[med-svn] [seqan2] 02/02: Test build of https://github.com/h-2/seqan/tree/fix/platform_issues
Michael Crusoe
misterc-guest at moszumanska.debian.org
Tue Oct 24 07:15:18 UTC 2017
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to tag debian/2.3.2.000platform-issues0-8ae7bc0+dfsg1
in repository seqan2.
commit 6c0a547a57a24cbd781a00e90e1c5180354f8d4f
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date: Mon Oct 23 10:01:37 2017 -0700
Test build of https://github.com/h-2/seqan/tree/fix/platform_issues
---
debian/changelog | 10 ++++++++++
debian/control | 3 ++-
debian/patches/series | 2 --
debian/patches/short-description | 34 ----------------------------------
debian/patches/skip-seqan-revision | 2 +-
debian/patches/spelling | 25 -------------------------
debian/rules | 23 ++++++++++++-----------
debian/source/lintian-overrides | 2 +-
8 files changed, 26 insertions(+), 75 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index f8dac25..ae03958 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,13 @@
+seqan2 (2.3.2.000platform-issues0-8ae7bc0+dfsg1-1) experimental; urgency=medium
+
+ * Patch for mips64el from bunk at debian.org (Closes: #878933)
+ * Temporarily enable all archs again
+ * Upstream source is pre-2.4.0, remove patches that they have merged:
+ short-description, spelling
+ * Cleaned up per-arch settings in debian/rules
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Mon, 23 Oct 2017 09:58:43 -0700
+
seqan2 (2.3.2+dfsg2-2) unstable; urgency=medium
* As per upstream, disable async-io for many platforms
diff --git a/debian/control b/debian/control
index 32e3cdb..1f4d6de 100644
--- a/debian/control
+++ b/debian/control
@@ -26,7 +26,8 @@ Vcs-Git: https://anonscm.debian.org/git/debian-med/seqan2.git
Homepage: http://www.seqan.de/
Package: seqan-apps
-Architecture: any-amd64 arm64 any-i386 mips64el powerpc ppc64el s390x alpha hppa m68k powerpcspe ppc64 sh4 sparc64 x32
+Architecture: any
+#Architecture: any-amd64 arm64 any-i386 mips64el powerpc ppc64el s390x alpha hppa m68k powerpcspe ppc64 sh4 sparc64 x32
# Skipping armel as per Adrian Bunk <bunk at debian.org> https://bugs.debian.org/877349
# Skipping arhmf due to lack of memory
Depends: ${shlibs:Depends},
diff --git a/debian/patches/series b/debian/patches/series
index dcf0532..18f492a 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,4 +1,2 @@
-spelling
-short-description
skip-seqan-revision
fix-version_check-test
diff --git a/debian/patches/short-description b/debian/patches/short-description
deleted file mode 100644
index b8d34d7..0000000
--- a/debian/patches/short-description
+++ /dev/null
@@ -1,34 +0,0 @@
-From: "Michael R. Crusoe" <michael.crusoe at gmail.com>
-Subject: Normalize some command line help to generate better manual pages
-Forwarded: https://github.com/seqan/seqan/pull/1999
---- seqan2.orig/apps/micro_razers/micro_razers.cpp
-+++ seqan2/apps/micro_razers/micro_razers.cpp
-@@ -212,6 +212,7 @@
-
-
- ArgumentParser parser("micro_razers");
-+ setShortDescription(parser, "Map small RNA reads possibly containing 3' adapter sequence");
- addUsageLine(parser, "[\\fIOPTIONS\\fP] <\\fIGENOME FILE\\fP> <\\fIREADS FILE\\fP>");
- addDescription(parser, "MicroRazerS uses a prefix-based mapping strategy to map "
- "small RNA reads possibly containing 3' adapter sequence. ");
---- seqan2.orig/apps/sgip/sgip.cpp
-+++ seqan2/apps/sgip/sgip.cpp
-@@ -168,7 +168,7 @@
- void _setupParser(TParser & parser)
- {
- setVersion(parser, SEQAN_APP_VERSION " [" SEQAN_REVISION "]");
-- addDescription(parser, " SGIP - Solution of Graph Isomorphism Problem");
-+ setShortDescription(parser, "Solution of Graph Isomorphism Problem");
- addUsageLine(parser, "-o <original graph> [Option]");
- addSection(parser, "Mandatory Options");
- addOption(parser, ArgParseOption("o", "original", "File containing original graph", ArgParseArgument::INPUT_FILE,"IN"));
---- seqan2.orig/apps/splazers/splazers.cpp
-+++ seqan2/apps/splazers/splazers.cpp
-@@ -303,6 +303,7 @@
- #ifdef RAZERS_MATEPAIRS
- addUsageLine(parser, "[\\fIOPTIONS\\fP] <\\fIGENOME FILE\\fP> <\\fIREADS FILE 1\\fP> <\\fIREADS FILE 2\\fP>");
- #endif
-+ setShortDescription(parser, "Split-map read sequences");
- addDescription(parser,
- "SplazerS uses a prefix-suffix mapping strategy to split-map read sequences."
