * debian/rules: Added targets build-indep and build-arch * debian/control: Standards version 3.9.2 -- Philipp Benner Wed, 02 Nov 2011 20:23:52 +0000 mcl (1:10-201-21) unstable; urgency=low * New upstream version * debian/control: - Added myself to uploaders - Fixed spelling of Debian Med - Standards-Version: 3.9.1 (no changes needed) - debhelper 7 - removed versioned conflicts for mcl-doc from quite old mcl version which seems to be useless these days * debian/source/format: 3.0 (quilt) * debian/rules, debian/patches/01-manpage-errors.patch: Use sed on installed packages to get the same effect as the patch but there is no need to change the patch for new versions -- Andreas Tille Mon, 24 Jan 2011 15:58:07 +0100 mcl (1:10-148-1) unstable; urgency=low * New upstream release -- Philipp Benner Tue, 01 Jun 2010 10:44:22 +0200 mcl (1:09-308-1) unstable; urgency=low * New upstream release * Moved repository to debian-med -- Philipp Benner Tue, 24 Nov 2009 20:43:56 +0000 mcl (1:09-261-1) unstable; urgency=low * New upstream release -- Philipp Benner Wed, 30 Sep 2009 10:54:28 +0000 mcl (1:09-182-1) unstable; urgency=low * New upstream release * New maintainer e-mail address * Removed DMUA -- Philipp Benner Fri, 24 Jul 2009 08:15:19 +0000 mcl (1:09-149-1) unstable; urgency=low * New upstream release. * Standards version 3.8.2. -- Philipp Benner Sat, 27 Jun 2009 20:33:54 +0000 mcl (1:08-312-1) unstable; urgency=low * New upstream release. * Added debian/patches/manpages-whatis-fix.patch. * Added debian/patches/perl-interpreter-path.patch * Build-depends on zoem and tidy to regenerate manuals. -- Philipp Benner Sun, 25 Jan 2009 12:29:28 +0000 mcl (1:06-058-2) unstable; urgency=low * New maintainer e-mail address. * debian/control: Added DM-Upload-Allowed: yes. * debian/mcl-doc.doc-base.mcxio: fixed typo. * Changed the doc-base section according to the new policy. -- Philipp Benner Mon, 31 Mar 2008 11:04:53 +0200 mcl (1:06-058-1) unstable; urgency=low * Adopting package (Closes: #452405). * Standards version 3.7.2. * Added Vcs-Browser and Vcs-Svn field to debian/control. * Machine interpretable copyright file. * Improved config.{guess,sub} handling. * New upstream release. -- Philipp Benner Mon, 26 Nov 2007 14:37:21 +0100 mcl (1:06-021-2) unstable; urgency=low * Orphaning this package (per Bug #452405). Set maintainer to Debian QA Group. * Move Homepage to control field. -- Joost van Baal Sat, 24 Nov 2007 00:35:03 +0100 mcl (1:06-021-1) unstable; urgency=low * New stable upstream release: Analysis and cache modes have been improved. This mcl binary in this release displays a citation reference on STDERR. Of course we honor upstream's wishes here, and do not suppress this helpful reminder. See the comments in debian/rules for hints on how to operate if you disagree. * debian/control: found out how to add Homepage pseudo-field (finally!) * debian/control: we no longer ship plain text manpages in mcl-doc, adjust description. -- Joost van Baal Tue, 07 Feb 2006 21:05:31 +0100 mcl (1:05-321-1) unstable; urgency=low * New stable upstream release. (Missed 05-272, 05-300, 05-314.) Some rephrased snippets from the announcement messages: + mcl-05-321: This mainly adds 'transformation' functionality, which complements the label-value streaming stuff. It means you can apply quite complex transformations on values, albeit only context-insensive transformations. + mcl-05-314: MCL can now read in label input in a simple line based format where each lines contains two labels and an optional value separated by whitespace. Output clusters are returned as lines of tab-separated labels. The BLAST parser can stream this format directly to mcl creating a very concise and easy to manage sequence clustering pipeline. The mcl(1) manual now has a 'getting started' section with some examples. New utility mcxload(1) with many custom options for reading in label data and transforming the associated numerical values, storing mappings in tab files and saving a graph in native mcl input format. + mcl-05-300: Important for mcxassemble users: Changed mcxassemble to pick the