[med-svn] [Git][med-team/gff2aplot][master] 8 commits: README files in examples are actually scripts - fix PATH to gff2aplot
Andreas Tille
gitlab at salsa.debian.org
Mon Dec 10 09:28:52 GMT 2018
Andreas Tille pushed to branch master at Debian Med / gff2aplot
Commits:
43d849a8 by Andreas Tille at 2018-12-10T06:38:51Z
README files in examples are actually scripts - fix PATH to gff2aplot
- - - - -
4e5053f5 by Andreas Tille at 2018-12-10T06:44:11Z
Add autopkgtest
- - - - -
574d9f43 by Andreas Tille at 2018-12-10T06:51:31Z
Fix issue with Perl 5.28
- - - - -
b727e01b by Andreas Tille at 2018-12-10T08:09:15Z
avoid useless install step to /usr/local/bin
- - - - -
9d46dc60 by Andreas Tille at 2018-12-10T08:11:38Z
Fix definition of CP in upstream makefile; Make sure sprint buffers have proper size
- - - - -
9fb1e11d by Andreas Tille at 2018-12-10T08:23:11Z
Add comment about not fully working patch
- - - - -
e377e8db by Andreas Tille at 2018-12-10T08:24:43Z
Properly install examples
- - - - -
4e7aefe1 by Andreas Tille at 2018-12-10T08:39:20Z
Make sure .pl files will be renamed
- - - - -
8 changed files:
- debian/changelog
- + debian/patches/enhance_sprintf_buffer.patch
- + debian/patches/fix_install_ali2gff.patch
- + debian/patches/perl_5.28.patch
- debian/patches/series
- debian/rules
- + debian/tests/control
- + debian/tests/run-unit-test
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+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 at 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
=====================================
@@ -0,0 +1,47 @@
+Author: Andreas Tille <tille at 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
=====================================
@@ -0,0 +1,26 @@
+Author: Andreas Tille <tille at 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
=====================================
@@ -0,0 +1,15 @@
+Author: Andreas Tille <tille at 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
=====================================
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,20 @@
+#!/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
View it on GitLab: https://salsa.debian.org/med-team/gff2aplot/compare/0dd91f60236262da22b5927f5421e363e1ab52bc...4e7aefe1271969e6b27353bf32d3827c7483f589
--
View it on GitLab: https://salsa.debian.org/med-team/gff2aplot/compare/0dd91f60236262da22b5927f5421e363e1ab52bc...4e7aefe1271969e6b27353bf32d3827c7483f589
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