[phenixbb] phenix fails to configure on fedora 20

Billy Poon bkpoon at lbl.gov
Thu Nov 3 23:53:06 PDT 2016


Hi Abhisek,

Can you provide the output to

/usr/local/phenix-1.11.1-2575/base/bin/python
/usr/local/phenix-1.11.1-2575/modules/cctbx_project/libtbx/configure.py
--current_working_directory /usr/local/phenix-1.11.1-2575/build
--command_version_suffix 1.11.1-2575 phenix phaser solve_resolve labelit

That's the command that is failing, and I'm assuming you did not delete the
installation directory that was created from running the install command.

--
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 Thu, Nov 3, 2016 at 11:31 PM, abhisek Mondal <abhisek.mndl at gmail.com>
wrote:

> Hi,
>
> The nightly build version is giving me the same error. I think something
> is going wrong during configuring the built.
>
> Please have a look.
> Thank you.
>
> On Tue, Nov 1, 2016 at 11:02 PM, Dr. Robert Oeffner <rdo20 at cam.ac.uk>
> wrote:
>
>> Dear Abhisek,
>>
>> Version 1.10 is quite old and there have been several bug fixes and new
>> features since then. We’re just about to release version 1.11 so the
>> current nightly builds on the website should be quite stable. If you detect
>> otherwise we would be interested to hear back.
>>
>> Regards,
>>
>> Robert
>>
>> *From:* abhisek Mondal
>> *Sent:* Tuesday, November 1, 2016 5:07 PM
>> *To:* rdo20 at cam.ac.uk ; phenixbb at phenix-online.org
>> *Subject:* RE: [phenixbb] phenix fails to configure on fedora 20
>>
>>
>> I'll try...
>> But, my concern is, when I tried to install the same version in my
>> workstation it worked cool.
>> Is this some sort of issue with my laptop ?
>> Nightly builds are beta right ? Won't it cause any stability issue ?
>>
>> On Nov 1, 2016 3:07 PM, <rdo20 at cam.ac.uk> wrote:
>>
>>> Have you tried one of the recent nightly builds or the centos5 version?
>>>
>>>
>>>
>>> Rob
>>>
>>>
>>>
>>> Sent from my Windows 10 phone
>>> --
>>> Robert Oeffner, Ph.D.
>>> Research Associate, The Read Group
>>> Department of Haematology,
>>> Cambridge Institute for Medical Research
>>> University of Cambridge
>>> Cambridge Biomedical Campus
>>> Wellcome Trust/MRC Building
>>> Hills Road
>>> Cambridge CB2 0XY
>>>
>>> www.cimr.cam.ac.uk/investigators/read/index.html
>>> tel: +44(0)1223 763234
>>> mobile: +44(0)7712 887162
>>>
>>>
>>>
>>> *From: *abhisek Mondal
>>> *Sent: *01 November 2016 07:39
>>> *To: *phenixbb at phenix-online.org
>>> *Subject: *[phenixbb] phenix fails to configure on fedora 20
>>>
>>>
>>>
>>> Hi,
>>>
>>> I'm using Fedora 20 on a 4 core laptop. When I tried to install phenix
>>> it gave following error.
>>>
>>>
>>>
>>> Same version installed fine in my workstation but keep failing here.
>>>
>>>
>>>
>>> Please help me out here.
>>>
>>> Thanks.
>>>
>>>
>>>
>>>
>>>
>>> *[root at viralhost
>>> phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6]# ./install *
>>>
>>>
>>>
>>> *
>>> ==========================================================================*
>>>
>>> *                          Phenix Installation*
>>>
>>>
>>>
>>> *                          version: 1.10.1-2155*
>>>
>>> *                     machine type: intel-linux-2.6*
>>>
>>> *                       OS version: 3.19.8-100.fc20.i686*
>>>
>>> *                      destination: /usr/local/phenix-1.10.1-2155*
>>>
>>> *                  # of processors: 4*
>>>
>>> *
>>> =========================================================================*
>>>
>>>
>>>
>>> *Configuring Phenix components...*
>>>
>>> *Traceback (most recent call last):*
>>>
>>> *  File "./bin/install.py", line 262, in <module>*
>>>
>>> *    installer(sys.argv[1:]).install()*
>>>
>>> *  File
>>> "/home/abhisek/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py",
>>> line 185, in install*
>>>
>>> *    self.install_from_binary()*
>>>
>>> *  File
>>> "/home/abhisek/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py",
>>> line 295, in install_from_binary*
>>>
>>> *    self.reconfigure(log=log)*
>>>
>>> *  File
>>> "/home/abhisek/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py",
>>> line 460, in reconfigure*
>>>
>>> *    call(args=args, log=log, verbose=self.options.verbose)*
>>>
>>> *  File
>>> "/home/abhisek/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/installer_utils.py",
>>> line 81, in call*
>>>
>>> *    raise RuntimeError("Call to '%s' failed with exit code %d" % (args,
>>> rc))*
>>>
>>> *RuntimeError: Call to '/usr/local/phenix-1.10.1-2155/base/bin/python
>>> /usr/local/phenix-1.10.1-2155/modules/cctbx_project/libtbx/configure.py
>>> --current_working_directory /usr/local/phenix-1.10.1-2155/build
>>> --command_version_suffix 1.10.1-2155 phenix phaser solve_resolve labelit'
>>> failed with exit code 126*
>>>
>>>
>>>
>>> --
>>>
>>> Abhisek Mondal
>>>
>>> *Research Fellow*
>>>
>>> *Structural Biology and Bioinformatics Division*
>>>
>>> *CSIR-Indian Institute of Chemical Biology*
>>>
>>> *Kolkata 700032*
>>>
>>> *INDIA*
>>>
>>>
>>>
>>
>
>
> --
> Abhisek Mondal
>
> *Research Fellow*
>
> *Structural Biology and Bioinformatics Division*
> *CSIR-Indian Institute of Chemical Biology*
>
> *Kolkata 700032*
>
> *INDIA*
>
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