[med-svn] r9507 - in trunk/packages/blimps: . trunk trunk/debian trunk/debian/patches trunk/debian/source
Laszlo Kajan
lkajan-guest at alioth.debian.org
Tue Jan 31 17:21:49 UTC 2012
Author: lkajan-guest
Date: 2012-01-31 17:21:48 +0000 (Tue, 31 Jan 2012)
New Revision: 9507
Added:
trunk/packages/blimps/tags/
trunk/packages/blimps/trunk/
trunk/packages/blimps/trunk/debian/
trunk/packages/blimps/trunk/debian/README.Debian
trunk/packages/blimps/trunk/debian/README.source
trunk/packages/blimps/trunk/debian/blimps-data.install
trunk/packages/blimps/trunk/debian/blimps-utils.install
trunk/packages/blimps/trunk/debian/changelog
trunk/packages/blimps/trunk/debian/compat
trunk/packages/blimps/trunk/debian/control
trunk/packages/blimps/trunk/debian/copyright
trunk/packages/blimps/trunk/debian/libblimps3-dev.install
trunk/packages/blimps/trunk/debian/libblimps3.install
trunk/packages/blimps/trunk/debian/patches/
trunk/packages/blimps/trunk/debian/patches/Makefile
trunk/packages/blimps/trunk/debian/patches/patch_001.diff
trunk/packages/blimps/trunk/debian/patches/patch_002.diff
trunk/packages/blimps/trunk/debian/patches/series
trunk/packages/blimps/trunk/debian/rules
trunk/packages/blimps/trunk/debian/source/
trunk/packages/blimps/trunk/debian/source/format
Modified:
trunk/packages/blimps/
Log:
initial Debianization essentially copied from the Debianization done by Laszlo Kajan at the Rost Lab
Property changes on: trunk/packages/blimps
___________________________________________________________________
Added: svn:ignore
+ build-area
tarballs
Added: trunk/packages/blimps/trunk/debian/README.Debian
===================================================================
--- trunk/packages/blimps/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/blimps/trunk/debian/README.Debian 2012-01-31 17:21:48 UTC (rev 9507)
@@ -0,0 +1,8 @@
+blimps for Debian
+-----------------
+
+Out of the many binaries from the upstream blimps package only fastaseqs is
+included in blimps-utils. The reason for this is that only that utility is
+needed by the sift package, which depends on blimps.
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Wed, 25 Nov 2009 12:26:22 +0100
Added: trunk/packages/blimps/trunk/debian/README.source
===================================================================
--- trunk/packages/blimps/trunk/debian/README.source (rev 0)
+++ trunk/packages/blimps/trunk/debian/README.source 2012-01-31 17:21:48 UTC (rev 9507)
@@ -0,0 +1,11 @@
+blimps for Debian
+-----------------
+
+Patches
+.......
+
+??:
+* ??
+
+# vim:et:ts=2:
+
Added: trunk/packages/blimps/trunk/debian/blimps-data.install
===================================================================
--- trunk/packages/blimps/trunk/debian/blimps-data.install (rev 0)
+++ trunk/packages/blimps/trunk/debian/blimps-data.install 2012-01-31 17:21:48 UTC (rev 9507)
@@ -0,0 +1 @@
+usr/share/blimps
Added: trunk/packages/blimps/trunk/debian/blimps-utils.install
===================================================================
--- trunk/packages/blimps/trunk/debian/blimps-utils.install (rev 0)
+++ trunk/packages/blimps/trunk/debian/blimps-utils.install 2012-01-31 17:21:48 UTC (rev 9507)
@@ -0,0 +1,4 @@
+usr/bin/fastaseqs
+usr/share/man
+usr/share/doc/blimps/README
+usr/share/doc/blimps/UPDATES
Added: trunk/packages/blimps/trunk/debian/changelog
===================================================================
--- trunk/packages/blimps/trunk/debian/changelog (rev 0)
+++ trunk/packages/blimps/trunk/debian/changelog 2012-01-31 17:21:48 UTC (rev 9507)
@@ -0,0 +1,6 @@
+blimps (3.9-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #657897)
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Sun, 29 Jan 2012 18:48:44 +0000
+
Added: trunk/packages/blimps/trunk/debian/compat
===================================================================
--- trunk/packages/blimps/trunk/debian/compat (rev 0)
+++ trunk/packages/blimps/trunk/debian/compat 2012-01-31 17:21:48 UTC (rev 9507)
@@ -0,0 +1 @@
+7
Added: trunk/packages/blimps/trunk/debian/control
===================================================================
--- trunk/packages/blimps/trunk/debian/control (rev 0)
+++ trunk/packages/blimps/trunk/debian/control 2012-01-31 17:21:48 UTC (rev 9507)
@@ -0,0 +1,51 @@
+Source: blimps
+Priority: extra
+Maintainer: Laszlo Kajan <lkajan at rostlab.org>
+Build-Depends: debhelper (>= 7.0.50~)
+Standards-Version: 3.9.2
+Section: libs
+Homepage: http://blocks.fhcrc.org/blocks/uploads/blimps
+
+Package: blimps-utils
+Section: science
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, libblimps3
+Recommends: blimps-data
+Description: blocks database improved searcher
+ BLIMPS (BLocks IMProved Searcher) is a searching tool that scores
+ a sequence against blocks or a block against sequences.
+ .
+ This package contains the binaries.
+
+Package: blimps-data
+Section: science
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: blocks database improved searcher
+ BLIMPS (BLocks IMProved Searcher) is a searching tool that scores
+ a sequence against blocks or a block against sequences.
+ .
+ This package contains data files such as matrices.
+
+Package: libblimps3-dev
+Section: libdevel
+Architecture: any
+Depends: ${misc:Depends}, libblimps3 (= ${binary:Version})
+Suggests: blimps-utils
+Provides: libblimps-dev
+Description: blocks database improved searcher
+ BLIMPS (BLocks IMProved Searcher) is a searching tool that scores
+ a sequence against blocks or a block against sequences.
+ .
+ This package provides the library development headers and the static library.
+
+Package: libblimps3
+Section: libs
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Suggests: blimps-utils
+Description: blocks database improved searcher
+ BLIMPS (BLocks IMProved Searcher) is a searching tool that scores
+ a sequence against blocks or a block against sequences.
+ .
+ This package provides the shared library.
Added: trunk/packages/blimps/trunk/debian/copyright
===================================================================
--- trunk/packages/blimps/trunk/debian/copyright (rev 0)
+++ trunk/packages/blimps/trunk/debian/copyright 2012-01-31 17:21:48 UTC (rev 9507)
@@ -0,0 +1,145 @@
+This package was debianized by Laszlo Kajan <lkajan at rostlab.org> on
+Wed, 25 Nov 2009 12:26:22 +0100.
+
+It was downloaded from http://blocks.fhcrc.org/blocks/uploads/blimps .
+
+Upstream Author:
+
+ J. Henikoff
+
+Copyright:
+
+ Copyright 1998, Fred Hutchinson Cancer Research Center
+
+License:
+
+ (C) Copyright 1993-2007, Fred Hutchinson Cancer Research Center
+
+ LICENSE -- License and copyright information for BLOCKS and BLIMPS
+
+
+
+ ---------------------------------------------------------------------------
+ FHCRC NONCOMMERCIAL LICENSE
+ Fred Hutchinson Cancer Research Center
+ 1100 Fairview AV N
+ Seattle, WA 98109-1024
+
+
+ This license may be copied and distributed but may not be modified in
+ any way.
+
+ RECITALS:
+
+ A. Fred Hutchinson Cancer Research Center is a nonprofit
+ corporation dedicated to investigating the nature and causes of cancer
+ and methods of cancer prevention and treatment and for conducting
+ education in all phases of cancer research.
+
+ B. This license is designed to permit certain activities with
+ respect to any computer programs to which it applies on the terms
+ stated in this license.
+
+ TERMS AND CONDITIONS:
+
+ 1. Definitions.
+
+ "Program" means the computer software and associated
+ documentation in whatever form or format including source and object
+ code.
+
+ "Derivative Work" means any modification, addition, upgrade,
+ update or improvement of the Program and any other work constituting a
+ derivative work under the copyright laws.
+
+ "Licensee" means licensee of the Program under this license.
+
+ "FHCRC" means Fred Hutchinson Cancer Research Center.
+
+ 2. License, Copy, Distribute and Create Derivative Work. FHCRC
+ hereby grants Licensee and Licensee accepts, subject to the terms and
+ conditions of this Agreement, a nonexclusive, royalty-free license to
+ use, copy and sublicense the Program and prepare and sublicense
+ Derivative Works. This license is expressly limited as follows:
+
+ a. All copies of the Program must conspicuously show an
+ appropriate copyright notice and disclaimer of warranty and must
+ expressly refer to this license. In addition, Derivative Works must
+ conspicuously state that the Program has been modified and the date of
+ any modification.
+
+ b. Licensee may not charge any fee or royalty for copies
+ of the Program or Derivative Work. Licensee is authorized to
+ sublicense the Program and any Derivative Work to third parties on a
+ royalty-free basis subject to the terms of this license but may not
+ otherwise distribute the Program or any Derivative Work.
+ Notwithstanding the foregoing, Licensee may be reimbursed for any
+ actual expenses it incurs in reproducing or delivering a copy of the
+ Program or any Derivative Work.
+
+ c. This license does not apply to a work written entirely
+ by Licensee.
+
+ d. Licensee agrees to make available to any person to whom
+ it sublicenses this Program or a Derivative Work source code and
+ object code for the Program or Derivative Work.
+
+ e. Licensee may not impose any terms in addition to the
+ terms of this license on any third party to whom it distributes the
+ Program, any Derivative Work or any copy thereof.
+
+ 3. Reservation of Rights to FHCRC. FHCRC hereby reserves to
+ itself all rights of any nature whatsoever with respect to the
+ Program. Any Derivative Work created by FHCRC or its employees or
+ agents is not subject to the terms of this license.
+
+ 4. Termination of license. This license precludes any copying,
+ modification, sublicensing or other distribution of any Program or
+ Derivative Work except as expressly permitted under this license.
+ Violation of the terms of this license by Licensee will be deemed an
+ automatic termination of Licensee's rights under this license;
+ provided, however, that sublicenses derived from Licensee will remain
+ in full force and effect provided that any such sublicensees do not
+ breach the terms of this license.
+
+ 5. Acceptance of Terms of License. Licensee agrees that by
+ copying or distributing this Program or by creating, copying or
+ distributing any Derivative Work, Licensee has agreed to the terms of
+ this license.
+
+ 6. Limitation of Remedies and Indemnity. Because this Program
+ is licensed on a royalty-free basis, FHCRC and any person distributing
+ this Program or any Derivative Work expressly disclaim all warranties
+ express or implied including, without limitation, any implied warranty
+ of merchantability or fitness for a particular purpose. Neither FHCRC
+ nor any other party distributing the Program or any Derivative Work
+ will be liable for any damages arising from or related to the use of
+ the Program or such Derivative Work, including, without limitation,
+ incidental or consequential damages caused by the use or inability to
+ use the Program or loss or damage to data.
+
+ Licensee agrees to indemnify, defend and hold FHCRC harmless
+ from and against any claims, causes of action, damages, liabilities
+ and expenses, including without limitation attorney's fees, arising
+ from or related to Licensee's use, copying or distribution of the
+ Program or any Derivative Work.
+
+ 7. Severability. If any provision of this license is held
+ invalid under any applicable law or for any other reason, such
+ invalidity shall not effect any other provision of this license that
+ can be given effect without the invalid provision.
+
+ 8. Notice. Persons wishing to communicate with FHCRC
+ concerning this license or the Program should address their
+ communications as follows:
+
+ Fred Hutchinson Cancer Research Center
+ Attn: Dr. Steven Henikoff
+ 1100 Fairview AV N, A1-162
+ PO Box 19024
+ Seattle, WA 98109-1024
+
+ ---------------------------------------------------------------------------
+
+The Debian packaging is (C) 2009, Laszlo Kajan <lkajan at rostlab.org> and
+is licensed under the GPL, see `/usr/share/common-licenses/GPL'.
Added: trunk/packages/blimps/trunk/debian/libblimps3-dev.install
===================================================================
--- trunk/packages/blimps/trunk/debian/libblimps3-dev.install (rev 0)
+++ trunk/packages/blimps/trunk/debian/libblimps3-dev.install 2012-01-31 17:21:48 UTC (rev 9507)
@@ -0,0 +1,3 @@
+usr/include/*
+usr/lib/lib*.a
+usr/lib/lib*.so
Added: trunk/packages/blimps/trunk/debian/libblimps3.install
===================================================================
--- trunk/packages/blimps/trunk/debian/libblimps3.install (rev 0)
+++ trunk/packages/blimps/trunk/debian/libblimps3.install 2012-01-31 17:21:48 UTC (rev 9507)
@@ -0,0 +1 @@
+usr/lib/lib*.so.*
Added: trunk/packages/blimps/trunk/debian/patches/Makefile
===================================================================
--- trunk/packages/blimps/trunk/debian/patches/Makefile (rev 0)
+++ trunk/packages/blimps/trunk/debian/patches/Makefile 2012-01-31 17:21:48 UTC (rev 9507)
@@ -0,0 +1,174 @@
+Index: blimps-3.9/Makefile
+===================================================================
+--- /dev/null 1970-01-01 00:00:00.000000000 +0000
++++ blimps-3.9/Makefile 2012-01-29 19:28:31.094364502 +0000
+@@ -0,0 +1,117 @@
++PACKAGE := blimps
++VERSION := 3.9
++DISTDIR := $(PACKAGE)-$(VERSION)
++
++BLIMPSDIR := blimps
++DOCSDIR := docs
++INCLUDEDIR := include
++PROTOMATDIR := protomat
++
++MAN1POD := fastaseqs.pod
++MAN1GZ := $(MAN1POD:%.pod=%.1.gz)
++
++libdir ?= $(prefix)/lib
++
++# export LD_LIBRARY_PATH=/mnt/home/lkajan/project/rostlab/blimps/blimps-3.9/blimps
++
++all: blimps protomat man
++
++blimps:
++ $(MAKE) -C $(BLIMPSDIR) -f Makefile.Linux VERSION=$(VERSION)
++
++protomat:
++ $(MAKE) -C $(PROTOMATDIR) -f Makefile.Linux VERSION=$(VERSION)
++
++man: $(MAN1GZ)
++
++$(MAN1GZ) : %.1.gz : %.pod
++ pod2man -c 'User Commands' -r "$(VERSION)" $< | gzip -c > $@
++
++# The sift package does not provide fastaseqs but expects it to exist. Fortunately this package provides it.
