From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from pigeon.gentoo.org ([208.92.234.80] helo=lists.gentoo.org) by finch.gentoo.org with esmtp (Exim 4.60) (envelope-from ) id 1PTEtc-0003Pq-Tr for garchives@archives.gentoo.org; Thu, 16 Dec 2010 14:33:34 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 5A4F4E0687; Thu, 16 Dec 2010 14:32:52 +0000 (UTC) Received: from mta-1.ms.rz.rwth-aachen.de (mta-1.ms.rz.RWTH-Aachen.DE [134.130.7.72]) by pigeon.gentoo.org (Postfix) with ESMTP id EAA0DE0687 for ; Thu, 16 Dec 2010 14:32:51 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-science@lists.gentoo.org Reply-to: gentoo-science@lists.gentoo.org MIME-version: 1.0 Content-transfer-encoding: 7BIT Content-type: Text/Plain; charset=iso-8859-15 Received: from ironport-out-1.rz.rwth-aachen.de ([134.130.5.40]) by mta-1.ms.rz.RWTH-Aachen.de (Sun Java(tm) System Messaging Server 6.3-7.04 (built Sep 26 2008)) with ESMTP id <0LDI004ZNZ2QXJA0@mta-1.ms.rz.RWTH-Aachen.de> for gentoo-science@lists.gentoo.org; Thu, 16 Dec 2010 15:32:51 +0100 (CET) X-IronPort-AV: E=Sophos;i="4.59,355,1288566000"; d="scan'208";a="85635914" Received: from relay-auth-2.ms.rz.rwth-aachen.de (HELO relay-auth-2) ([134.130.7.79]) by ironport-in-1.rz.rwth-aachen.de with ESMTP; Thu, 16 Dec 2010 15:32:51 +0100 Received: from localhost.localnet ([unknown] [137.226.40.42]) by relay-auth-2.ms.rz.rwth-aachen.de (Sun Java(tm) System Messaging Server 7.0-3.01 64bit (built Dec 9 2008)) with ESMTPA id <0LDI00L5OZ2QIX90@relay-auth-2.ms.rz.rwth-aachen.de> for gentoo-science@lists.gentoo.org; Thu, 16 Dec 2010 15:32:50 +0100 (CET) From: Jan Marten Simons Organization: Institut =?iso-8859-1?q?f=FCr?= Kristallographie To: gentoo-science@lists.gentoo.org Subject: Re: [gentoo-science] cctbx version-bump to 2010.12.13.0000? Date: Thu, 16 Dec 2010 15:32:50 +0100 User-Agent: KMail/1.13.5 (Linux/2.6.36-gentoo-r5; KDE/4.4.5; x86_64; ; ) References: <201012031548.42284.marten@xtal.rwth-aachen.de> <201012131325.31734.marten@xtal.rwth-aachen.de> <4D093556.4000504@gentoo.org> In-reply-to: <4D093556.4000504@gentoo.org> Message-id: <201012161532.50471.marten@xtal.rwth-aachen.de> X-Archives-Salt: 658ed3a6-0398-4f48-91d1-934f3c6620ca X-Archives-Hash: 70c5137098943a2bf70dea4b5d56b34f Am Mittwoch 15 Dezember 2010 22:38:30 schrieb Justin (jlec) Lecher: > Hi, > > I fixed the last ebuild in the tree, so that all the binary wrappers > should work now. And currently working on the bump. But it seems to not > be that smooth. So don't expect it do appear before Xmas. By now there's even a more recent build agin: 2010_12_13_0000 and I suppose there will be a new release after xmas as well ;). As I'just found a bug and got it fixed upstream (in svn) I'm using their svn-version in a local install at the moment. So the old version of cctbx in portage is no showstopper to me right now and as far as I'm concerned you can take your time to versionbump it. Now to some feedback: I tried emerging sci-libs/cctbx-2010.03.29.2334-r3 but encountered an error (sci-libs/cctbx-2010.03.29.2334-r1 compiles and installs). It looks like something in that update broke clipper somehow as you can see from the relevant parts of the log: * Package: sci-libs/cctbx-2010.03.29.2334-r3 * Repository: gentoo * Maintainer: jlec@gentoo.org sci-chemistry@gentoo.org * USE: amd64 elibc_glibc kernel_linux minimal multilib openmp userland_GNU >>> Unpacking source... >>> Unpacking cctbx-2010.03.29.2334.tar.gz to /var/tmp/portage/sci- libs/cctbx-2010.03.29.2334-r3/work >>> Source unpacked in /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r3/work >>> Preparing source in /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- r3/work ... * Applying 2010.03.29.2334-tst_server.py.patch ... [ ok ] * Applying 2010.03.29.2334-boost.patch ... [ ok ] * Applying 2010.03.29.2334-clipper.patch ... [ ok ] * Applying 2010.03.29.2334-flags.patch ... [ ok ] * Applying 2010.03.29.2334-soname.patch ... [ ok ] >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- r3/work ... * configuring with /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- r3/work/cctbx_sources/libtbx/configure.py --compiler=gcc --enable-openmp-if- possible=True --scan-boost --use_e nvironment_flags --current_working_directory=/var/tmp/portage/sci- libs/cctbx-2010.03.29.2334-r3/work/cctbx_build --build=release fftw3tbx rstbx smtbx mmtbx clipper_adaptbx fable Python: 2.6.5 "/usr/bin/python2.6" Compiler: gcc Build mode: release Warning level: 0 Static libraries: False Static exe: False Scan Boost headers: True Write full flex_fwd.h files: False Build Boost.Python extensions: True Define BOOST_PYTHON_NO_PY_SIGNATURES: False Define BOOST_PYTHON_BOOL_INT_STRICT: True Boost threads enabled: False Enable OpenMP if possible: True Use environment flags: True CXXFLAGS = -march=native -O2 -pipe CFLAGS = -march=native -O2 -pipe CPPFLAGS = LDFLAGS = -Wl,-O1 -Wl,--as-needed [...] g++ -o exe_dev/cctbx.convert_ccp4_symop_lib -Wl,-O1 -Wl,--as-needed -fopenmp