debian/0000755000000000000000000000000012153337166007175 5ustar debian/lutefisk-doc.manpages0000644000000000000000000000002712153337166013302 0ustar debian/lutefisk-doc.7 debian/lutefisk.manpages0000644000000000000000000000002312153337166012533 0ustar debian/lutefisk.1 debian/source/0000755000000000000000000000000012153337166010475 5ustar debian/source/format0000644000000000000000000000001512153337166011704 0ustar 3.0 (quilt) debian/lutefisk.install0000644000000000000000000000015612153337166012415 0ustar Lutefisk.details usr/share/lutefisk Lutefisk.residues usr/share/lutefisk debian/build-arch/lutefisk usr/bin debian/control0000644000000000000000000000233212153337166010600 0ustar Source: lutefisk Section: science Priority: optional Maintainer: The Debichem Group Uploaders: Filippo Rusconi DM-Upload-Allowed: yes Build-Depends: debhelper (>= 7), dpkg-dev (>= 1.16.1.1) Standards-Version: 3.9.4 Homepage: http://www.hairyfatguy.com/lutefisk/ Vcs-Git: git://git.debian.org/git/debichem/packages/lutefisk.git Vcs-Browser: http://git.debian.org/?p=debichem/packages/lutefisk.git Package: lutefisk Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: lutefisk-doc Description: de novo interpretation of peptide CID spectra Lutefisk performs a de novo interpreation of collision-induced decay (CID) spectra, providing the user with a file containing all the possible sequence candidates corresponding to the CID data. Package: lutefisk-doc Section: doc Architecture: all Depends: ${shlibs:Depends}, ${misc:Depends} Description: De novo interpretation of peptide CID spectra - documentation Lutefisk performs a de novo interpreation of collision-induced decay (CID) spectra, providing the user with a file containing all the possible sequence candidates corresponding to the CID data. . This package contains the manual in HTML format. debian/compat0000644000000000000000000000000212153337166010373 0ustar 7 debian/upstream0000644000000000000000000000075112153337166010763 0ustar Reference: Author: Richard S. Johnson and J. Alex Taylor Title: Searching sequence databases via de novo peptide sequencing by tandem mass spectrometry Journal: Molecular Biotechnology Year: 2002 Volume: 22 Number: 3 Pages: 301-315 DOI: 10.1385/MB:22:3:301 PMID: 12448884 URL: http://www.springerlink.com/content/3726h1m004207721/ eprint: http://www.springerlink.com/content/3726h1m004207721/fulltext.pdf Repository : http://sourceforge.net/projects/lutefiskxp/ debian/patches/0000755000000000000000000000000012153337166010624 5ustar debian/patches/build-flags0000644000000000000000000000042212153337166012736 0ustar Set an incremental CFLAGS flag using += instead of setting it using = so that the flags in debian/rules are not overwritten.--- a/src/Makefile.linux +++ b/src/Makefile.linux @@ -1,5 +1,5 @@ CC= gcc -O -CFLAGS= -D__LINUX +CFLAGS+=-D__LINUX LFLAGS= -lm -o NRAND= nrand48 debian/patches/series0000644000000000000000000000017712153337166012046 0ustar build-flags fix-html-doc-paragraph fix-math-h-include-header fix-global-definitions improve-feedback-to-user fix-pointer-stuff debian/patches/improve-feedback-to-user0000644000000000000000000001266112153337166015354 0ustar Improve the feedback to the user and make a better implementation of the usage explanations.