++install: install-utils install-lib-dev install-lib install-data install-doc
++
++install-data:
++ mkdir -p $(DESTDIR)$(prefix)/share/$(PACKAGE) && \
++ cp -a $(DOCSDIR) \
++ $(DESTDIR)$(prefix)/share/$(PACKAGE)/
++
++install-utils:
++ mkdir -p $(DESTDIR)$(prefix)/bin && \
++ cp -a $(BLIMPSDIR)/fastaseqs \
++ $(DESTDIR)$(prefix)/bin/
++ mkdir -p $(DESTDIR)$(prefix)/share/man/man1 && cp $(MAN1GZ) $(DESTDIR)$(prefix)/share/man/man1/
++
++install-lib-dev:
++ mkdir -p $(DESTDIR)$(prefix)/include/$(PACKAGE) && \
++ cp $(INCLUDEDIR)/*.h $(DESTDIR)$(prefix)/include/$(PACKAGE)/
++ mkdir -p $(DESTDIR)$(libdir) && \
++ cp -a $(BLIMPSDIR)/*.a $(BLIMPSDIR)/*.so \
++ $(DESTDIR)$(libdir)/
++
++install-lib:
++ mkdir -p $(DESTDIR)$(prefix)/lib && \
++ cp -a $(BLIMPSDIR)/*.so.* \
++ $(DESTDIR)$(libdir)/
++
++.PHONY: install-doc
++install-doc:
++ mkdir -p $(DESTDIR)$(prefix)/share/doc/$(PACKAGE) && \
++ cp -a LICENSE README UPDATES \
++ $(DESTDIR)$(prefix)/share/doc/$(PACKAGE)/
++
++clean: clean-blimps clean-protomat
++ rm -f *.[12345678].gz
++
++clean-blimps:
++ -if [ -d $(BLIMPSDIR) ]; then $(MAKE) -C $(BLIMPSDIR) -f Makefile.Linux clean; fi
++
++clean-protomat:
++ -if [ -d $(PROTOMATDIR) ]; then $(MAKE) -C $(PROTOMATDIR) -f Makefile.Linux clean; fi
++
++distclean: clean
++ -if [ -d "$(DISTDIR)" ]; then rm -rf $(DISTDIR); fi
++ rm -rf \
++ $(DISTDIR) \
++ $(DISTDIR).tar.gz
++
++dist: distdir
++ tar chof - "$(DISTDIR)" | gzip -c >$(DISTDIR).tar.gz
++ rm -rf $(DISTDIR)
++
++distdir:
++ rm -rf $(DISTDIR) && mkdir -p $(DISTDIR) && \
++ rsync -avCR \
++ --exclude /*-stamp \
++ --exclude .*.swp \
++ --exclude debian \
++ ChangeLog \
++ Makefile \
++ $(PACKAGE).spec \
++ $(MAN1POD) \
++ $(DISTDIR)/;
++
++help:
++ @echo "Rules:"
++ @echo "all*"
++ @echo "*blimps"
++ @echo "install+"
++ @echo "+install-data"
++ @echo "+install-lib"
++ @echo "+install-lib-dev"
++ @echo "+install-utils"
++ @echo "clean"
++ @echo "distclean"
++ @echo "dist"
++ @echo "help"
++ @echo "*man"
++ @echo "*protomat"
++ @echo
++ @echo "Variables:"
++ @echo "DESTDIR - install to DESTDIR"
++ @echo "prefix - common installation prefix for all files"
++ @echo "libdir - install libraries here, default: /$$(prefix)/lib"
++ @echo " use prefix=$$HOME to build for personal use"
++
++.PHONY: all bin clean-blimps clean diff dist distclean distdir help install install-data install-lib install-lib-dev install-utils man untar blimps protomat clean-protomat
++
++# vim:ai:
+Index: blimps-3.9/blimps/Makefile.Linux
+===================================================================
+--- blimps-3.9.orig/blimps/Makefile.Linux 2012-01-29 19:28:22.951946468 +0000
++++ blimps-3.9/blimps/Makefile.Linux 2012-01-29 19:28:31.094364502 +0000
+@@ -44,7 +44,7 @@
+ # so the Makefile continues to work.
+
+ # Linux
+-VERSION := 3.9-rg0
++VERSION := 3.9
+ SOVERSION := 3.0.0
+ SHORTSOVERSION := 3
+
+@@ -106,7 +106,7 @@
+
+ XXWARN = -Werror
+
+-INCLUDE_DIR = ../blimps-3.9/include
++INCLUDE_DIR = ../include
+ INCLUDES = -I$(INCLUDE_DIR)
+
+
+Index: blimps-3.9/fastaseqs.pod
+===================================================================
+--- /dev/null 1970-01-01 00:00:00.000000000 +0000
++++ blimps-3.9/fastaseqs.pod 2012-01-29 19:28:31.094364502 +0000
+@@ -0,0 +1,25 @@
++=head1 NAME
++
++fastaseqs - converts a file of sequences to FASTA format
++
++=head1 SYNOPSIS
++
++fastaseqs <INPUTFILE> <OUTPUTFILE>
++
++=head1 DESCRIPTION
++
++fastaseqs converts a file of sequences to FASTA format.
++
++=head1 AUTHOR
++
++J. Henikoff
++
++=head1 COPYRIGHT AND LICENSE
++
++Copyright 1998, Fred Hutchinson Cancer Research Center
++
++Please refer to /usr/share/doc/*blimps*/copyright for the license.
++
++=head1 SEE ALSO
++
++L<http://blocks.fhcrc.org/blocks/uploads/blimps/>
Added: trunk/packages/blimps/trunk/debian/patches/patch_001.diff
===================================================================
--- trunk/packages/blimps/trunk/debian/patches/patch_001.diff (rev 0)
+++ trunk/packages/blimps/trunk/debian/patches/patch_001.diff 2012-01-31 17:21:48 UTC (rev 9507)
@@ -0,0 +1,3078 @@
+Index: blimps-3.9/blimps/addseqs.c
+===================================================================
+--- blimps-3.9.orig/blimps/addseqs.c 2012-01-29 19:13:51.171871018 +0000
++++ blimps-3.9/blimps/addseqs.c 2012-01-29 19:13:53.404364908 +0000
+@@ -150,7 +150,7 @@
+ else
+ {
+ printf("\nEnter name of file containing blocks: ");
+- gets(infile);
++ fgets(infile, MAXNAME, stdin);
+ }
+ if ( (fblk=fopen(infile, "r")) == NULL)
+ {
+@@ -164,7 +164,7 @@
+ else
+ {
+ printf("\nEnter name of sequence file: ");
+- gets(seqsfile);
++ fgets(seqsfile, MAXNAME, stdin);
+ }
+ if ( (fseq=fopen(seqsfile, "r")) == NULL)
+ {
+@@ -177,7 +177,7 @@
+ else
+ {
+ printf("\nEnter name of output seqs file: ");
+- gets(outfile);
++ fgets(outfile, MAXNAME, stdin);
+ }
+ if ( (fout=fopen(outfile, "w")) == NULL)
+ {
+Index: blimps-3.9/blimps/biassed_blocks_finder.c
+===================================================================
+--- blimps-3.9.orig/blimps/biassed_blocks_finder.c 2012-01-29 19:13:51.151864652 +0000
++++ blimps-3.9/blimps/biassed_blocks_finder.c 2012-01-29 19:13:53.404364908 +0000
+@@ -25,6 +25,11 @@
+ void unescape_url(char *url);
+ void plustospace(char *str);
+ */
++// lkajan: very nice but util.c does not have an interface defined
++// lkajan: can't figure out where this came from but it certainly picked up the wrong fmakeword
++char *fmakeword(FILE *f, char stop, int *cl);
++char *makeword(char *line, char stop);
++
+
+ entry entries[10000];
+
+@@ -124,7 +129,7 @@
+
+
+ /* check that a block was specified */
+- if (BLOCK_Ptr->val[0] == NULL)
++ if (BLOCK_Ptr->val[0] == 0)
+ {
+ printf("<H1>Error</H1>\n");
+ printf("You need to enter a block by writing or pasting a block in the window.<P>\n");
+@@ -139,7 +144,7 @@
+
+
+ /* if block was pasted/written - */
+- if (BLOCK_Ptr->val[0] != NULL)
++ if (BLOCK_Ptr->val[0] != 0)
+ {
+
+ /* open up the block file to write to */
+@@ -264,7 +269,7 @@
+
+ /**********************************************************************/
+
+-void main(int argc, char *argv[]) {
++int main(int argc, char *argv[]) {
+
+ printf("Content-type: text/html\n\n\n");
+
+@@ -301,6 +306,6 @@
+
+ clean_temp_files() ;
+
+- exit(0) ;
++ return(0) ;
+ }
+
+Index: blimps-3.9/blimps/blalign.c
+===================================================================
+--- blimps-3.9.orig/blimps/blalign.c 2012-01-29 19:13:51.131877048 +0000
++++ blimps-3.9/blimps/blalign.c 2012-01-29 19:13:53.404364908 +0000
+@@ -119,7 +119,7 @@
+ else
+ {
+ printf("\nEnter name of file of blocks: ");
+- gets(bdbname);
++ fgets(bdbname, MAXNAME, stdin);
+ }
+ if ( (bfp=fopen(bdbname, "r")) == NULL)
+ {
+Index: blimps-3.9/blimps/bldist.c
+===================================================================
+--- blimps-3.9.orig/blimps/bldist.c 2012-01-29 19:13:50.811872358 +0000
++++ blimps-3.9/blimps/bldist.c 2012-01-29 19:13:53.404364908 +0000
+@@ -70,7 +70,7 @@
+ else
+ {
+ printf("\nEnter name of file of fasta multiple alignments: ");
+- gets(bdbname);
++ fgets(bdbname, MAXNAME, stdin);
+ }
+ if ( (ifp=fopen(bdbname, "r")) == NULL)
+ {
+@@ -94,7 +94,7 @@
+ else
+ {
+ printf("\nEnter name of file containing substitution matrix: ");
+- gets(sijname);
++ fgets(sijname, MAXNAME, stdin);
+ }
+ if ( (sfp=fopen(sijname, "r")) == NULL)
+ {
+@@ -127,7 +127,7 @@
+ else
+ {
+ printf("\nEnter name of output file: ");
+- gets(outname);
++ fgets(outname, MAXNAME, stdin);
+ }
+ if ( (ofp=fopen(outname, "w")) == NULL)
+ {
+@@ -140,7 +140,7 @@
+ else
+ {
+ printf("\nEnter type (S=similarity, D=dissimilarity, C=correlation): ");
+- gets(ctemp);
++ fgets(ctemp, MAXNAME, stdin);
+ }
+ OutType = 1; /* similarity is default */
+ if (ctemp[0] == 'd' || ctemp[0] == 'D' || ctemp[0] == '2') OutType = 2;
+Index: blimps-3.9/blimps/blDR.c
+===================================================================
+--- blimps-3.9.orig/blimps/blDR.c 2012-01-29 19:13:51.011863238 +0000
++++ blimps-3.9/blimps/blDR.c 2012-01-29 19:13:53.404364908 +0000
+@@ -56,7 +56,7 @@
+ else
+ {
+ printf("\nEnter name of blocks database: ");
+- gets(bdbname);
++ fgets(bdbname, MAXNAME, stdin);
+ }
+ if ( (bfp=fopen(bdbname, "r")) == NULL)
+ {
+@@ -69,7 +69,7 @@
+ {
+ printf("\nSequence database must be in fasta format:");
+ printf("\nEnter name of sequence database: ");
+- gets(sdbname);
++ fgets(sdbname, MAXNAME, stdin);
+ }
+ if ( (sfp=fopen(sdbname, "r")) == NULL)
+ {
+@@ -81,7 +81,7 @@
+ else
+ {
+ printf("\nEnter name of new blocks database: ");
+- gets(outname);
++ fgets(outname, MAXNAME, stdin);
+ }
+ if ( (ofp=fopen(outname, "w")) == NULL)
+ {
+Index: blimps-3.9/blimps/blexplode.c
+===================================================================
