[med-svn] r21057 - in trunk/packages/aegean/tags: . 0.15.1+dfsg-1/debian 0.15.1+dfsg-1/debian/man 0.15.1+dfsg-1/debian/patches 0.15.1+dfsg-1/debian/tests
Sascha Steinbiss
sascha-guest at moszumanska.debian.org
Sat Jan 9 14:26:07 UTC 2016
Author: sascha-guest
Date: 2016-01-09 14:26:06 +0000 (Sat, 09 Jan 2016)
New Revision: 21057
Added:
trunk/packages/aegean/tags/0.15.1+dfsg-1/
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/aegean.docs
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/aegean.install
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/changelog
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/control
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/canon-gff3.1
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/gaeval.1
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/locuspocus.1
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/parseval.1
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/pmrna.1
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/tidygff3.1
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/xtractore.1
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/add_hardening
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/add_version
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/adjust_datapath
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/fix_m64_on_some_archs
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/follow_links
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/includepaths
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/remove_license
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/series
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/spelling
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/rules
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/tests/
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/tests/control
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/tests/functional-tests
Removed:
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/aegean.docs
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/aegean.install
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/changelog
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/control
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/canon-gff3.1
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/gaeval.1
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/locuspocus.1
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/parseval.1
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/pmrna.1
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/xtractore.1
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/add_hardening
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/add_version
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/adjust_datapath
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/fix_m64_on_some_archs
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/follow_links
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/includepaths
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/remove_license
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/series
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/rules
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/tests/control
trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/tests/functional_tests
Log:
[svn-buildpackage] Tagging aegean 0.15.1+dfsg-1
Deleted: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/aegean.docs
===================================================================
--- trunk/packages/aegean/trunk/debian/aegean.docs 2016-01-03 13:49:42 UTC (rev 20945)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/aegean.docs 2016-01-09 14:26:06 UTC (rev 21057)
@@ -1,3 +0,0 @@
-README.md
-VERSION
-CHANGELOG.md
Copied: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/aegean.docs (from rev 21050, trunk/packages/aegean/trunk/debian/aegean.docs)
===================================================================
--- trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/aegean.docs (rev 0)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/aegean.docs 2016-01-09 14:26:06 UTC (rev 21057)
@@ -0,0 +1 @@
+README.md
Deleted: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/aegean.install
===================================================================
--- trunk/packages/aegean/trunk/debian/aegean.install 2016-01-03 13:49:42 UTC (rev 20945)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/aegean.install 2016-01-09 14:26:06 UTC (rev 21057)
@@ -1,7 +0,0 @@
-bin/parseval usr/bin
-bin/locuspocus usr/bin
-bin/xtractore usr/bin
-bin/canon-gff3 usr/bin
-bin/pmrna usr/bin
-bin/gaeval usr/bin
-share/aegean usr/share
Copied: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/aegean.install (from rev 21053, trunk/packages/aegean/trunk/debian/aegean.install)
===================================================================
--- trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/aegean.install (rev 0)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/aegean.install 2016-01-09 14:26:06 UTC (rev 21057)
@@ -0,0 +1,8 @@
+bin/parseval usr/bin
+bin/locuspocus usr/bin
+bin/xtractore usr/bin
+bin/canon-gff3 usr/bin
+bin/pmrna usr/bin
+bin/gaeval usr/bin
+bin/tidygff3 usr/bin
+share/aegean usr/share
Deleted: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/changelog
===================================================================
--- trunk/packages/aegean/trunk/debian/changelog 2016-01-03 13:49:42 UTC (rev 20945)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/changelog 2016-01-09 14:26:06 UTC (rev 21057)
@@ -1,32 +0,0 @@
-aegean (0.14.1+dfsg2-2) unstable; urgency=low
-
- * d/rules: build w/o parallelism, set LC_ALL
- * patch Makefile to remove nondeterminism
-
- -- Sascha Steinbiss <sascha at steinbiss.name> Sun, 29 Nov 2015 19:19:01 +0000
-
-aegean (0.14.1+dfsg2-1) unstable; urgency=medium
-
- * Exclude DataTables JS source, add Depends to new package
- Closes: #798900
- * Remove now redundant Lintian override
-
- -- Sascha Steinbiss <sascha at steinbiss.name> Fri, 27 Nov 2015 22:35:59 +0000
-
-aegean (0.14.1+dfsg-1) unstable; urgency=low
-
- * New upstream release.
-
- -- Sascha Steinbiss <sascha at steinbiss.name> Sat, 10 Oct 2015 09:43:34 +0000
-
-aegean (0.13.0+dfsg-1) unstable; urgency=low
-
- * New upstream release.
-
- -- Sascha Steinbiss <sascha at steinbiss.name> Tue, 28 Jul 2015 08:50:09 +0000
-
-aegean (0.10.2+dfsg-1) unstable; urgency=low
-
- * Initial release (Closes: #769162)
-
- -- Sascha Steinbiss <sascha at steinbiss.name> Tue, 11 Nov 2014 11:14:11 +0000
Copied: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/changelog (from rev 21056, trunk/packages/aegean/trunk/debian/changelog)
===================================================================
--- trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/changelog (rev 0)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/changelog 2016-01-09 14:26:06 UTC (rev 21057)
@@ -0,0 +1,38 @@
+aegean (0.15.1+dfsg-1) unstable; urgency=medium
+
+ * New upstream release.
+
+ -- Sascha Steinbiss <sascha at steinbiss.name> Sat, 09 Jan 2016 14:16:31 +0000
+
+aegean (0.14.1+dfsg2-2) unstable; urgency=low
+
+ * d/rules: build w/o parallelism, set LC_ALL
+ * patch Makefile to remove nondeterminism
+
+ -- Sascha Steinbiss <sascha at steinbiss.name> Sun, 29 Nov 2015 19:19:01 +0000
+
+aegean (0.14.1+dfsg2-1) unstable; urgency=medium
+
+ * Exclude DataTables JS source, add Depends to new package
+ Closes: #798900
+ * Remove now redundant Lintian override
+
+ -- Sascha Steinbiss <sascha at steinbiss.name> Fri, 27 Nov 2015 22:35:59 +0000
+
+aegean (0.14.1+dfsg-1) unstable; urgency=low
+
+ * New upstream release.
+
+ -- Sascha Steinbiss <sascha at steinbiss.name> Sat, 10 Oct 2015 09:43:34 +0000
+
+aegean (0.13.0+dfsg-1) unstable; urgency=low
+
+ * New upstream release.
+
+ -- Sascha Steinbiss <sascha at steinbiss.name> Tue, 28 Jul 2015 08:50:09 +0000
+
+aegean (0.10.2+dfsg-1) unstable; urgency=low
+
+ * Initial release (Closes: #769162)
+
+ -- Sascha Steinbiss <sascha at steinbiss.name> Tue, 11 Nov 2014 11:14:11 +0000
Deleted: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/control
===================================================================
--- trunk/packages/aegean/trunk/debian/control 2016-01-03 13:49:42 UTC (rev 20945)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/control 2016-01-09 14:26:06 UTC (rev 21057)
@@ -1,40 +0,0 @@
-Source: aegean
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Sascha Steinbiss <sascha at steinbiss.name>
-Section: science
-Priority: optional
-Build-Depends: debhelper (>= 9),
- libcairo2-dev,
- libgenometools0-dev,
- python,
- git
-Standards-Version: 3.9.6
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/aegean/trunk/
-Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/aegean/trunk/
-Homepage: http://standage.github.io/AEGeAn
-
-Package: aegean
-Architecture: any
-Depends: ${shlibs:Depends},
- ${misc:Depends},
- libjs-jquery,
- libjs-jquery-datatables,
- libjs-mootools,
- libgenometools0
-Description: integrated genome analysis toolkit
- The AEGeAn Toolkit is designed for the Analysis and Evaluation of Genome
- Annotations. The toolkit includes a variety of analysis programs, e.g. for
- comparing distinct sets of gene structure annotations (ParsEval), computation
- of gene loci (LocusPocus) and more.
-
-Package: aegean-dbg
-Architecture: any
-Section: debug
-Priority: extra
-Depends: ${shlibs:Depends},
- ${misc:Depends},
- aegean (= ${binary:Version})
-Description: integrated genome analysis toolkit, with debug symbols
- This package contains debug information stripped from AEGeAn.
- You may decide to install it to help identifying issues, typically
- to help communication with upstream developers.
