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 <[email protected]> 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 [email protected] (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 <[email protected]> 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 <[email protected]> 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" <[email protected]> -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 <[email protected]> -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 [email protected] 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 ([email protected])\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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/seqan2.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
