[sharp-discuss] SHARP/autoSHARP installation on Mac OS X 10.5.6

[Masato Akutsu]

Dear Clemens,

Finally, I could install sharp on Macbook.
(I installed another Macbook. Somehow, previous iMac still does not  
accept sharp install)
I should report what was the difference between these two Mac.
…But I do not know what was problem.
Only I can tell you now is Sharp is running on my Macbook.

Thank you very much for your kind help.

Best regards,
Masato Akutsu

On 30 Mar 2009, at 08:57, Clemens Vonrhein wrote:

> Dear Masato,
>
> On Fri, Mar 27, 2009 at 02:11:42PM +0000, Masato Akutsu wrote:
>> Do you want to start the httpd now ? [y]es/[n]o > y
>>
>> Error: Apache has not been designed to serve pages while
>> running as root. There are known race conditions that
>> will allow any local user to read any file on the system.
>> If you still desire to serve pages as root then
>> add -DBIG_SECURITY_HOLE to the EXTRA_CFLAGS line in your
>> src/Configuration file and rebuild the server. It is
>> strongly suggested that you instead modify the User
>> directive in your httpd.conf file to list a non-root
>> user.
>>
>> ERROR : something went wrong - please see any message above
>> and also try running the httpd binary
>> /usr/local/xtal/sharp/helpers/darwin/httpd by hand.
>> Maybe this binary isn't working on that particular
>> platform/operating system? See the file(s)
>> /usr/local/xtal/sharp/helpers/*/httpd.README_GPhL.
>
> It seems you're installing SHARP/autoSHARP as root - which is usually
> ok for software that doesn't involve something like a httpd. Remember
> that all files created by the running httpd (meaning: all
> SHARP/autoSHARP output) will then be owned by root. This might not be
> ideal.
>
> Furthermore, it seems that on your machine the httpd isn't happy to be
> run as 'root' and would need to be compiled differently (with that
> -DBIG_SECURITY_HOLE flag ... which has a very telling name).
>
> I would recommend installing our software under a generic 'software'
> account (you could name it 'sharp' if you want to use it only for
> SHARP/autoSHARP - or 'software', 'xray', 'xtal' or anything else if
> you want to use it for all crystallographic software as well).
>
> You could also install our software under your own account if you're
> going to be the only peason using it on that particular machine
> anyway. Just run the installation in a directory like ~/sharp or such.
>
> If you want to use only the CCP4i autoSHARP interface (the one that
> comes with the latest CCP4 6.1.1 - but see the 'problems' page on
> www.ccp4.ac.uk for updated files!): no running httpd is needed anyway
> and you could just skip that step. However, the CCP4i interface to
> autoSHARP has significantly less functionality: all those well and
> tightly integrated tools for analysis of residual maps, density
> modification and fine-tuning SHARP aren't in there. It will runn the
> same autoSHARP steps though ...
>
> Cheers
>
> Clemens
>
>>
>>
>> NOTE : unable to start httpd on this port - try next one
>>
>> Continue [y]es/[n]o/[e]xit/[s]kip >
>>> ***************************************************************
>>
>>
>> I am afraid I do not know how to run this by hand.
>> Do I need to do something with
>> /usr/local/xtal/sharp/helpers/darwin/httpd.README_GPhL ?
>>
>> Best regards,
>> Masato
>>
>>
>> On 27 Mar 2009, at 08:07, Clemens Vonrhein wrote:
>>
>>> Dear Masato,
>>>
>>> On Fri, Mar 27, 2009 at 01:10:23AM +0000, Masato Akutsu wrote:
>>>> However, I got another WARNING message at the section of server
>>>> setup as
>>>> below.
>>>> 4. list of directories for
>>>>    LD_LIBRARY_PATH/DYLD_LIBRARY_PATH variable :
>>>>    [/usr/local/ccp4-6.1.1/share/XIAROOT/xia2//binaries/mac_386:] >
>>>> WARNING : invalid answer - try again.
>>>
>>> Yes, that installation part is maybe a bit picky: it basically tests
>>> that each directory in that DYLD_LIBRARY_PATH variable (picked up  
>>> rom
>>> your environment) exists. So there are two possible explanations:
>>>
>>> a) the directory
>>> /usr/local/ccp4-6.1.1/share/XIAROOT/xia2//binaries/mac_386 doesnt
>>> exist
>>>
>>> b) it is confused by that extra ':' at the end
>>>
>>>> I would be most grateful if anyone could give me a hint.
>>>
>>> Ideally, try fixing your DYLD_LIBRARY_PATH settings before running
>>> 'installSHARP -F'. I'm not sure where this is set (maybe in one of  
>>> the
>>> CCP4 setup scripts?) though.
>>>
>>> Or when you get stuck at that point, give it a valid entry like
>>>
>>> /usr/local/ccp4-6.1.1/share/XIAROOT/xia2/binaries/mac_386
>>>
>>> (i.e. without the trailing ':').
>>>
>>> Cheers
>>>
>>> Clemens
>>>
>>> -- 
>>>
>>> ***************************************************************
>>> * Clemens Vonrhein, Ph.D.     vonrhein AT GlobalPhasing DOT com
>>> *
>>> *  Global Phasing Ltd.
>>> *  Sheraton House, Castle Park
>>> *  Cambridge CB3 0AX, UK
>>> *--------------------------------------------------------------
>>> * BUSTER Development Group      (http://www.globalphasing.com)
>>> ***************************************************************
>>
>
> -- 
>
> ***************************************************************
> * Clemens Vonrhein, Ph.D.     vonrhein AT GlobalPhasing DOT com
> *
> *  Global Phasing Ltd.
> *  Sheraton House, Castle Park
> *  Cambridge CB3 0AX, UK
> *--------------------------------------------------------------
> * BUSTER Development Group      (http://www.globalphasing.com)
> ***************************************************************