diff -Nru theseus-3.3.0/debian/changelog theseus-3.3.0/debian/changelog --- theseus-3.3.0/debian/changelog 2017-08-06 13:48:51.000000000 +0000 +++ theseus-3.3.0/debian/changelog 2017-08-24 13:31:38.000000000 +0000 @@ -1,8 +1,14 @@ -theseus (3.3.0-5ubuntu1) artful; urgency=medium +theseus (3.3.0-6) unstable; urgency=medium - * Build with -Wno-error=format-overflow to build with GCC 7. + * Move packaging from SVN to Git + * debhelper 10 + * Standards-Version: 4.1.0 (no changes needed) + * Use DEB_SOURCE in d/rules + * Increase string length of string buffer to build with gcc-7 + Closes: #853681 + * Hardening - -- Matthias Klose Sun, 06 Aug 2017 13:48:51 +0000 + -- Andreas Tille Thu, 24 Aug 2017 15:31:38 +0200 theseus (3.3.0-5) unstable; urgency=medium diff -Nru theseus-3.3.0/debian/compat theseus-3.3.0/debian/compat --- theseus-3.3.0/debian/compat 2012-03-24 07:32:09.000000000 +0000 +++ theseus-3.3.0/debian/compat 2017-08-24 13:31:38.000000000 +0000 @@ -1 +1 @@ -9 +10 diff -Nru theseus-3.3.0/debian/control theseus-3.3.0/debian/control --- theseus-3.3.0/debian/control 2016-04-29 11:28:37.000000000 +0000 +++ theseus-3.3.0/debian/control 2017-08-24 13:31:38.000000000 +0000 @@ -3,11 +3,11 @@ Uploaders: Andreas Tille Section: science Priority: optional -Build-Depends: debhelper (>= 9), +Build-Depends: debhelper (>= 10), libgsl-dev -Standards-Version: 3.9.8 -Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/theseus/trunk -Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/theseus/trunk/ +Standards-Version: 4.1.0 +Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/theseus.git +Vcs-Git: https://anonscm.debian.org/git/debian-med/theseus.git Homepage: http://www.theseus3d.org Package: theseus diff -Nru theseus-3.3.0/debian/patches/30_fix_gcc_options.patch theseus-3.3.0/debian/patches/30_fix_gcc_options.patch --- theseus-3.3.0/debian/patches/30_fix_gcc_options.patch 2017-08-06 13:48:47.000000000 +0000 +++ theseus-3.3.0/debian/patches/30_fix_gcc_options.patch 2017-08-24 13:31:38.000000000 +0000 @@ -4,8 +4,6 @@ Default options seem to be addressing MacOS by default - just enable clean on Linux -Index: b/make.inc -=================================================================== --- a/make.inc +++ b/make.inc @@ -3,10 +3,10 @@ @@ -42,7 +40,7 @@ #OPT = -O0 -ggdb -#WARN = -Wall -Werror -pedantic -std=c99 -Wno-unused-result -#CFLAGS = $(WARN) -pthread -+WARN = -Wall -Werror -Wno-error=format-overflow -pedantic -std=c99 -Wno-unused-result ++WARN = -Wall -Werror -pedantic -std=c99 -Wno-unused-result +CFLAGS = $(WARN) -pthread #CC = /usr/local/bin/gcc diff -Nru theseus-3.3.0/debian/patches/gcc-7.patch theseus-3.3.0/debian/patches/gcc-7.patch --- theseus-3.3.0/debian/patches/gcc-7.patch 1970-01-01 00:00:00.000000000 +0000 +++ theseus-3.3.0/debian/patches/gcc-7.patch 2017-08-24 13:31:38.000000000 +0000 @@ -0,0 +1,47 @@ +Author: Andreas Tille +Last-Update: Thu, 24 Aug 2017 15:20:58 +0200 +Bug-Debian: https://bugs.debian.org/853681 +Description: Increase string length of string buffer to build with gcc-7 + +--- a/libmsa/msa.c ++++ b/libmsa/msa.c +@@ -607,7 +607,7 @@ MSA + *MSAfixnamesphy(MSA *msa) + { + int i, j, cnt, dig; +- int len = 10; ++ int len = 11; + char digit[len]; + + for(i = 0; i < msa->seqnum; ++i) +--- a/PCAstats.c ++++ b/PCAstats.c +@@ -49,7 +49,7 @@ CalcPCA(CdsArray *cdsA) + double **CovMat = cdsA->CovMat; + double sum, runsum; + PDBCds *pdbave = NULL; +- char pcafile_name[256]; ++ char pcafile_name[4117]; + FILE *pcavecs_fp = NULL, *pcastats_fp = NULL; + double biggest, bstick; + char aster; +@@ -209,7 +209,7 @@ Calc3NPCA(CdsArray *cdsA) + double **evecs = NULL, *evals = NULL; + double sum, runsum; + PDBCds *pdbave = NULL; +- char pcafile_name[256]; ++ char pcafile_name[4109]; + FILE *pcavecs_fp = NULL, *pcastats_fp = NULL; + double biggest, bstick; + char aster; +--- a/GibbsMet.c ++++ b/GibbsMet.c +@@ -2110,7 +2111,7 @@ GibbsMet(CdsArray *cdsA) + int i; + const int cnum = cdsA->cnum, vlen = cdsA->vlen; + int burn = algo->bayes; +- char paramfname[256], maxfname[256]; ++ char paramfname[4120], maxfname[4120]; + //char tmpname[256]; + double **theta = MatAlloc(cnum, 3); + double invtr, mlik, hmlik, blik, amlik, diff, ediff, liksi; diff -Nru theseus-3.3.0/debian/patches/series theseus-3.3.0/debian/patches/series --- theseus-3.3.0/debian/patches/series 2015-05-21 14:26:27.000000000 +0000 +++ theseus-3.3.0/debian/patches/series 2017-08-24 13:31:38.000000000 +0000 @@ -1 +1,2 @@ 30_fix_gcc_options.patch +gcc-7.patch diff -Nru theseus-3.3.0/debian/rules theseus-3.3.0/debian/rules --- theseus-3.3.0/debian/rules 2016-04-29 11:54:25.000000000 +0000 +++ theseus-3.3.0/debian/rules 2017-08-24 13:31:38.000000000 +0000 @@ -1,26 +1,22 @@ #!/usr/bin/make -f -# rules file using dh for theseus -# Copyright (C) Andreas Tille -# License: GPL - -pkg=theseus - -# This -# export DEB_BUILD_MAINT_OPTIONS = hardening=+pie -# leads to -# /usr/bin/ld: theseus.o: relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC -DEB_BUILD_MAINT_OPTIONS=hardening=+all,-pie + +DEB_BUILD_MAINT_OPTIONS=hardening=+all + +include /usr/share/dpkg/default.mk %: dh $@ +override_dh_auto_build: + dh_auto_build --no-parallel + override_dh_auto_install-arch: - make install INSTALLDIR=$(CURDIR)/debian/$(pkg)/usr/bin + make install INSTALLDIR=$(CURDIR)/debian/$(DEB_SOURCE)/usr/bin # Fix wrong path used in upstream script. Fixing it here is safer than # changing the patch for any new upstream release sed -e 's?/usr/local/bin?/usr/bin?' \ -e 's?/usr/bin/sed?/bin/sed?' \ - theseus_align > debian/$(pkg)/usr/bin/theseus_align + theseus_align > debian/$(DEB_SOURCE)/usr/bin/theseus_align override_dh_auto_install-indep: # nothing to do here