Your message dated Tue, 24 Oct 2017 07:34:12 +0000 with message-id <e1e6tj2-000dpg...@fasolo.debian.org> and subject line Bug#878933: fixed in seqan2 2.3.2.000platform-issues0-8ae7bc0+dfsg1-1 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: ;
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--- Begin Message ---Source: seqan2 Source-Version: 2.3.2.000platform-issues0-8ae7bc0+dfsg1-1 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: Mon, 23 Oct 2017 09:58:43 -0700 Source: seqan2 Binary: seqan-apps libseqan2-dev Architecture: source Version: 2.3.2.000platform-issues0-8ae7bc0+dfsg1-1 Distribution: experimental 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 (2.3.2.000platform-issues0-8ae7bc0+dfsg1-1) experimental; urgency=medium . * Patch for mips64el from b...@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 Checksums-Sha1: ed88dbbf33648ad89128345ff62f52297466e00e 2386 seqan2_2.3.2.000platform-issues0-8ae7bc0+dfsg1-1.dsc e1f70713d9e0e3aa40f4dc950fcc0ac254e5a172 98490624 seqan2_2.3.2.000platform-issues0-8ae7bc0+dfsg1.orig.tar.gz ba721b7d50c2a3f08e4494b7a6f8bcfea640822c 10916 seqan2_2.3.2.000platform-issues0-8ae7bc0+dfsg1-1.debian.tar.xz dcfb5815736c68f496cce91ddb992888ac551f78 6287 seqan2_2.3.2.000platform-issues0-8ae7bc0+dfsg1-1_source.buildinfo Checksums-Sha256: 60ba0513d7087d0593a6b8d05b498c04dc12816cb06863ac05fcdd261b8e74bf 2386 seqan2_2.3.2.000platform-issues0-8ae7bc0+dfsg1-1.dsc 64d7dc8efd2cb938a8b640b9a45ea23e2d71fba2ff6d78ede8714cda3ada4fbd 98490624 seqan2_2.3.2.000platform-issues0-8ae7bc0+dfsg1.orig.tar.gz 15cfd2830750d3471a5ef12426854d8eb5c61e6aa52a2a6ae34be90b06c3bede 10916 seqan2_2.3.2.000platform-issues0-8ae7bc0+dfsg1-1.debian.tar.xz d104fd0affcfa8350aa2b0842924c9b5c30dcefcf3e038ec247d05b689b65f32 6287 seqan2_2.3.2.000platform-issues0-8ae7bc0+dfsg1-1_source.buildinfo Files: f05010ab2461f425035c9aa945164ad7 2386 science optional seqan2_2.3.2.000platform-issues0-8ae7bc0+dfsg1-1.dsc 51d018dd278f490b673f9e2afb204849 98490624 science optional seqan2_2.3.2.000platform-issues0-8ae7bc0+dfsg1.orig.tar.gz ffdca8ff78774bc09ea2d4b35347eb47 10916 science optional seqan2_2.3.2.000platform-issues0-8ae7bc0+dfsg1-1.debian.tar.xz e86b6110dc87fcad8f01776000d0a55e 6287 science optional seqan2_2.3.2.000platform-issues0-8ae7bc0+dfsg1-1_source.buildinfo -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAlnu57YACgkQPCZ2P2xn 5uL0jBAArIfzRkUaq1JDhFm9asSSKLJENCEMQ4GqbcdX/q/qgFivF8fx5STZrI/U GWpvWQiSxg2u3w3DJSw5A8amjv8VzfqMB8dAsXmg2kuWcCDQWibfUN99jmjD4FWC lJl2A98fK6z3lPmvcR/vLgjk5AZ/sjuOIjAbYzH01QcBCx+PJcp83I/N1S9qyzbb Vmr78j8Xgg3FCNXJa3j1M4Dn6faGLt9fWXgwDdl6H0AIMgYdakzwLnLcVTCZGrDh 7Ja/1Pmsjab3v+YUbiKiAElM/6G5cZCRucyHUNOn7XR/0gKJh7oxs9Qq/cV+Uso5 mJh20m3lUse5rnLRmVq8Y0iSIXlzCK2ENbQ7M4YnWEMLl1A44MwFCkjCHz0qoN6v OLS6aZwS8SnzsBqEY6GUuUjg8B1bMjCjulNmAyo5yoJ+E2m6eHKEbxi8drbzqmfP ffFoAXhiLN0Bj/Kyqy53mJ9S6QJFbXI3JzZcLV0sJleQDaE9tEUjq/YCxht0vi3y sXfclX8+fRhDVaS4IIujyd2P/1GIHuYFW2PRmkBl9JTjbTO1NAdhCfdh9GB7aorG 4pGEXIbJebS0olFNg5U6jHLr6qcNUpHl2I7h3/5zjJIoK6G8LB/ZVBQe3gNetlp3 F0GofV3WxikHh+CxGpMrjRHCQ9dMOteoIiUIQ1WwsSQRjjaA5a0= =DQq4 -----END PGP SIGNATURE-----
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