Copied: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/control (from rev 21054, trunk/packages/aegean/trunk/debian/control)
===================================================================
--- trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/control (rev 0)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/control 2016-01-09 14:26:06 UTC (rev 21057)
@@ -0,0 +1,41 @@
+Source: aegean
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Sascha Steinbiss <sascha at steinbiss.name>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ libcairo2-dev,
+ libgenometools0-dev,
+ python,
+ git
+Standards-Version: 3.9.6
+Testsuite: autopkgtest
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/aegean/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/aegean/trunk/
+Homepage: http://standage.github.io/AEGeAn
+
+Package: aegean
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ libjs-jquery,
+ libjs-jquery-datatables,
+ libjs-mootools,
+ libgenometools0
+Description: integrated genome analysis toolkit
+ The AEGeAn Toolkit is designed for the Analysis and Evaluation of Genome
+ Annotations. The toolkit includes a variety of analysis programs, e.g. for
+ comparing distinct sets of gene structure annotations (ParsEval), computation
+ of gene loci (LocusPocus) and more.
+
+Package: aegean-dbg
+Architecture: any
+Section: debug
+Priority: extra
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ aegean (= ${binary:Version})
+Description: integrated genome analysis toolkit, with debug symbols
+ This package contains debug information stripped from AEGeAn.
+ You may decide to install it to help identifying issues, typically
+ to help communication with upstream developers.
Deleted: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/canon-gff3.1
===================================================================
--- trunk/packages/aegean/trunk/debian/man/canon-gff3.1 2016-01-03 13:49:42 UTC (rev 20945)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/canon-gff3.1 2016-01-09 14:26:06 UTC (rev 21057)
@@ -1,29 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
-.TH CANON-GFF3 "1" "July 2015" "canon-gff3 0.13" "User Commands"
-.SH NAME
-canon-gff3 \- create canonical GFF3
-.SH SYNOPSIS
-.B canon-gff3
-[\fI\,options\/\fR] \fI\,gff3file1 \/\fR[\fI\,gff3file2 \/\fR...]
-.SH DESCRIPTION
-.IP
-Options:
-.TP
-\fB\-h\fR|\-\-help
-print this help message and exit
-.TP
-\fB\-i\fR|\-\-infer
-for transcript features lacking an explicitly
-declared gene feature as a parent, create this
-feature on\-they\-fly
-.TP
-\fB\-o\fR|\-\-outfile: STRING
-name of file to which GFF3 data will be
-written; default is terminal (stdout)
-.TP
-\fB\-s\fR|\-\-source: STRING
-reset the source of each feature to the given
-value
-.TP
-\fB\-v\fR|\-\-version
-print version number and exit
Copied: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/canon-gff3.1 (from rev 21052, trunk/packages/aegean/trunk/debian/man/canon-gff3.1)
===================================================================
--- trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/canon-gff3.1 (rev 0)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/canon-gff3.1 2016-01-09 14:26:06 UTC (rev 21057)
@@ -0,0 +1,29 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
+.TH CANON-GFF3 "1" "January 2016" "canon-gff3 0.15.1" "User Commands"
+.SH NAME
+canon-gff3 \- create canonical GFF3
+.SH SYNOPSIS
+.B canon-gff3
+[\fI\,options\/\fR] \fI\,gff3file1 \/\fR[\fI\,gff3file2 \/\fR...]
+.SH DESCRIPTION
+.IP
+Options:
+.TP
+\fB\-h\fR|\-\-help
+print this help message and exit
+.TP
+\fB\-i\fR|\-\-infer
+for transcript features lacking an explicitly
+declared gene feature as a parent, create this
+feature on\-they\-fly
+.TP
+\fB\-o\fR|\-\-outfile: STRING
+name of file to which GFF3 data will be
+written; default is terminal (stdout)
+.TP
+\fB\-s\fR|\-\-source: STRING
+reset the source of each feature to the given
+value
+.TP
+\fB\-v\fR|\-\-version
+print version number and exit
Deleted: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/gaeval.1
===================================================================
--- trunk/packages/aegean/trunk/debian/man/gaeval.1 2016-01-03 13:49:42 UTC (rev 20945)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/gaeval.1 2016-01-09 14:26:06 UTC (rev 21057)
@@ -1,42 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
-.TH GAEVAL "1" "July 2015" "gaeval 0.13" "User Commands"
-.SH NAME
-gaeval \- calculate coverage and intergrity scores for gene models based on transcript alignments
-.SH SYNOPSIS
-.B gaeval
-[\fI\,options\/\fR] \fI\,alignments.gff3 genes.gff3 \/\fR[\fI\,moregenes.gff3 \/\fR...]
-.SH DESCRIPTION
-.IP
-Basic options:
-.TP
-\fB\-h\fR|\-\-help
-print this help message and exit
-.TP
-\fB\-v\fR|\-\-version
-print version number and exit
-.IP
-Weights for calculating integrity score (must add up to 1.0):
-.TP
-\fB\-a\fR|\-\-alpha: DOUBLE
-introns confirmed, or % expected CDS length for
-single\-exon genes; default is 0.6
-.TP
-\fB\-b\fR|\-\-beta: DOUBLE
-exon coverage; default is 0.3
-.TP
-\fB\-g\fR|\-\-gamma: DOUBLE
-% expected 5' UTR length; default is 0.05
-.TP
-\fB\-e\fR|\-\-epsilon: DOUBLE
-% expected 3' UTR length; default is 0.05
-.IP
-Expected feature lengths for calculating integrity score:
-.TP
-\fB\-c\fR|\-\-exp\-cds: INT
-expected CDS length (in bp); default is 400
-.TP
-\fB\-5\fR|\-\-exp\-5putr: INT
-expected 5' UTR length; default is 200
-.TP
-\fB\-3\fR|\-\-exp\-3putr: INT
-expected 3' UTR length; default is 100
Copied: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/gaeval.1 (from rev 21052, trunk/packages/aegean/trunk/debian/man/gaeval.1)
===================================================================
--- trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/gaeval.1 (rev 0)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/gaeval.1 2016-01-09 14:26:06 UTC (rev 21057)
@@ -0,0 +1,41 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
+.TH GAEVAL "1" "January 2016" "gaeval 0.15.1" "User Commands"
+.SH NAME
+gaeval \- calculate coverage and intergrity scores for gene models based on transcript alignments
+.SH SYNOPSIS
+.B gaeval
+[\fI\,options\/\fR] \fI\,alignments.gff3 genes.gff3 \/\fR[\fI\,moregenes.gff3 \/\fR...]
+.SH DESCRIPTION
+Basic options:
+.TP
+\fB\-h\fR|\-\-help
+print this help message and exit
+.TP
+\fB\-v\fR|\-\-version
+print version number and exit
+.IP
+Weights for calculating integrity score (must add up to 1.0):
+.TP
+\fB\-a\fR|\-\-alpha: DOUBLE
+introns confirmed, or % expected CDS length for
+single\-exon genes; default is 0.6
+.TP
+\fB\-b\fR|\-\-beta: DOUBLE
+exon coverage; default is 0.3
+.TP
+\fB\-g\fR|\-\-gamma: DOUBLE
+% expected 5' UTR length; default is 0.05
+.TP
+\fB\-e\fR|\-\-epsilon: DOUBLE
+% expected 3' UTR length; default is 0.05
+.IP
+Expected feature lengths for calculating integrity score:
+.TP
+\fB\-c\fR|\-\-exp\-cds: INT
+expected CDS length (in bp); default is 400
+.TP
+\fB\-5\fR|\-\-exp\-5putr: INT
+expected 5' UTR length; default is 200
+.TP
+\fB\-3\fR|\-\-exp\-3putr: INT
+expected 3' UTR length; default is 100
Deleted: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/locuspocus.1
===================================================================
--- trunk/packages/aegean/trunk/debian/man/locuspocus.1 2016-01-03 13:49:42 UTC (rev 20945)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/locuspocus.1 2016-01-09 14:26:06 UTC (rev 21057)
@@ -1,82 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
-.TH LOCUSPOCUS "1" "July 2015" "locuspocus 0.13" "User Commands"
-.SH NAME
-locuspocus \- calculate locus coordinates for the given gene annotation
-.SH SYNOPSIS
-.B locuspocus
-[\fI\,options\/\fR] \fI\,gff3file1 \/\fR[\fI\,gff3file2 gff3file3 \/\fR...]
