Hi Haiguang, Is it related to the DYLD_LIBRARY_PATH environment variable? We had an issue with Phenix and Rosetta on 10.11. I changed the fully_buffered class and call function in libtbx/easy_run.py to bypass SIP for OS X. Maybe there are more places that need the fix or maybe more environment variables need to be passed? Also, the new macOS 10.12 seems to use randomized installation paths for unsigned applications. I think our command-line installer will be fine, but I'm not sure about the graphical installer that puts things in /Applications. -- 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, Sep 20, 2016 at 4:49 AM, wrote:

Dear Haiguang,

I for one have been using OS X El Capitan for a good long while now with no problems…

Please could you give more information as to what the exact problem is? I.e. where you are trying to install and so on.

Thanks & best wishes Graeme

*From:* [email protected] [mailto:cctbxbb-bounces@ phenix-online.org] *On Behalf Of *Haiguang Liu *Sent:* 20 September 2016 12:47 *To:* [email protected] *Subject:* [cctbxbb] rpath problem on Mac system

Dear CCTBX developing team,

Is there already a solution for the run path problem in the new Mac OS?

The System Integrity Protection https://support.apple.com/en-us/HT204899 does not allow relative run path. I temporarily disabled this feature to run the programs that requires boost (for example).

If there is already a solution, please let me know.

Thanks,

Haiguang

--

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Hey Haiguang, There is a relatively new way of getting cctbx and its dependencies. Just run svn export svn:// svn.code.sf.net/p/cctbx/code/trunk/libtbx/auto_build/bootstrap.py python bootstrap.py --builder=cctbx The bootstrap.py file will download all the sources anonymously. If you want, you can provide your cci username and sourceforge username with the --cciuser and --sfuser flags to bootstrap.py, respectively. I don't think sastbx is supported, though. If you do provide the usernames, just make sure to have an ssh agent running with the appropriate key. -- 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, Sep 20, 2016 at 4:37 PM, Haiguang Liu wrote:

Dear Graeme, and Billy

Thanks for the quick reply.

This is not from the standard cctbx or phenix source installation.

It is based on an older version (the code might be dated back to 2013), from which Peter and I wrote some program for saxs analysis. I have not updated the cctbx source tree since then. That's why I was asking whether someone encountered this. After reading the mail list, I found there is one thread saying about AUTO_BUILD, where a rpath.py is available.

I can try to update the cctbx source (but the code is not available online any more?) Do you know where to download the new version cctbx source?

Thanks, Haiguang

On Tue, Sep 20, 2016 at 7:49 PM, wrote:

...

Dear Haiguang,

I for one have been using OS X El Capitan for a good long while now with no problems…

Please could you give more information as to what the exact problem is? I.e. where you are trying to install and so on.

Thanks & best wishes Graeme

*From:* [email protected] [mailto:cctbxbb-bounces@phenix -online.org] *On Behalf Of *Haiguang Liu *Sent:* 20 September 2016 12:47 *To:* [email protected] *Subject:* [cctbxbb] rpath problem on Mac system

Dear CCTBX developing team,

Is there already a solution for the run path problem in the new Mac OS?

The System Integrity Protection https://support.apple.com/en-us/HT204899 does not allow relative run path. I temporarily disabled this feature to run the programs that requires boost (for example).

If there is already a solution, please let me know.

Thanks,

Haiguang

--

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

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