+--- blimps-3.9.orig/blimps/blexplode.c 2012-01-29 19:13:50.831863443 +0000
++++ blimps-3.9/blimps/blexplode.c 2012-01-29 19:13:53.404364908 +0000
+@@ -29,7 +29,7 @@
+ else
+ {
+ printf("\nEnter name of blocks database: ");
+- gets(bdbname);
++ fgets(bdbname, MAXNAME, stdin);
+ }
+ if ( (bfp=fopen(bdbname, "r")) == NULL)
+ {
+Index: blimps-3.9/blimps/blk2DR.c
+===================================================================
+--- blimps-3.9.orig/blimps/blk2DR.c 2012-01-29 19:13:50.921862682 +0000
++++ blimps-3.9/blimps/blk2DR.c 2012-01-29 19:13:53.404364908 +0000
+@@ -31,7 +31,7 @@
+ else
+ {
+ printf("\nEnter name of blocks database: ");
+- gets(bdbname);
++ fgets(bdbname, MAXNAME, stdin);
+ }
+ if ( (bfp=fopen(bdbname, "r")) == NULL)
+ {
+Index: blimps-3.9/blimps/blk2GC.c
+===================================================================
+--- blimps-3.9.orig/blimps/blk2GC.c 2012-01-29 19:13:51.101863908 +0000
++++ blimps-3.9/blimps/blk2GC.c 2012-01-29 19:13:53.404364908 +0000
+@@ -30,7 +30,7 @@
+ else
+ {
+ printf("\nEnter name of blocks database: ");
+- gets(bdbname);
++ fgets(bdbname, MAXNAME, stdin);
+ }
+ if ( (bfp=fopen(bdbname, "r")) == NULL)
+ {
+Index: blimps-3.9/blimps/blk2lis.c
+===================================================================
+--- blimps-3.9.orig/blimps/blk2lis.c 2012-01-29 19:13:50.841864585 +0000
++++ blimps-3.9/blimps/blk2lis.c 2012-01-29 19:13:53.404364908 +0000
+@@ -30,7 +30,7 @@
+ else
+ {
+ printf("\nEnter name of blocks database: ");
+- gets(bdbname);
++ fgets(bdbname, MAXNAME, stdin);
+ }
+ if ( (bfp=fopen(bdbname, "r")) == NULL)
+ {
+Index: blimps-3.9/blimps/blk2mot.c
+===================================================================
+--- blimps-3.9.orig/blimps/blk2mot.c 2012-01-29 19:13:51.081864026 +0000
++++ blimps-3.9/blimps/blk2mot.c 2012-01-29 19:13:53.404364908 +0000
+@@ -43,7 +43,7 @@
+ char Seqname[MAXSEQS][SNAMELEN];
+
+ /*=======================================================================*/
+-void main(argc, argv)
++int main(argc, argv)
+ int argc;
+ char *argv[];
+ {
+@@ -71,7 +71,7 @@
+ else
+ {
+ printf("\nEnter name of file containing sequences: ");
+- gets(seqfile);
++ fgets(seqfile, FNAMELEN, stdin);
+ }
+ if ( (fseq=fopen(seqfile, "r")) == NULL)
+ {
+@@ -92,7 +92,7 @@
+ else
+ {
+ printf("\nEnter name of blocks file: ");
+- gets(blkfile);
++ fgets(blkfile, FNAMELEN, stdin);
+ }
+ if ( (fblk=fopen(blkfile, "r")) == NULL)
+ {
+@@ -126,7 +126,7 @@
+ else
+ {
+ printf("\nEnter name of new motomat file: ");
+- gets(motfile);
++ fgets(motfile, FNAMELEN, stdin);
+ }
+ if ( (fmot=fopen(motfile, "wb")) == NULL)
+ {
+@@ -135,7 +135,7 @@
+ }
+ write_motifs(fmot, info, motif);
+ fclose(fmot);
+- exit(0);
++ return(0);
+ } /* end of main */
+
+ /*======================================================================
+Index: blimps-3.9/blimps/blk2pssm.c
+===================================================================
+--- blimps-3.9.orig/blimps/blk2pssm.c 2012-01-29 19:13:50.861864270 +0000
++++ blimps-3.9/blimps/blk2pssm.c 2012-01-29 19:13:53.404364908 +0000
+@@ -67,7 +67,8 @@
+ Block *block;
+ Matrix *matrix, *logodds;
+ char bdbname[MAXNAME], conname[MAXNAME];
+- char ctemp[10];
++#define BLK2PSSM_CTEMPLEN 10
++ char ctemp[BLK2PSSM_CTEMPLEN];
+ int format, type, itemp;
+
+ ErrorLevelReport = 5; /* No blimps errors reported */
+@@ -87,7 +88,7 @@
+ else
+ {
+ printf("\nEnter name of BLOCKS input file: ");
+- gets(bdbname);
++ fgets(bdbname, MAXNAME, stdin);
+ }
+ if ( (bfp=fopen(bdbname, "r")) == NULL)
+ {
+@@ -100,7 +101,7 @@
+ else
+ {
+ printf("\nEnter name of PSSM output file: ");
+- gets(conname);
++ fgets(conname, MAXNAME, stdin);
+ }
+ if ( (ofp=fopen(conname, "w")) == NULL)
+ {
+@@ -115,7 +116,7 @@
+ else
+ {
+ printf("\nEnter PSSM format type (B=blimps, M=mast, G=Gribskov, P=Psi-Blast) [B]: ");
+- gets(ctemp);
++ fgets(ctemp, BLK2PSSM_CTEMPLEN, stdin );
+ }
+ if (strlen(ctemp) && (ctemp[0] == 'm' || ctemp[0] == 'M'))
+ { format = 1; type = 6; }
+Index: blimps-3.9/blimps/blk2slx.c
+===================================================================
+--- blimps-3.9.orig/blimps/blk2slx.c 2012-01-29 19:13:50.931870624 +0000
++++ blimps-3.9/blimps/blk2slx.c 2012-01-29 19:13:53.404364908 +0000
+@@ -35,7 +35,7 @@
+ else
+ {
+ printf("\nEnter name of blocks database: ");
+- gets(bdbname);
++ fgets(bdbname, MAXNAME, stdin);
+ }
+ if ( (bfp=fopen(bdbname, "r")) == NULL)
+ {
+@@ -48,7 +48,7 @@
+ else
+ {
+ printf("\nEnter name of new slx database: ");
+- gets(conname);
++ fgets(conname, MAXNAME, stdin);
+ }
+ if ( (ofp=fopen(conname, "w")) == NULL)
+ {
+Index: blimps-3.9/blimps/blklis.c
+===================================================================
+--- blimps-3.9.orig/blimps/blklis.c 2012-01-29 19:13:50.871863612 +0000
++++ blimps-3.9/blimps/blklis.c 2012-01-29 19:13:53.404364908 +0000
+@@ -34,7 +34,7 @@
+ else
+ {
+ printf("\nEnter name of file of blocks: ");
+- gets(infile);
++ fgets(infile, 80, stdin);
+ }
+ if ( (fin=fopen(infile, "r")) == NULL)
+ {
+@@ -46,7 +46,7 @@
+ else
+ {
+ printf("\nEnter name of output file: ");
+- gets(outfile);
++ fgets(outfile, 80, stdin );
+ }
+ if ( (fout=fopen(outfile, "w+")) == NULL)
+ {
+Index: blimps-3.9/blimps/blkprob.c
+===================================================================
+--- blimps-3.9.orig/blimps/blkprob.c 2012-01-29 19:13:50.891864377 +0000
++++ blimps-3.9/blimps/blkprob.c 2012-01-29 19:13:53.404364908 +0000
+@@ -325,7 +325,7 @@
+ {
+ printf("\nEnter number of hits to report or ");
+ printf("blimps configuration file name [%d]: ", MaxHit);
+- gets(ctemp);
++ fgets(ctemp, FNAMELEN, stdin);
+ }
+ if (!strlen(ctemp)) strcpy(ctemp, "0");
+ for (i=0; i<strlen(ctemp); i++)
+@@ -353,7 +353,7 @@
+ else
+ {
+ printf("\nEnter name of file containing blocks search results: ");
+- gets(homfile);
++ fgets(homfile, FNAMELEN, stdin);
+ }
+ /*------------- arg 3: blocks database file -----------------------*/
+ db[0] = '\0';
+@@ -362,7 +362,7 @@
+ else
+ {
+ printf("\nEnter name of blocks database searched: ");
+- gets(datfile);
++ fgets(datfile, FNAMELEN, stdin);
+ }
+ if (strlen(datfile))
+ {
+Index: blimps-3.9/blimps/blocks.c
+===================================================================
+--- blimps-3.9.orig/blimps/blocks.c 2012-01-29 19:13:50.961863689 +0000
++++ blimps-3.9/blimps/blocks.c 2012-01-29 19:13:53.404364908 +0000
+@@ -891,7 +891,7 @@
+ }
+ }
+ else {
+- printf("??) \t");
++ printf("??" ") \t");
+ for(k=0; k<block->clusters[i].sequences[j].length; k++) {
+ printf("%c", aa_btoa[block->clusters[i].sequences[j].sequence[k]]);
+ }
+Index: blimps-3.9/blimps/blocks_search.c
+===================================================================
+--- blimps-3.9.orig/blimps/blocks_search.c 2012-01-29 19:13:51.151864652 +0000
++++ blimps-3.9/blimps/blocks_search.c 2012-01-29 19:13:53.404364908 +0000
+@@ -302,8 +302,9 @@
+ else if (!strncmp(entries[i].val, "pfam", 9))
+ { Pfam_Flag = TRUE; }
+ }
+- else if (!strncmp(entries[i].name, "bias", 4))
+- { strcpy(Minus_Flag, entries[i].val); }
++// lkajan: what was the intention here? Looks like this would copy entries[i].val to the value of boolean Minus_Flag interpreted as a pointer - trigger to segfault?
++// else if (!strncmp(entries[i].name, "bias", 4))
++// { strcpy(Minus_Flag, entries[i].val); }
+ else if (!strncmp(entries[i].name, "ty", 2))
+ { strcpy(type, entries[i].val); }
+ else if (!strncmp(entries[i].name, "st", 2))
+@@ -379,7 +380,7 @@
+
+ cshp = fopen(csh_file, "w");
+
+- fprintf(cshp, "\#\!/bin/csh\n");
++ fprintf(cshp, "#!/bin/csh\n");
+ fprintf(cshp, "unalias mv\n");
+ fprintf(cshp, "%s %s >& /dev/null\n", blimps, cs_file);
+ if (Title_Ptr != NULL)
+@@ -419,7 +420,7 @@
+ mailprog, email_addr, buf, Address_Ptr->val, blksort_output);
+ }
+ }
+- fprintf(cshp, "exit\(0\)\n");
++ fprintf(cshp, "exit(0)\n");
+ fclose(cshp);
+ sprintf(buf, "chmod a+x %s", csh_file);
+ system(buf);
+@@ -433,7 +434,7 @@
+ Boolean loop = TRUE;
+ int tot, sum;
+
+- if (Sequence_Ptr->val[0] == NULL) {
++ if (Sequence_Ptr->val[0] == 0) {
+ printf("<H1>Search Error</H1>\n");
+ printf("You need to enter a sequence to search with.<P>\n");
+ exit(0);
+@@ -590,7 +591,7 @@
+
+
+ /*=======================================================================*/
+-void main(int argc, char *argv[]) {
++int main(int argc, char *argv[]) {
+
+
+ /*
+@@ -655,5 +656,5 @@
+ /*
+ fclose(jgh);
+ */
+- exit(0);
++ return(0);
+ } /* end of main */
+Index: blimps-3.9/blimps/block_vis.c
+===================================================================
+--- blimps-3.9.orig/blimps/block_vis.c 2012-01-29 19:13:50.831863443 +0000
++++ blimps-3.9/blimps/block_vis.c 2012-01-29 19:13:53.404364908 +0000
+@@ -868,7 +868,7 @@
+ * each input file. The only actual work done here is interpreting
+ * '*' in the output filename.
