Yes, that is a general "problem" with sudo, with the latest version
distributed in OS X.

Briefly, sudo (and I have noticed other programs, like screen) don't
inherit the environment, so

sudo ccp4i

no longer works.

sudo -s

spawns a root shell.

Then you can source the environment file, and then it will all work.


This PITA is supposedly a security enhancement. (Big Brother knows what is
best for you.)


On Fri, April 25, 2008 2:57 pm, Patrick Loll wrote:
> 1.  I was sourcing /sw/bin/init.csh, so that wasn't the problem...but:
>
> 2.  I did find the problem (at least for the precompiled version from
> UC Santa Cruz):  For some reason "sudo ccp4i" gave the error message,
> but just "ccp4i" (without the sudo) worked OK.  (Although I thought
> the first time you launched ccp4i you were supposed to do it using
> sudo...??).  Anyway, I'm good (although peeved at my continuing
> inability to master sudo.  I miss living on the edge with root).
>
> 3. I didn't try to debug the binaries I got from the ccp4 site, since
> I now have a working package.  However, Iain Kerr kindly provided
> this info, which may prove useful to other small brains out there:
>
>> ccp4.setup is in ccp4-6.0.2/bin...it used to be in include..is that
>> your problem ?
>>
>> Also, there's no ccp4i folder....the ccp4i binary is in bin/ also.
>
>
> Note to the long-suffering folks at the secret underground world
> headquarters of ccp4:  Small brain or no, I spent a lot of time
> looking around for some clue as to how to complete the install for
> the ccp4 package, to no avail; a README file to accompany the
> installer would not be unwelcome...
>
> Thanks,
>
> Pat
>
>
> On 25 Apr 2008, at 4:56 PM, William Scott wrote:
>
>> You need to run
>>
>> source /sw/bin/init.sh
>>
>> if you use bash or zsh
>>
>> or
>>
>> source /sw/bin/init.csh
>>
>> if you use tcsh.
>>
>> this will automatically set up the environment variables and then
>> it will do what you want it to (which is to set up the ccp4
>> environment according to whichever shell you might be using).
>>
>>
>> On Apr 25, 2008, at 1:19 PM, Patrick Loll wrote:
>>
>>> Accck!
>>>
>>> 1.  I tried to install Bill Scott's precompiled ccp4 on an intel
>>> mac running OS X 10.5.  When attempting launch ccp4i, I receive
>>> this error message:
>>>
>>> /sw/share/xtal/ccp4-6.0.2/ccp4i/bin/ccp4i: line 4 /bltwish: no
>>> such file or directory
>>>
>>> Typing "which bltwish" returns /sw/bin/bltwish, which jibes with
>>> the definition of $CCP4I_TCLTK, so I'm not sure where the problem
>>> is...
>>>
>>> 2.  Pfui.  So next I tried jettisoning the apt-get installation,
>>> and instead used the installer downloaded from the ccp4 site
>>> (ccp4-6.0.2-osx-i386.dmg.gz).  This goes swimmingly, until I
>>> actually try to do something.   Commands like "ccp4i" or "mtzdump"
>>> aren't recognized, so I go looking for the ccp4.setup file; but
>>> it's not there.  Huh?  Also, there's no folder named ccp4i, even
>>> though this install is supposed to include it...
>>>
>>> It's Friday, and I'm at the nadir of my weekly brain function, so
>>> perhaps some kind soul will tell me where I'm going astray.
>>>
>>> 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
>>> [log in to unmask]
>>>
>
> ------------------------------------------------------------------------
> ---------------
> 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
> [log in to unmask]
>
>



William G. Scott

Contact info:
http://chemistry.ucsc.edu/~wgscott/