debian/changelog

+gff2aplot (2.0-11) UNRELEASED; urgency=medium
+
+  * README files in examples are actually scripts - fix PATH to gff2aplot
+  * Add autopkgtest
+    Closes: #890789
+  * Fix issue with Perl 5.28
+  * Fix definition of CP in upstream makefile
+  * Make sure sprint buffers have proper size
+
+ -- Andreas Tille <tille@debian.org>  Mon, 10 Dec 2018 07:36:57 +0100
+
 gff2aplot (2.0-10) unstable; urgency=medium
 
   * debhelper 11

debian/patches/enhance_sprintf_buffer.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Mon, 10 Dec 2018 07:36:57 +0100
+Description: Enhance print buffer to avoid:
+  /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 36 and 3418 bytes into a destination of size 1000
+ Finally this patch is not fully working since the enhanced buffers
+ make sprint assume that even larger buffers are needed.
+
+--- a/src/ali2gff/ali2gff.c
++++ b/src/ali2gff/ali2gff.c
+@@ -234,7 +234,7 @@ void processGFFfile() {
+ 	unsigned long int yseqLen_4 = LONG_MAX;
+ 	
+ 	float score;
+-	char scores[MAXSTRING];
++	char scores[2*MAXSTRING];
+ 	
+ 	char strand1;
+ 	char strand2;
+@@ -426,8 +426,8 @@ void processMumfile() {
+ 	time_t now;
+ 	char nowString[100];
+ 	
+-	char nextMUM[MAXSTRING] = "";
+-	char nextGAP[MAXSTRING] = "";
++	char nextMUM[5*MAXSTRING] = "";
++	char nextGAP[3*MAXSTRING] = "";
+ 	
+ 	
+ 	char seq1[MAX_SEQUENCE_LENGTH];
+@@ -974,7 +974,7 @@ void processSimfile() {
+ 	FILE *simfile;
+ 
+ 	char line[MAXSTRING];							/*----- read line 		-----*/
+-	char seqboundsline[MAXSTRING];
++	char seqboundsline[2*MAXSTRING];
+ 	char *ptr;										/*----- pointer to line -----*/
+ 	char waste[MAXSTRING];
+ 	
+@@ -1000,7 +1000,7 @@ void processSimfile() {
+ 	unsigned long int yrev; 			/* start position + end position of y sequence --- this term is used to calculate positions of rev. compl. fragments on forward strand */   			
+ 	
+ 	unsigned short int aliPrinted = 0;
+-	char aliPrintString[MAXSTRING];
++	char aliPrintString[4*MAXSTRING];
+ 
+ 		
+ 	/*----- open alignment file -----*/

debian/patches/fix_install_ali2gff.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Mon, 10 Dec 2018 07:36:57 +0100
+Description: Make sure target dir exists when performing parallel builds
+ Somehow CP is resolved to "cp 1" - no idea why, just force proper copy statement
+
+--- a/Makefile
++++ b/Makefile
+@@ -84,7 +84,7 @@
+ 
+          RM = $(firstword $(shell which rm   )) $(V)
+          RD = $(firstword $(shell which rmdir)) $(V)
+-         CP = $(firstword $(shell which cp   )) $(V)
++         CP = cp -v
+          MV = $(firstword $(shell which mv   )) $(V)
+          LN = $(firstword $(shell which ln   )) $(V)
+          MD = $(firstword $(shell which mkdir)) $(V)
+@@ -145,7 +145,8 @@ installbin : $(BINCODE)
+ ### FINISHING CODE
+ 
+ $(addprefix $(BIN)/, $(ALI2GFF)) : $(addprefix $(ALI2GFFD)/, $(ALI2GFF))
+-	@${CP} $(addprefix $(ALI2GFFD)/, $(ALI2GFF)) \
++	mkdir -p $(BIN)
++	cp $(addprefix $(ALI2GFFD)/, $(ALI2GFF)) \
+            $(addprefix $(BIN)/, $(ALI2GFF))
+ 
+ $(addprefix $(ALI2GFFD)/, $(ALI2GFF)) : $(addprefix $(addprefix $(ALI2GFFD)/, $(ALI2GFF)), .h .c)

debian/patches/perl_5.28.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Mon, 10 Dec 2018 07:36:57 +0100
+Description: Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /usr/bin/gff2aplot line 1737.
+
+--- a/src/gff2aplot.pl
++++ b/src/gff2aplot.pl
+@@ -1733,7 +1733,7 @@ sub varscheck() {
+       || return $F;
+     $flag && do {
+         my @tmpary = ();
+-        defined( @{ $varec->{$class}{ $$rec[1] } } ) || do {
++        @{ $varec->{$class}{ $$rec[1] } } || do {
+             @{ $varec->{$class}{ $$rec[1] } } = ();
+         };
+         @tmpary = &find_regexp( $$rec[0] );

debian/patches/series

@@ -3,3 +3,6 @@
 use-dpkg-buildflags.patch
 mayhem.patch
 fis-privacy-breach.patch
+perl_5.28.patch
+fix_install_ali2gff.patch
+enhance_sprintf_buffer.patch

debian/rules

@@ -10,6 +10,10 @@
 override_dh_auto_clean:
 	rm -f src/ali2gff/ali2gff bin/ali2gff
 
-# We need to rename some *.pl files
+# We need to rename some *.pl files (done in dh_auto_install to avoid useless install step to /usr/local/bin)
 override_dh_auto_install:
 	for script in `find bin -name "*.pl"` ; do mv $$script bin/`basename $$script .pl` ; done
+
+override_dh_installexamples:
+	dh_installexamples
+	find debian/*/usr/share/doc/*/examples -name README -exec sed -i 's?^$$BIN/gff2aplot.pl?gff2aplot?' \{\} \;

debian/tests/control

+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr

debian/tests/run-unit-test

+#!/bin/bash
+set -e
+
+pkg=gff2aplot
+
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+  AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+  trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
+
+cd $AUTOPKGTEST_TMP
+gunzip -r *
+
+for script in `find . -name README` ; do
+   cd $(dirname $script)
+   sh README
+   cd ..
+done