Hi, This is really a ccp4-provoked question, but it relates to phaser & cctbx (I think), so I'll try here as well: After an install of ccp4 on a MacBook Pro running Snow Leopard and on a MacPro running Leopard, the command: source /sw*/bin/init.csh (where /sw* is either /sw64 on the machine running 10.6, or /sw on the machine running 10.5) gives the error: ******************************************* Fatal Error: Incomplete libtbx environment! ******************************************* Please re-run the libtbx/configure.py command. If I go to ...ccp4.../src/phaser/phaser-2.1.4/libtbx/ and type python configure.py Then it tells me that the md5 module is deprecated, and that the cool kids use hashlib instead. Does this mean that I need to go to an earlier version of python? Will that mess up other things? Curiously, one machines giving this problem has python 2.5.1, while the other has 2.6. However, I currently have python 2.5.1 running on another machine (albeit with a slightly earlier version of ccp4) and it doesn't give me this problem. Ideas? Thanks, Pat --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 [email protected]
Hi,
Are you sure the error is from CCP4, and not Phenix? I got this error
from installing Phenix badly (IIRC).
Did you install Phenix by just moving the directory from one system to
another, but which also involved changing the path? If so, it's easiest to
re-run the installer:
./install --prefix=/where/you/want/to/install/phenix
http://www.phenix-online.org/pipermail/phenixbb/2008-January/000689.html
Otherwise, copying the entire directory tree, but keeping the paths the
same on all systems worked for me when installing on multiple systems.
HTH
Mark
P.S. The configure.py to run would be "/cctbx_project/libtbx/configure.py"
from PHENIX in that case, I guess.
On 9 March 2010 22:01, Patrick Loll
Hi,
This is really a ccp4-provoked question, but it relates to phaser & cctbx (I think), so I'll try here as well:
After an install of ccp4 on a MacBook Pro running Snow Leopard and on a MacPro running Leopard, the command:
source /sw*/bin/init.csh (where /sw* is either /sw64 on the machine running 10.6, or /sw on the machine running 10.5)
gives the error:
******************************************* Fatal Error: Incomplete libtbx environment! ******************************************* Please re-run the libtbx/configure.py command.
If I go to ...ccp4.../src/phaser/phaser-2.1.4/libtbx/ and type
python configure.py
Then it tells me that the md5 module is deprecated, and that the cool kids use hashlib instead. Does this mean that I need to go to an earlier version of python? Will that mess up other things?
Curiously, one machines giving this problem has python 2.5.1, while the other has 2.6. However, I currently have python 2.5.1 running on another machine (albeit with a slightly earlier version of ccp4) and it doesn't give me this problem.
Ideas?
Thanks,
Pat
---------------------------------------------------------------------------------------
Patrick J. Loll, Ph. D.
Professor of Biochemistry & Molecular Biology
Director, Biochemistry Graduate Program
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA 19102-1192 USA
(215) 762-7706
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- Skype: markabrooks
Hi Pat,
source /sw*/bin/init.csh (where /sw* is either /sw64 on the machine running 10.6, or /sw on the machine running 10.5)
gives the error:
******************************************* Fatal Error: Incomplete libtbx environment! ******************************************* Please re-run the libtbx/configure.py command.
I wrote the script which produces this error, but I'm not sure I can help much... The message comes from an auto-generated "setpaths.csh" file which contains full path names to the Python used to configure the cctbx-based build, and a utility script. Apparently, those full path names aren't valid on your system. If you can find the "setpaths.csh" script maybe the pathnames will give you a clue what's wrong. Under 10.6 there are several things that can go wrong in addition, related to 32-bit vs. 64-bit.
If I go to ...ccp4.../src/phaser/phaser-2.1.4/libtbx/ and type
python configure.py
Users shouldn't have to run this command themselves. It is meant to be part of the package-specific installation scripts. If you run it manually you have to have the "build" directory as your current working directory, i.e. the same directory where you find the "setpaths.csh" script (which will be overwritten). Also, importantly, you have to get the right python executable, matching the pre-compiled binaries. I hope you'll get better help from the people who made the ccp4 installer you're using. Ralf
Hi Folks,
Regarding these errors I do remember seeing these when I did a binary
installation, but forgot to run binary.setup. I'm not sure if you need
to do the same on a mac though - I don't remember doing such on my Mac
OS X.5 installation.
Certainly used to happen on Linux if you just downloaded the binary
tarball, unpack and then edit and source the setup script.
Best wishes,
Graeme
On 10 March 2010 16:20, Ralf W. Grosse-Kunstleve
Hi Pat,
source /sw*/bin/init.csh (where /sw* is either /sw64 on the machine running 10.6, or /sw on the machine running 10.5)
gives the error:
******************************************* Fatal Error: Incomplete libtbx environment! ******************************************* Please re-run the libtbx/configure.py command.
I wrote the script which produces this error, but I'm not sure I can help much...
The message comes from an auto-generated "setpaths.csh" file which contains full path names to the Python used to configure the cctbx-based build, and a utility script. Apparently, those full path names aren't valid on your system. If you can find the "setpaths.csh" script maybe the pathnames will give you a clue what's wrong. Under 10.6 there are several things that can go wrong in addition, related to 32-bit vs. 64-bit.
If I go to ...ccp4.../src/phaser/phaser-2.1.4/libtbx/ and type
python configure.py
Users shouldn't have to run this command themselves. It is meant to be part of the package-specific installation scripts. If you run it manually you have to have the "build" directory as your current working directory, i.e. the same directory where you find the "setpaths.csh" script (which will be overwritten). Also, importantly, you have to get the right python executable, matching the pre-compiled binaries.
I hope you'll get better help from the people who made the ccp4 installer you're using.
Ralf _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
participants (4)
-
Graeme Winter -
Mark Brooks -
Patrick Loll -
Ralf W. Grosse-Kunstleve