-.SH DESCRIPTION
-.IP
-Basic options:
-.TP
-\fB\-d\fR|\-\-debug
-print detailed debugging messages to terminal
-(standard error)
-.TP
-\fB\-h\fR|\-\-help
-print this help message and exit
-.TP
-\fB\-v\fR|\-\-version
-print version number and exit
-.IP
-iLocus parsing:
-.TP
-\fB\-l\fR|\-\-delta: INT
-when parsing interval loci, use the following
-delta to extend gene loci and include potential
-regulatory regions; default is 500
-.TP
-\fB\-s\fR|\-\-skipends
-when enumerating interval loci, exclude gene\-less
-iLoci at either end of the sequence
-.TP
-\fB\-e\fR|\-\-endsonly
-report only empty iLoci at the ends of sequences
-(complement of \fB\-\-skipends\fR)
-.TP
-\fB\-y\fR|\-\-skipempty
-do not report empty iLoci
-.IP
-Output options:
-.TP
-\fB\-I\fR|\-\-idformat: STR
-provide a printf\-style format string to override
-the default ID format for newly created loci;
-default is 'locus%lu' (locus1, locus2, etc) for
-loci and 'iLocus%lu' (iLocus1, iLocus2, etc) for
-interval loci; note the format string should
-include a single %lu specifier to be filled in
-with a long unsigned integer value
-.TP
-\fB\-g\fR|\-\-genemap: FILE
-print a mapping from each gene annotation to its
-corresponding locus to the given file
-.TP
-\fB\-o\fR|\-\-outfile: FILE
-name of file to which results will be written;
-default is terminal (standard output)
-.TP
-\fB\-t\fR|\-\-transmap: FILE
-print a mapping from each transcript annotation
-to its corresponding locus to the given file
-.TP
-\fB\-V\fR|\-\-verbose
-include all locus subfeatures (genes, RNAs, etc)
-in the GFF3 output; default includes only locus
-features
-.IP
-Input options:
-.TP
-\fB\-f\fR|\-\-filter: TYPE
-comma\-separated list of feature types to use in
-constructing loci/iLoci; default is 'gene'
-.TP
-\fB\-p\fR|\-\-parent: CT:PT
-if a feature of type $CT exists without a parent,
-create a parent for this feature with type $PT;
-for example, mRNA:gene will create a gene feature
-as a parent for any top\-level mRNA feature;
-this option can be specified multiple times
-.TP
-\fB\-u\fR|\-\-pseudo
-correct erroneously labeled pseudogenes
Copied: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/locuspocus.1 (from rev 21052, trunk/packages/aegean/trunk/debian/man/locuspocus.1)
===================================================================
--- trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/locuspocus.1 (rev 0)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/locuspocus.1 2016-01-09 14:26:06 UTC (rev 21057)
@@ -0,0 +1,108 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
+.TH LOCUSPOCUS "1" "January 2016" "locuspocus 0.15.1" "User Commands"
+.SH NAME
+locuspocus \- calculate locus coordinates for the given gene annotation
+.SH SYNOPSIS
+.B locuspocus
+[\fI\,options\/\fR] \fI\,gff3file1 \/\fR[\fI\,gff3file2 gff3file3 \/\fR...]
+.SH DESCRIPTION
+Basic options:
+.TP
+\fB\-d\fR|\-\-debug
+print detailed debugging messages to terminal
+(standard error)
+.TP
+\fB\-h\fR|\-\-help
+print this help message and exit
+.TP
+\fB\-v\fR|\-\-version
+print version number and exit
+.IP
+iLocus parsing:
+.TP
+\fB\-l\fR|\-\-delta: INT
+when parsing interval loci, use the following
+delta to extend gene loci and include potential
+regulatory regions; default is 500
+.TP
+\fB\-s\fR|\-\-skipends
+when enumerating interval loci, exclude
+unannotated (and presumably incomplete) iLoci at
+either end of the sequence
+.TP
+\fB\-e\fR|\-\-endsonly
+report only incomplete iLocus fragments at the
+unannotated ends of sequences (complement of
+\fB\-\-skipends\fR)
+.TP
+\fB\-y\fR|\-\-skipiiloci
+do not report intergenic iLoci
+.IP
+Refinement options:
+.TP
+\fB\-r\fR|\-\-refine
+by default genes are grouped in the same iLocus
+if they have any overlap; 'refine' mode allows
+for a more nuanced handling of overlapping genes
+.TP
+\fB\-c\fR|\-\-cds
+use CDS rather than UTRs for determining gene
+overlap; implies 'refine' mode
+.TP
+\fB\-m\fR|\-\-minoverlap: INT
+the minimum number of nucleotides two genes must
+overlap to be grouped in the same iLocus; default
+is 1
+.IP
+Output options:
+.TP
+\fB\-n\fR|\-\-namefmt: STR
+provide a printf\-style format string to override
+the default ID format for newly created loci;
+default is 'locus%lu' (locus1, locus2, etc) for
+loci and 'iLocus%lu' (iLocus1, iLocus2, etc) for
+interval loci; note the format string should
+include a single %lu specifier to be filled in
+with a long unsigned integer value
+.TP
+\fB\-i\fR|\-\-ilens: FILE
+create a file with the lengths of each intergenic
+iLocus
+.TP
+\fB\-g\fR|\-\-genemap: FILE
+print a mapping from each gene annotation to its
+corresponding locus to the given file
+.TP
+\fB\-o\fR|\-\-outfile: FILE
+name of file to which results will be written;
+default is terminal (standard output)
+.TP
+\fB\-T\fR|\-\-retainids
+retain original feature IDs from input files;
+conflicts will arise if input contains duplicated
+ID values
+.TP
+\fB\-t\fR|\-\-transmap: FILE
+print a mapping from each transcript annotation
+to its corresponding locus to the given file
+.TP
+\fB\-V\fR|\-\-verbose
+include all locus subfeatures (genes, RNAs, etc)
+in the GFF3 output; default includes only locus
+features
+.IP
+Input options:
+.TP
+\fB\-f\fR|\-\-filter: TYPE
+comma\-separated list of feature types to use in
+constructing loci/iLoci; default is 'gene'
+.TP
+\fB\-p\fR|\-\-parent: CT:PT
+if a feature of type $CT exists without a parent,
+create a parent for this feature with type $PT;
+for example, mRNA:gene will create a gene feature
+as a parent for any top\-level mRNA feature;
+this option can be specified multiple times
+.TP
+\fB\-u\fR|\-\-pseudo
+correct erroneously labeled pseudogenes
Deleted: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/parseval.1
===================================================================
--- trunk/packages/aegean/trunk/debian/man/parseval.1 2016-01-03 13:49:42 UTC (rev 20945)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/parseval.1 2016-01-09 14:26:06 UTC (rev 21057)
@@ -1,80 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
-.TH PARSEVAL "1" "July 2015" "parseval 0.13" "User Commands"
-.SH NAME
-parseval \- comparative analysis of two alternative sources of annotation
-.SH SYNOPSIS
-.B parseval
-[\fI\,options\/\fR] \fI\,reference.gff3 prediction.gff3\/\fR
-.SH DESCRIPTION
-.IP
-Basic options:
-.TP
-\fB\-d\fR|\-\-debug:
-Print debugging messages
-.TP
-\fB\-h\fR|\-\-help:
-Print help message and exit
-.TP
-\fB\-l\fR|\-\-delta: INT
-Extend gene loci by this many nucleotides;
-default is 0
-.TP
-\fB\-V\fR|\-\-verbose:
-Print verbose warning messages
-.TP
-\fB\-v\fR|\-\-version:
-Print version number and exit
-.IP
-Output options:
-.TP
-\fB\-a\fR|\-\-datashare: STRING
-Location from which to copy shared data for