+ */
+-void main(int argc, char *argv[])
++int main(int argc, char *argv[])
+ {
+ int i1, i2, i3, i4;
+ char out_filename[80];
+@@ -910,5 +910,7 @@
+ /* No arguments? Give the user some help (and skip the warning above) */
+ if (argc == 1)
+ do_help();
++
++ return(0);
+ }
+
+Index: blimps-3.9/blimps/blpssm.c
+===================================================================
+--- blimps-3.9.orig/blimps/blpssm.c 2012-01-29 19:13:50.901871518 +0000
++++ blimps-3.9/blimps/blpssm.c 2012-01-29 19:13:53.404364908 +0000
+@@ -241,7 +241,7 @@
+ else
+ {
+ printf("\nEnter name of configuration file: ");
+- gets(cfname);
++ fgets(cfname, FNAMELEN, stdin);
+ }
+ if ( (cfp=fopen(cfname, "r")) == NULL)
+ {
+Index: blimps-3.9/blimps/blweight.c
+===================================================================
+--- blimps-3.9.orig/blimps/blweight.c 2012-01-29 19:13:51.021862940 +0000
++++ blimps-3.9/blimps/blweight.c 2012-01-29 19:13:53.404364908 +0000
+@@ -92,7 +92,8 @@
+ FILE *bfp, *ofp;
+ Block *block, *cblock;
+ int wtype, clus, stype;
+- char bdbname[MAXNAME], conname[MAXNAME], ctemp[10];
++#define BLWEIGHT_CTEMPLEN 10
++ char bdbname[MAXNAME], conname[MAXNAME], ctemp[BLWEIGHT_CTEMPLEN];
+ struct timeval tv;
+
+ ErrorLevelReport = 5; /* don't want to see them */
+@@ -119,7 +120,7 @@
+ else
+ {
+ printf("\nEnter name of blocks database: ");
+- gets(bdbname);
++ fgets( bdbname, MAXNAME, stdin );
+ }
+ if ( (bfp=fopen(bdbname, "r")) == NULL)
+ {
+@@ -132,7 +133,7 @@
+ else
+ {
+ printf("\nEnter name of new weighted blocks database: ");
+- gets(conname);
++ fgets( conname, MAXNAME, stdin );
+ }
+ if ( (ofp=fopen(conname, "w")) == NULL)
+ {
+@@ -149,7 +150,7 @@
+ {
+ printf("\nEnter weighting scheme (P=position-based, V=Voronoi, ");
+ printf("\n A=Vingron & Argos, Cn = n-percent cluster [P]: ");
+- gets(ctemp);
++ fgets( ctemp, BLWEIGHT_CTEMPLEN, stdin );
+ }
+ if (strlen(ctemp))
+ {
+@@ -187,7 +188,7 @@
+ else
+ {
+ printf("\nEnter scale (M=>max=100, N=>sum=#seq, ###=>sum=###) [M]: ");
+- gets(ctemp);
++ fgets( ctemp, BLWEIGHT_CTEMPLEN, stdin );
+ }
+ if (strlen(ctemp))
+ {
+Index: blimps-3.9/blimps/cobbler.c
+===================================================================
+--- blimps-3.9.orig/blimps/cobbler.c 2012-01-29 19:13:50.811872358 +0000
++++ blimps-3.9/blimps/cobbler.c 2012-01-29 19:13:53.404364908 +0000
+@@ -256,7 +256,7 @@
+ else
+ {
+ printf("\nEnter name of configuration file: ");
+- gets(cfname);
++ fgets(cfname, MAXNAME, stdin);
+ }
+ if ( (cfp=fopen(cfname, "r")) == NULL)
+ {
+Index: blimps-3.9/blimps/coduse.c
+===================================================================
+--- blimps-3.9.orig/blimps/coduse.c 2012-01-29 19:13:50.951863548 +0000
++++ blimps-3.9/blimps/coduse.c 2012-01-29 19:13:53.404364908 +0000
+@@ -65,7 +65,7 @@
+ else
+ {
+ printf("\nEnter name of CUTG spsum file: ");
+- gets(infile);
++ fgets(infile, MAXNAME, stdin );
+ }
+ if ( (fin=fopen(infile, "r")) == NULL)
+ {
+@@ -78,7 +78,7 @@
+ else
+ {
+ printf("Enter organism name (leave blank for first organism in file): ");
+- gets(organism);
++ fgets(organism, MAXNAME, stdin);
+ }
+ if (strlen(organism))
+ {
+@@ -95,7 +95,7 @@
+ else
+ {
+ printf("\nEnter name of Blimps codon usage output file: ");
+- gets(outfile);
++ fgets(outfile, MAXNAME, stdin);
+ }
+ if ( (fout=fopen(outfile, "w")) == NULL)
+ {
+Index: blimps-3.9/blimps/email.c
+===================================================================
+--- blimps-3.9.orig/blimps/email.c 2012-01-29 19:13:50.961863689 +0000
++++ blimps-3.9/blimps/email.c 2012-01-29 19:13:53.404364908 +0000
+@@ -35,7 +35,7 @@
+ else
+ {
+ printf("\nEnter name of sequence file: ");
+- gets(filename);
++ fgets(filename, MAXNAME, stdin);
+ }
+ if ( (bfp=fopen(filename, "r")) == NULL)
+ {
+Index: blimps-3.9/blimps/fastaseqs.c
+===================================================================
+--- blimps-3.9.orig/blimps/fastaseqs.c 2012-01-29 19:13:51.141863309 +0000
++++ blimps-3.9/blimps/fastaseqs.c 2012-01-29 19:13:53.404364908 +0000
+@@ -39,7 +39,7 @@
+ else
+ {
+ printf("\nEnter name of input sequence file: ");
+- gets(infile);
++ fgets(infile, MAXNAME, stdin);
+ }
+ if ( (fin=fopen(infile, "r")) == NULL)
+ {
+@@ -52,7 +52,7 @@
+ else
+ {
+ printf("\nEnter name of output file: ");
+- gets(outfile);
++ fgets(outfile, MAXNAME, stdin);
+ }
+ if ( (fout=fopen(outfile, "w")) == NULL)
+ {
+Index: blimps-3.9/blimps/find_biassed_blocks.c
+===================================================================
+--- blimps-3.9.orig/blimps/find_biassed_blocks.c 2012-01-29 19:13:51.051872323 +0000
++++ blimps-3.9/blimps/find_biassed_blocks.c 2012-01-29 19:13:53.404364908 +0000
+@@ -290,7 +290,7 @@
+ else /* get input file interactively */
+ {
+ printf("\nEnter name of a file with blocks or block matrices: ");
+- gets(bdbname);
++ fgets(bdbname, MAXNAME, stdin);
+ }
+
+ if ( (*bfp=fopen(bdbname, "r")) == NULL)
+Index: blimps-3.9/blimps/format_block.c
+===================================================================
+--- blimps-3.9.orig/blimps/format_block.c 2012-01-29 19:13:51.041864902 +0000
++++ blimps-3.9/blimps/format_block.c 2012-01-29 19:13:53.404364908 +0000
+@@ -242,14 +242,14 @@
+ }
+
+ /*
+- * resize_block_sequences
++ * fb_resize_block_sequences
+ * Increases the memory for the storage of the sequences of a block.
+ * Parameter:
+ * Block *block: the block to resize
+ * Error codes: none
+ */
+
+-static void resize_block_sequences(block)
++static void fb_resize_block_sequences(block)
+ Block *block;
+ {
+ int i;
+@@ -315,13 +315,13 @@
+ /* check that obligatory fields have something */
+
+ /* Note if sequence names and start positions not supplied */
+- if (SEQ_NAMES_Ptr->val[0] == NULL) no_seq_names = 1 ;
++ if (SEQ_NAMES_Ptr->val[0] == 0) no_seq_names = 1 ;
+ else no_seq_names = 0 ;
+
+- if (SEQ_POS_Ptr->val[0] == NULL) no_seq_pos = 1 ;
++ if (SEQ_POS_Ptr->val[0] == 0) no_seq_pos = 1 ;
+ else no_seq_pos = 0 ;
+
+- if (SEQS_Ptr->val[0] == NULL)
++ if (SEQS_Ptr->val[0] == 0)
+ {
+ printf("<H1>Error</H1>\n");
+ printf("No sequences specified.<P>\n");
+@@ -403,7 +403,7 @@
+ exit(0);
+ }
+
+- if (MA_WIDTH_Ptr->val[0] != NULL &&
++ if (MA_WIDTH_Ptr->val[0] != 0 &&
+ block->width != atoi (MA_WIDTH_Ptr->val))
+ {
+ printf("<H2>Warning</H2>\n");
+@@ -470,15 +470,15 @@
+ if (seq_header)
+ {
+ /* skip blanks */
+- for(; isspace(SEQS_Ptr->val[i]) && SEQS_Ptr->val[i] != '/n' &&
+- SEQS_Ptr->val[i] != '/0'; i++) ;
+- if (SEQS_Ptr->val[i] == '/n') /* no name is found in line */
++ for(; isspace(SEQS_Ptr->val[i]) && SEQS_Ptr->val[i] != '\n' &&
++ SEQS_Ptr->val[i] != '\0'; i++) ;
++ if (SEQS_Ptr->val[i] == '\n') /* no name is found in line */
+ sprintf(block->sequences[block->num_sequences].name,
+ "%s%d", UNKNOWN_SEQ_NAME, block->num_sequences+1) ;
+ else
+ /* copy first 20 chars or until a space is reached */
+ for(k=0; !(isspace(SEQS_Ptr->val[i])) && k<20 &&
+- SEQS_Ptr->val[i] != '/n' ; i++, k++)
++ SEQS_Ptr->val[i] != '\n' ; i++, k++)
+ block->sequences[block->num_sequences].name[k] = SEQS_Ptr->val[i];
+
+ /* end string */
+@@ -520,7 +520,7 @@
+ string[j] = '\0' ;
+
+ if (block->max_sequences <= block->num_sequences+1)
+- resize_block_sequences(block) ;
++ fb_resize_block_sequences(block) ;
+
+ /* process the sequence */
+
+@@ -623,7 +623,7 @@
+ string[j] = '\0' ;
+
+ if (block->max_sequences <= k)
+- resize_block_sequences(block) ;
++ fb_resize_block_sequences(block) ;
+
+ /* copy up to first 20 chars of name */
+ strncpy(block->sequences[k].name,string,20) ;
+@@ -681,7 +681,7 @@
+ }
+ string[j] = '\0' ;
+
+- if (block->max_sequences <= k+1) resize_block_sequences(block) ;
++ if (block->max_sequences <= k+1) fb_resize_block_sequences(block) ;
+
+ block->sequences[k].position = atoi(string) ;
+
+@@ -703,7 +703,7 @@
+
+ /* check that actual number of sequences is equal to
+ what the user gave */
+- if (MA_SEQS_Ptr->val[0] != NULL &&
++ if (MA_SEQS_Ptr->val[0] != 0 &&
+ block->num_sequences != atoi (MA_SEQS_Ptr->val))
+ {
+ printf("<H2>Warning</H2>\n");
+@@ -719,7 +719,7 @@
+
+ /* get block header data */
+
+- if (ID_Ptr->val[0] == NULL)
++ if (ID_Ptr->val[0] == 0)
+ strcpy(block->id, "None") ;
+ else
+ strncpy(block->id,ID_Ptr->val, SMALL_BUFF_LENGTH) ;
+@@ -727,7 +727,7 @@
+ strcat(block->id, "; BLOCK") ;
+
+
+- if (AC_Ptr->val[0] == NULL)
++ if (AC_Ptr->val[0] == 0)
+ {
+ strncpy(block->number, block->sequences[0].name, MAXAC) ;
+ }
+@@ -746,7 +746,7 @@
+
+ strcpy(block->ac,block->number) ;
+
+- if (MIN_DIST_Ptr->val[0] == NULL)
++ if (MIN_DIST_Ptr->val[0] == 0)
+ {
+ j = 10000 ;
+ for(i=0; i<block->num_sequences; i++)
+@@ -758,7 +758,7 @@
+ block->ac, j) ;
+
+
+- if (MAX_DIST_Ptr->val[0] == NULL)
++ if (MAX_DIST_Ptr->val[0] == 0)
+ {
+ j = 0 ;
+ for(i=0; i<block->num_sequences; i++)
+@@ -769,12 +769,12 @@
+ sprintf(block->ac, "%s,%d)",
+ block->ac, j) ;
+
+- if (DE_Ptr->val[0] == NULL)
++ if (DE_Ptr->val[0] == 0)
+ strcpy(block->de, "None") ;
+ else
+ strncpy(block->de,DE_Ptr->val, SMALL_BUFF_LENGTH) ;
+
+- if (MA_METH_Ptr->val[0] != NULL)
++ if (MA_METH_Ptr->val[0] != 0)