--- a/src/LutefiskMain.c +++ b/src/LutefiskMain.c @@ -81,6 +81,27 @@ char versionString[256] = "LutefiskXP v1.0.7\nCopyright 1996-1906 Richard S. Johnson\n\n"; + +static void usage(void) +{ + /* print usage */ + puts("\nUSAGE: lutefisk [options] [CID file pathname]\n"); + puts( " The following options are available:\n"); + puts( " -o = output file pathname"); + puts( " -q = quiet mode ON (default OFF)"); + puts( " -m = precursor ion mass"); + puts( " -d = details file pathname"); + puts( " Default: /usr/share/lutefisk/Lutefisk.details"); + puts( " -p = params file pathname"); + puts( " -r = residues file pathname"); + puts( " Default: /usr/share/lutefisk/Lutefisk.residues"); + puts( " -s = pathnane of file with database sequences to score"); + puts( " -v = verbose mode ON (default OFF)"); + puts( " -h = print this help text"); + puts( "" ); + puts("\n"); +} + /* //-------------------------------------------------------------------------------- // main() @@ -604,82 +625,94 @@ strcpy(gParam.outputFile,""); - strcpy(gParam.detailsFilename,"Lutefisk.details"); - - strcpy(gParam.residuesFilename,"Lutefisk.residues"); + strcpy(gParam.detailsFilename,"/usr/share/lutefisk/Lutefisk.details"); + strcpy(gParam.residuesFilename,"/usr/share/lutefisk/Lutefisk.residues"); + /* get command-line parameters */ + + if (argc < 2) + { + usage(); + exit(1); + } - /* get command-line parameters */ - - while ((c = getopt(argc, argv, "?hqvd:o:m:p:r:s:")) != -1) - { + while ((c = getopt(argc, argv, "?hqvd:o:m:p:r:s:")) != -1) + { switch (c) - { + { - case 'o': + case 'o': /* output file name */ - strncpy(gParam.outputFile, optarg, sizeof(gParam.outputFile)); - break; + if (memccpy(gParam.outputFile, optarg, '\x0', sizeof(gParam.outputFile)) == NULL) + { + fprintf(stderr, "Argument filename max length = %d caracters", sizeof(gParam.outputFile) - 1 ); + exit(1); + } + break; - case 'd': + case 'd': /* details file name */ - strncpy(gParam.detailsFilename, optarg, sizeof(gParam.detailsFilename)); + if (memccpy(gParam.detailsFilename, optarg, '\x0', sizeof(gParam.detailsFilename)) == NULL) + { + fprintf(stderr, "Argument filename max length = %d caracters", sizeof(gParam.detailsFilename) - 1 ); + exit(1); + } break; - case 'm': + case 'm': /* peptide MW */ gParam.peptideMW = atof(optarg); break; - case 'p': + case 'p': /* param file name */ - strncpy(gParam.paramFile, optarg, sizeof(gParam.paramFile)); + if (memccpy(gParam.paramFile, optarg, '\x0', sizeof(gParam.paramFile)) == NULL) + { + fprintf(stderr, "Argument filename max length = %d caracters", sizeof(gParam.paramFile) - 1 ); + exit(1); + } break; - case 'q': + case 'q': /* QUIET! */ gParam.fMonitor = FALSE; gParam.fVerbose = FALSE; break; - case 'r': - /* residues file name */ - strncpy(gParam.residuesFilename, optarg, sizeof(gParam.residuesFilename)); - break; - - case 's': - /* database sequences file */ - strncpy(gParam.databaseSequences, optarg, sizeof(gParam.databaseSequences)); - break; - - case 'v': + case 'r': + /* residues file name */ + if (memccpy(gParam.residuesFilename, optarg, '\x0', sizeof(gParam.residuesFilename)) == NULL) + { + fprintf(stderr, "Argument filename max length = %d caracters", sizeof(gParam.residuesFilename) - 1 ); + exit(1); + } + break; + + case 's': + /* database sequences file */ + if (memccpy(gParam.databaseSequences, optarg, '\x0', sizeof(gParam.databaseSequences)) == NULL) + { + fprintf(stderr, "Argument filename max length = %d caracters", sizeof(gParam.databaseSequences) - 1 ); + exit(1); + } + break; + + case 'v': /* verbose */ gParam.fVerbose = TRUE; break; - case '?': - case 'h': - /* print usage */ - puts("\nUSAGE: lutefisk [options] [CID file pathname]\n"); - puts( " -o = output file pathname"); - puts( " -q = quiet mode ON (default OFF)"); - puts( " -m = precursor ion mass"); - puts( " -d = details file pathname"); - puts( " -p = params file pathname"); - puts( " -r = residues file pathname"); - puts( " -s = pathnane of file with database sequences to score"); - puts( " -v = verbose mode ON (default OFF)"); - puts( " -h = print this help text"); - puts( "" ); - puts("\n"); - exit(1); - - break; - } - } - + case '?': + case 'h': + /* print usage */ + usage(); + exit(1); + + break; + } + } /* report flag state */ debian/patches/fix-pointer-stuff0000644000000000000000000000066312153337166014145 0ustar Fix some NULL pointer stuff.