[med-svn] [mothur] 04/05: d/patches: refresh
Tomasz Buchert
tomasz at moszumanska.debian.org
Mon Jun 13 07:11:07 UTC 2016
This is an automated email from the git hooks/post-receive script.
tomasz pushed a commit to branch master
in repository mothur.
commit 7c23422319b52ffac1f0020f8718dc0886ab65b1
Author: Tomasz Buchert <tomasz at debian.org>
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 <debian-med-packaging at lists.alioth.debian.org>
+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 $LDFLAGS >> mk.stdout 2>> tmp.stderr
+ cat tmp.stderr
+ cat tmp.stderr >> mk.stderr
+ rm -f tmp.stderr
diff --git a/debian/patches/0003-Fix-VERSION-in-Makefile.patch b/debian/patches/0003-Fix-VERSION-in-Makefile.patch
new file mode 100644
index 0000000..210c6ae
--- /dev/null
+++ b/debian/patches/0003-Fix-VERSION-in-Makefile.patch
@@ -0,0 +1,35 @@
+From: Tomasz Buchert <tomasz at debian.org>
+Date: Sun, 12 Jun 2016 20:34:56 +0200
+Subject: Fix VERSION in Makefiles.
+
+---
+ Makefile | 2 +-
+ source/makefile | 2 +-
+ 2 files changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index 5cfd853..bd35b41 100755
+--- a/Makefile
++++ b/Makefile
+@@ -15,7 +15,7 @@ USEBOOST ?= yes
+ BOOST_LIBRARY_DIR="\"Enter_your_boost_library_path_here\""
+ MOTHUR_FILES="\"Enter_your_default_path_here\""
+ RELEASE_DATE = "\"4/18/2016\""
+-VERSION = "\"1.37.1\""
++VERSION = "\"1.37.5\""
+
+ ifeq ($(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 <tille at debian.org>
-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
--
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