debian/changelog

+abyss (2.1.5-7) unstable; urgency=medium
+
+  * Add myself as an uploader.
+  * The package openmpi-bin is now a required dependency for the abyss
+    binary package. Many thanks to ci.debian.org for bringing this to light.
+  * Fix "implicit declaration of function"s in dialign/museq.c
+  * Fix some spelling typos
+  * Register the flowchart PDFs with doc-base
+
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Sun, 17 Feb 2019 05:19:54 -0800
+
 abyss (2.1.5-6) unstable; urgency=high
 
   * Team upload.

debian/control

 Source: abyss
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille@debian.org>
+Uploaders: Andreas Tille <tille@debian.org>,
+           Michael R. Crusoe <michael.crusoe@gmail.com>
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 12~),
@@ -11,7 +12,8 @@ Build-Depends: debhelper (>= 12~),
                libtext-multimarkdown-perl,
                libgtest-dev,
                libsqlite3-dev,
-	       pkg-config
+	       pkg-config,
+	       help2man
 Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/abyss
 Vcs-Git: https://salsa.debian.org/med-team/abyss.git
@@ -24,8 +26,10 @@ Depends: make,
          ${misc:Depends},
          ${perl:Depends},
          bsdmainutils,
-	 openmpi-common
-Suggests: openmpi-bin
+# For openmpi error messages:
+	 openmpi-common,
+# for /usr/bin/orted and possibly other MPI components:
+	 openmpi-bin
 Description: de novo, parallel, sequence assembler for short reads
  ABySS is a de novo, parallel, sequence assembler that is designed for
  short reads. It may be used to assemble genome or transcriptome

debian/doc-base

+Document: abyss-flowcharts
+Title: ABySS flowcharts
+Author: Tbe ABySS authors
+Abstract: The ABySS assembly pipeline and its intermediate files
+Section: Science/Biology
+
+Format: pdf
+Files: /usr/share/doc/abyss/flowchart*.pdf.gz

debian/docs

-README.md
+debian/tmp/usr/share/doc/abyss/README.md
 README.html
-doc/flowchart.pdf
+debian/tmp/usr/share/doc/abyss/flowchart*.pdf
+debian/tmp/usr/share/doc/abyss/CITATION*
 debian/tests/run-unit-test
 debian/tests/test-data
 debian/README.test

debian/manpages

-doc/*.1
+debian/tmp/usr/share/man/man1/*.1

debian/not-installed

+usr/share/doc/abyss/LICENSE
+usr/share/doc/abyss/COPYRIGHT
+
+# not true, but done in another way
+usr/share/doc/abyss/ChangeLog

debian/patches/abyss-32-bit.patch

 Author: Graham Inggs <graham@nerve.org.za>
 Last-Update: Thu, 16 Jul 2015 10:44:56 +0200
+Forwarded: https://github.com/bcgsc/abyss/pull/278
 Bug-Debian: http://bugs.debian.org/780409
 Description: Fix FTBFS on 32-bit architectures
  Version 1.5.2-1 of abyss FTBFS on 32-bit architectures (armhf, i386 and

debian/patches/big_endian.patch

 Author: Daniel Knezevic <Daniel.Knezevic@imgtec.com>
 Last-Update: Fri, 9 Dec 2016 15:27:02 UTC
 Bug-Debian: https://bugs.debian.org/847574
+Forwarded: https://github.com/bcgsc/abyss/pull/279
 Description: Fix FTBFS on mips and other big-endian architectures
 
 --- a/Common/Kmer.cpp

debian/patches/fix_bash_script.patch

 Author: Andreas Tille <tille@debian.org>
 Last-Update: Thu, 16 Jul 2015 10:50:15 +0200
+Forwarded: https://github.com/bcgsc/abyss/pull/280
 Description: Script uses bash syntax so request bash interpreter
 
 --- a/DataBase/abyss-db-txt

debian/patches/fix_implicit-function-declaration

+From: Michael R. Crusoe <michael.crusoe@gmail.com>
+Subject: Fix "implicit declaration of function"s
+Forwarded: https://github.com/bcgsc/abyss/pull/277
+
+Issues discovered courtesy the Debian Build Log Scanner
+
+--- abyss.orig/dialign/museq.c
++++ abyss/dialign/museq.c
+@@ -38,6 +38,7 @@
+ //extern void calc_weight(struct diag* dg, struct scr_matrix* smatrix, 
+ //		 struct prob_dist *pdist);
+ //extern struct diag_col *create_diag_col(int seq_amount);
++extern void free_diag(struct diag* dg);
+ extern void free_diag_col(struct diag_col* dcol);
+ extern struct diag_col *find_all_diags(struct scr_matrix *smatrix, 
+ 				struct prob_dist *pdist, 
+@@ -51,6 +52,7 @@
+ extern struct prob_dist* calc_score_dist(struct scr_matrix *smatrix, int mxdlen);
+ 
+ // alig.c
++extern void free_alignment(struct alignment *algn);
+ extern struct alignment* create_empty_alignment(struct seq_col *scol);
+ //extern char adapt_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg);
+ extern int  simple_aligner(struct seq_col *scol, struct diag_col *dcol, 