- "If a SAM file of mapped reads is given as input, all unmapped but anchored"
diff --git a/debian/patches/skip-seqan-revision b/debian/patches/skip-seqan-revision
index d710814..693e57f 100644
--- a/debian/patches/skip-seqan-revision
+++ b/debian/patches/skip-seqan-revision
@@ -3,7 +3,7 @@ Description: Don't look for a git directory, as the Debian packaging confuses
the build system
--- seqan2.orig/util/cmake/SeqAnBuildSystem.cmake
+++ seqan2/util/cmake/SeqAnBuildSystem.cmake
-@@ -651,14 +651,15 @@
+@@ -663,14 +663,15 @@
set (_SEQAN_GIT_DIR "${CMAKE_SOURCE_DIR}/.git")
message (STATUS " Selected repository dir: ${CMAKE_SOURCE_DIR}")
# Get Git information.
diff --git a/debian/patches/spelling b/debian/patches/spelling
deleted file mode 100644
index 8bf818e..0000000
--- a/debian/patches/spelling
+++ /dev/null
@@ -1,25 +0,0 @@
-From: Michael R. Crusoe <michael.crusoe at gmail.com>
-Subject: Fix a typo: recieve -> receive
-Forwarded: https://github.com/seqan/seqan/pull/2001
---- seqan2.orig/include/seqan/arg_parse/arg_parse_version_check.h
-+++ seqan2/include/seqan/arg_parse/arg_parse_version_check.h
-@@ -70,16 +70,16 @@
- static constexpr char const * const MESSAGE_SEQAN_UPDATE =
- "[SEQAN INFO] :: There is a newer SeqAn version available!\n"
- "[SEQAN INFO] :: Please visit www.seqan.de for an update or inform the developer of this app.\n"
-- "[SEQAN INFO] :: If you don't want to recieve this message again set --version-check OFF\n\n";
-+ "[SEQAN INFO] :: If you don't want to receive this message again set --version-check OFF\n\n";
- static constexpr char const * const MESSAGE_APP_UPDATE =
- "[APP INFO] :: There is a newer version of this application available.\n"
- "[APP INFO] :: If this app is developed by SeqAn, visit www.seqan.de for updates.\n"
-- "[APP INFO] :: If you don't want to recieve this message again set --version_check OFF\n\n";
-+ "[APP INFO] :: If you don't want to receive this message again set --version_check OFF\n\n";
- static constexpr char const * const MESSAGE_UNREGISTERED_APP =
- "[SEQAN INFO] :: Thank you for using SeqAn!\n"
- "[SEQAN INFO] :: You might want to regsiter you app for support and version check features?\n"
- "[SEQAN INFO] :: Just send us an email to seqan at team.fu-berlin.de with your app name and version number.\n"
-- "[SEQAN INFO] :: If you don't want to recieve this message anymore set --version_check OFF\n\n";
-+ "[SEQAN INFO] :: If you don't want to receive this message anymore set --version_check OFF\n\n";
- static constexpr char const * const MESSAGE_REGISTERED_APP_UPDATE =
- "[APP INFO] :: We noticed the app version you use is newer than the one registered with us.\n"
- "[APP INFO] :: Please send us an email with the new version so we can correct it (support at seqan.de)\n\n";
diff --git a/debian/rules b/debian/rules
index 920eab1..bd8b9de 100755
--- a/debian/rules
+++ b/debian/rules
@@ -11,8 +11,6 @@ export HOME=$(shell echo $$PWD"/fakehome")
