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To: gentoo-science@g.o
From: Jan Marten Simons <marten@...>
Subject: Re: cctbx version-bump to 2010.12.13.0000?
Date: Thu, 16 Dec 2010 15:32:50 +0100
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-
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::<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:
 *     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


Replies:
Re: cctbx version-bump to 2010.12.13.0000?
-- Jan Marten Simons
References:
cctbx version-bump to 2010.09.15.2318?
-- Jan Marten Simons
Re: cctbx version-bump to 2010.09.15.2318?
-- Jan Marten Simons
Re: cctbx version-bump to 2010.09.15.2318?
-- Justin (jlec) Lecher
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