-HTML output (if `make install' has not yet
-been run)
-.TP
-\fB\-f\fR|\-\-outformat: STRING
-Indicate desired output format; possible
-options: 'csv', 'text', or 'html'
-(default='text'); in 'text' or 'csv' mode,
-will create a single file; in 'html' mode,
-will create a directory
-.TP
-\fB\-g\fR|\-\-nogff3:
-Do no print GFF3 output corresponding to each
-comparison
-.TP
-\fB\-o\fR|\-\-outfile: FILENAME
-File/directory to which output will be
-written; default is the terminal (STDOUT)
-.TP
-\fB\-p\fR|\-\-png:
-Generate individual PNG graphics for each
-gene locus (HTML mode only)
-.TP
-\fB\-s\fR|\-\-summary:
-Only print summary statistics, do not print
-individual comparisons
-.TP
-\fB\-w\fR|\-\-overwrite:
-Force overwrite of any existing output files
-.TP
-\fB\-x\fR|\-\-refrlabel: STRING
-Optional label for reference annotations
-.TP
-\fB\-y\fR|\-\-predlabel: STRING
-Optional label for prediction annotations
-.IP
-Filtering options:
-.TP
-\fB\-k\fR|\-\-makefilter
-Create a default configuration file for
-filtering reported results and quit,
-performing no comparisons
-.TP
-\fB\-r\fR|\-\-filterfile: STRING
-Use the indicated configuration file to
-filter reported results;
-.TP
-\fB\-t\fR|\-\-maxtrans: INT
-Maximum transcripts allowed per locus; use 0
-to disable limit; default is 32
Copied: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/parseval.1 (from rev 21052, trunk/packages/aegean/trunk/debian/man/parseval.1)
===================================================================
--- trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/parseval.1 (rev 0)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/parseval.1 2016-01-09 14:26:06 UTC (rev 21057)
@@ -0,0 +1,79 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
+.TH PARSEVAL "1" "January 2016" "parseval 0.15.1" "User Commands"
+.SH NAME
+parseval \- comparative analysis of two alternative sources of annotation
+.SH SYNOPSIS
+.B parseval
+[\fI\,options\/\fR] \fI\,reference.gff3 prediction.gff3\/\fR
+.SH DESCRIPTION
+Basic options:
+.TP
+\fB\-d\fR|\-\-debug:
+Print debugging messages
+.TP
+\fB\-h\fR|\-\-help:
+Print help message and exit
+.TP
+\fB\-l\fR|\-\-delta: INT
+Extend gene loci by this many nucleotides;
+default is 0
+.TP
+\fB\-V\fR|\-\-verbose:
+Print verbose warning messages
+.TP
+\fB\-v\fR|\-\-version:
+Print version number and exit
+.IP
+Output options:
+.TP
+\fB\-a\fR|\-\-datashare: STRING
+Location from which to copy shared data for
+HTML output (if `make install' has not yet
+been run)
+.TP
+\fB\-f\fR|\-\-outformat: STRING
+Indicate desired output format; possible
+options: 'csv', 'text', or 'html'
+(default='text'); in 'text' or 'csv' mode,
+will create a single file; in 'html' mode,
+will create a directory
+.TP
+\fB\-g\fR|\-\-nogff3:
+Do no print GFF3 output corresponding to each
+comparison
+.TP
+\fB\-o\fR|\-\-outfile: FILENAME
+File/directory to which output will be
+written; default is the terminal (STDOUT)
+.TP
+\fB\-p\fR|\-\-nopng:
+In HTML output mode, skip generation of PNG
+graphics for each gene locus
+.TP
+\fB\-s\fR|\-\-summary:
+Only print summary statistics, do not print
+individual comparisons
+.TP
+\fB\-w\fR|\-\-overwrite:
+Force overwrite of any existing output files
+.TP
+\fB\-x\fR|\-\-refrlabel: STRING
+Optional label for reference annotations
+.TP
+\fB\-y\fR|\-\-predlabel: STRING
+Optional label for prediction annotations
+.IP
+Filtering options:
+.TP
+\fB\-k\fR|\-\-makefilter
+Create a default configuration file for
+filtering reported results and quit,
+performing no comparisons
+.TP
+\fB\-r\fR|\-\-filterfile: STRING
+Use the indicated configuration file to
+filter reported results;
+.TP
+\fB\-t\fR|\-\-maxtrans: INT
+Maximum transcripts allowed per locus; use 0
+to disable limit; default is 32
Deleted: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/pmrna.1
===================================================================
--- trunk/packages/aegean/trunk/debian/man/pmrna.1 2016-01-03 13:49:42 UTC (rev 20945)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/pmrna.1 2016-01-09 14:26:06 UTC (rev 21057)
@@ -1,28 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
-.TH PMRNA "1" "July 2015" "pmrna 0.13" "User Commands"
-.SH NAME
-pmrna \- filter out all but the primary isoform from each gene of the input
-.SH SYNOPSIS
-.B pmrna
-[\fI\,options\/\fR] \fI\,< annot.gff3 > new.gff3\/\fR
-.SH DESCRIPTION
-.IP
-Options:
-.TP
-\fB\-h\fR|\-\-help
-print this help message and exit
-.TP
-\fB\-i\fR|\-\-introns
-flag indicating that introns are declared explicitly
-and do not need to be inferred from exon features;
-default is to infer introns
-.TP
-\fB\-l\fR|\-\-locus
-report a single representative mRNA for each locus
-instead of each gene
-.TP
-\fB\-m\fR|\-\-map: FILE
-write each gene/mRNA mapping to the specified file
-.TP
-\fB\-p\fR|\-\-pseudogenes
-disable pseudogene detection and correction
Copied: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/pmrna.1 (from rev 21052, trunk/packages/aegean/trunk/debian/man/pmrna.1)
===================================================================
--- trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/pmrna.1 (rev 0)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/pmrna.1 2016-01-09 14:26:06 UTC (rev 21057)
@@ -0,0 +1,27 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
+.TH PMRNA "1" "January 2016" "pmrna 0.15.1" "User Commands"
+.SH NAME
+pmrna \- filter out all but the primary isoform from each gene of the input
+.SH SYNOPSIS
+.B pmrna
+[\fI\,options\/\fR] \fI\,< annot.gff3 > new.gff3\/\fR
+.SH DESCRIPTION
+Options:
+.TP
+\fB\-h\fR|\-\-help
+print this help message and exit
+.TP
+\fB\-i\fR|\-\-introns
+flag indicating that introns are declared explicitly
+and do not need to be inferred from exon features;
+default is to infer introns
+.TP
+\fB\-l\fR|\-\-locus
+report a single representative mRNA for each locus
+instead of each gene
+.TP
+\fB\-m\fR|\-\-map: FILE
+write each gene/mRNA mapping to the specified file
+.TP
+\fB\-p\fR|\-\-pseudogenes
+disable pseudogene detection and correction
Copied: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/tidygff3.1 (from rev 21052, trunk/packages/aegean/trunk/debian/man/tidygff3.1)
===================================================================
--- trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/tidygff3.1 (rev 0)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/tidygff3.1 2016-01-09 14:26:06 UTC (rev 21057)
@@ -0,0 +1,11 @@
+.TH TIDYGFF3 "1" "January 2016" "tidygff3 0.15.1" "User Commands"
+.SH NAME
+tidygff3 \- tidy GFF3 file
+.SH SYNOPSIS
+.B tidygff3
+<
+.IR features.gff3
+.SH DESCRIPTION
+.IP
+Cleans up GFF3 format files read from stdin for further use in AEGeAn by
+printing the clean version on stdout.