cctbx/examples/convert_ccp4_symop_lib.o -Llib -L/var/tmp/portage/sci- libs/cctbx-2010.03.29.2334-r3/work /cctbx_sources/lib -lcctbx_sgtbx_asu -lcctbx -lm /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- r3/work/cctbx_sources/clipper/examples/symtest.cpp:1:29: error: clipper/clipper.h: No such file or directory g++ -o chiltbx/handle_test -Wl,-O1 -Wl,--as-needed -fopenmp chiltbx/handle_test.o -Llib -L/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- r3/work/cctbx_sources/lib /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- r3/work/cctbx_sources/clipper_adaptbx/sanity_check.cpp:1:39: error: clipper/core/clipper_util.h: No such file or directory g++ -o exe_dev/cctbx.find_distances -Wl,-O1 -Wl,--as-needed -fopenmp cctbx/examples/find_distances.o -Llib -L/var/tmp/portage/sci- libs/cctbx-2010.03.29.2334-r3/work/cctbx_sources/l ib -lcctbx_sgtbx_asu -lcctbx -lm g++ -o exe_dev/cctbx.getting_started -Wl,-O1 -Wl,--as-needed -fopenmp cctbx/examples/getting_started.o -Llib -L/var/tmp/portage/sci- libs/cctbx-2010.03.29.2334-r3/work/cctbx_sources /lib -lcctbx_sgtbx_asu -lcctbx -lm /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- r3/work/cctbx_sources/clipper/examples/symtest.cpp:6: error: 'clipper' is not a namespace-name /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- r3/work/cctbx_sources/clipper/examples/symtest.cpp:6: error: expected namespace-name before ';' token /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- r3/work/cctbx_sources/clipper/examples/symtest.cpp: In function 'int main()': [...] scons: *** [clipper/examples/symtest.o] Error 1 /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- r3/work/cctbx_sources/clipper_adaptbx/sanity_check.cpp: In function 'void clipper::::show_as_unsigned(const char*, const FloatType&)': /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- r3/work/cctbx_sources/clipper_adaptbx/sanity_check.cpp:39: error: 'Util' has not been declared /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- r3/work/cctbx_sources/clipper_adaptbx/sanity_check.cpp:40: error: 'Util' has not been declared /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- r3/work/cctbx_sources/clipper_adaptbx/sanity_check.cpp:41: error: 'Util' has not been declared /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- r3/work/cctbx_sources/clipper_adaptbx/sanity_check.cpp: In function 'void clipper::::sanity_check()': /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- r3/work/cctbx_sources/clipper_adaptbx/sanity_check.cpp:54: error: 'itype32' was not declared in this scope /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- r3/work/cctbx_sources/clipper_adaptbx/sanity_check.cpp:55: error: 'uitype32' was not declared in this scope /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- r3/work/cctbx_sources/clipper_adaptbx/sanity_check.cpp:56: error: 'ftype32' was not declared in this scope /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- r3/work/cctbx_sources/clipper_adaptbx/sanity_check.cpp:57: error: 'itype64' was not declared in this scope /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- r3/work/cctbx_sources/clipper_adaptbx/sanity_check.cpp:58: error: 'uitype64' was not declared in this scope /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- r3/work/cctbx_sources/clipper_adaptbx/sanity_check.cpp:59: error: 'ftype64' was not declared in this scope /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- r3/work/cctbx_sources/clipper_adaptbx/sanity_check.cpp:60: error: 'Util' has not been declared /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- r3/work/cctbx_sources/clipper_adaptbx/sanity_check.cpp:61: error: 'Util' has not been declared /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- r3/work/cctbx_sources/clipper_adaptbx/sanity_check.cpp:64: error: 'Util' has not been declared /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- r3/work/cctbx_sources/clipper_adaptbx/sanity_check.cpp:69: error: 'Util' has not been declared /var/tmp/portage/sci-libs/cctbx-2010.03.29.2334- r3/work/cctbx_sources/clipper_adaptbx/sanity_check.cpp:73: error: 'sqrt' was not declared in this scope scons: *** [clipper_adaptbx/sanity_check.o] Error 1 scons: building terminated because of errors. * ERROR: sci-libs/cctbx-2010.03.29.2334-r3 failed: * make failed * * Call stack: * ebuild.sh, line 56: Called src_compile * environment, line 4448: Called die * The specific snippet of code: * libtbx.scons ${makeopts_exp} . || die "make failed" * * If you need support, post the output of 'emerge --info =sci- libs/cctbx-2010.03.29.2334-r3', * the complete build log and the output of 'emerge -pqv =sci- libs/cctbx-2010.03.29.2334-r3'. * The complete build log is located at '/var/tmp/portage/sci- libs/cctbx-2010.03.29.2334-r3/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci- libs/cctbx-2010.03.29.2334-r3/temp/environment'. * S: '/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r3/work' With regards, Jan Simons Institute of Crystallography RWTH Aachen University