# See https://wiki.debian.org/Hardening#Notes_for_packages_using_CMake
DPKG_EXPORT_BUILDFLAGS = 1
include /usr/share/dpkg/buildflags.mk
-CFLAGS+=$(CPPFLAGS) -O3
-CXXFLAGS+=$(CPPFLAGS) -O3
# Droping -fstack-protector flag helps **drastically** reducing memory consumption when building the package!!!!
# export CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS | sed 's/-fstack-protector *//') ## don't do this, it simply triggers #759978
@@ -22,8 +20,16 @@ CXXFLAGS+=$(CPPFLAGS) -O3
DEB_HOST_ARCH ?= $(shell dpkg-architecture -qDEB_HOST_ARCH)
DEB_BUILD_ARCH ?= $(shell dpkg-architecture -qDEB_BUILD_ARCH)
-ifneq (,$(filter mips mipsel,$(DEB_BUILD_ARCH)))
- export CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS | sed 's/-O[1-9]//') -O1 -mxgot
+ifneq (,$(filter mips mipsel kfreebsd% hurd%,$(DEB_BUILD_ARCH)))
+ CXXFLAGS+=-O1
+ CFLAGS+=-01
+else
+ CXXFLAGS+=-O3
+ CFLAGS+=-O3
+endif
+
+ifneq (,$(filter mips mipsel mips64el,$(DEB_BUILD_ARCH)))
+ export CXXFLAGS+=-mxgot
endif
# Disable parallel building on some build archs to save memory
ifneq (,$(filter armhf mips kfreebsd%,$(DEB_BUILD_ARCH)))
@@ -33,15 +39,10 @@ ifneq (,$(filter armhf mips kfreebsd%,$(DEB_BUILD_ARCH)))
endif
$(info $$DEB_BUILD_OPTIONS is [${DEB_BUILD_OPTIONS}])
-# Try to save memory on kfreebsd-* and hurd-i386
-ifneq (,$(filter kfreebsd% hurd%,$(DEB_BUILD_ARCH)))
- export CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS | sed 's/-O[1-9]//') -O1
-endif
-
ifneq (,$(filter mips64el ppc64el s390x alpha hppa powerpc ppc64 sparc64,$(DEB_HOST_ARCH)))
# Disable async io on certain target archs, as per upstream
# https://github.com/seqan/seqan/issues/1861#issuecomment-336484553
-NOASYNC=-DCMAKE_CXX_FLAGS="-DSEQAN_ASYNC_IO=0"
+CXXFLAGS+="-DSEQAN_ASYNC_IO=0"
endif
pkgapps=seqan-apps
@@ -54,7 +55,7 @@ override_dh_auto_configure-arch:
# dh_auto_configure -- -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_APPS -DSEQAN_STATIC_APPS=False # skip the tests for now
dh_auto_configure -- -DSEQAN_BUILD_SYSTEM=DEVELOP \
-DSEQAN_STATIC_APPS=False -DSEQAN_NO_DOX=1 \
- -DSEQAN_DISABLE_VERSION_CHECK=YES $(NOASYNC)
+ -DSEQAN_DISABLE_VERSION_CHECK=YES
override_dh_auto_configure-indep: ;
diff --git a/debian/source/lintian-overrides b/debian/source/lintian-overrides
index c493f4b..dec1714 100644
--- a/debian/source/lintian-overrides
+++ b/debian/source/lintian-overrides
@@ -1 +1 @@
-seqan2 source: debian-rules-sets-DEB_BUILD_OPTIONS line 32
+seqan2 source: debian-rules-sets-DEB_BUILD_OPTIONS line 38
--
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