\ No newline at end of file
Deleted: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/xtractore.1
===================================================================
--- trunk/packages/aegean/trunk/debian/man/xtractore.1 2016-01-03 13:49:42 UTC (rev 20945)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/xtractore.1 2016-01-09 14:26:06 UTC (rev 21057)
@@ -1,37 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
-.TH XTRACTORE "1" "July 2015" "xtractore 0.13" "User Commands"
-.SH NAME
-xtractore \- extract sequences corresponding to annotated features from the given sequence file
-.SH SYNOPSIS
-.B xtractore
-[\fI\,options\/\fR] \fI\,features.gff3 sequences.fasta\/\fR
-.SH DESCRIPTION
-.IP
-Options:
-.TP
-\fB\-h\fR|\-\-help
-print this help message and exit
-.TP
-\fB\-i\fR|\-\-idfile: FILE
-file containing a list of feature IDs (1 per line
-with no spaces); if provided, only features with
-IDs in this file will be extracted
-.TP
-\fB\-o\fR|\-\-outfile: FILE
-file to which output sequences will be written;
-default is terminal (stdout)
-.TP
-\fB\-t\fR|\-\-type: STRING
-feature type to extract; can be used multiple
-times to extract features of multiple types
-.TP
-\fB\-v\fR|\-\-version
-print version number and exit
-.TP
-\fB\-V\fR|\-\-verbose
-print verbose warning and error messages
-.TP
-\fB\-w\fR|\-\-width: INT
-width of each line of sequence in the Fasta
-output; default is 80; set to 0 for no
-formatting
Copied: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/xtractore.1 (from rev 21052, trunk/packages/aegean/trunk/debian/man/xtractore.1)
===================================================================
--- trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/xtractore.1 (rev 0)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/man/xtractore.1 2016-01-09 14:26:06 UTC (rev 21057)
@@ -0,0 +1,39 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
+.TH XTRACTORE "1" "January 2016" "xtractore 0.15.1" "User Commands"
+.SH NAME
+xtractore \- extract sequences corresponding to annotated features from the given sequence file
+.SH SYNOPSIS
+.B xtractore
+[\fI\,options\/\fR] \fI\,features.gff3 sequences.fasta\/\fR
+.SH DESCRIPTION
+Options:
+.TP
+\fB\-d\fR|\-\-debug
+print debugging output
+.TP
+\fB\-h\fR|\-\-help
+print this help message and exit
+.TP
+\fB\-i\fR|\-\-idfile: FILE
+file containing a list of feature IDs (1 per line
+with no spaces); if provided, only features with
+IDs in this file will be extracted
+.TP
+\fB\-o\fR|\-\-outfile: FILE
+file to which output sequences will be written;
+default is terminal (stdout)
+.TP
+\fB\-t\fR|\-\-type: STRING
+feature type to extract; can be used multiple
+times to extract features of multiple types
+.TP
+\fB\-v\fR|\-\-version
+print version number and exit
+.TP
+\fB\-V\fR|\-\-verbose
+print verbose warning and error messages
+.TP
+\fB\-w\fR|\-\-width: INT
+width of each line of sequence in the Fasta
+output; default is 80; set to 0 for no
+formatting
Deleted: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/add_hardening
===================================================================
--- trunk/packages/aegean/trunk/debian/patches/add_hardening 2016-01-03 13:49:42 UTC (rev 20945)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/add_hardening 2016-01-09 14:26:06 UTC (rev 21057)
@@ -1,12 +0,0 @@
-Description: Add_hardening
---- a/Makefile
-+++ b/Makefile
-@@ -48,7 +48,7 @@
- ifneq ($(debug),no)
- CFLAGS += -g
- endif
--LDFLAGS=-lgenometools -lm \
-+LDFLAGS+=-lgenometools -lm \
- -L$(prefix)/lib \
- -L/usr/local/lib
- ifdef lib
Copied: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/add_hardening (from rev 21050, trunk/packages/aegean/trunk/debian/patches/add_hardening)
===================================================================
--- trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/add_hardening (rev 0)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/add_hardening 2016-01-09 14:26:06 UTC (rev 21057)
@@ -0,0 +1,70 @@
+Description: Add hardening
+Author: Sascha Steinbiss <sascha at steinbiss.name>
+--- a/Makefile
++++ b/Makefile
+@@ -49,7 +49,7 @@
+ ifneq ($(debug),no)
+ CFLAGS += -g
+ endif
+-LDFLAGS=-lgenometools -lm -ldl \
++LDFLAGS+=-lgenometools -lm -ldl \
+ -L$(prefix)/lib \
+ -L/usr/local/lib
+ ifdef lib
+@@ -99,47 +99,47 @@
+ $(AGN_OBJS): obj/%.o : src/core/%.c inc/core/%.h inc/core/AgnVersion.h
+ @- mkdir -p obj
+ @ echo "[compile $*]"
+- @ $(CC) $(CFLAGS) $(INCS) -c -o $@ $<
++ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -c -o $@ $<
+
+ $(PE_EXE): src/ParsEval/parseval.c src/ParsEval/pe_options.c src/ParsEval/pe_utils.c src/ParsEval/pe_options.h src/ParsEval/pe_utils.h $(AGN_OBJS)
+ @ mkdir -p bin
+ @ echo "[compile ParsEval]"
+- @ $(CC) $(CFLAGS) $(INCS) -I src/ParsEval -o $@ $(AGN_OBJS) src/ParsEval/parseval.c src/ParsEval/pe_options.c src/ParsEval/pe_utils.c $(LDFLAGS)
++ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -I src/ParsEval -o $@ $(AGN_OBJS) src/ParsEval/parseval.c src/ParsEval/pe_options.c src/ParsEval/pe_utils.c $(LDFLAGS)
+
+ $(CN_EXE): src/canon-gff3.c $(AGN_OBJS)
+ @ mkdir -p bin
+ @ echo "[compile CanonGFF3]"
+- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/canon-gff3.c $(LDFLAGS)
++ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/canon-gff3.c $(LDFLAGS)
+
+ $(LP_EXE): src/locuspocus.c $(AGN_OBJS)
+ @ mkdir -p bin
+ @ echo "[compile LocusPocus]"
+- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/locuspocus.c $(LDFLAGS)
++ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/locuspocus.c $(LDFLAGS)
+
+ $(GV_EXE): src/gaeval.c $(AGN_OBJS)
+ @ mkdir -p bin
+ @ echo "[compile GAEVAL]"
+- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/gaeval.c $(LDFLAGS)
++ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/gaeval.c $(LDFLAGS)
+
+ $(XT_EXE): src/xtractore.c $(AGN_OBJS)
+ @ mkdir -p bin
+ @ echo "[compile Xtractore]"
+- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/xtractore.c $(LDFLAGS)
++ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/xtractore.c $(LDFLAGS)
+
+ $(RP_EXE): src/pmrna.c $(AGN_OBJS)
+ @ mkdir -p bin
+ @ echo "[compile $@]"
+- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/pmrna.c $(LDFLAGS)
++ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/pmrna.c $(LDFLAGS)
+
+ $(TD_EXE): src/tidygff3.c $(AGN_OBJS)
+ @ mkdir -p bin
+ @ echo "[compile $@]"
+- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/tidygff3.c $(LDFLAGS)
++ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/tidygff3.c $(LDFLAGS)
+
+ $(UT_EXE): test/unittests.c $(AGN_OBJS)
+ @ mkdir -p bin
+ @ echo "[compile unit tests]"
+- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) test/unittests.c $(LDFLAGS)
++ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) test/unittests.c $(LDFLAGS)
+
+ libaegean.a: $(AGN_OBJS)
+ @ echo "[create libaegean]"
Deleted: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/add_version
===================================================================
--- trunk/packages/aegean/trunk/debian/patches/add_version 2016-01-03 13:49:42 UTC (rev 20945)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/add_version 2016-01-09 14:26:06 UTC (rev 21057)
@@ -1,60 +0,0 @@
-Description: Add_version
---- a/Makefile
-+++ b/Makefile
-@@ -95,47 +95,47 @@
- $(AGN_OBJS): obj/%.o : src/core/%.c inc/core/%.h inc/core/AgnVersion.h
- @- mkdir -p obj
- @ echo "[compile $*]"
-- @ $(CC) $(CFLAGS) $(INCS) -c -o $@ $<
-+ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -c -o $@ $<
-
- $(PE_EXE): src/ParsEval/parseval.c src/ParsEval/pe_options.c src/ParsEval/pe_utils.c src/ParsEval/pe_options.h src/ParsEval/pe_utils.h $(AGN_OBJS)
- @ mkdir -p bin
- @ echo "[compile ParsEval]"
-- @ $(CC) $(CFLAGS) $(INCS) -I src/ParsEval -o $@ $(AGN_OBJS) src/ParsEval/parseval.c src/ParsEval/pe_options.c src/ParsEval/pe_utils.c $(LDFLAGS)
-+ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -I src/ParsEval -o $@ $(AGN_OBJS) src/ParsEval/parseval.c src/ParsEval/pe_options.c src/ParsEval/pe_utils.c $(LDFLAGS)
-
- $(CN_EXE): src/canon-gff3.c $(AGN_OBJS)
- @ mkdir -p bin
- @ echo "[compile CanonGFF3]"
-- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/canon-gff3.c $(LDFLAGS)
-+ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/canon-gff3.c $(LDFLAGS)
-
- $(LP_EXE): src/locuspocus.c $(AGN_OBJS)
- @ mkdir -p bin
