debian/blimps-utils.manpages

-usr/share/man/man1/fastaseqs.1.gz
+debian/fastaseqs.1

debian/changelog

-blimps (3.9+ds-1) unstable; urgency=medium
+blimps (3.9+ds-1) UNRELEASED; urgency=medium
 
   * Homepage vanished - point to waybackmachine as homepage
   * Rebuild tarball by droping all binaries
@@ -6,6 +6,8 @@ blimps (3.9+ds-1) unstable; urgency=medium
   * debhelper 12
   * Point Vcs fields to salsa.debian.org
   * Standards-Version: 4.3.0
+  * hardening=+all
+  * Refactor single patch
 
  -- Andreas Tille <tille@debian.org>  Thu, 10 Jan 2019 22:19:40 +0100
 

debian/fastaseqs.1

+.\" Automatically generated by Pod::Man 4.10 (Pod::Simple 3.35)
+.\"
+.\" Standard preamble:
+.\" ========================================================================
+.de Sp \" Vertical space (when we can't use .PP)
+.if t .sp .5v
+.if n .sp
+..
+.de Vb \" Begin verbatim text
+.ft CW
+.nf
+.ne \\$1
+..
+.de Ve \" End verbatim text
+.ft R
+.fi
+..
+.\" Set up some character translations and predefined strings.  \*(-- will
+.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left
+.\" double quote, and \*(R" will give a right double quote.  \*(C+ will
+.\" give a nicer C++.  Capital omega is used to do unbreakable dashes and
+.\" therefore won't be available.  \*(C` and \*(C' expand to `' in nroff,
+.\" nothing in troff, for use with C<>.
+.tr \(*W-
+.ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p'
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+.    if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch
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+.    ds L" ""
+.    ds R" ""
+.    ds C` ""
+.    ds C' ""
+'br\}
+.el\{\
+.    ds -- \|\(em\|
+.    ds PI \(*p
+.    ds L" ``
+.    ds R" ''
+.    ds C`
+.    ds C'
+'br\}
+.\"
+.\" Escape single quotes in literal strings from groff's Unicode transform.
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\"
+.\" If the F register is >0, we'll generate index entries on stderr for
+.\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index
+.\" entries marked with X<> in POD.  Of course, you'll have to process the
+.\" output yourself in some meaningful fashion.
+.\"
+.\" Avoid warning from groff about undefined register 'F'.
+.de IX
+..
+.nr rF 0
+.if \n(.g .if rF .nr rF 1
+.if (\n(rF:(\n(.g==0)) \{\
+.    if \nF \{\
+.        de IX
+.        tm Index:\\$1\t\\n%\t"\\$2"
+..
+.        if !\nF==2 \{\
+.            nr % 0
+.            nr F 2
+.        \}
+.    \}
+.\}
+.rr rF
+.\"
+.\" Accent mark definitions (@(#)ms.acc 1.5 88/02/08 SMI; from UCB 4.2).
+.\" Fear.  Run.  Save yourself.  No user-serviceable parts.
+.    \" fudge factors for nroff and troff
+.if n \{\
+.    ds #H 0
+.    ds #V .8m
+.    ds #F .3m
+.    ds #[ \f1
+.    ds #] \fP
+.\}
+.if t \{\
+.    ds #H ((1u-(\\\\n(.fu%2u))*.13m)
+.    ds #V .6m
+.    ds #F 0
+.    ds #[ \&
+.    ds #] \&
+.\}
+.    \" simple accents for nroff and troff
+.if n \{\
+.    ds ' \&
+.    ds ` \&
+.    ds ^ \&
+.    ds , \&
+.    ds ~ ~
+.    ds /
+.\}
+.if t \{\
+.    ds ' \\k:\h'-(\\n(.wu*8/10-\*(#H)'\'\h"|\\n:u"
+.    ds ` \\k:\h'-(\\n(.wu*8/10-\*(#H)'\`\h'|\\n:u'
+.    ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'^\h'|\\n:u'
+.    ds , \\k:\h'-(\\n(.wu*8/10)',\h'|\\n:u'
+.    ds ~ \\k:\h'-(\\n(.wu-\*(#H-.1m)'~\h'|\\n:u'
+.    ds / \\k:\h'-(\\n(.wu*8/10-\*(#H)'\z\(sl\h'|\\n:u'
+.\}
+.    \" troff and (daisy-wheel) nroff accents
+.ds : \\k:\h'-(\\n(.wu*8/10-\*(#H+.1m+\*(#F)'\v'-\*(#V'\z.\h'.2m+\*(#F'.\h'|\\n:u'\v'\*(#V'
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+.ds D- D\\k:\h'-\w'D'u'\v'-.11m'\z\(hy\v'.11m'\h'|\\n:u'
+.ds th \*(#[\v'.3m'\s+1I\s-1\v'-.3m'\h'-(\w'I'u*2/3)'\s-1o\s+1\*(#]
+.ds Th \*(#[\s+2I\s-2\h'-\w'I'u*3/5'\v'-.3m'o\v'.3m'\*(#]
+.ds ae a\h'-(\w'a'u*4/10)'e
+.ds Ae A\h'-(\w'A'u*4/10)'E
+.    \" corrections for vroff
+.if v .ds ~ \\k:\h'-(\\n(.wu*9/10-\*(#H)'\s-2\u~\d\s+2\h'|\\n:u'
+.if v .ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'\v'-.4m'^\v'.4m'\h'|\\n:u'
+.    \" for low resolution devices (crt and lpr)
+.if \n(.H>23 .if \n(.V>19 \
+\{\
+.    ds : e
+.    ds 8 ss
+.    ds o a
+.    ds d- d\h'-1'\(ga
+.    ds D- D\h'-1'\(hy
+.    ds th \o'bp'
+.    ds Th \o'LP'
+.    ds ae ae
+.    ds Ae AE
+.\}
+.rm #[ #] #H #V #F C
+.\" ========================================================================
+.\"
+.IX Title "FASTASEQS 1"
+.TH FASTASEQS 1 "2019-01-11" "3.9" "User Commands"
+.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
+.\" way too many mistakes in technical documents.
+.if n .ad l
+.nh
+.SH "NAME"
+fastaseqs \- converts a file of sequences to FASTA format
+.SH "SYNOPSIS"
+.IX Header "SYNOPSIS"
+fastaseqs <\s-1INPUTFILE\s0> <\s-1OUTPUTFILE\s0>
+.SH "DESCRIPTION"
+.IX Header "DESCRIPTION"
+fastaseqs converts a file of sequences to \s-1FASTA\s0 format.
+.SH "AUTHOR"
+.IX Header "AUTHOR"
+J. Henikoff
+.SH "COPYRIGHT AND LICENSE"
+.IX Header "COPYRIGHT AND LICENSE"
+Copyright 1998, Fred Hutchinson Cancer Research Center
+.PP
+Please refer to /usr/share/doc/*blimps*/copyright for the license.
+.SH "SEE ALSO"
+.IX Header "SEE ALSO"
+<http://blocks.fhcrc.org/blocks/uploads/blimps/>

