Gentoo Archives: gentoo-science

From: Jan Marten Simons <marten@××××××××××××××××.de>
To: gentoo-science@l.g.o
Subject: Re: [gentoo-science] cctbx version-bump to 2010.12.13.0000?
Date: Thu, 16 Dec 2010 14:33:34
In Reply to: Re: [gentoo-science] cctbx version-bump to 2010.09.15.2318? by "Justin (jlec) Lecher"
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@g.o sci-chemistry@g.o * 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-
>>> 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 ... [ 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/ --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::<unnamed>::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::<unnamed>::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: *, 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


Subject Author
Re: [gentoo-science] cctbx version-bump to 2010.12.13.0000? Jan Marten Simons <marten@××××××××××××××××.de>