- @ echo "[compile LocusPocus]"
-- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/locuspocus.c $(LDFLAGS)
-+ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/locuspocus.c $(LDFLAGS)
-
- $(GV_EXE): src/gaeval.c $(AGN_OBJS)
- @ mkdir -p bin
- @ echo "[compile GAEVAL]"
-- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/gaeval.c $(LDFLAGS)
-+ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/gaeval.c $(LDFLAGS)
-
- $(XT_EXE): src/xtractore.c $(AGN_OBJS)
- @ mkdir -p bin
- @ echo "[compile Xtractore]"
-- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/xtractore.c $(LDFLAGS)
-+ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/xtractore.c $(LDFLAGS)
-
- $(RP_EXE): src/pmrna.c $(AGN_OBJS)
- @ mkdir -p bin
- @ echo "[compile $@]"
-- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/pmrna.c $(LDFLAGS)
-+ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/pmrna.c $(LDFLAGS)
-
- $(TD_EXE): src/tidygff3.c $(AGN_OBJS)
- @ mkdir -p bin
- @ echo "[compile $@]"
-- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/tidygff3.c $(LDFLAGS)
-+ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/tidygff3.c $(LDFLAGS)
-
- $(UT_EXE): test/unittests.c $(AGN_OBJS)
- @ mkdir -p bin
- @ echo "[compile unit tests]"
-- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) test/unittests.c $(LDFLAGS)
-+ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) test/unittests.c $(LDFLAGS)
-
- libaegean.a: $(AGN_OBJS)
- @ echo "[create libaegean]"
Copied: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/add_version (from rev 21050, trunk/packages/aegean/trunk/debian/patches/add_version)
===================================================================
--- trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/add_version (rev 0)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/add_version 2016-01-09 14:26:06 UTC (rev 21057)
@@ -0,0 +1,60 @@
+Description: Add_version
+--- a/Makefile
++++ b/Makefile
+@@ -99,47 +99,47 @@
+ $(AGN_OBJS): obj/%.o : src/core/%.c inc/core/%.h inc/core/AgnVersion.h
+ @- mkdir -p obj
+ @ echo "[compile $*]"
+- @ $(CC) $(CFLAGS) $(INCS) -c -o $@ $<
++ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -c -o $@ $<
+
+ $(PE_EXE): src/ParsEval/parseval.c src/ParsEval/pe_options.c src/ParsEval/pe_utils.c src/ParsEval/pe_options.h src/ParsEval/pe_utils.h $(AGN_OBJS)
+ @ mkdir -p bin
+ @ echo "[compile ParsEval]"
+- @ $(CC) $(CFLAGS) $(INCS) -I src/ParsEval -o $@ $(AGN_OBJS) src/ParsEval/parseval.c src/ParsEval/pe_options.c src/ParsEval/pe_utils.c $(LDFLAGS)
++ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -I src/ParsEval -o $@ $(AGN_OBJS) src/ParsEval/parseval.c src/ParsEval/pe_options.c src/ParsEval/pe_utils.c $(LDFLAGS)
+
+ $(CN_EXE): src/canon-gff3.c $(AGN_OBJS)
+ @ mkdir -p bin
+ @ echo "[compile CanonGFF3]"
+- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/canon-gff3.c $(LDFLAGS)
++ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/canon-gff3.c $(LDFLAGS)
+
+ $(LP_EXE): src/locuspocus.c $(AGN_OBJS)
+ @ mkdir -p bin
+ @ echo "[compile LocusPocus]"
+- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/locuspocus.c $(LDFLAGS)
++ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/locuspocus.c $(LDFLAGS)
+
+ $(GV_EXE): src/gaeval.c $(AGN_OBJS)
+ @ mkdir -p bin
+ @ echo "[compile GAEVAL]"
+- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/gaeval.c $(LDFLAGS)
++ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/gaeval.c $(LDFLAGS)
+
+ $(XT_EXE): src/xtractore.c $(AGN_OBJS)
+ @ mkdir -p bin
+ @ echo "[compile Xtractore]"
+- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/xtractore.c $(LDFLAGS)
++ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/xtractore.c $(LDFLAGS)
+
+ $(RP_EXE): src/pmrna.c $(AGN_OBJS)
+ @ mkdir -p bin
+ @ echo "[compile $@]"
+- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/pmrna.c $(LDFLAGS)
++ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/pmrna.c $(LDFLAGS)
+
+ $(TD_EXE): src/tidygff3.c $(AGN_OBJS)
+ @ mkdir -p bin
+ @ echo "[compile $@]"
+- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/tidygff3.c $(LDFLAGS)
++ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) src/tidygff3.c $(LDFLAGS)
+
+ $(UT_EXE): test/unittests.c $(AGN_OBJS)
+ @ mkdir -p bin
+ @ echo "[compile unit tests]"
+- @ $(CC) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) test/unittests.c $(LDFLAGS)
++ @ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -o $@ $(AGN_OBJS) test/unittests.c $(LDFLAGS)
+
+ libaegean.a: $(AGN_OBJS)
+ @ echo "[create libaegean]"
Deleted: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/adjust_datapath
===================================================================
--- trunk/packages/aegean/trunk/debian/patches/adjust_datapath 2016-01-03 13:49:42 UTC (rev 20945)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/adjust_datapath 2016-01-09 14:26:06 UTC (rev 21057)
@@ -1,43 +0,0 @@
-Description: Adjust_datapath
---- a/Makefile
-+++ b/Makefile
-@@ -27,7 +27,7 @@
-
- # Compilation settings
- CC=gcc
--CFLAGS += -Wall -DAGN_DATA_PATH='"$(prefix)/share/aegean"' -Wno-unused-result
-+CFLAGS += -Wall -DAGN_DATA_PATH='"/usr/share/aegean"' -Wno-unused-result
- GTFLAGS=prefix=$(prefix)
- SYSTEM:=$(shell uname -s)
- MACHINE:=$(shell uname -m)
-@@ -87,13 +87,13 @@
- @ mkdir -p $(prefix)/bin/
- cp data/scripts/*.p? $(prefix)/bin/.
-
--uninstall:
-+uninstall:
- for exe in $(INSTALL_BINS); do rm -r $(prefix)/$$exe; done
- rm -r $(prefix)/include/aegean/
- rm -r $(prefix)/share/aegean/
- rm $(prefix)/lib/libaegean.a
-
--clean:
-+clean:
- rm -rf README $(BINS) libaegean.a $(AGN_OBJS) inc/core/AgnVersion.h bin/*.dSYM
-
- $(AGN_OBJS): obj/%.o : src/core/%.c inc/core/%.h inc/core/AgnVersion.h
-@@ -145,12 +145,12 @@
- @ echo "[create libaegean]"
- @ ar ru libaegean.a $(AGN_OBJS)
-
--inc/core/AgnVersion.h:
-+inc/core/AgnVersion.h:
- @ echo "[print $@]"
- @ data/scripts/version.py > $@
-
- test: agn-test
--
-+
-
- agn-test: all
- @ $(MEMCHECK) bin/unittests
Copied: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/adjust_datapath (from rev 21050, trunk/packages/aegean/trunk/debian/patches/adjust_datapath)
===================================================================
--- trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/adjust_datapath (rev 0)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/adjust_datapath 2016-01-09 14:26:06 UTC (rev 21057)
@@ -0,0 +1,29 @@
+Description: Adjust datapath
+ Debian uses /usr/share.
+Author: Sascha Steinbiss <sascha at steinbiss.name>
+--- a/Makefile
++++ b/Makefile
+@@ -29,7 +29,7 @@
+
+ # Compilation settings
+ CC=gcc
+-CFLAGS=-Wall -DAGN_DATA_PATH='"$(prefix)/share/aegean"' -Wno-unused-result
++CFLAGS+=-Wall -DAGN_DATA_PATH='"/usr/share/aegean"' -Wno-unused-result
+ GTFLAGS=prefix=$(prefix)
+ SYSTEM:=$(shell uname -s)
+ MACHINE:=$(shell uname -m)
+@@ -149,12 +149,12 @@
+ @ echo "[create libaegean]"
+ @ ar ru libaegean.a $(AGN_OBJS)
+
+-inc/core/AgnVersion.h:
++inc/core/AgnVersion.h:
+ @ echo "[print $@]"
+ @ data/scripts/version.py > $@
+
+ test: agn-test
+-
++
+
+ agn-test: all
+ @ $(MEMCHECK) bin/unittests
Deleted: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/fix_m64_on_some_archs
===================================================================
--- trunk/packages/aegean/trunk/debian/patches/fix_m64_on_some_archs 2016-01-03 13:49:42 UTC (rev 20945)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/fix_m64_on_some_archs 2016-01-09 14:26:06 UTC (rev 21057)
@@ -1,43 +0,0 @@
-Description: Fix_m64_on_some_archs
---- a/Makefile
-+++ b/Makefile
-@@ -29,6 +29,8 @@
- CC=gcc
- CFLAGS += -Wall -DAGN_DATA_PATH='"$(prefix)/share/aegean"' -Wno-unused-result
- GTFLAGS=prefix=$(prefix)
-+SYSTEM:=$(shell uname -s)
-+MACHINE:=$(shell uname -m)
- ifeq ($(cairo),no)
- CFLAGS += -DWITHOUT_CAIRO
- GTFLAGS += cairo=no
-@@ -40,8 +42,10 @@
- CFLAGS += -O3
- endif
- ifneq ($(64bit),no)
-- CFLAGS += -m64
-- GTFLAGS += 64bit=yes
-+ ifeq (,$(filter $(MACHINE),ia64 alpha mips64 mips64el aarch64))
-+ CFLAGS += -m64
-+ GTFLAGS += 64bit=yes
-+ endif
- endif
- ifneq ($(debug),no)
- CFLAGS += -g
-@@ -66,7 +70,7 @@
-
- # Targets
- all: $(BINS) libaegean.a
--
-+
-
- install: all
- @ mkdir -p $(prefix)/bin/
-@@ -142,7 +146,7 @@
- @ ar ru libaegean.a $(AGN_OBJS)
-
- inc/core/AgnVersion.h:
-- @- echo "[print $@]"
-+ @ echo "[print $@]"