debian/fastaseqs.pod

+=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/>

debian/get-patch

-#!/bin/sh -e
-
-wget -N https://web.archive.org/web/20170703191319/http://blocks.fhcrc.org/blocks/uploads/blimps/blimps.patch.txt

debian/patches/hardening.patch

+Description: Propagate hardening options
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Thu, 10 Jan 2019 22:19:40 +0100
+
+--- a/Makefile
++++ b/Makefile
+@@ -14,10 +14,10 @@ libdir ?= $(prefix)/lib
+ all: blimps protomat
+ 
+ blimps:
+-	$(MAKE) -C $(BLIMPSDIR) -f Makefile.Linux VERSION=$(VERSION)
++	$(MAKE) -C $(BLIMPSDIR) -f Makefile.Linux VERSION=$(VERSION) DEBCFLAGS="$(CFLAGS)" DEBLDFLAGS="$(LDFLAGS)"
+ 
+ protomat:
+-	$(MAKE) -C $(PROTOMATDIR) -f Makefile.Linux VERSION=$(VERSION)
++	$(MAKE) -C $(PROTOMATDIR) -f Makefile.Linux VERSION=$(VERSION) DEBCFLAGS="$(CFLAGS)" DEBLDFLAGS="$(LDFLAGS)"
+ 
+ # 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
+--- a/blimps/Makefile.Linux
++++ b/blimps/Makefile.Linux
+@@ -112,11 +112,11 @@ INCLUDES = -I$(INCLUDE_DIR)
+ 
+ # C Flags to compiler
+ #CFLAGS = `getconf LFS_CFLAGS` $(OPTIMIZ) $(DEFINES) $(INCLUDES)
+-CFLAGS = $(OPTIMIZ) $(DEFINES) $(INCLUDES) -fpic
++CFLAGS = $(DEBCFLAGS) $(OPTIMIZ) $(DEFINES) $(INCLUDES) -fpic
+ 
+ 
+ # Linker Flags
+-LDFLAGS = $(CFLAGS)
++LDFLAGS = $(DEBLDFLAGS)
+ LDLIBS = -lblimps -lm
+ LDOPTIONS = $(LDFLAGS) $(LDDIR)
+ # cc ld options

debian/patches/series

-patch001
+gets.patch
+makefile.patch
+hardening.patch

debian/rules

@@ -3,6 +3,10 @@
 # In order to make dh verbose set this to 1:
 # export DH_VERBOSE=1
 
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
+include /usr/share/dpkg/default.mk
+
 %:
 	dh $@
 
@@ -10,8 +14,11 @@ override_dh_auto_install:
 	dh_auto_install -- prefix=/usr
 	find debian/tmp -name LICENSE -delete
 
-override_dh_dwz:
-	echo "Optimization of DWARF debug information in ELF binaries via dwz does not work"
+#override_dh_dwz:
+#	echo "Optimization of DWARF debug information in ELF binaries via dwz does not work"
 
 override_dh_clean:
 	dh_clean blimps/deps.mk
+
+manpage:
+	pod2man -c 'User Commands' -r "$(DEB_VERSION_UPSTREAM)" debian/fastaseqs.pod > debian/fastaseqs.1