debian/patches/hurd.patch

 From: Samuel Thibault <sthibault@debian.org>
 Date: Wed, 23 Jan 2019 09:45:27 +0100
 Bug-Debian: https://bugs.debian.org/920240
+Forwarded: https://github.com/bcgsc/abyss/pull/281
 Description: Fix build on hurd due to missing header file
 
 --- a/Common/MemoryUtil.h

debian/patches/series

@@ -5,3 +5,5 @@ fix_bash_script.patch
 big_endian.patch
 strict_alignment.patch
 hurd.patch
+fix_implicit-function-declaration
+spelling

debian/patches/spelling

+From: Michael R. Crusoe <michael.crusoe@gmail.com>
+Subject: Fix spelling
+Forwarded: https://github.com/bcgsc/abyss/pull/282
+
+Spelling typos found via the Debian lintian checks
+--- abyss.orig/Consensus/Consensus.cpp
++++ abyss/Consensus/Consensus.cpp
+@@ -453,7 +453,7 @@
+ 		} else if (opt::verbose > 0) {
+ 			cerr << "warning: Contig " << it->first
+ 				<< " was not supported by a complete read "
+-				"and was ommited.\n";
++				"and was omitted.\n";
+ 		}
+ 	}
+ }
+--- abyss.orig/dialign/parameters.c
++++ abyss/dialign/parameters.c
+@@ -300,7 +300,7 @@
+ 	printf("  -n\tmaximum number of consecutive positions for window containing\n     \tlow scoring positions \n \t\t[DEFAULT PROTEIN: 4]\n\t\t[DEFAULT DNA: 4]\n");
+ 	printf("  -g\tglobal minimum fragment length for stop criterion \n \t\t[DEFAULT PROTEIN: 40] \n\t\t[DEFAULT DNA: 40]\n");
+ 	printf("  -m\tminimal allowed average score in frag window containing low \n     \tscoring positions \n \t\t[DEFAULT PROTEIN: 4.0]\n\t\t[DEFAULT DNA: 0.25]\n");
+-	printf("  -o\twether overlap weights are calculated or not [DEFAULT 0]\n");
++	printf("  -o\twhether overlap weights are calculated or not [DEFAULT 0]\n");
+ 	printf("  -f\tminimum fragment length [DEFAULT 1]\n");
+ 	printf("  -r\tthreshold weight to consider the fragment at all [DEFAULT 0.0]\n");
+ 	printf("  -u\t[DEFAULT 0]\n");
+--- abyss.orig/dialign/parameters.h
++++ abyss/dialign/parameters.h
+@@ -90,7 +90,7 @@
+ 	 *
+ 	 *****************************/
+ 
+-	// wether overlap weights are calculated or not
++	// whether overlap weights are calculated or not
+ 	int DO_OVERLAP; // = 0;
+ 
+ 	// minimum diag length
+--- abyss.orig/SimpleGraph/SimpleGraph.cpp
++++ abyss/SimpleGraph/SimpleGraph.cpp
+@@ -806,7 +806,7 @@
+ 			<< g_minNumPairsUsed << ".\n";
+ 		if (g_minNumPairs < g_minNumPairsUsed)
+ 			cout << "Consider increasing the number of pairs "
+-				"threshold paramter, n, to " << g_minNumPairsUsed
++				"threshold parameter, n, to " << g_minNumPairsUsed
+ 				<< ".\n";
+ 	}
+ 
+--- abyss.orig/DataLayer/abyss-tofastq.cc
++++ abyss/DataLayer/abyss-tofastq.cc
+@@ -34,8 +34,8 @@
+ "\n"
+ "      --cat               concatenate the records [default]\n"
+ "  -i, --interleave        interleave the records\n"
+-"      --fastq             ouput FASTQ format [default]\n"
+-"      --fasta             ouput FASTA format\n"
++"      --fastq             output FASTQ format [default]\n"
++"      --fasta             output FASTA format\n"
+ "      --bx                copy SAM BX tag to output FASTA comment\n"
+ "      --chastity          discard unchaste reads [default]\n"
+ "      --no-chastity       do not discard unchaste reads\n"
+--- abyss.orig/Konnector/konnector.cc
++++ abyss/Konnector/konnector.cc
+@@ -128,7 +128,7 @@
+ "                               use 'nolimit' for no limit [nolimit]\n"
+ "\n"
+ "  Note: --max-branches was not effective for truncating expensive searches,\n"
+-"  and has been superceded by the --max-cost option.\n"
++"  and has been superseded by the --max-cost option.\n"
+ "\n"
+ "Report bugs to <" PACKAGE_BUGREPORT ">.\n";
+ 
+@@ -864,7 +864,7 @@
+ 
+ 	updateCounters(params, result);
+ 
+-	/* ouput merged / unmerged reads */
++	/* output merged / unmerged reads */
+ 
+ 	if (result.pathResult == FOUND_PATH &&
+ 		!exceedsMismatchThresholds(params, result)) {
+--- abyss.orig/Sealer/sealer.cc
++++ abyss/Sealer/sealer.cc
+@@ -124,12 +124,12 @@
+ "  -F, --max-frag=N             max fragment size in base pairs\n"
+ "\n"
+ "  Note 1: --max-branches was not effective for truncating expensive searches,\n"
+-"  and has been superceded by the --max-cost option.\n"
++"  and has been superseded by the --max-cost option.\n"
+ "\n"
+ "  Note 2: --max-frag was formerly used to determine the maximum gap\n"
+ "  size that abyss-sealer would attempt to close, according to the formula\n"
+ "  max_gap_size = max_frag - 2 * flank_length, where flank_length is\n"
+-"  determined by the -L option.  --max-frag is superceded by the more\n"
++"  determined by the -L option.  --max-frag is superseded by the more\n"
+ "  intuitive -G (--max-gap-length) option. The related option --min-frag\n"
+ "  does not seem to have any practical use.\n"
+ "\n"
+--- abyss.orig/doc/abyss-pe.1
++++ abyss/doc/abyss-pe.1
+@@ -24,7 +24,7 @@
+ .TP
+ .B lib
+ a quoted list of whitespace-separated paired-end library names. Use
+-this varible when assembling data from multiple paired-end libraries.
++this variable when assembling data from multiple paired-end libraries.
+ For each library name in lib, the user must define a variable on
+ the command line with the same name, which indicates the read files for
+ that library. See \fBEXAMPLES\fR below for a concrete example of usage.