- @ data/scripts/version.py > $@
-
- test: agn-test
Copied: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/fix_m64_on_some_archs (from rev 21050, trunk/packages/aegean/trunk/debian/patches/fix_m64_on_some_archs)
===================================================================
--- trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/fix_m64_on_some_archs (rev 0)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/fix_m64_on_some_archs 2016-01-09 14:26:06 UTC (rev 21057)
@@ -0,0 +1,44 @@
+Description: Fix -m64 on some archs
+Author: Sascha Steinbiss <sascha at steinbiss.name>
+--- a/Makefile
++++ b/Makefile
+@@ -31,6 +31,8 @@
+ CC=gcc
+ CFLAGS=-Wall -DAGN_DATA_PATH='"$(prefix)/share/aegean"' -Wno-unused-result
+ GTFLAGS=prefix=$(prefix)
++SYSTEM:=$(shell uname -s)
++MACHINE:=$(shell uname -m)
+ ifeq ($(cairo),no)
+ CFLAGS += -DWITHOUT_CAIRO
+ GTFLAGS += cairo=no
+@@ -43,8 +45,10 @@
+ CFLAGS += -O3
+ endif
+ ifneq ($(64bit),no)
+- CFLAGS += -m64
+- GTFLAGS += 64bit=yes
++ ifeq (,$(filter $(MACHINE),ia64 alpha mips64 mips64el aarch64))
++ CFLAGS += -m64
++ GTFLAGS += 64bit=yes
++ endif
+ endif
+ ifneq ($(debug),no)
+ CFLAGS += -g
+@@ -70,7 +74,7 @@
+
+ # Targets
+ all: $(BINS) libaegean.a
+-
++
+
+ install: all
+ @ mkdir -p $(prefix)/bin/
+@@ -146,7 +150,7 @@
+ @ ar ru libaegean.a $(AGN_OBJS)
+
+ inc/core/AgnVersion.h:
+- @- echo "[print $@]"
++ @ echo "[print $@]"
+ @ data/scripts/version.py > $@
+
+ test: agn-test
Deleted: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/follow_links
===================================================================
--- trunk/packages/aegean/trunk/debian/patches/follow_links 2016-01-03 13:49:42 UTC (rev 20945)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/follow_links 2016-01-09 14:26:06 UTC (rev 21057)
@@ -1,12 +0,0 @@
-Description: Follow_links
---- a/src/ParsEval/pe_options.c
-+++ b/src/ParsEval/pe_options.c
-@@ -265,7 +265,7 @@
- }
-
- char copy_cmd[1024];
-- sprintf(copy_cmd,"cp -r %s/* %s", options->data_path, options->outfilename);
-+ sprintf(copy_cmd,"cp -LR %s/* %s", options->data_path, options->outfilename);
- if(options->debug)
- fprintf(stderr, "debug: copying shared data: '%s'\n", copy_cmd);
- if(system(copy_cmd) != 0)
Copied: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/follow_links (from rev 21050, trunk/packages/aegean/trunk/debian/patches/follow_links)
===================================================================
--- trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/follow_links (rev 0)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/follow_links 2016-01-09 14:26:06 UTC (rev 21057)
@@ -0,0 +1,14 @@
+Description: Follow links
+ Honor symlinks when copying files.
+Author: Sascha Steinbiss <sascha at steinbiss.name>
+--- a/src/ParsEval/pe_options.c
++++ b/src/ParsEval/pe_options.c
+@@ -262,7 +262,7 @@
+ }
+
+ char copy_cmd[1024];
+- sprintf(copy_cmd,"cp -r %s/* %s", options->data_path, options->outfilename);
++ sprintf(copy_cmd,"cp -LR %s/* %s", options->data_path, options->outfilename);
+ if(options->debug)
+ fprintf(stderr, "debug: copying shared data: '%s'\n", copy_cmd);
+ if(system(copy_cmd) != 0)
Deleted: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/includepaths
===================================================================
--- trunk/packages/aegean/trunk/debian/patches/includepaths 2016-01-03 13:49:42 UTC (rev 20945)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/includepaths 2016-01-09 14:26:06 UTC (rev 21057)
@@ -1,38 +0,0 @@
-Description: Includepaths
---- a/Makefile
-+++ b/Makefile
-@@ -1,8 +1,6 @@
- #---Begin configuration---#
- #---Begin configuration---#
-
--prefix=/usr/local
--
- #----End configuration----#
- #----End configuration----#
-
-@@ -29,7 +27,7 @@
-
- # Compilation settings
- CC=gcc
--CFLAGS=-Wall -DAGN_DATA_PATH='"$(prefix)/share/aegean"' -Wno-unused-result
-+CFLAGS += -Wall -DAGN_DATA_PATH='"$(prefix)/share/aegean"' -Wno-unused-result
- GTFLAGS=prefix=$(prefix)
- ifeq ($(cairo),no)
- CFLAGS += -DWITHOUT_CAIRO
-@@ -57,6 +55,7 @@
- INCS=$(shell pkg-config --silence-errors --cflags-only-I cairo) \
- -I inc/core \
- -I /usr/local/include/genometools \
-+ -I /usr/include/genometools \
- -I $(prefix)/include/genometools
- ifeq ($(memcheck),yes)
- MEMCHECK=valgrind --leak-check=full --show-reachable=yes --error-exitcode=1 \
-@@ -91,7 +90,7 @@
- rm $(prefix)/lib/libaegean.a
-
- clean:
-- rm -rf $(BINS) libaegean.a $(AGN_OBJS) inc/core/AgnVersion.h bin/*.dSYM
-+ rm -rf README $(BINS) libaegean.a $(AGN_OBJS) inc/core/AgnVersion.h bin/*.dSYM
-
- $(AGN_OBJS): obj/%.o : src/core/%.c inc/core/%.h inc/core/AgnVersion.h
- @- mkdir -p obj
Copied: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/includepaths (from rev 21050, trunk/packages/aegean/trunk/debian/patches/includepaths)
===================================================================
--- trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/includepaths (rev 0)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/includepaths 2016-01-09 14:26:06 UTC (rev 21057)
@@ -0,0 +1,13 @@
+Description: Adjust include paths
+ Debian uses /usr/include.
+Author: Sascha Steinbiss <sascha at steinbiss.name>
+--- a/Makefile
++++ b/Makefile
+@@ -62,6 +62,7 @@
+ INCS=$(shell pkg-config --silence-errors --cflags-only-I cairo) \
+ -I inc/core \
+ -I /usr/local/include/genometools \
++ -I /usr/include/genometools \
+ -I $(prefix)/include/genometools
+ ifeq ($(memcheck),yes)
+ MEMCHECK=valgrind --leak-check=full --show-reachable=yes --error-exitcode=1 \
Deleted: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/remove_license
===================================================================
--- trunk/packages/aegean/trunk/debian/patches/remove_license 2016-01-03 13:49:42 UTC (rev 20945)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/remove_license 2016-01-09 14:26:06 UTC (rev 21057)
@@ -1,17 +0,0 @@
-Description: Remove_license
---- a/data/share/LICENSE
-+++ /dev/null
-@@ -1,13 +0,0 @@
--Copyright (c) 2010-2014, Daniel S. Standage and CONTRIBUTORS
--
--Permission to use, copy, modify, and/or distribute this software for any
--purpose with or without fee is hereby granted, provided that the above
--copyright notice and this permission notice appear in all copies.
--
--THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
--WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
--MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
--ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
--WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
--ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
--OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
Copied: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/remove_license (from rev 21050, trunk/packages/aegean/trunk/debian/patches/remove_license)
===================================================================
--- trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/remove_license (rev 0)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/remove_license 2016-01-09 14:26:06 UTC (rev 21057)
@@ -0,0 +1,34 @@
+Description: Remove license file not to be installed in wrong location
+Author: Sascha Steinbiss <sascha at steinbiss.name>
+--- a/data/share/LICENSE
++++ /dev/null
+@@ -1,13 +0,0 @@
+-Copyright (c) 2010-2014, Daniel S. Standage and CONTRIBUTORS
+-
+-Permission to use, copy, modify, and/or distribute this software for any
+-purpose with or without fee is hereby granted, provided that the above
+-copyright notice and this permission notice appear in all copies.
+-
+-THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
+-WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
+-MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
+-ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
+-WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
+-ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
+-OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
+--- a/data/misc/amel-ogs-vs-ncbi-parseval-html/LICENSE
++++ /dev/null
+@@ -1,13 +0,0 @@
+-Copyright (c) 2010-2014, Daniel S. Standage and CONTRIBUTORS
+-
+-Permission to use, copy, modify, and/or distribute this software for any
+-purpose with or without fee is hereby granted, provided that the above
+-copyright notice and this permission notice appear in all copies.