--- a/src/LutefiskXCorr.c +++ b/src/LutefiskXCorr.c @@ -251,7 +251,7 @@ Determine the sequence length. */ pSeq = &currScorePtr->peptide[0]; - while(*pSeq != NULL) + while(*pSeq != '\x0') { seqLength++; pSeq++; @@ -552,8 +552,8 @@ */ pSeq = &currScorePtr->peptide[0]; seqLength = 0; - while(*pSeq != NULL) - { + while(*pSeq != '\x0') + { seqLength++; pSeq++; } debian/patches/fix-html-doc-paragraph0000644000000000000000000000063412153337166015010 0ustar Small fix to the user html-formatted documentation to better reflect the location of files on a Debian system.--- a/docs/index.html +++ b/docs/index.html @@ -499,7 +499,7 @@ Files

To run Lutefisk, you need to have four -files within the same directory or folder:

+files:

debian/patches/fix-global-definitions0000644000000000000000000000251512153337166015107 0ustar Improve global definitions.--- a/src/LutefiskDefinitions.h +++ b/src/LutefiskDefinitions.h @@ -143,6 +143,7 @@ #define BOOLEAN unsigned char #endif +#define MAX_FILENAME_SIZE 4096 /* Define a few constants. */ #define AMINO_ACID_NUMBER 25 /*Number of amino acids.*/ @@ -357,11 +358,11 @@ char fVerbose; clock_t startTicks; clock_t searchTime; - char paramFile[256]; - char outputFile[256]; - char cidFilename[256]; - char detailsFilename[256]; - char residuesFilename[256]; + char paramFile[MAX_FILENAME_SIZE]; + char outputFile[MAX_FILENAME_SIZE]; + char cidFilename[MAX_FILENAME_SIZE]; + char detailsFilename[MAX_FILENAME_SIZE]; + char residuesFilename[MAX_FILENAME_SIZE]; REAL_4 peptideMW; INT_4 chargeState; BOOLEAN maxent3; @@ -395,10 +396,10 @@ REAL_4 peptideErr; BOOLEAN autoTag; BOOLEAN edmanPresent; - char edmanFilename[256]; + char edmanFilename[MAX_FILENAME_SIZE]; REAL_4 ionsPerResidue; char CIDfileType; - char databaseSequences[256]; + char databaseSequences[MAX_FILENAME_SIZE]; BOOLEAN quality; INT_4 wrongSeqNum; @@ -416,7 +417,7 @@ REAL_4 modifiedNTerm_orig; REAL_4 modifiedCTerm_orig; INT_4 maxGapNum_orig; - char outputFile_orig[256]; + char outputFile_orig[MAX_FILENAME_SIZE]; }tParam; debian/patches/fix-math-h-include-header0000644000000000000000000000106712153337166015364 0ustar Add #include statements.--- a/src/LutefiskHaggis.c +++ b/src/LutefiskHaggis.c @@ -34,6 +34,7 @@ #include #include #include +#include /* Haggis headers */ #include "LutefiskPrototypes.h" @@ -2275,4 +2276,4 @@ } } return; -} \ No newline at end of file +} --- a/src/LutefiskMain.c +++ b/src/LutefiskMain.c @@ -52,6 +52,7 @@ #include #include #include +#include #if(defined(__MWERKS__) && __dest_os == __mac_os) /* Some Macintosh specific things */ debian/lutefisk-doc.install0000644000000000000000000000004212153337166013152 0ustar docs /usr/share/doc/lutefisk-doc debian/lutefisk.10000644000000000000000000000556212153337166011115 0ustar .TH "LUTEFISK" "1" "2009/04/29" "" "" .SH "NAME" lutefisk \- software for the de novo interpretation of peptide CID spectra .SH "SYNOPSIS" \fBlutefisk\fR [\-q ] [ \-m ] [ \-d] [ \-p ] [ \-r ] [ \-s ] [ \-v] [ \-h] [\-o ] .SH "DESCRIPTION" \fBlutefisk\fR is a software for the de novo interpretation of peptide CID spectra. It takes peptide CID data and some ancillary data files (of which the location is specified on the command line) and outputs a results file containing all the sequences hypothetically matching the CID data. When you invoke \fBlutefisk\fR with the \fB\-h\fR option, the program lists to the command line all the options that are available. .SH "OPTIONS" .TP .B \-h Print a list of options .TP .B \-q Run in quiet mode .TP .B \-m Precursor ion mass .TP .B \-d Pathname to the details file .TP .B \-p Pathname to the params file .TP .B \-r Pathname to the residues file .TP .B \-s Pathname to the file