Adding --use-conda seems to make it work: python bootstrap.py --builder=phenix --cciuser=afonine --use-conda Pavel On 4/6/19 11:39, Pavel Afonine wrote:

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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