+ strncpy(block->bl,MA_METH_Ptr->val, SMALL_BUFF_LENGTH-25) ;
+ else
+ strcpy(block->bl,"Method unspecified") ;
+@@ -881,7 +881,7 @@
+ }
+
+
+-void main(int argc, char *argv[]) {
++int main(int argc, char *argv[]) {
+
+ printf("Content-type: text/html\n\n\n");
+
+@@ -918,6 +918,6 @@
+
+ clean_temp_files() ;
+
+- exit(0) ;
++ return(0) ;
+ }
+
+Index: blimps-3.9/blimps/htmlize-codehop.c
+===================================================================
+--- blimps-3.9.orig/blimps/htmlize-codehop.c 2012-01-29 19:13:51.121863948 +0000
++++ blimps-3.9/blimps/htmlize-codehop.c 2012-01-29 19:13:53.404364908 +0000
+@@ -47,7 +47,7 @@
+ void condense();
+
+ /*======================================================================*/
+-void main(argc, argv)
++int main(argc, argv)
+ int argc;
+ char *argv[];
+ {
+@@ -250,7 +250,7 @@
+ printf("\n%d blocks, %d oligos processed\n", nblock, noligo);
+ */
+
+- exit(0);
++ return(0);
+ } /* end of main */
+ /*=========================================================================*/
+ struct olist *make_olist()
+Index: blimps-3.9/blimps/htmlize-LAMA.c
+===================================================================
+--- blimps-3.9.orig/blimps/htmlize-LAMA.c 2012-01-29 19:13:50.941863566 +0000
++++ blimps-3.9/blimps/htmlize-LAMA.c 2012-01-29 19:13:53.404364908 +0000
+@@ -13,6 +13,7 @@
+
+ #include <stdlib.h>
+ #include <stdio.h>
++#include <string.h>
+
+
+ #define TRUE 1
+Index: blimps-3.9/blimps/interpro.c
+===================================================================
+--- blimps-3.9.orig/blimps/interpro.c 2012-01-29 19:13:51.071862806 +0000
++++ blimps-3.9/blimps/interpro.c 2012-01-29 19:13:53.404364908 +0000
+@@ -94,7 +94,7 @@
+ else
+ {
+ printf("\nEnter name of interpro xml file: ");
+- gets(iprfile);
++ fgets(iprfile, MAXNAME, stdin);
+ }
+ if ( (fip=fopen(iprfile, "r")) == NULL)
+ {
+@@ -108,7 +108,7 @@
+ else
+ {
+ printf("\nEnter name of interpro entry or all : ");
+- gets(iprname);
++ fgets(iprname, MAXAC, stdin);
+ }
+ if (!strlen(iprname)) strcpy(iprname, "all");
+ All = NO;
+Index: blimps-3.9/blimps/LAMA.c
+===================================================================
+--- blimps-3.9.orig/blimps/LAMA.c 2012-01-29 19:13:50.821864381 +0000
++++ blimps-3.9/blimps/LAMA.c 2012-01-29 19:13:53.404364908 +0000
+@@ -400,12 +400,12 @@
+ else /* get input file(s) interactively */
+ {
+ printf("\nEnter name of a file with blocks or block matrices: ");
+- gets(bdbname[0]);
++ fgets(bdbname[0], MAXNAME, stdin);
+
+ printf("\nThe blocks/matrices in this file will be intercompared.\n");
+ printf("If you wish to compare them against blocks/matrices in\n");
+ printf("another file enter that file name (else just hit <ENTER>).\n");
+- gets(bdbname[1]);
++ fgets(bdbname[1], MAXNAME, stdin);
+
+ if (bdbname[1][0] == '\0') *inpfiles = 1 ;
+ else *inpfiles = 2 ;
+@@ -426,7 +426,7 @@
+ else
+ {
+ printf("\nEnter name of output file: ");
+- gets(outname);
++ fgets(outname, MAXNAME, stdin);
+ }
+
+ if ( (*out=fopen(outname, "w")) == NULL)
+Index: blimps-3.9/blimps/LAMA_search.c
+===================================================================
+--- blimps-3.9.orig/blimps/LAMA_search.c 2012-01-29 19:13:50.791864833 +0000
++++ blimps-3.9/blimps/LAMA_search.c 2012-01-29 19:13:53.404364908 +0000
+@@ -281,7 +281,7 @@
+
+
+ /* check that a block was specified */
+- if (Qblock_Ptr->val[0] == NULL)
++ if (Qblock_Ptr->val[0] == 0)
+ {
+ printf("<H1>Search Error</H1>\n");
+ printf("You need to enter a block to search with by writing or pasting a block in the query block window.<P>\n");
+@@ -296,7 +296,7 @@
+
+
+ /* if block was pasted/written - */
+- if (Qblock_Ptr->val[0] != NULL)
++ if (Qblock_Ptr->val[0] != 0)
+ {
+
+ /* open up the block file to write to */
+@@ -579,7 +579,7 @@
+ /* mail the person the results */
+ /* NOTE: need to echo the header lines for the LAMA output :P */
+ /* NOTE: all this should need to do is to cat the ouput file. */
+- sprintf(buf, "%s %s '(cat %s) | /usr/bin/mailx -s \"LAMA Results\" -r \"blocks\@fhcrc.org\" %s'", add_queue_entry, LAMA_queue, LAMA_output, Address_Ptr->val);
++ sprintf(buf, "%s %s '(cat %s) | /usr/bin/mailx -s \"LAMA Results\" -r \"blocks at fhcrc.org\" %s'", add_queue_entry, LAMA_queue, LAMA_output, Address_Ptr->val);
+ system(buf);
+
+
+@@ -666,7 +666,7 @@
+
+ } /* end of run Cyrca */
+
+-void main(int argc, char *argv[]) {
++int main(int argc, char *argv[]) {
+
+ printf("Content-type: text/html\n\n\n");
+
+@@ -715,5 +715,5 @@
+
+ clean_temp_files() ;
+
+- exit(0) ;
++ return(0) ;
+ }
+Index: blimps-3.9/blimps/lisblk.c
+===================================================================
+--- blimps-3.9.orig/blimps/lisblk.c 2012-01-29 19:13:50.901871518 +0000
++++ blimps-3.9/blimps/lisblk.c 2012-01-29 19:13:53.404364908 +0000
+@@ -33,7 +33,7 @@
+ char Title[MAXLINE];
+
+ /*======================================================================*/
+-void main(argc, argv)
++int main(argc, argv)
+ int argc;
+ char *argv[];
+ {
+@@ -53,7 +53,7 @@
+ else
+ {
+ printf("\nEnter name of file containing list of sequences: ");
+- gets(lisfile);
++ fgets(lisfile, FNAMELEN, stdin);
+ }
+ if ( (flis=fopen(lisfile, "r")) == NULL)
+ {
+@@ -69,7 +69,7 @@
+ else
+ {
+ printf("\nEnter name of block file: ");
+- gets(blkfile);
++ fgets(blkfile, FNAMELEN, stdin);
+ }
+
+ if ((fblk=fopen(blkfile, "r")) == NULL)
+@@ -85,7 +85,7 @@
+ if ((fblk=fopen(blkfile, "r")) == NULL)
+ {
+ printf("\nEnter name of block file: ");
+- gets(blkfile);
++ fgets(blkfile, FNAMELEN, stdin);
+ }
+ }
+ if (fblk == NULL)
+@@ -147,7 +147,7 @@
+ fclose(fout);
+
+ printf("\n");
+- exit(0);
++ return(0);
+ } /* end of main */
+ /*================================================================*/
+ int flag_ids(block, ids)
+Index: blimps-3.9/blimps/mablock.c
+===================================================================
+--- blimps-3.9.orig/blimps/mablock.c 2012-01-29 19:13:51.031863121 +0000
++++ blimps-3.9/blimps/mablock.c 2012-01-29 19:13:53.404364908 +0000
+@@ -102,7 +102,8 @@
+ {
+ FILE *ifp, *bfp, *sfp;
+ Sequence *seqs[MAXSEQ];
+- char ctemp[MAXNAME], bdbname[MAXNAME], outtype[10], *ptr;
++#define MABLOCK_OUTTYPELEN 10
++ char ctemp[MAXNAME], bdbname[MAXNAME], outtype[MABLOCK_OUTTYPELEN], *ptr;
+ int db_type, seq_type, nseq, i, bflag, ftype;
+ struct blocks_list *blocks;
+ Block *block;
+@@ -127,7 +128,7 @@
+ else
+ {
+ printf("\nEnter name of blocks database: ");
+- gets(bdbname);
++ fgets( bdbname, MAXNAME, stdin );
+ }
+ if ( (ifp=fopen(bdbname, "r")) == NULL)
+ {
+@@ -157,7 +158,7 @@
+ else
+ {
+ printf("\nEnter name of output file: ");
+- gets(OutName);
++ fgets( OutName, MAXNAME, stdin );
+ }
+ strcpy(ctemp, OutName); strcat(ctemp, ".blks");
+ if ( (bfp=fopen(ctemp, "w")) == NULL)
+@@ -177,7 +178,7 @@
+ else
+ {
+ printf("\nEnter type of output file [B=blocks|F=fasta]: ");
+- gets(outtype);
++ fgets( outtype, MABLOCK_OUTTYPELEN, stdin );
+ }
+ if (outtype[0] == 'F' || outtype[0] == 'f') ftype = 1;
+ /* ------------4th arg = optional min trimming size--------------------*/
+Index: blimps-3.9/blimps/Makefile.Linux
+===================================================================
+--- blimps-3.9.orig/blimps/Makefile.Linux 2012-01-29 19:13:50.931870624 +0000
++++ blimps-3.9/blimps/Makefile.Linux 2012-01-29 19:13:53.414372010 +0000
+@@ -44,19 +44,25 @@
+ # so the Makefile continues to work.
+
+ # Linux
++VERSION := 3.9-rg0
++SOVERSION := 3.0.0
++SHORTSOVERSION := 3
++
+ DEFINES =
+ SYSTEM =
+-OPTIMIZ = -Wall -O2
++#OPTIMIZ = -Wall -O2
++OPTIMIZ = -Wuninitialized -O2
++#OPTIMIZ = -Werror -O2
+ RANLIB = ls
+
+ MAKE = make
+-DEPEND = makedepend
++DEPEND = $(CC)
+
+ # ar -t libpssm.a for table of contents
+ AR = ar
+ RM = rm -f
+ MV = mv -f
+-CP = cp
++CP = cp -af
+
+
+ # C compiler
+@@ -106,12 +112,12 @@
+
+ # C Flags to compiler
+ #CFLAGS = `getconf LFS_CFLAGS` $(OPTIMIZ) $(DEFINES) $(INCLUDES)
+-CFLAGS = $(OPTIMIZ) $(DEFINES) $(INCLUDES)
++CFLAGS = $(OPTIMIZ) $(DEFINES) $(INCLUDES) -fpic
+
+
+ # Linker Flags
+ LDFLAGS = $(CFLAGS)
+-LDLIBS = -lblimps -ly -lm
++LDLIBS = -lblimps -lm
+ LDOPTIONS = $(LDFLAGS) $(LDDIR)
+ # cc ld options
+
+@@ -120,6 +126,9 @@
+ LIBRARY_DIR = ./
+ LDDIR = -L$(LIBRARY_DIR)
+
++#SHARED_LIB_DIR := ./.libs
++SHARED_LIB_DIR := .
++
+
+ # source files
+ SRCS = blimps-mem.c \
+@@ -197,34 +206,36 @@
+ OTHER_OBJS_DEBUG = /usr/lib/debug/malloc.o \
+ /usr/lib/debug/mallocmap.o
+
+-LIBOBJS = pattern.o \
+- files.o \
+- frequency.o \
+- convert.o \
++LIBOBJS = \
++ blimps.o \
++ blimps-mem.o \
+ blocks.o \
++ config.o \
++ convert.o \
+ errors.o \
++ files.o \
++ frequency.o \
+ gcode.o \
++ lists.o \
+ matrix.o \
+ memory.o \
+- sequences.o \
+- strutil.o \
+- sl.o \
+- version.o \
+ options.o \
+- blimps-mem.o \
+- config.o \
+- lists.o \
++ p2clib.o \
++ pattern.o \
++ protomat.o \
+ scores.o \
+ scoring.o \
+- p2clib.o \
++ sequences.o \
++ sl.o \
++ strutil.o \
+ util.o \
+- protomat.o
++ version.o
+
+
+ # need malloc.o for malloc_debug() which will have free() raise SIGABRT
+ # if it is unable to free the space.