with database sequences to score .TP .B \-v Run in verbose mode .TP .B \-o Output file .TP .B CID data file .SH "PROGRAM DATA" The data required to run the program are located in \fI\%/usr/share/lutefisk\fP. .SH "EXAMPLE DATA" Example data are located in \fI\%/usr/share/doc/lutefisk/examples\fP. .SH "BIBLIOGRAPHICAL REFERENCES TO BE CITED" R. S. Johnson and J. A. Taylor (2002) "Searching sequence databases via de novo peptide sequencing by tandem mass spectrometry", Mol. Biotechnology Vol. 22, No. 3. (November 2002), pp. 301\-315. .PP J. A. Taylor and R. S. Johnson (2000) "Implementation and uses of automated de novo peptide sequencing by tandem mass spectrometry". Anal. Chem. 73:2594\-2604. .PP R. S. Johnson and J. A. Taylor (2000) "Searching sequence databases via de novo peptide sequencing by tandem mass spectrometry", "Protein and Peptide Analysis: Advances in the Use of Mass Spectrometry", 146:41\-61 (Methods in Molecular Biology series, Humana Press). .PP J. A. Taylor and R. S. Johnson (1997) "Sequence database searches via de novo peptide sequencing by tandem mass spectrometry". Rapid Comm. Mass Spec. 11:1067-1075. .SH "SEE ALSO" .BR lutefisk\-doc (7). .SH "AUTHORS" \fB Richard S. Johnson\fR <\&jsrichar@alum.mit.edu\&>. .sp -1n .IP "" 4 Program author. .PP \fBFilippo Rusconi\fR <\&rusconi\-debian@laposte.net\&>. .sp -1n .IP "" 4 Man\-page author for the Debian distribution\&. .SH "COPYRIGHT" Copyright \(co 1995\-1999 Richard S. Johnson .PP Copyright \(co 2009 Filippo Rusconi .PP This manual page was written for the Debian system (but may be used by others). .PP Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 3 or (at your option) any later version published by the Free Software Foundation\&. .PP On a Debian system the complete text of the GNU General Public License version 3 can be found in the file `\fI\%/usr/share/common-licenses/GPL\-3\fP'. debian/copyright0000644000000000000000000000627212153337166011137 0ustar This package was debianized by Filippo Rusconi on Wed, 13 May 2009 18:48:36 +0200. It was downloaded from http://sourceforge.net/projects/lutefiskxp/ Author: Richard S. Johnson Lutefisk Copyright © 1995-1999 Richard S. Johnson License for Lutefisk: GNU General Public License This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. 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. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. On Debian systems, the GNU General Public License, is available as the file `/usr/share/common-licenses/GPL-2'. License for Lutefisk documentation files: GNU General Public License Although the main documentation file has the following two lines Copyright © 2005 Rich Johnson (jsrichar@alum.mit.edu)
All rights reserved worldwide the documentation is under GPLv2, as shown in the transcript of mails exchanged with the upstream author. ~~~~~~~~~~~~~~~~~~~~~~~~ BEGIN TRANSCRIPT ~~~~~~~~~~~~~~~~~~~~~~~~ From toxothurston@gmail.com Thu Apr 30 07:45:12 2009 In-Reply-To: <20090428162709.GE3730@biophypfr> References: <20090428162709.GE3730@biophypfr> Date: Wed, 29 Apr 2009 17:37:43 -0700 Message-ID: Subject: Re: Lutefisk enquiry, specifically the documentation From: Richard Johnson To: Filippo Rusconi Yes, its all under the same license. Rich On Tue, Apr 28, 2009 at 9:27 AM, Filippo Rusconi wrote: > Greetings, > > I am starting the packaging of Lutefisk for GNU/Linux (Debian, > specifically). I would also like to package the documentation, as the > set of files that come along with the source tarball. Could you please > tell me if the docs/* files are all under the same license as the > program itself (GPL v2)? > > Thank you for choosing the GPL for publishing your work. > > Sincerely, Filippo > > -- > Filippo Rusconi, PhD - CNRS - public key C78F687C > Author of ``massXpert'' at http://www.massxpert.org > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.9 (GNU/Linux) > > iEYEARECAAYFAkn3Ll0ACgkQTTOs5MePaHwxmACffAUYh8AmoCIyhypXBnPrr5L/ > UNoAoKErhXRK/ssTzRo2jHbVTfU1t1I8 > =g+of > -----END PGP SIGNATURE----- ~~~~~~~~~~~~~~~~~~~~~~ END TRANSCRIPT ~~~~~~~~~~~~~~~~~~~~~~ The Debian packaging is © 2009 Filippo Rusconi and is licensed under the GPL, see `/usr/share/common-licenses/GPL-3'. debian/rules0000755000000000000000000000426312153337166010262 0ustar #!