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 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, [email protected] mailto:[email protected] 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: [email protected] mailto:[email protected] mailto:[email protected]> on behalf of Luc Bourhis mailto:[email protected]> 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

-- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Hi Billy, using conda did it! Thanks for the info! Best wishes, Luc J Bourhis

On 13 Aug 2019, at 18:16, Billy Poon wrote:

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 bootstrap.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 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 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, [email protected] 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: [email protected] on behalf of Luc Bourhis 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

-- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

---

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