+
+-LIBRARIES = libblimps.a
++LIBRARIES = libblimps.a $(SHARED_LIB_DIR)/libblimps.so.$(SOVERSION)
+
+
+ ########################################################################
+@@ -235,10 +246,10 @@
+ ########################################################################
+ ########################################################################
+
+-install: clean all move-lib move-bin
+-
+ all: lib blimps blweight blalign bldist blk2pssm rank_matrix retblock codehop htmlize-codehop oligo_melt mablock cobbler addseqs fastaseqs LAMA find_biassed_blocks makeblockmap prints2blocks lisblk coduse narrow blk2slx blkprob interpro pssmdist pssmBL papssm matrix_logob makelogob blocks_search LAMA_search block_vis format_block biassed_blocks_finder htmlize-LAMA show_aligned_blocks makelis blk2mot
+
++install: clean all move-lib move-bin
++
+ blimps: $(LIBRARIES) blimps.o $(LIBOBJS)
+ $(RM) $@
+ $(CC) -o $@ blimps.o $(LDOPTIONS) $(LDLIBS) $(SYSLIBS) $(EXTRA_LOAD_FLAGS)
+@@ -427,7 +438,15 @@
+ #
+
+ libblimps.a: $(LIBOBJS)
+- $(AR) cr $@ $(LIBOBJS) ; $(RANLIB) $@
++ $(AR) cr $@ $(LIBOBJS)
++
++$(SHARED_LIB_DIR):
++ mkdir -p $@
++
++$(SHARED_LIB_DIR)/libblimps.so.$(SOVERSION): $(LIBOBJS) | $(SHARED_LIB_DIR)
++ $(CC) $(LDFLAGS) -shared -Wl,-soname,libblimps.so.$(SHORTSOVERSION) -o $@ -lm $(LIBOBJS)
++ /sbin/ldconfig -n $(SHARED_LIB_DIR)
++ rm -f $(SHARED_LIB_DIR)/libblimps.so && ln -sf libblimps.so.$(SOVERSION) $(SHARED_LIB_DIR)/libblimps.so
+
+ ########################################################################
+ ########################################################################
+@@ -480,57 +499,61 @@
+ etags ./*.[ch] $(INCLUDE_DIR)/*.[ch]
+
+
+-depend:
+- $(DEPEND) -- $(CFLAGS) -- -s "# DO NOT DELETE" -- $(SRCS)
++depend: deps.mk
+
+
+-clean::
++clean:
+ $(RM) blimps blweight blalign bldist blk2pssm rank_matrix retblock codehop htmlize-codehop oligo_melt mablock makeblockmap prints2blocks lisblk coduse narrow blkprob blk2slx LAMA find_biassed_blocks fastaseqs addseqs cobbler interpro pssmdist pssmBL papssm matrix_logob makelogob blocks_search LAMA_search block_vis format_block biassed_blocks_finder htmlize-LAMA show_aligned_blocks makelis blk2mot
+ $(RM) *.a *.o *~
++ if [ "$(SHARED_LIB_DIR)" != "." ]; then $(RM) -r $(SHARED_LIB_DIR); fi
++ rm -f $(SHARED_LIB_DIR)/libblimps.so*
+ @echo " "
+
++distclean: clean
++ $(RM) deps.mk
++
+ move-lib:
+- $(MV) lib*.a ../lib
++ $(CP) lib*.a $(SHARED_LIB_DIR)/*.so ../lib
+
+ move-bin:
+- $(MV) blimps ../bin
+- $(MV) blweight ../bin
+- $(MV) blalign ../bin
+- $(MV) bldist ../bin
+- $(MV) blk2pssm ../bin
+- $(MV) rank_matrix ../bin
+- $(MV) retblock ../bin
+- $(MV) codehop ../bin
+- $(MV) htmlize-codehop ../bin
+- $(MV) oligo_melt ../bin
+- $(MV) mablock ../bin
+- $(MV) makeblockmap ../bin
+- $(MV) prints2blocks ../bin
+- $(MV) lisblk ../bin
+- $(MV) coduse ../bin
+- $(MV) narrow ../bin
+- $(MV) blkprob ../bin
+- $(MV) blk2slx ../bin
+- $(MV) LAMA ../bin
+- $(MV) find_biassed_blocks ../bin
+- $(MV) fastaseqs ../bin
+- $(MV) addseqs ../bin
+- $(MV) cobbler ../bin
+- $(MV) interpro ../bin
+- $(MV) pssmdist ../bin
+- $(MV) pssmBL ../bin
+- $(MV) papssm ../bin
+- $(MV) matrix_logob ../bin
+- $(MV) makelogob ../bin
+- $(MV) blocks_search ../bin
+- $(MV) LAMA_search ../bin
+- $(MV) block_vis ../bin
+- $(MV) format_block ../bin
+- $(MV) biassed_blocks_finder ../bin
+- $(MV) htmlize-LAMA ../bin
+- $(MV) show_aligned_blocks ../bin
+- $(MV) makelis ../bin
+- $(MV) blk2mot ../bin
++ $(CP) blimps ../bin
++ $(CP) blweight ../bin
++ $(CP) blalign ../bin
++ $(CP) bldist ../bin
++ $(CP) blk2pssm ../bin
++ $(CP) rank_matrix ../bin
++ $(CP) retblock ../bin
++ $(CP) codehop ../bin
++ $(CP) htmlize-codehop ../bin
++ $(CP) oligo_melt ../bin
++ $(CP) mablock ../bin
++ $(CP) makeblockmap ../bin
++ $(CP) prints2blocks ../bin
++ $(CP) lisblk ../bin
++ $(CP) coduse ../bin
++ $(CP) narrow ../bin
++ $(CP) blkprob ../bin
++ $(CP) blk2slx ../bin
++ $(CP) LAMA ../bin
++ $(CP) find_biassed_blocks ../bin
++ $(CP) fastaseqs ../bin
++ $(CP) addseqs ../bin
++ $(CP) cobbler ../bin
++ $(CP) interpro ../bin
++ $(CP) pssmdist ../bin
++ $(CP) pssmBL ../bin
++ $(CP) papssm ../bin
++ $(CP) matrix_logob ../bin
++ $(CP) makelogob ../bin
++ $(CP) blocks_search ../bin
++ $(CP) LAMA_search ../bin
++ $(CP) block_vis ../bin
++ $(CP) format_block ../bin
++ $(CP) biassed_blocks_finder ../bin
++ $(CP) htmlize-LAMA ../bin
++ $(CP) show_aligned_blocks ../bin
++ $(CP) makelis ../bin
++ $(CP) blk2mot ../bin
+
+
+ ##########
+@@ -687,1272 +710,14 @@
+ $(VERSIONDISTRIB)/blimps.$(TXTVER)/docs/INSTALL $(FTPDIR)
+ @echo " "
+
+-
++deps.mk:
++ $(DEPEND) -MM $(CFLAGS) $(SRCS) > $@
+
+ ###########################################################################
+
++.PHONY: depend all clean distclean dist
+
+ ###########################################################################
+-# dependencies generated by makedepend
+-
+-# DO NOT DELETE
++# dependencies
++include deps.mk
+
+-blimps-mem.o: ../include/global.h /usr/include/stdlib.h
+-blimps-mem.o: /usr/include/features.h /usr/include/sys/cdefs.h
+-blimps-mem.o: /usr/include/gnu/stubs.h
+-blimps-mem.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
+-blimps-mem.o: /usr/include/stdio.h /usr/include/bits/types.h
+-blimps-mem.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
+-blimps-mem.o: /usr/include/libio.h /usr/include/_G_config.h
+-blimps-mem.o: /usr/include/wchar.h /usr/include/bits/wchar.h
+-blimps-mem.o: /usr/include/gconv.h
+-blimps-mem.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
+-blimps-mem.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
+-blimps-mem.o: /usr/include/string.h /usr/include/ctype.h
+-blimps-mem.o: /usr/include/endian.h /usr/include/bits/endian.h
+-blimps-mem.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
+-blimps-mem.o: ../include/errors.h ../include/memory.h blimps-mem.h blimps.h
+-blimps-mem.o: lists.h ../include/skiplist.h
+-blimps.o: /usr/include/math.h /usr/include/features.h
+-blimps.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
+-blimps.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
+-blimps.o: /usr/include/bits/mathcalls.h /usr/include/signal.h
+-blimps.o: /usr/include/bits/sigset.h /usr/include/bits/types.h
+-blimps.o: /usr/include/bits/wordsize.h
+-blimps.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
+-blimps.o: /usr/include/bits/typesizes.h /usr/include/bits/signum.h
+-blimps.o: ../include/global.h /usr/include/stdlib.h /usr/include/stdio.h
+-blimps.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
+-blimps.o: /usr/include/bits/wchar.h /usr/include/gconv.h
+-blimps.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
+-blimps.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
+-blimps.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
+-blimps.o: /usr/include/bits/endian.h /usr/include/malloc.h
+-blimps.o: ../include/license.h ../include/strutil.h ../include/errors.h
+-blimps.o: ../include/memory.h ../include/version.h ../include/residues.h
+-blimps.o: ../include/blastapp.h /usr/include/limits.h
+-blimps.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
+-blimps.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
+-blimps.o: ../include/gcode.h ../include/files.h ../include/blocks.h
+-blimps.o: ../include/output.h ../include/sequences.h ../include/matrix.h
+-blimps.o: ../include/pattern.h ../include/convert.h ../include/frequency.h
+-blimps.o: ../include/options.h blimps.h blimps-mem.h config.h scores.h
+-blimps.o: scoring.h lists.h ../include/skiplist.h
+-blweight.o: ../include/blocksprogs.h /usr/include/stdlib.h
+-blweight.o: /usr/include/features.h /usr/include/sys/cdefs.h
+-blweight.o: /usr/include/gnu/stubs.h
+-blweight.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
+-blweight.o: /usr/include/stdio.h /usr/include/bits/types.h
+-blweight.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
+-blweight.o: /usr/include/libio.h /usr/include/_G_config.h
+-blweight.o: /usr/include/wchar.h /usr/include/bits/wchar.h
+-blweight.o: /usr/include/gconv.h
+-blweight.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
+-blweight.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
+-blweight.o: /usr/include/string.h /usr/include/math.h
+-blweight.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
+-blweight.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
+-blweight.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
+-blweight.o: /usr/include/ctype.h /usr/include/endian.h
+-blweight.o: /usr/include/bits/endian.h ../include/global.h
+-blweight.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
+-blweight.o: ../include/errors.h ../include/memory.h ../include/residues.h
+-blweight.o: ../include/blastapp.h /usr/include/limits.h
+-blweight.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
+-blweight.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
+-blweight.o: ../include/gcode.h ../include/blocks.h ../include/output.h
+-blweight.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
+-blweight.o: ../include/convert.h ../include/frequency.h ../include/files.h
+-blweight.o: ../include/protomat.h /usr/include/sys/time.h /usr/include/time.h
+-blweight.o: /usr/include/bits/time.h /usr/include/sys/select.h
+-blweight.o: /usr/include/bits/select.h /usr/include/bits/sigset.h
+-blalign.o: ../include/blocksprogs.h /usr/include/stdlib.h
+-blalign.o: /usr/include/features.h /usr/include/sys/cdefs.h
+-blalign.o: /usr/include/gnu/stubs.h
+-blalign.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
+-blalign.o: /usr/include/stdio.h /usr/include/bits/types.h
+-blalign.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
+-blalign.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
+-blalign.o: /usr/include/bits/wchar.h /usr/include/gconv.h
+-blalign.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
+-blalign.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
+-blalign.o: /usr/include/string.h /usr/include/math.h
+-blalign.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
+-blalign.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
+-blalign.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
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+-convert.o: ../include/output.h ../include/sequences.h ../include/matrix.h
+-convert.o: ../include/pattern.h ../include/residues.h ../include/blastapp.h
+-convert.o: /usr/include/limits.h
+-convert.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
+-convert.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
+-convert.o: ../include/gcode.h ../include/frequency.h ../include/protomat.h
+-convert.o: ../include/convert.h blimps.h
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+-errors.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
+-errors.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
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+-errors.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
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+-errors.o: /usr/include/bits/wchar.h /usr/include/gconv.h
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+-errors.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
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+-errors.o: /usr/include/bits/endian.h /usr/include/malloc.h
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+-errors.o: ../include/memory.h
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+-files.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
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+-files.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
+-files.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
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+-files.o: /usr/include/bits/endian.h /usr/include/malloc.h
+-files.o: ../include/license.h ../include/strutil.h ../include/errors.h
+-files.o: ../include/memory.h ../include/files.h ../include/sequences.h
+-frequency.o: ../include/global.h /usr/include/stdlib.h
+-frequency.o: /usr/include/features.h /usr/include/sys/cdefs.h
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+-frequency.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
+-frequency.o: /usr/include/stdio.h /usr/include/bits/types.h
+-frequency.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
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+-frequency.o: /usr/include/wchar.h /usr/include/bits/wchar.h
+-frequency.o: /usr/include/gconv.h
+-frequency.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
+-frequency.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
+-frequency.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
+-frequency.o: /usr/include/bits/endian.h /usr/include/malloc.h
+-frequency.o: ../include/license.h ../include/strutil.h ../include/errors.h
+-frequency.o: ../include/memory.h ../include/blocks.h ../include/output.h
+-frequency.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
+-frequency.o: ../include/frequency.h ../include/convert.h ../include/files.h
+-frequency.o: ../include/residues.h ../include/blastapp.h
+-frequency.o: /usr/include/limits.h
+-frequency.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
+-frequency.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
+-frequency.o: ../include/gcode.h
+-gcode.o: ../include/global.h /usr/include/stdlib.h /usr/include/features.h
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+-gcode.o: /usr/include/stdio.h /usr/include/bits/types.h
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+-gcode.o: /usr/include/bits/endian.h /usr/include/malloc.h
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+-gcode.o: ../include/memory.h ../include/residues.h ../include/blastapp.h
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+-gcode.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
+-gcode.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
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+-lists.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
+-lists.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
+-lists.o: /usr/include/stdio.h /usr/include/bits/types.h
+-lists.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
+-lists.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
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+-lists.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
+-lists.o: /usr/include/bits/endian.h /usr/include/malloc.h
+-lists.o: ../include/license.h ../include/strutil.h ../include/errors.h
+-lists.o: ../include/memory.h ../include/blocks.h ../include/output.h
+-lists.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
+-lists.o: lists.h ../include/skiplist.h blimps.h scores.h
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+-matrix.o: /usr/include/stdio.h /usr/include/bits/types.h
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+-matrix.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
+-matrix.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
+-matrix.o: /usr/include/bits/endian.h /usr/include/malloc.h
+-matrix.o: ../include/license.h ../include/strutil.h ../include/errors.h
+-matrix.o: ../include/memory.h ../include/blocks.h ../include/output.h
+-matrix.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
+-matrix.o: ../include/residues.h ../include/blastapp.h /usr/include/limits.h
+-matrix.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
+-matrix.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
+-matrix.o: ../include/gcode.h
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+-memory.o: /usr/include/stdio.h /usr/include/bits/types.h