debian/patches/strict_alignment.patch

 Author: David Matthew Mattli <dmm@mattli.us>
 Last-Change: Fri, 2 Feb 2018 15:28:32 +0000 (by James Clarke <jrtc27@debian.org>)
 Bug-Debian: https://bugs.debian.org/889147
+Forwarded: https://github.com/bcgsc/abyss/pull/279
 Description: Fix strict alignment violation on sparc64
 
 --- a/Common/Kmer.cpp

debian/rules

@@ -19,6 +19,12 @@ override_dh_auto_build:
 
 override_dh_auto_install:
 	dh_auto_install --destdir=debian/tmp
+	PATH=debian/tmp/usr/bin:$(PATH) help2man --no-info \
+	     -n "Estimate distances between contigs using paired-end alignments." \
+	     DistanceEst > debian/tmp/usr/share/man/man1/DistanceEst.1
+	PATH=debian/tmp/usr/bin:$(PATH) help2man --no-info \
+	     -n "Fill the paired-end fields of SAM alignments" abyss-fixmate \
+	     > debian/tmp/usr/share/man/man1/abyss-fixmate.1
 
 override_dh_install:
 	dh_install

debian/tests/run-unit-test

@@ -2,20 +2,23 @@
 
 pkg=abyss
 
-if [ "$ADTTMP" = "" ] ; then
-  ADTTMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
-  trap "rm -rf $ADTTMP" 0 INT QUIT ABRT PIPE TERM
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+  # Double quote below to expand the temporary directory variable now versus
+  # later is on purpose.
+  # shellcheck disable=SC2064
+  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
 fi
 
-cd $ADTTMP
+cd "${AUTOPKGTEST_TMP}"
 
 cp -a /usr/share/doc/${pkg}/test-data/ .
-gunzip -r *
+gunzip -r ./*
 
 abyss-pe k=25 name=test in='test-data/reads1.fastq test-data/reads2.fastq'
 
-echo Testing mpi compilation
-/usr/lib/abyss/ABYSS-P --help
-
-
-
+# It is okay if the echo comman can't respect "-n" and includes a newline
+# shellcheck disable=SC2039
+echo -n Testing mpi compilation: ...
+/usr/lib/abyss/ABYSS-P --help > /dev/null
+echo " success!"