[cctbxbb] cannot compile Phenix

Pavel Afonine pafonine at lbl.gov
Sat Apr 6 11:39:11 PDT 2019


No luck.. Running

python bootstrap.py --builder=phenix --cciuser=afonine

in an empty directory results in another crash:

Installing OpenSSL...
   log file is /Users/pafonine/phenix/base_tmp/OpenSSL_install_log
   getting package openssl-1.0.2r.tar.gz...
     downloading from 
https://gitcdn.link/repo/dials/dependencies/master/ : Traceback (most 
recent call last):
   File 
"modules/cctbx_project/libtbx/auto_build/install_base_packages.py", line 
1674, in <module>
     installer(args=sys.argv, log=sys.stdout)
   File 
"modules/cctbx_project/libtbx/auto_build/install_base_packages.py", line 
250, in __init__
     self.build_dependencies(packages=packages)
   File 
"modules/cctbx_project/libtbx/auto_build/install_base_packages.py", line 
774, in build_dependencies
     getattr(self, 'build_%s'%i)()
   File 
"modules/cctbx_project/libtbx/auto_build/install_base_packages.py", line 
1228, in build_openssl
     pkg = self.fetch_package(pkg_name=pkg_name, pkg_url=pkg_url)
   File 
"/Users/pafonine/phenix/modules/cctbx_project/libtbx/auto_build/package_defs.py", 
line 240, in __call__
     size = self.toolbox.download_to_file(full_url, output_file, 
log=self.log)
   File 
"/Users/pafonine/phenix/modules/cctbx_project/libtbx/auto_build/bootstrap.py", 
line 265, in download_to_file
     socket = urllib2.urlopen(url_request)
   File 
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", 
line 154, in urlopen
     return opener.open(url, data, timeout)
   File 
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", 
line 437, in open
     response = meth(req, response)
   File 
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", 
line 550, in http_response
     'http', request, response, code, msg, hdrs)
   File 
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", 
line 475, in error
     return self._call_chain(*args)
   File 
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", 
line 409, in _call_chain
     result = func(*args)
   File 
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", 
line 558, in http_error_default
     raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
urllib2.HTTPError: HTTP Error 500: Internal Server Error
Process failed with return code 1

Pavel

P.S.: Are we really ready for Phenix release?


On 4/6/19 11:16, Pavel Afonine wrote:
> Oh, thanks Rob! Now trying from scratch in an empty folder! Let's see 
> how it goes!
> Pavel
>
> On 4/6/19 11:15, R. D. Oeffner wrote:
>> From the messages on the cctbx github mailing list it seems that 
>> Dials people have been extricating dxtbx from cctbx_project.
>>
>> Rob
>>
>> -----Original Message----- From: Pavel Afonine
>> Sent: Saturday, April 6, 2019 7:07 PM
>> To: phenixdev
>> Subject: cannot compile Phenix
>>
>> Hi,
>>
>> anyone knows why current Phenix code is broken:
>>
>> python bootstrap.py --builder=phenix --sfuser=afonine --cciuser=afonine
>> update
>> python bootstrap.py --builder=phenix --sfuser=afonine --cciuser=afonine
>> build --nproc=12
>>
>> leads to
>>
>> (...)
>> AttributeError: 'empty' object has no attribute 'dxtbx_include':
>>   File "/Users/pafonine/phenix/build/SConstruct", line 31:
>>     SConscript("spotfinder/SConscript")
>>   File
>> "/Users/pafonine/phenix/modules/scons/engine/SCons/Script/SConscript.py", 
>>
>> line 607:
>>     return method(*args, **kw)
>>   File
>> "/Users/pafonine/phenix/modules/scons/engine/SCons/Script/SConscript.py", 
>>
>> line 544:
>>     return _SConscript(self.fs, *files, **subst_kw)
>>   File
>> "/Users/pafonine/phenix/modules/scons/engine/SCons/Script/SConscript.py", 
>>
>> line 253:
>>     call_stack[-1].globals)
>>   File
>> "/Users/pafonine/phenix/modules/cctbx_project/spotfinder/SConscript",
>> line 22:
>>     env_etc.dxtbx_include,
>> usr+sys time: 1.94 seconds
>> wall clock time: 4.51 seconds
>> Process failed with return code 2
>>
>> Any idea for a workaround?
>>
>> Pavel
>>
>>
>>
>> ---
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>>
>



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