maximum between repeated entries by default. Other noteworthy changes: mcxdump can now also be used to restrict tab files, and: Fixed mcxsubs bug, introduced in last release, where selections never materialize unless one mysteriously specifies --rand-merge. No changes in mcl, only stuff done to the graph manipulation programs. + mcl-05-272: Major changes in clmimac, a noticeable change in mclblastline, a minor addition to mcxdeblast, improved dump functionality in mcl. If you just use mcl there is little need for upgrading. mcl-05-272 adds some extra stuff to doc/mcl/examples/ . As always, read changelog for details. * debian/mcl-doc.doc-base.mcxload: added * debian/{compat,control,rules}: move from debhelper compatibility level 3 to 4 (add ${misc:Depends} to Depends) * debian/copyright: new snailmail address of FSF. * debian/watch: make sure it doesn't match the symlink mcl-latest.tar.gz. * debian/rules, debian/mcl-doc.install: no longer install upstream TODO file: it's not useful for users. * debian/control: fix versioned conflicts syntax * debian/rules: make proper use of comments: don't clobber build output. * debian/control: Standards Version bumped from 3.6.1.0 to 3.6.2.0 (no changes needed). -- Joost van Baal Wed, 23 Nov 2005 16:36:39 +0100 mcl (1:05-118-1) unstable; urgency=low * New stable upstream release: a lot faster on large graphs because a clunky input routine was fixed. * debian/rules: Make sure config.{guess,sub} are up to date. (Upstream _does_ ship these.) * debian/mcl-doc.doc-base.mcl, debian/mcl-doc.doc-base.mclfaq: We are no longer shipping documentation in txt format. -- Joost van Baal Wed, 25 May 2005 08:09:54 +0200 mcl (1:05-096-1) unstable; urgency=low * New upstream development release. (Missed mcl-04-314, mcl-05-090.) The only difference between mcl 05-096 and the official 05-090 release is the addition of a clmorder(1) manpage. Here's a rephrased snippet from the 05-090 announcement message: Nothing changed in the core clustering algorithm. But: - Better support for diagnostics: mcl can now dump iterand submatrices. - Helper applications for analyzing cluster structure added: clxdo, clxcoarse (primitive hierarchical clustering, undocumented shell scripts, installed in /usr/share/doc/mcl/scripts) and clmorder. - Improvement of sibling applications: large mcxsubs rewrite - cleaner specification language and new modes and options. Also, rewrite of the IO library (umpteenth). Read changelog for details. * Install upstream TODO file. * Removed maintainer scripts: not needed for this package. * mcl-doc.doc-base.clmdist: fixed typo. -- Joost van Baal Wed, 06 Apr 2005 09:50:10 +0200 mcl (1:04-250-2) unstable; urgency=medium * control: Fixed embarrasing typo in description (closes: #285424). This is the reason urgency=medium rather than high: it'd be very nice if this package made it to sarge, so that not too many people get exposed to this ugly typo: s/computer sciense/computer science/. * mcl 04-314 is out, but might not get packaged: it has no shocking improvements, and a new upstream is likely to get published soon. -- Joost van Baal Sun, 16 Jan 2005 16:27:12 +0100 mcl (1:04-250-1) unstable; urgency=low * New upstream release. (Missed mcl-04-230.) * watch: added, so that http://qa.debian.org/developer.php?gpg_key=969457F0 looks even more spiffy. -- Joost van Baal Wed, 08 Sep 2004 15:04:32 +0200 mcl (1:04-189-1) unstable; urgency=low * New upstream release. (Missed mcl-04-174, 04-185, 04-187.) However, beware! mcl-04-103 might be considered non-free by some. LICENSE in this release is more clear, and free. debian/copyright updated accoringly. Furthermore, zoem >= 04-173 is needed for parsing cmlformat(1)'s zoem output. Such a zoem release is not yet packaged for Debian. * control: added Enhances: blast2, ncbi-tools-bin, bioperl. -- Joost van Baal Thu, 08 Jul 2004 12:13:30 +0200 mcl (1:04-103-1) unstable; urgency=low * New upstream development release. (Upstream has published six other development releases since 03-277.) * Splitted in mcl and mcl-doc binary packages. * No longer installs HTML documentation in plain