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 <[email protected]> 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 <[email protected]> +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 <[email protected]> +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 <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org.
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