/usr/bin/make -f # Based on the initial work of Joey Hess and Craig Small. # Uncomment this to turn on verbose mode. export DH_VERBOSE=1 DEB_HOST_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_HOST_GNU_TYPE) DEB_BUILD_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE) PACKAGE=lutefisk BUILD_DIR = $(CURDIR)/debian/build-arch ifneq (,$(filter parallel=%,$(DEB_BUILD_OPTIONS))) NUMJOBS = $(patsubst parallel=%,%,$(filter parallel=%,$(DEB_BUILD_OPTIONS))) MAKEFLAGS += -j$(NUMJOBS) endif $(info "---------------------------------------") $(info NUMJOBS: $(NUMJOBS)) $(info MAKEFLAGS: $(MAKEFLAGS)) $(info DEB_BUILD_OPTIONS: $(DEB_BUILD_OPTIONS)) $(info "---------------------------------------") # Hardening stuff, see http://wiki.debian.org/Hardening # export DEB_BUILD_MAINT_OPTIONS = hardening=+all # DPKG_EXPORT_BUILDFLAGS = 1 # include /usr/share/dpkg/buildflags.mk # $(info CFLAGS: $(CFLAGS)) # Uncomment to monitor the log of package building (pdebuild log) # .NOTPARALLEL: .PHONY: clean clean: dh_testdir dh_testroot dh_clean rm -rf $(BUILD_DIR) configure-stamp: dh_testdir mkdir -p $(BUILD_DIR) cp -rpf src/* $(BUILD_DIR) ln -s $(BUILD_DIR)/Makefile.linux $(BUILD_DIR)/Makefile touch configure-stamp .PHONY: build build: build-indep build-arch .PHONY: build-indep build-indep: .PHONY: build-arch build-arch: build-arch-stamp build-arch-stamp: configure-stamp dh_testdir dh_prep -a cd $(BUILD_DIR) && $(MAKE) all touch build-arch-stamp # Build architecture-independent files here. .PHONY: binary-indep binary-indep: dh_testdir -i dh_testroot -i dh_installchangelogs HISTORY.txt -i dh_installdocs -i dh_install -i dh_installman -i dh_compress -i dh_fixperms -i dh_installdeb -i dh_gencontrol -i dh_md5sums -i dh_builddeb -i # Build architecture-dependent files here. .PHONY: binary-arch binary-arch: build-arch dh_testdir -a dh_testroot -a dh_installchangelogs HISTORY.txt -a dh_installdocs -a dh_installexamples -a dh_install -a dh_installman -a dh_strip -a dh_compress -a dh_fixperms -a dh_installdeb -a dh_shlibdeps -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a .PHONY: binary binary: binary-indep binary-arch debian/get-orig-source.sh0000755000000000000000000000145412153337166012553 0ustar #!/bin/sh set -ex UPSTREAM_VERSION=$2 ORIG_TARBALL=$3 REAL_TARBALL=`readlink -f ${ORIG_TARBALL}` WORKING_DIR=`dirname ${ORIG_TARBALL}` ORIG_TARBALL_DFSG=`echo ${ORIG_TARBALL} | sed -e "s/\(${UPSTREAM_VERSION}\)\(\.orig\)/\1+dfsg\2/g"` ORIG_TARBALL_DIR=`echo ${ORIG_TARBALL_DFSG} | sed -e "s/_\(${UPSTREAM_VERSION}\)/-\1/g" -e "s/\.tar\.gz//g"` ORIG_TARBALL_DIR_STRIP=`basename ${ORIG_TARBALL_DIR}` mkdir -p ${ORIG_TARBALL_DIR} tar --directory=${ORIG_TARBALL_DIR} --strip 1 -xzf ${REAL_TARBALL} || exit 1 rm -f ${ORIG_TARBALL} ${REAL_TARBALL} rm -rf ${ORIG_TARBALL_DIR}/windoze/ mv -f "${ORIG_TARBALL_DIR}/docs/LutefiskXP Operators Manual.htm" "${ORIG_TARBALL_DIR}/docs/index.html" GZIP=-9 tar --remove-files --directory ${WORKING_DIR} -czf ${ORIG_TARBALL_DFSG} ${ORIG_TARBALL_DIR_STRIP} || exit 1 exit 0 debian/lutefisk-doc.70000644000000000000000000000251512153337166011661 0ustar .TH "LUTEFISK" "7" "2009/04/25" "" "" .SH "NAME" lutefisk-doc \- software for the de novo interpretation of peptide CID spectra (documentation) .SH "DESCRIPTION" This