text too. * Some manpages no longer register via doc-base; just the "major" ones do now. * Debian Policy compliance: bumped from Standards Version 3.5.9 to Standards-Version: 3.6.1.0: debian/rules now honors DEB_BUILD_OPTIONS. -- Joost van Baal Tue, 13 Apr 2004 07:59:47 +0200 mcl (1:03-277-1) unstable; urgency=low * New upstream release. This is the same as http://micans.org/mcl/src/mcl-03-276.tar.gz, the version number is the only thing which differs. * doc-base.clmmate: added. Upstream ships a clmmate manpage now: our package is lintian clean again. -- Joost van Baal Sun, 05 Oct 2003 12:27:53 +0200 mcl (1:03-276-1) unstable; urgency=low * New upstream _development_ release (missed formal releases 03-154, 03-178, 03-185, 03-245). * copyright: added note on citations when using the software in writing scientific papers. * rules: build and install BLAST parsing scripts. Do not build tribe stuff. See README for details. * doc-base.*: new docs: clmformat, mclblastline, mclpipeline, mcxassemble, mcxdeblast, mcxio. removed docs: clmconf, mcxformat. -- Joost van Baal Fri, 03 Oct 2003 11:48:46 +0200 mcl (1:03-010-2) unstable; urgency=low * Removed bogus mcximac doc-base file: mcximac does not exist. Tnx Laurent Bonnaud. (closes: #193058) -- Joost van Baal Thu, 15 May 2003 10:58:17 +0200 mcl (1:03-010-1) unstable; urgency=low * New upstream release. * Registered new docs using doc-base: clmimac, clmresidue, mcxmap. mcl and mclfaq now get installed in plain text format too. * debian/control: Standards 3.5.2 -> 3.5.9 (no changes needed). -- Joost van Baal Sat, 10 May 2003 10:29:04 +0200 mcl (1:02-277-1) unstable; urgency=low * New upstream release. -- Joost van Baal Fri, 25 Oct 2002 11:31:34 +0200 mcl (1:02-172-1) unstable; urgency=low * New upstream release. * debian/rules: no longer uses touch-hack to work around timeskew problems: upstreams uses AM_MAINTAINER_MODE now. -- Joost van Baal Mon, 24 Jun 2002 14:44:11 +0200 mcl (1:02-116-1) unstable; urgency=low * New upstream release. -- Joost van Baal Sat, 27 Apr 2002 22:59:49 +0200 mcl (1:02-113-cvs-1) unstable; urgency=low * build from current cvs, pre-release * debian/rules: set configure flags based on check equality of DEB_BUILD_GNU_TYPE and DEB_HOST_GNU_TYPE, cf current autotools-dev ideas. * debian/control, debian/copyright: MCL found a new home on the www. * debian/copyright: added note on contrib/tribe/ copyright holder. * doc-base.*: added doc-base.mclfaq and doc-base.mcximac -- Joost van Baal Tue, 23 Apr 2002 23:30:37 +0200 mcl (1:02-035-1) unstable; urgency=low * First release for the Debian archive (closes: #132283). * copyright: new download location, refer to /usr/share/common-licenses/GPL . * rules: applied some of Henrique de Moraes Holschuh's autotools-dev voodoo, got rid of some NOP dh_ calls. * docs: no longer installs NEWS; this file is not yet maintained upstream. -- Joost van Baal Wed, 6 Feb 2002 10:20:17 +0100 mcl (1:02-034-1) unstable; urgency=low * New upstream release. -- Joost van Baal Mon, 4 Feb 2002 08:33:36 +0100 mcl (1:02-030-1) unstable; urgency=low * Snapshot build from CVS. * Use epoch in version numbering, since upstream made order-breaking version numbering policy change. * Use docbase for all .ps and .html manpages. -- Joost van Baal Wed, 30 Jan 2002 22:46:28 +0100 mcl (20020116-1) unstable; urgency=low * Snapshot build from CVS. -- Joost van Baal Wed, 16 Jan 2002 21:08:22 +0100 mcl (20011211-1) unstable; urgency=low * New upstream release. Now registers documentation using doc-base. -- Joost van Baal Tue, 11 Dec 2001 20:19:42 +0100 mcl (20011012-1) unstable; urgency=low * Initial Release. -- Joost van Baal Fri, 12 Oct 2001 22:43:08 +0200 debian/README.source0000644000000000000000000000035012101236635011342 0ustar 01-manpage-errors.patch: remove spaces in the program name (which is not allowed in manuals) 02-wrong-interpreter-path.patch: fix perl interpreter paths -- Philipp Benner , Thu, 1 Oct 2009 13:38:53 +0000 debian/watch0000644000000000000000000000011112101236635010207 0ustar version=3 http://micans.org/mcl/src/mcl-(..-.*)\.tar\.gz debian uupdate