Your message dated Wed, 25 Oct 2017 12:51:47 +0000
with message-id <e1e7l9v-000deq...@fasolo.debian.org>
and subject line Bug#878933: fixed in seqan2 2.3.2+dfsg2-3
has caused the Debian Bug report #878933,
regarding seqan2 FTBFS on mips64el
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
878933: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=878933
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: seqan2
Version: 2.3.2+dfsg2-2
Severity: serious
Tags: patch
Changes:
- don't add the CFLAGS/CPPFLAGS again when appending
(cosmetic issue resulting in some options being set twice)
- pass -mxgot to fix link error on mips64el
(re-using code for the no longer built mips/mipsel)
- don't overwrite CXXFLAGS with setting -DSEQAN_ASYNC_IO=0
one of the unintended side effects was building without
any optimization at all
--- debian/rules.old 2017-10-17 08:01:14.653184226 +0000
+++ debian/rules 2017-10-17 08:05:18.754594240 +0000
@@ -11,8 +11,8 @@
# 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
+CFLAGS+=-O3
+CXXFLAGS+=-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 +22,8 @@
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 (,$(filter mips64el,$(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)))
@@ -41,7 +41,7 @@
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 +54,7 @@
# 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: ;
--- End Message ---
--- Begin Message ---
Source: seqan2
Source-Version: 2.3.2+dfsg2-3
We believe that the bug you reported is fixed in the latest version of
seqan2, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 878...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Michael R. Crusoe <michael.cru...@gmail.com> (supplier of updated seqan2
package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Tue, 24 Oct 2017 04:56:12 -0700
Source: seqan2
Binary: seqan-apps libseqan2-dev
Architecture: source
Version: 2.3.2+dfsg2-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Michael R. Crusoe <michael.cru...@gmail.com>
Description:
libseqan2-dev - C++ library for the analysis of biological sequences
(development
seqan-apps - C++ library for the analysis of biological sequences
Closes: 878933
Changes:
seqan2 (2.3.2+dfsg2-3) unstable; urgency=medium
.
* Patch for mips64el from b...@debian.org (Closes: #878933)
* Cleaned up per-arch settings in debian/rules
* Disable parallel building on sh4
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