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+-memory.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
+-memory.o: /usr/include/bits/endian.h /usr/include/malloc.h
+-memory.o: ../include/license.h ../include/strutil.h ../include/errors.h
+-memory.o: ../include/memory.h
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+-pattern.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
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+-pattern.o: ../include/license.h ../include/strutil.h ../include/errors.h
+-pattern.o: ../include/memory.h ../include/files.h ../include/blocks.h
+-pattern.o: ../include/output.h ../include/sequences.h ../include/matrix.h
+-pattern.o: ../include/pattern.h ../include/residues.h ../include/blastapp.h
+-pattern.o: /usr/include/limits.h
+-pattern.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
+-pattern.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
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+-scores.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
+-scores.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
+-scores.o: /usr/include/bits/mathcalls.h ../include/global.h
+-scores.o: /usr/include/stdlib.h
+-scores.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
+-scores.o: /usr/include/stdio.h /usr/include/bits/types.h
+-scores.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
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+-scores.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
+-scores.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
+-scores.o: /usr/include/string.h /usr/include/ctype.h /usr/include/endian.h
+-scores.o: /usr/include/bits/endian.h /usr/include/malloc.h
+-scores.o: ../include/license.h ../include/strutil.h ../include/errors.h
+-scores.o: ../include/memory.h ../include/blocks.h ../include/output.h
+-scores.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
+-scores.o: scores.h blimps.h scoring.h lists.h ../include/skiplist.h
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+-scoring.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
+-scoring.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
+-scoring.o: /usr/include/bits/mathcalls.h ../include/global.h
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+-sequences.o: /usr/include/features.h /usr/include/sys/cdefs.h
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+-protomat.o: /usr/include/dirent.h /usr/include/bits/dirent.h
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+-interpro.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
+-interpro.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
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+-show_aligned_blocks.o: /usr/include/bits/mathdef.h
+-show_aligned_blocks.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
+-show_aligned_blocks.o: /usr/include/bits/posix_opt.h
+-show_aligned_blocks.o: /usr/include/bits/confname.h /usr/include/ctype.h
+-show_aligned_blocks.o: /usr/include/endian.h /usr/include/bits/endian.h
+-show_aligned_blocks.o: ../include/global.h /usr/include/malloc.h
+-show_aligned_blocks.o: ../include/license.h ../include/strutil.h
+-show_aligned_blocks.o: ../include/errors.h ../include/memory.h
+-show_aligned_blocks.o: ../include/residues.h ../include/blastapp.h
+-show_aligned_blocks.o: /usr/include/limits.h
+-show_aligned_blocks.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
+-show_aligned_blocks.o: ../include/alphabet.h ../include/aabet.h
+-show_aligned_blocks.o: ../include/ntbet.h ../include/gcode.h
+-show_aligned_blocks.o: ../include/blocks.h ../include/output.h
+-show_aligned_blocks.o: ../include/sequences.h ../include/matrix.h
+-show_aligned_blocks.o: ../include/pattern.h ../include/convert.h
+-show_aligned_blocks.o: ../include/frequency.h ../include/files.h
+-show_aligned_blocks.o: ../include/protomat.h
+-blk2mot.o: ../include/blocksprogs.h /usr/include/stdlib.h
+-blk2mot.o: /usr/include/features.h /usr/include/sys/cdefs.h
+-blk2mot.o: /usr/include/gnu/stubs.h
+-blk2mot.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stddef.h
+-blk2mot.o: /usr/include/stdio.h /usr/include/bits/types.h
+-blk2mot.o: /usr/include/bits/wordsize.h /usr/include/bits/typesizes.h
+-blk2mot.o: /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h
+-blk2mot.o: /usr/include/bits/wchar.h /usr/include/gconv.h
+-blk2mot.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/stdarg.h
+-blk2mot.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
+-blk2mot.o: /usr/include/string.h /usr/include/math.h
+-blk2mot.o: /usr/include/bits/huge_val.h /usr/include/bits/mathdef.h
+-blk2mot.o: /usr/include/bits/mathcalls.h /usr/include/unistd.h
+-blk2mot.o: /usr/include/bits/posix_opt.h /usr/include/bits/confname.h
+-blk2mot.o: /usr/include/ctype.h /usr/include/endian.h
+-blk2mot.o: /usr/include/bits/endian.h ../include/global.h
+-blk2mot.o: /usr/include/malloc.h ../include/license.h ../include/strutil.h
+-blk2mot.o: ../include/errors.h ../include/memory.h ../include/residues.h
+-blk2mot.o: ../include/blastapp.h /usr/include/limits.h
+-blk2mot.o: /usr/lib/gcc-lib/i586-suse-linux/3.3.3/include/limits.h
+-blk2mot.o: ../include/alphabet.h ../include/aabet.h ../include/ntbet.h
+-blk2mot.o: ../include/gcode.h ../include/blocks.h ../include/output.h
+-blk2mot.o: ../include/sequences.h ../include/matrix.h ../include/pattern.h
+-blk2mot.o: ../include/convert.h ../include/frequency.h ../include/files.h
+-blk2mot.o: ../include/protomat.h
+Index: blimps-3.9/blimps/makelogob.c
+===================================================================
+--- blimps-3.9.orig/blimps/makelogob.c 2012-01-29 19:13:50.851865048 +0000
++++ blimps-3.9/blimps/makelogob.c 2012-01-29 19:13:53.414372010 +0000
+@@ -797,7 +797,7 @@
+ *w = NULL;
+ return;
+ }
+- *w = (waveparam *)Malloc(sizeof(waveparam));
++ *w = (waveparam *)malloc(sizeof(waveparam));
+ p = *w;
+ while (!BUFEOF(afile->f)) {
+ fscanf(afile->f, "%c%*[^\n]", &p->extreme);
+@@ -831,7 +831,7 @@
+ }
+ }
+ if (!BUFEOF(afile->f)) {
+- p->next = (waveparam *)Malloc(sizeof(waveparam));
++ p->next = (waveparam *)malloc(sizeof(waveparam));
+ p = p->next;
+ } else
+ p->next = NULL;
+@@ -2007,7 +2007,7 @@
+ return;
+ }
+
+- *thestrings = (strings *)Malloc(sizeof(strings));
++ *thestrings = (strings *)malloc(sizeof(strings));
+ stringspot = *thestrings;
+ for (n = 1; n <= numberstrings; n++) {
+ if (BUFEOF(theplace->f)) {
+@@ -2023,7 +2023,7 @@
+ halt();
+ }
+ if (n < numberstrings) {
+- stringspot->next = (strings *)Malloc(sizeof(strings));
++ stringspot->next = (strings *)malloc(sizeof(strings));
+ stringspot = stringspot->next;
+ } else
+ stringspot->next = NULL;
+Index: blimps-3.9/blimps/matrix_logob.c
+===================================================================
+--- blimps-3.9.orig/blimps/matrix_logob.c 2012-01-29 19:13:50.991863315 +0000
++++ blimps-3.9/blimps/matrix_logob.c 2012-01-29 19:13:53.414372010 +0000
+@@ -331,7 +331,7 @@
+ else
+ {
+ printf("\nEnter name of BLOCK or MATRIX file: ");
+- gets(bdbname);
++ fgets(bdbname, MAXNAME, stdin);
+ }
+
+ /* Read stdin if the filename starts with '-' */
+@@ -347,7 +347,7 @@
+ else /* get input file(s) interactively */
+ {
+ printf("\nEnter AC in %s or - to make logos for all: ", bdbname);
+- gets(blockAC);
++ fgets(blockAC, MAXNAME, stdin);
+ }
+
+ /* ------------3rd arg = file name suffix ------------------------------JGH*/
+@@ -356,7 +356,7 @@
+ else
+ {
+ printf("\nEnter file name suffix: ");
+- gets(suffix);
++ fgets(suffix, MAXNAME, stdin);
+ printf("Logos will be written to logo.%s\n", suffix);
+ }
+
+@@ -588,7 +588,7 @@
+ printf(" after viewing you can also choose to print,\n") ;
+ printf(" P to print logo (%s %s).)\n", PSprint, outname) ;
+
+- gets(ans) ;
++ fgets(ans, 2, stdin) ;
+
+ switch (toupper(ans[0]))
+ {
+Index: blimps-3.9/blimps/narrow.c
+===================================================================
+--- blimps-3.9.orig/blimps/narrow.c 2012-01-29 19:13:51.171871018 +0000
++++ blimps-3.9/blimps/narrow.c 2012-01-29 19:13:53.414372010 +0000
+@@ -93,7 +93,7 @@
+ else
+ {
+ printf("\nEnter type of input file (Block|Frequencies|Weights): ");
+- gets(ctemp);
++ fgets(ctemp, 80, stdin);
+ }
+ if (ctemp[0] == 'F' || ctemp[0] == 'f') type = 1;
+ else if (ctemp[0] == 'W' || ctemp[0] == 'w') type = 2;
+@@ -104,7 +104,7 @@
+ else
+ {
+ printf("\nEnter name of input file: ");
+- gets(chkname);
++ fgets(chkname, 80, stdin);
+ }
+ if ( (chk=fopen(chkname, "r")) == NULL)
+ {
+Index: blimps-3.9/blimps/oligo_melt.c
+===================================================================
+--- blimps-3.9.orig/blimps/oligo_melt.c 2012-01-29 19:13:50.881864474 +0000
++++ blimps-3.9/blimps/oligo_melt.c 2012-01-29 19:13:53.414372010 +0000
+@@ -75,7 +75,7 @@
+ else
+ {
+ printf("Enter name of file containing oligos: ");
+- gets(fname);
++ fgets(fname, 80, stdin);
+ }
+ if (!strlen(fname) ) inpf = stdin;
+ else if ((inpf=fopen(fname, "r")) == NULL)
+Index: blimps-3.9/blimps/papssm.c
+===================================================================
+--- blimps-3.9.orig/blimps/papssm.c 2012-01-29 19:13:51.001864057 +0000
++++ blimps-3.9/blimps/papssm.c 2012-01-29 19:13:53.414372010 +0000
+@@ -163,7 +163,7 @@
+
+ int read_cf();
+ int load_frequencies();
+-double read_freq();
++static double read_freq();
+ void load_subst();
+ double nrgamma();
+ double addlogs();
+@@ -250,7 +250,7 @@
+ else
+ {
+ printf("\nEnter name of configuration file: ");
+- gets(cfname);
++ fgets(cfname, FNAMELEN, stdin);
+ }
+ if ( (cfp=fopen(cfname, "r")) == NULL)
+ {
+Index: blimps-3.9/blimps/prints2blocks.c
+===================================================================
+--- blimps-3.9.orig/blimps/prints2blocks.c 2012-01-29 19:13:50.911864660 +0000
++++ blimps-3.9/blimps/prints2blocks.c 2012-01-29 19:13:53.414372010 +0000
+@@ -63,7 +63,7 @@
+ {
+ printf(
+ "\nEnter name of input file (Prints protein motifs database): ");
+- gets(inpfname);
++ fgets(inpfname, MAXNAME, stdin);
+ }
+
+ if ( (inpf=fopen(inpfname, "r")) == NULL)
+Index: blimps-3.9/blimps/protomat.c
+===================================================================
+--- blimps-3.9.orig/blimps/protomat.c 2012-01-29 19:13:51.001864057 +0000
++++ blimps-3.9/blimps/protomat.c 2012-01-29 19:13:53.414372010 +0000
+@@ -438,7 +438,8 @@
+ char *dir_unix(line)
+ char *line;
+ {
+- char tname[FNAMELEN], mem[MAXLINE], pros[FNAMELEN], *ptr;
++ char tname[FNAMELEN], mem[MAXLINE], *ptr;
++ static char pros[FNAMELEN];
+ int test;
+ DIR *dp;
+
+Index: blimps-3.9/blimps/protxblk.c
+===================================================================
+--- blimps-3.9.orig/blimps/protxblk.c 2012-01-29 19:13:51.091863167 +0000
++++ blimps-3.9/blimps/protxblk.c 2012-01-29 19:13:53.414372010 +0000
+@@ -37,7 +37,7 @@
+ else
+ {
+ printf("\nEnter name of blocks database: ");
+- gets(bdbname);
++ fgets(bdbname, MAXNAME, stdin);
+ }
+ if ( (bfp=fopen(bdbname, "r")) == NULL)
+ {
+@@ -50,7 +50,7 @@
+ else
+ {
+ printf("\nEnter name of output file: ");
+- gets(conname);
++ fgets(conname, MAXNAME, stdin);
+ }
+ if ( (ofp=fopen(conname, "w")) == NULL)
+ {
+Index: blimps-3.9/blimps/pssmBL.c
+===================================================================
+--- blimps-3.9.orig/blimps/pssmBL.c 2012-01-29 19:13:50.801864376 +0000
++++ blimps-3.9/blimps/pssmBL.c 2012-01-29 19:13:53.414372010 +0000
+@@ -29,7 +29,7 @@
+ else
+ {
+ printf("\nEnter name of pssmdist.dat file: ");
+- gets(pssmname);
++ fgets(pssmname, MAXNAME, stdin);
+ }
+ if ( (pfp=fopen(pssmname, "r")) == NULL)
+ {
+@@ -42,7 +42,7 @@
+ else
+ {
+ printf("\nEnter name of blocks database: ");
+- gets(bdbname);
++ fgets(bdbname, MAXNAME, stdin);
+ }
+ if ( (bfp=fopen(bdbname, "r")) == NULL)
+ {
+@@ -55,7 +55,7 @@
+ else
+ {
+ printf("\nEnter name of new blocks database: ");
+- gets(conname);
++ fgets(conname, MAXNAME, stdin);
+ }
+ if ( (ofp=fopen(conname, "a")) == NULL)
+ {
+Index: blimps-3.9/blimps/pssmdist.c
+===================================================================
+--- blimps-3.9.orig/blimps/pssmdist.c 2012-01-29 19:13:51.101863908 +0000
++++ blimps-3.9/blimps/pssmdist.c 2012-01-29 19:13:53.414372010 +0000
+@@ -81,7 +81,7 @@
+
+ int compute();
+ int load_freqs();
+-double read_a_freq();
++static double read_a_freq();
+ void fix_freqs();
+ int count_tps();
+
+@@ -113,7 +113,7 @@
+ else
+ {
+ printf("\nEnter name of matrix database: ");
+- gets(mname);
++ fgets(mname, MAXNAME, stdin);
+ }
+ if ( (mfp=fopen(mname, "r")) == NULL)
+ {
+@@ -126,7 +126,7 @@
+ else
+ {
+ printf("\nEnter name of observed frequencies database: ");
+- gets(oname);
++ fgets(oname, MAXNAME, stdin);
+ }
+ if ( (ofp=fopen(oname, "r")) == NULL)
+ {
+@@ -138,7 +138,7 @@
+ else
+ {
+ printf("\nEnter name of frequency file: ");
+- gets(fname);
++ fgets(fname, MAXNAME,stdin);
+ }
+ if ( (ffp=fopen(fname, "r")) == NULL)
+ {
+@@ -155,7 +155,7 @@
+ {
+ printf("\nEnter number of sequences in a typical search [%.0f]: ",
+ Search);
+- gets(ctemp);
++ fgets(ctemp, MAXNAME, stdin);
+ }
+ if (strlen(ctemp)) Search = atof(ctemp);
+ /* ------------5th arg = #aas in a search--------------------*/
+@@ -166,7 +166,7 @@
+ {
+ printf("\nEnter number of amino acids in a typical database [%.0f]: ",
+ SearchAA);
+- gets(ctemp);
++ fgets(ctemp, MAXNAME, stdin);
+ }
+ if (strlen(ctemp)) SearchAA = atof(ctemp);
+ printf ("Assuming %.0f sequences, %.0f amino acids in a search\n",
+Index: blimps-3.9/blimps/rank_matrix.c
+===================================================================
+--- blimps-3.9.orig/blimps/rank_matrix.c 2012-01-29 19:13:51.111864408 +0000
++++ blimps-3.9/blimps/rank_matrix.c 2012-01-29 19:13:53.414372010 +0000
+@@ -39,7 +39,7 @@
+ else
+ {
+ printf("\nEnter name of scoring matrix: ");
+- gets(matname);
++ fgets(matname, MAXNAME, stdin);
+ }
+ if ( (fmat=fopen(matname, "r")) == NULL)
+ {
+Index: blimps-3.9/blimps/readchk.c
+===================================================================
+--- blimps-3.9.orig/blimps/readchk.c 2012-01-29 19:13:51.161863795 +0000
++++ blimps-3.9/blimps/readchk.c 2012-01-29 19:13:53.414372010 +0000
+@@ -20,7 +20,7 @@
+ else
+ {
+ printf("\nEnter name of configuration file: ");
+- gets(chkname);
++ fgets(chkname, 80, stdin);
+ }
+ if ( (chk=fopen(chkname, "r")) == NULL)
+ {
+Index: blimps-3.9/blimps/readmast.c
+===================================================================
+--- blimps-3.9.orig/blimps/readmast.c 2012-01-29 19:13:50.971862551 +0000
++++ blimps-3.9/blimps/readmast.c 2012-01-29 19:13:53.414372010 +0000
+@@ -26,7 +26,7 @@
+ else
+ {
+ printf("\nEnter name of configuration file: ");
+- gets(chkname);
++ fgets(chkname, 80, stdin);
+ }
+ if ( (chk=fopen(chkname, "r")) == NULL)
+ {
+Index: blimps-3.9/blimps/retblock.c
+===================================================================
+--- blimps-3.9.orig/blimps/retblock.c 2012-01-29 19:13:51.191865064 +0000
++++ blimps-3.9/blimps/retblock.c 2012-01-29 19:13:53.414372010 +0000
+@@ -50,7 +50,7 @@
+ else
+ {
+ printf("\nEnter name of blocks database: ");
+- gets(bdbname);
++ fgets(bdbname, MAXNAME, stdin);
+ }
+ if ( (bfp=fopen(bdbname, "r")) == NULL)
+ {
+@@ -66,7 +66,7 @@
+ {
+ strcpy(acname, "all");
+ printf("\nEnter AC of blocks to extract, or all [%s]: ", acname);
+- gets(acname);
++ fgets(acname, MAXNAME, stdin);
+ }
+ if (strcasecmp(acname, "all") == 0) allflag = TRUE;
+
+Index: blimps-3.9/blimps/sequences.c
+===================================================================
+--- blimps-3.9.orig/blimps/sequences.c 2012-01-29 19:13:51.061863185 +0000
++++ blimps-3.9/blimps/sequences.c 2012-01-29 19:13:53.414372010 +0000
+@@ -665,7 +665,7 @@
+ stemp is a huge negative number ...
