[gentoo-science] cctbx version-bump to 2010.09.15.2318?

[gentoo-science] cctbx version-bump to 2010.09.15.2318?

[Jan Marten Simons]

Hi,

I recently found out cctbx has released a new version (see 
http://cci.lbl.gov/cctbx_build/). I tried to do a version-bump with the 
ebuild, but as some code changed some patches don't apply anymore.

I found out, tst-server.py.patch can be dropped, as the code it tries to 
correct has been removed upstream.


Aditionally I found a bug:

/usr/lib64/cctbx/cctbx_build/bin/cctbx.python is refering to paths in 
/var/tmp/portage, which don't exist post-install and therefore calling 
cctbx.python does not give a useable environment. After fixing up those paths 
(manually) I got a working python shell where import cctbx works like it 
should.

I'll gladly help in debugging/testing an ebuld of the most recent version of 
cctbx.

With regards,

Jan Simons

Institute of Crystallography
RWTH Aachen University

Re: [gentoo-science] cctbx version-bump to 2010.09.15.2318?

[Jan Marten Simons]

[-- Attachment #1: Type: Text/Plain, Size: 1693 bytes --]

Am Freitag 03 Dezember 2010 15:48:42 schrieb Jan Marten Simons:
> Hi,
> 
> I recently found out cctbx has released a new version (see
> http://cci.lbl.gov/cctbx_build/). I tried to do a version-bump with the
> ebuild, but as some code changed some patches don't apply anymore.

By now there is another new release: 2010_12_06_2139 availiable at 
http://cci.lbl.gov/cctbx_build/: 

http://cci.lbl.gov/cctbx_build/results/2010_12_06_2139/cctbx_bundle.tar.gz

As one of the changes is "Migration to Python 2.7.1" it might be neccessary to 
depend on python >=2.7.1
 

I did a simple version-bump with the most recent ebuild in tree and found out: 

* -tst-server.py.patch can be dropped, as the code it tries to correct has 
been removed upstream
* -clipper.patch still applies.
* -boost.patch, -flags.patch and -soname.patch both don't apply to the new 
version and I'm not sure if I know enough about Scons to fix them up.

More details on the bug I found:
(/usr/lib64/cctbx/cctbx_build/bin/cctbx.python is refering to paths in
/var/tmp/portage, which don't exist post-install and therefore calling
cctbx.python does not give a useable environment. After fixing up those
paths (manually) I got a working python shell where import cctbx works
like it should.)

I attached a diff between the broken version (installed by the ebuild) and my 
working version. A solution would be to either fix the paths post build via sed 
or to get the build to write correct paths, which might be much more difficult.


I'll gladly help in debugging/testing an ebuld of the most recent version
of cctbx. I've joined irc as well.

With regards,
 
 Jan Simons
 
Institute of Crystallography
RWTH Aachen University

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--- /usr/lib64/cctbx/cctbx_build/bin/cctbx.python	2010-11-23 12:38:18.944000011 +0100
+++ /usr/lib64/cctbx/cctbx_build/bin/cctbx.pythonfixed	2010-11-23 14:21:56.061000008 +0100
@@ -21,29 +21,29 @@
 unset PYTHONHOME
 LC_ALL=C
 export LC_ALL
-LIBTBX_BUILD="/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r1/work/cctbx_build"
+LIBTBX_BUILD="/usr/lib64/cctbx/cctbx_build"
 export LIBTBX_BUILD
 LIBTBX_DISPATCHER_NAME="cctbx.python"
 export LIBTBX_DISPATCHER_NAME
 if [ -n "$PYTHONPATH" ]; then
-  PYTHONPATH="/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r1/work/cctbx_sources:/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r1/work/cctbx_sources/PyCifRW:/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r1/work/cctbx_sources/clipper_adaptbx:/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r1/work/cctbx_sources/boost_adaptbx:/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r1/work/cctbx_sources/libtbx/pythonpath:/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r1/work/cctbx_build/lib:$PYTHONPATH"
+  PYTHONPATH="/usr/lib64/cctbx/cctbx_sources:/usr/lib64/cctbx/cctbx_sources/PyCifRW:/usr/lib64/cctbx/cctbx_sources/clipper_adaptbx:/usr/lib64/cctbx/cctbx_sources/boost_adaptbx:/usr/lib64/cctbx/cctbx_sources/libtbx/pythonpath:/usr/lib64/cctbx/cctbx_build/lib:$PYTHONPATH"
   export PYTHONPATH
 else
-  PYTHONPATH="/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r1/work/cctbx_sources:/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r1/work/cctbx_sources/PyCifRW:/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r1/work/cctbx_sources/clipper_adaptbx:/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r1/work/cctbx_sources/boost_adaptbx:/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r1/work/cctbx_sources/libtbx/pythonpath:/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r1/work/cctbx_build/lib"
+  PYTHONPATH="/usr/lib64/cctbx/cctbx_sources:/usr/lib64/cctbx/cctbx_sources/PyCifRW:/usr/lib64/cctbx/cctbx_sources/clipper_adaptbx:/usr/lib64/cctbx/cctbx_sources/boost_adaptbx:/usr/lib64/cctbx/cctbx_sources/libtbx/pythonpath:/usr/lib64/cctbx/cctbx_build/lib"
   export PYTHONPATH
 fi
 if [ -n "$LD_LIBRARY_PATH" ]; then
-  LD_LIBRARY_PATH="/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r1/work/cctbx_build/lib:$LD_LIBRARY_PATH"
+  LD_LIBRARY_PATH="/usr/lib64/cctbx/cctbx_build/lib:$LD_LIBRARY_PATH"
   export LD_LIBRARY_PATH
 else
-  LD_LIBRARY_PATH="/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r1/work/cctbx_build/lib"
+  LD_LIBRARY_PATH="/usr/lib64/cctbx/cctbx_build/lib"
   export LD_LIBRARY_PATH
 fi
 if [ -n "$PATH" ]; then
-  PATH="/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r1/work/cctbx_build/bin:$PATH"
+  PATH="/usr/lib64/cctbx/cctbx_build/bin:$PATH"
   export PATH
 else
-  PATH="/var/tmp/portage/sci-libs/cctbx-2010.03.29.2334-r1/work/cctbx_build/bin"
+  PATH="/usr/lib64/cctbx/cctbx_build/bin"
   export PATH
 fi
 if [ -n "$LIBTBX__VALGRIND_FLAG__" ]; then

Re: [gentoo-science] cctbx version-bump to 2010.09.15.2318?

[Justin (jlec) Lecher]

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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.

justin


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Re: [gentoo-science] cctbx version-bump to 2010.12.13.0000?

[Jan Marten Simons]

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::<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

Re: [gentoo-science] cctbx version-bump to 2010.12.13.0000?

[Jan Marten Simons]

Am Donnerstag 16 Dezember 2010 15:32:50 schrieb Jan Marten Simons:
> 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.

> ...
> 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).
 
Justin hit me to it: I was missing sci-libs/clipper. -r1 built fine because it 
used the bundled version from upstream, -r3 removed clipper via patch to build 
against the system installed version but did not add a dependency.

So after unmasking and emerge -1 clipper cctbx-2010.03.29.2334-r3 installed 
and I can confirm that now the wrappers work like expected. cctbx also seems to 
be working like before according to my simple test suite.
 
With regards and best thanks,

 Jan Simons
 
Institute of Crystallography
RWTH Aachen University