[cctbxbb] Booststrap fails: zlib.h missing on Mojave with Xcode 10.3

Tue Aug 13 09:16:51 PDT 2019

Hi Luc,

I would recommend using conda for building with Python 3. Just add the
"--use-conda" flag to your bootstrap command so that it looks like

python *boots*trap.py --git-ssh --python3 --builder cctbxlite *--use-conda*

The builds on Azure pipelines are being run with conda environments and are
built with different versions of Xcode (supposed to be nightly, but the
scheduling is not behaving as expect.

When you do use the "--use-conda" flag, make sure that you're not in an
active conda environment. Otherwise, that one will be used instead of a new
one being created. That behavior will be changed so that the active
environment is not always used.

Also, the default Python 3 currently is Python 3.6 and the default
environment has a bunch of extra dependencies not in cctbxlite. That will
also be changed so that a minimal set of dependencies will be installed for
the cctbxlite builder.

--
Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Tel: (510) 486-5709
Fax: (510) 486-5909
Web: https://phenix-online.org

On Tue, Aug 13, 2019 at 7:30 AM Luc Bourhis <luc_j_bourhis at mac.com> wrote:

> Fails later. As can be seen below, the symlinks are bogus: python3 ends up
> being a link to ../../python3.7 and then of course, kaboom!
>
> Oh, my!
>
> Trying conda…
>
> Installing wxPython 4.0.3...
> Cross platform GUI toolkit for Python, "Phoenix" version
>   log file is /Users/luc/Developer/cctbx/base_tmp/wxPython_install_log
>   verifying wxPython installation in
> /Users/luc/Developer/cctbx/base/bin/python3 OK
>   package wxpython took 7.5s to install
> Dependencies finished building.
> Regenerating symlinks with relative paths...
>   creating symlink to ../../2to3-3.7
>   creating symlink to ../../python3.7
>   creating symlink to ../../python3.7m-config
>   creating symlink to ../../libpng16-config
>   creating symlink to ../../idle3.7
>   creating symlink to ../python3.7m-config
>   creating symlink to ../../pyvenv-3.7
>   creating symlink to ../../pydoc3.7
> ===== Running in build: run configure.py
> Traceback (most recent call last):
>   File "bootstrap.py", line 2695, in <module>
>     run()
>   File "bootstrap.py", line 2690, in run
>     use_conda=options.use_conda,
>   File "bootstrap.py", line 1166, in run
>     i.run()
>   File "bootstrap.py", line 189, in run
>     raise RuntimeError("Could not run %s: File not found" % executable)
> RuntimeError: Could not run base/bin/python3: File not found
>
>
> On 13 Aug 2019, at 15:58, Luc Bourhis <luc_j_bourhis at mac.com> wrote:
>
> I see a message should have been printed to advise me to do that but it
> was not. Buffering maybe? In any case, yes, it helps!
> Sorry, I missed that closed issue…
>
> On 13 Aug 2019, at 15:40, richard.gildea at diamond.ac.uk wrote:
>
> Hi Luc,
>
>
> Does this help? https://github.com/cctbx/cctbx_project/issues/333
>
>
> I.e. have you also run:
>
>
> sudo installer -pkg
> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
> -target /
>
>
> See also: https://github.com/cctbx/cctbx_project/issues/240 and
> https://github.com/cctbx/cctbx_project/pull/334
>
>
> Cheers,
>
>
> Richard
>
>
> Dr Richard Gildea
> Data Analysis Scientist
> Tel: +441235 77 8078
>
> Diamond Light Source Ltd.
> Diamond House
> Harwell Science & Innovation Campus
> Didcot
> Oxfordshire
> OX11 0DE
> ________________________________
> From: cctbxbb-bounces at phenix-online.org <cctbxbb-bounces at phenix-online.org>
> on behalf of Luc Bourhis <luc_j_bourhis at mac.com>
> Sent: 13 August 2019 14:28:05
> To: cctbx mailing list
> Subject: [cctbxbb] Booststrap fails: zlib.h missing on Mojave with Xcode
> 10.3
>
> Hi,
>
> I am trying to setup a Python 3 cctbx. I did
>
> python bootstrap.py --git-ssh --python3 --builder cctbxlite
>
> But it fails at the installation of OpenSSL. Clang version is "Apple LLVM
> version 10.0.1 (clang-1001.0.46.4)”. I attached the OpenSSL install log but
> I don’t see any error in it. And the advice to run xcode-select is bogus: I
> have it already setup.
> Best wishes,
>
> Luc
>
> Installing OpenSSL...
>  log file is /Users/luc/Developer/cctbx/base_tmp/OpenSSL_install_log
>  getting package openssl-1.0.2r.tar.gz...
>    downloading from
> https://gitcdn.link/repo/dials/dependencies/master/openssl-1.0.2r.tar.gz
> : 5223 kB
>  installing openssl-1.0.2r.tar.gz...
>  package openssl took 219.5s to install
>
>
> --------------------------------------------------------------------------------
>
> zlib.h missing -- try running 'xcode-select --install' first
> Process failed with return code 1
>
>
>
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