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commit 7c23422319b52ffac1f0020f8718dc0886ab65b1 Author: Tomasz Buchert <[email protected]> Date: Sun Jun 12 20:05:38 2016 +0200 d/patches: refresh --- ...mmand.patch => 0001-Fix-catchall-command.patch} | 2 ++ debian/patches/0002-Add-hardening-flags.patch | 38 ++++++++++++++++++++++ debian/patches/0003-Fix-VERSION-in-Makefile.patch | 35 ++++++++++++++++++++ debian/patches/hardening.patch | 15 --------- debian/patches/series | 5 +-- 5 files changed, 78 insertions(+), 17 deletions(-) diff --git a/debian/patches/0008-Fix-catchall-command.patch b/debian/patches/0001-Fix-catchall-command.patch similarity index 91% rename from debian/patches/0008-Fix-catchall-command.patch rename to debian/patches/0001-Fix-catchall-command.patch index a1ab000..9da2780 100644 --- a/debian/patches/0008-Fix-catchall-command.patch +++ b/debian/patches/0001-Fix-catchall-command.patch @@ -12,6 +12,8 @@ information. source/commands/catchallcommand.cpp | 6 ++++++ 1 file changed, 6 insertions(+) +diff --git a/source/commands/catchallcommand.cpp b/source/commands/catchallcommand.cpp +index 74f02e1..8d22971 100644 --- a/source/commands/catchallcommand.cpp +++ b/source/commands/catchallcommand.cpp @@ -199,6 +199,7 @@ int CatchAllCommand::execute() { diff --git a/debian/patches/0002-Add-hardening-flags.patch b/debian/patches/0002-Add-hardening-flags.patch new file mode 100644 index 0000000..29d3c7b --- /dev/null +++ b/debian/patches/0002-Add-hardening-flags.patch @@ -0,0 +1,38 @@ +From: Debian Med Packaging Team <[email protected]> +Date: Sun, 12 Jun 2016 19:59:04 +0200 +Subject: Add hardening flags. + +--- + source/uchime_src/mk | 7 +++++-- + 1 file changed, 5 insertions(+), 2 deletions(-) + +diff --git a/source/uchime_src/mk b/source/uchime_src/mk +index 8cd6282..8ac4acf 100755 +--- a/source/uchime_src/mk ++++ b/source/uchime_src/mk +@@ -1,4 +1,7 @@ + #!/bin/bash ++ ++set -eux ++ + CPPNames='addtargets2 alignchime alignchimel alnparams alpha alpha2 fractid getparents globalalign2 make3way mx myutils path searchchime seqdb setnucmx sfasta tracebackbit uchime_main usort viterbifast writechhit' + ObjNames='addtargets2.o alignchime.o alignchimel.o alnparams.o alpha.o alpha2.o fractid.o getparents.o globalalign2.o make3way.o mx.o myutils.o path.o searchchime.o seqdb.o setnucmx.o sfasta.o tracebackbit.o uchime_main.o usort.o viterbifast.o writechhit.o' + +@@ -7,7 +10,7 @@ rm -f *.o mk.stdout mk.stderr tmp.stderr + for CPPName in $CPPNames + do + echo $CPPName >&2 +- g++ $ENV_GCC_OPTS -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 $CPPName.cpp -o $CPPName.o >> mk.stdout 2>> tmp.stderr ++ g++ $CPPFLAGS $CXXFLAGS ${ENV_GCC_OPTS:-} -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 $CPPName.cpp -o $CPPName.o >> mk.stdout 2>> tmp.stderr + cat tmp.stderr + cat tmp.stderr >> mk.stderr + rm -f tmp.stderr +@@ -17,7 +20,7 @@ LINK_OPTS= + #if [ `uname -s` == Linux ] ; then + # LINK_OPTS=-static + #fi +-g++ $LINK_OPTS $ENV_LINK_OPTS -g -o uchime $ObjNames >> mk.stdout 2>> tmp.stderr ++g++ $LINK_OPTS ${ENV_LINK_OPTS:-} -g -o uchime $ObjNames $LDFLAGS >> mk.stdout 2>> tmp.stderr + cat tmp.stderr + cat tmp.stderr >> mk.stderr + rm -f tmp.stderr diff --git a/debian/patches/0003-Fix-VERSION-in-Makefile.patch b/debian/patches/0003-Fix-VERSION-in-Makefile.patch new file mode 100644 index 0000000..210c6ae --- /dev/null +++ b/debian/patches/0003-Fix-VERSION-in-Makefile.patch @@ -0,0 +1,35 @@ +From: Tomasz Buchert <[email protected]> +Date: Sun, 12 Jun 2016 20:34:56 +0200 +Subject: Fix VERSION in Makefiles. + +--- + Makefile | 2 +- + source/makefile | 2 +- + 2 files changed, 2 insertions(+), 2 deletions(-) + +diff --git a/Makefile b/Makefile +index 5cfd853..bd35b41 100755 +--- a/Makefile ++++ b/Makefile +@@ -15,7 +15,7 @@ USEBOOST ?= yes + BOOST_LIBRARY_DIR="\"Enter_your_boost_library_path_here\"" + MOTHUR_FILES="\"Enter_your_default_path_here\"" + RELEASE_DATE = "\"4/18/2016\"" +-VERSION = "\"1.37.1\"" ++VERSION = "\"1.37.5\"" + + ifeq ($(strip $(64BIT_VERSION)),yes) + CXXFLAGS += -DBIT_VERSION +diff --git a/source/makefile b/source/makefile +index fe1d1d4..6ede471 100644 +--- a/source/makefile ++++ b/source/makefile +@@ -16,7 +16,7 @@ MOTHUR_FILES="\"Enter_your_default_path_here\"" + BOOST_INCLUDE_DIR="/usr/local/include/" + BOOST_LIBRARY_DIR="/usr/local/lib/" + RELEASE_DATE = "\"4/22/2015\"" +-VERSION = "\"1.35.1\"" ++VERSION = "\"1.37.5\"" + FORTAN_COMPILER = gfortran + FORTRAN_FLAGS = + diff --git a/debian/patches/hardening.patch b/debian/patches/hardening.patch deleted file mode 100644 index b30d72f..0000000 --- a/debian/patches/hardening.patch +++ /dev/null @@ -1,15 +0,0 @@ -Dscription: propagate hardening options to uchime build -Author: Andreas Tille <[email protected]> -Last-Update: Sat, 07 May 2016 16:01:33 +0200 - ---- a/source/uchime_src/mk -+++ b/source/uchime_src/mk -@@ -17,7 +17,7 @@ LINK_OPTS= - #if [ `uname -s` == Linux ] ; then - # LINK_OPTS=-static - #fi --g++ $LINK_OPTS $ENV_LINK_OPTS -g -o uchime $ObjNames >> mk.stdout 2>> tmp.stderr -+g++ $LINK_OPTS $ENV_LINK_OPTS -g -o uchime $ObjNames $(LDFLAGS) >> mk.stdout 2>> tmp.stderr - cat tmp.stderr - cat tmp.stderr >> mk.stderr - rm -f tmp.stderr diff --git a/debian/patches/series b/debian/patches/series index 8813742..1e031b2 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,2 +1,3 @@ -0008-Fix-catchall-command.patch -hardening.patch +0001-Fix-catchall-command.patch +0002-Add-hardening-flags.patch +0003-Fix-VERSION-in-Makefile.patch -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/mothur.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