+ */
+ if (seq_type == AA_SEQ) {
+- while ( (c != NULL) && (c != '\0') && (num_seen < room_left) ) {
++ while ( (c != 0) && (c != '\0') && (num_seen < room_left) ) {
+ stemp = aa_atob[c];
+ if (stemp < 0 || stemp > AAID_MAX) stemp = AAID_MAX + 1;
+ if ( stemp <= AAID_MAX ) {
+@@ -1201,7 +1201,7 @@
+ }
+ }
+ else {
+- printf("??) \t");
++ printf("??"") \t");
+ printf("\n");
+ for(k=0; k<seq->length; k++) {
+ printf("%c", aa_btoa[seq->sequence[k]]);
+Index: blimps-3.9/blimps/sortblk.c
+===================================================================
+--- blimps-3.9.orig/blimps/sortblk.c 2012-01-29 19:13:50.981863453 +0000
++++ blimps-3.9/blimps/sortblk.c 2012-01-29 19:13:53.414372010 +0000
+@@ -58,7 +58,7 @@
+ else
+ {
+ printf("\nEnter name of blocks database: ");
+- gets(bdbname);
++ fgets(bdbname, MAXNAME, stdin);
+ }
+ if ( (bfp=fopen(bdbname, "r")) == NULL)
+ {
+@@ -71,7 +71,7 @@
+ else
+ {
+ printf("\nEnter name of new sorted blocks database: ");
+- gets(conname);
++ fgets(conname, MAXNAME, stdin);
+ }
+ if ( (ofp=fopen(conname, "w")) == NULL)
+ {
+Index: blimps-3.9/blimps/translate.c
+===================================================================
+--- blimps-3.9.orig/blimps/translate.c 2012-01-29 19:13:51.071862806 +0000
++++ blimps-3.9/blimps/translate.c 2012-01-29 19:13:53.414372010 +0000
+@@ -29,7 +29,7 @@
+ else
+ {
+ printf("\nEnter name of sequence database: ");
+- gets(sname);
++ fgets(sname, MAXNAME, stdin);
+ }
+ if ( (bfp=fopen(sname, "r")) == NULL)
+ {
+@@ -50,7 +50,7 @@
+ else
+ {
+ printf("\nEnter name of new translated sequence database: ");
+- gets(outname);
++ fgets(outname, MAXNAME, stdin);
+ }
+ if ( (ofp=fopen(outname, "w")) == NULL)
+ {
+@@ -62,7 +62,7 @@
+ else
+ {
+ printf("\nEnter translation frame: ");
+- gets(ctemp);
++ fgets(ctemp, MAXNAME, stdin);
+ frame = atoi(ctemp);
+ }
+ if (frame == 0 || frame < -3 || frame > 3) frame = 1;
+@@ -74,7 +74,7 @@
+ for (code = 0; code < NUMBER_OF_GENETIC_CODES; code++)
+ printf("\n %d %s", code, gcodes[code].name);
+ printf("\nEnter genetic code: ");
+- gets(ctemp);
++ fgets(ctemp, MAXNAME, stdin);
+ code = atoi(ctemp);
+ }
+ if (code < 0 || code > 8) code = 0;
+Index: blimps-3.9/blimps/util.c
+===================================================================
+--- blimps-3.9.orig/blimps/util.c 2012-01-29 19:13:50.871863612 +0000
++++ blimps-3.9/blimps/util.c 2012-01-29 19:13:53.414372010 +0000
+@@ -1,5 +1,6 @@
+ #include <stdlib.h>
+ #include <stdio.h>
++#include <string.h>
+
+ #define LF 10
+ #define CR 13
+@@ -92,7 +93,7 @@
+ return -1;
+ }
+
+-int getline(char *s, int n, FILE *f) {
++int blimps_getline(char *s, int n, FILE *f) {
+ register int i=0;
+
+ while(1) {
+Index: blimps-3.9/protomat/Makefile.Linux
+===================================================================
+--- blimps-3.9.orig/protomat/Makefile.Linux 2012-01-29 19:13:50.781871971 +0000
++++ blimps-3.9/protomat/Makefile.Linux 2012-01-29 19:13:53.414372010 +0000
+@@ -3,52 +3,65 @@
+ # Type "make blksort" to compile blksort program
+ CC = gcc
+ CFLAGS = -Wall -O2 -c
+-CL = gcc
+-LFLAGS = -lm -o
++LDFLAGS = -lm -o
+ RM = /bin/rm -f
+ MV = /bin/mv -f
++CP = cp -af
++
++BIN := blksort getblock getseq multimat motifj motomat uextract blosum blastdat
+ #
+-install: clean all
+-clean:
+- $(RM) *.o blksort getblock getseq multimat motifj motomat uextract blosum blastdat
+-all: blksort getblock getseq multimat motifj motomat uextract blosum blastdat
++all: $(BIN)
+ #
++install: $(BIN)
++ $(CP) blksort ../bin
++ $(CP) getblock ../bin
++ $(CP) getseq ../bin
++ $(CP) multimat ../bin
++ $(CP) motifj ../bin
++ $(CP) motomat ../bin
++ $(CP) uextract ../bin
++ $(CP) blosum ../bin
++ $(CP) blastdat ../bin
++
++clean:
++ $(RM) *.o $(BIN)
++
+ # blksort: Analyze results of a BLOCKS search
+ blksort: blksort.o motmisc.o
+- $(CL) blksort.o motmisc.o $(LFLAGS) blksort
+- mv blksort ../bin
++ $(CC) blksort.o motmisc.o $(LDFLAGS) blksort
++
+ # getblock: Retrieve BLOCKs
+ getblock: getblock.o motmisc.o
+- $(CL) getblock.o motmisc.o $(LFLAGS) getblock
+- mv getblock ../bin
++ $(CC) getblock.o motmisc.o $(LDFLAGS) getblock
++
+ # getseq: Retrieve a sequence
+ getseq: getseq.o motmisc.o
+- $(CL) getseq.o motmisc.o $(LFLAGS) getseq
+- mv getseq ../bin
++ $(CC) getseq.o motmisc.o $(LDFLAGS) getseq
++
+ # multimat: Analyze results of a MATRIX search
+ multimat: multimat.o motmisc.o
+- $(CL) multimat.o motmisc.o $(LFLAGS) multimat
+- mv multimat ../bin
++ $(CC) multimat.o motmisc.o $(LDFLAGS) multimat
++
+ # motifj: Make blocks using Ham Smith's motif algorithm
+ motifj: motifj.o motmisc.o
+- $(CL) motifj.o motmisc.o $(LFLAGS) motifj
+- mv motifj ../bin
++ $(CC) motifj.o motmisc.o $(LDFLAGS) motifj
++
+ # motomat: Assemble blocks from motifj
+ motomat: motomat.o motmisc.o
+- $(CL) motomat.o motmisc.o $(LFLAGS) motomat
+- mv motomat ../bin
++ $(CC) motomat.o motmisc.o $(LDFLAGS) motomat
++
+ # uextract: Extract protein families from prosite.dat
+ uextract: uextract.o motmisc.o
+- $(CL) uextract.o motmisc.o $(LFLAGS) uextract
+- mv uextract ../bin
++ $(CC) uextract.o motmisc.o $(LDFLAGS) uextract
++
+ # blosum: Make substitution matrices from blocks
+ blosum: blosum.o motmisc.o
+- $(CL) blosum.o motmisc.o $(LFLAGS) blosum
+- mv blosum ../bin
++ $(CC) blosum.o motmisc.o $(LDFLAGS) blosum
++
+ # blastdat: Read blast output
+ blastdat: blastdat.o motmisc.o
+- $(CL) blastdat.o motmisc.o $(LFLAGS) blastdat
+- mv blastdat ../bin
++ $(CC) blastdat.o motmisc.o $(LDFLAGS) blastdat
++
+ #
+ blksort.o: blksort.c motifj.h
+ $(CC) $(CFLAGS) blksort.c
Added: trunk/packages/blimps/trunk/debian/patches/patch_002.diff
===================================================================
--- trunk/packages/blimps/trunk/debian/patches/patch_002.diff (rev 0)
+++ trunk/packages/blimps/trunk/debian/patches/patch_002.diff 2012-01-31 17:21:48 UTC (rev 9507)
@@ -0,0 +1,13 @@
+Index: blimps-3.9/blimps/Makefile.Linux
+===================================================================
+--- blimps-3.9.orig/blimps/Makefile.Linux 2012-01-29 19:13:53.414372010 +0000
++++ blimps-3.9/blimps/Makefile.Linux 2012-01-29 19:28:22.951946468 +0000
+@@ -106,7 +106,7 @@
+
+ XXWARN = -Werror
+
+-INCLUDE_DIR = ../include
++INCLUDE_DIR = ../blimps-3.9/include
+ INCLUDES = -I$(INCLUDE_DIR)
+
+
Added: trunk/packages/blimps/trunk/debian/patches/series
===================================================================
--- trunk/packages/blimps/trunk/debian/patches/series (rev 0)
+++ trunk/packages/blimps/trunk/debian/patches/series 2012-01-31 17:21:48 UTC (rev 9507)
@@ -0,0 +1,3 @@
+patch_001.diff
+patch_002.diff
+Makefile
Added: trunk/packages/blimps/trunk/debian/rules
===================================================================
--- trunk/packages/blimps/trunk/debian/rules (rev 0)
+++ trunk/packages/blimps/trunk/debian/rules 2012-01-31 17:21:48 UTC (rev 9507)
@@ -0,0 +1,11 @@
+#!/usr/bin/make -f
+
+# In order to make dh verbose set this to 1:
+export DH_VERBOSE=1
+
+%:
+ dh --parallel $@
+
+.PHONY: override_dh_auto_install
+override_dh_auto_install:
+ dh_auto_install -- prefix=/usr
Property changes on: trunk/packages/blimps/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/blimps/trunk/debian/source/format
===================================================================
--- trunk/packages/blimps/trunk/debian/source/format (rev 0)
+++ trunk/packages/blimps/trunk/debian/source/format 2012-01-31 17:21:48 UTC (rev 9507)
@@ -0,0 +1 @@
+3.0 (quilt)
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