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Commits (8)
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
......
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 -----*/
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)
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] );
......@@ -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
......@@ -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?' \{\} \;
Tests: run-unit-test
Depends: @
Restrictions: allow-stderr
#!/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