+-
+-THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
+-WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
+-MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
+-ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
+-WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
+-ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
+-OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
Deleted: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/series
===================================================================
--- trunk/packages/aegean/trunk/debian/patches/series 2016-01-03 13:49:42 UTC (rev 20945)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/series 2016-01-09 14:26:06 UTC (rev 21057)
@@ -1,8 +0,0 @@
-add_hardening
-remove_license
-includepaths
-add_version
-fix_m64_on_some_archs
-adjust_datapath
-follow_links
-sort_source_files
Copied: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/series (from rev 21050, trunk/packages/aegean/trunk/debian/patches/series)
===================================================================
--- trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/series (rev 0)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/series 2016-01-09 14:26:06 UTC (rev 21057)
@@ -0,0 +1,7 @@
+add_hardening
+fix_m64_on_some_archs
+remove_license
+adjust_datapath
+follow_links
+includepaths
+spelling
Copied: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/spelling (from rev 21050, trunk/packages/aegean/trunk/debian/patches/spelling)
===================================================================
--- trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/spelling (rev 0)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/patches/spelling 2016-01-09 14:26:06 UTC (rev 21057)
@@ -0,0 +1,14 @@
+Description: Fix spelling unknow->unknown
+Author: Sascha Steinbiss <sascha at steinbiss.name>
+Forwarded: https://github.com/standage/AEGeAn/pull/161
+--- a/src/core/AgnLocus.c
++++ b/src/core/AgnLocus.c
+@@ -344,7 +344,7 @@
+ break;
+ default:
+ desc = NULL;
+- fprintf(stderr, "error: unknow comp classification %d\n", c);
++ fprintf(stderr, "error: unknown comp classification %d\n", c);
+ break;
+ }
+ desc->comparison_count++;
Deleted: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/rules
===================================================================
--- trunk/packages/aegean/trunk/debian/rules 2016-01-03 13:49:42 UTC (rev 20945)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/rules 2016-01-09 14:26:06 UTC (rev 21057)
@@ -1,39 +0,0 @@
-#!/usr/bin/make -f
-# -*- makefile -*-
-
-DH_VERBOSE=1
-DEBVERS := $(shell dpkg-parsechangelog | sed -n -e 's/^Version: //p')
-VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[[:digit:]]*://' -e 's/[~-].*//')
-OVERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[[:digit:]]*://' -e 's/[+].*//')
-export DESTDIR=$(CURDIR)/debian/tmp
-export LC_ALL=C.UTF-8
-
-BITS:=$(shell dpkg-architecture | grep DEB_BUILD_ARCH_BITS | cut -f 2 -d'=')
-ifeq ($(BITS),64)
- 64BIT:=yes
-else
- 64BIT:=no
-endif
-
-%:
- dh $@
-
-override_dh_auto_build:
- dh_auto_build -- prefix=$(DESTDIR) 64bit=$(64BIT) errorcheck=no
-
-override_dh_auto_test:
- #dh_auto_test -- useshared=yes 64bit=$(64BIT) testthreads=5
-
-override_dh_auto_install:
- dh_auto_install -- 64bit=$(64BIT) prefix=$(DESTDIR)
-
-override_dh_strip:
- dh_strip --dbg-package=aegean-dbg
-
-override_dh_installdocs:
- cp $(CURDIR)/README.md $(CURDIR)/README
- dh_installdocs
-
-get-orig-source:
- uscan --verbose --force-download --repack --compression xz --destdir=..
- mv ../aegean_$(OVERSION).orig.tar.xz ../aegean_$(VERSION).orig.tar.xz
Copied: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/rules (from rev 21051, trunk/packages/aegean/trunk/debian/rules)
===================================================================
--- trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/rules (rev 0)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/rules 2016-01-09 14:26:06 UTC (rev 21057)
@@ -0,0 +1,39 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+DH_VERBOSE=1
+DEBVERS := $(shell dpkg-parsechangelog | sed -n -e 's/^Version: //p')
+VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[[:digit:]]*://' -e 's/[~-].*//')
+OVERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[[:digit:]]*://' -e 's/[+].*//')
+export DESTDIR=$(CURDIR)/debian/tmp
+export LC_ALL=C.UTF-8
+
+BITS:=$(shell dpkg-architecture | grep DEB_BUILD_ARCH_BITS | cut -f 2 -d'=')
+ifeq ($(BITS),64)
+ 64BIT:=yes
+else
+ 64BIT:=no
+endif
+
+%:
+ dh $@
+
+override_dh_auto_build:
+ dh_auto_build -- prefix=$(DESTDIR) 64bit=$(64BIT) errorcheck=no
+
+override_dh_auto_test:
+ dh_auto_test -- useshared=yes 64bit=$(64BIT) testthreads=5
+
+override_dh_auto_install:
+ dh_auto_install -- 64bit=$(64BIT) prefix=$(DESTDIR)
+
+override_dh_strip:
+ dh_strip --dbg-package=aegean-dbg
+
+override_dh_installdocs:
+ cp $(CURDIR)/README.md $(CURDIR)/README
+ dh_installdocs
+
+get-orig-source:
+ uscan --verbose --force-download --repack --compression xz --destdir=..
+ mv ../aegean_$(OVERSION).orig.tar.xz ../aegean_$(VERSION).orig.tar.xz
Deleted: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/tests/control
===================================================================
--- trunk/packages/aegean/trunk/debian/tests/control 2016-01-09 14:12:05 UTC (rev 21054)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/tests/control 2016-01-09 14:26:06 UTC (rev 21057)
@@ -1,2 +0,0 @@
-Tests: functional_tests
-Depends: @, python
Copied: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/tests/control (from rev 21055, trunk/packages/aegean/trunk/debian/tests/control)
===================================================================
--- trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/tests/control (rev 0)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/tests/control 2016-01-09 14:26:06 UTC (rev 21057)
@@ -0,0 +1,2 @@
+Tests: functional-tests
+Depends: @, python
Copied: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/tests/functional-tests (from rev 21055, trunk/packages/aegean/trunk/debian/tests/functional-tests)
===================================================================
--- trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/tests/functional-tests (rev 0)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/tests/functional-tests 2016-01-09 14:26:06 UTC (rev 21057)
@@ -0,0 +1,27 @@
+#!/bin/sh
+# autopkgtest check: Run test cases for installed AEGeAn tools
+# Author: Sascha Steinbiss <sascha at steinbiss.name>
+set -e
+
+ORIGDIR=$(pwd)
+WORKDIR=$(mktemp -d)
+trap "rm -rf $WORKDIR" 0 INT QUIT ABRT PIPE TERM
+
+# change paths to reflect installed binaries
+for f in test/*.sh; do
+ sed -r 's/(^|[^/])bin\//\1/g' $f > $WORKDIR/`basename $f`;
+ chmod +x $WORKDIR/`basename $f`;
+done
+cp -pr $ORIGDIR/data $WORKDIR
+cd $WORKDIR
+
+# adjust test data
+sed -r -i 's/(^|[^/])bin\//\1/g' `grep -Rl bin data`
+
+# run tests
+for f in *.sh; do
+ ./$f;
+done
+
+echo "run: OK"
+
Deleted: trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/tests/functional_tests
===================================================================
--- trunk/packages/aegean/trunk/debian/tests/functional_tests 2016-01-09 14:12:05 UTC (rev 21054)
+++ trunk/packages/aegean/tags/0.15.1+dfsg-1/debian/tests/functional_tests 2016-01-09 14:26:06 UTC (rev 21057)
@@ -1,27 +0,0 @@
-#!/bin/sh
-# autopkgtest check: Run test cases for installed AEGeAn tools
-# Author: Sascha Steinbiss <sascha at steinbiss.name>
-set -e
-
-ORIGDIR=$(pwd)
-WORKDIR=$(mktemp -d)
-trap "rm -rf $WORKDIR" 0 INT QUIT ABRT PIPE TERM
-
-# change paths to reflect installed binaries
-for f in test/*.sh; do
- sed -r 's/(^|[^/])bin\//\1/g' $f > $WORKDIR/`basename $f`;
- chmod +x $WORKDIR/`basename $f`;
-done
-cp -pr $ORIGDIR/data $WORKDIR
-cd $WORKDIR
-
-# adjust test data
-sed -r -i 's/(^|[^/])bin\//\1/g' `grep -Rl bin data`
-
-# run tests
-for f in *.sh; do
- ./$f;
-done
-
-echo "run: OK"
-
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