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

Luc Bourhis luc_j_bourhis at mac.com
Tue Aug 13 07:29:21 PDT 2019

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>
  File "bootstrap.py", line 2690, in run
  File "bootstrap.py", line 1166, in 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 <mailto:richard.gildea at diamond.ac.uk> wrote:
>> Hi Luc,
>> Does this help? https://github.com/cctbx/cctbx_project/issues/333 <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 <https://github.com/cctbx/cctbx_project/issues/240> and https://github.com/cctbx/cctbx_project/pull/334 <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 <mailto:cctbxbb-bounces at phenix-online.org> <cctbxbb-bounces at phenix-online.org <mailto:cctbxbb-bounces at phenix-online.org>> on behalf of Luc Bourhis <luc_j_bourhis at mac.com <mailto: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 <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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