manual page documents briefly the \fBlutefisk\-doc\fR package. This package contains the user manual for the \fBlutefisk\fR software package. The documentation is provided in the form of a set of HTML files. The files are located in /usr/share/doc/lutefisk\-doc. Note that the documentation is also available at \fI\%http://www.hairyfatguy.com/lutefisk/docs/\fP. .SH "SEE ALSO" .BR lutefisk (1). .SH "AUTHORS" \fB Richard S. Johnson\fR <\&jsrichar@alum.mit.edu\&>. .sp -1n .IP "" 4 Program author. .PP \fBFilippo Rusconi\fR <\&rusconi\-debian@laposte.net\&>. .sp -1n .IP "" 4 Man\-page author for the Debian distribution\&. .SH "COPYRIGHT" Copyright \(co 1995\-1999 Richard S. Johnson .PP Copyright \(co 2009 Filippo Rusconi .PP This manual page was written for the Debian system (but may be used by others). .PP Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 3 or (at your option) any later version published by the Free Software Foundation\&. .PP On a Debian system the complete text of the GNU General Public License version 3 can be found in the file `\fI\%/usr/share/common-licenses/GPL\-3\fP'. debian/lutefisk.dirs0000644000000000000000000000001112153337166011676 0ustar usr/bin debian/watch0000644000000000000000000000021712153337166010226 0ustar version=3 opts=dversionmangle=s/\+dfsg$// \ http://sf.net/lutefiskxp/LutefiskXPv([\d.]+)\.tar\.gz \ debian /bin/sh debian/get-orig-source.sh debian/lutefisk-doc.doc-base0000644000000000000000000000055412153337166013171 0ustar Document: lutefisk-documentation Title: lutefisk Author: Richard S. Johnson Abstract: This manual describes what lutefisk is and how it can be used to perform de novo interpretations of peptide CID spectra. Section: Science/Chemistry Format: HTML Index: /usr/share/doc/lutefisk-doc/docs/index.html Files: /usr/share/doc/lutefisk-doc/docs debian/changelog0000644000000000000000000000355112153337166011053 0ustar lutefisk (1.0.7+dfsg-1) unstable; urgency=low * new upstream version; * applied patches as for previous version, but this time using the dquilt setup. For that set the source format to 3.0 (quilt); * debian/control: Standards-Version: 3.9.4 and set address to lopippo@debian.org; * set the basis for hardening stuff but commented out because would require a lot of work. I let that for another release; * set dpkg-dev (>= 1.16.1.1) to build depends for hardening stuff; * debian/watch: new version of watch file from kind contribution of Daniel Leidert ; * debian/get-orig-source.sh: script to get the original source, clean it and make an orig tarball. Kind contribution from Daniel; Leidert. (Closes: #675830; sorry Daniel that I somehow skipped the bug report for so long); * change debian/get-orig-source.sh so that awful doc file name is moved to index.html; * debian/rules: remove the renaming of the doc file since performed at orig tarball constitution. -- Filippo Rusconi Tue, 04 Jun 2013 12:06:36 +0200 lutefisk (1.0.5a.cleaned-1) unstable; urgency=low * Initial release (Closes: #527141); * Removed file windoze/lutefisk.exe that was shipped in the upstream tarball; * Fixed glitches in the upstream source that had gcc emit warning (#include in two files and and replace 'NULL' with '\x0' to test end of array in one file); * Move the main HTML documentation file (space-ridden filename) to index.html; * Look for default files in /usr/share/lutefisk/, not current directory. * Display usage help when no argument given. * Protect against too long filenames (and raise the limit). * Sponsored upload done by Lionel Elie Mamane . -- Filippo Rusconi Wed, 09 Dec 2009 22:42:38 +0100 debian/lutefisk.examples0000644000000000000000000000014612153337166012564 0ustar database.sequence Lutefisk.lcq_params Lutefisk.qtof_params Qtof_ELVISLIVESK.dta Qtof_ELVISLIVESK.lut