[ome-users] Mcpp install failure during OMERO install attempt under Mac OS X 10.6

Thu Jun 3 14:46:03 BST 2010

Hello Listserv!

I just thought I would chime in on this.  

The reason why we did everything from source was so that we knew what was being installed where and what dependencies were being used. If you use an RPM or any other type of automatic installer, make sure you know where the files are going so that you can use them for other dependencies or for OMERO itself.

As for MCPP.  When you download the "Third Party" tarball from ICE's site for 3.3.1 (3.4.x will NOT work now unless Chris says otherwise), look into the readme file included with that on how to patch MCPP correctly.  On top of that patch, delete the lines from that header file as outlined in my install guide.  

If you have any questions about the install guide let me know!

-Ken

-----Original Message-----
From: Chris Allan [mailto:callan at lifesci.dundee.ac.uk] 
Sent: Thursday, June 03, 2010 3:58 AM
To: ome-users at lists.openmicroscopy.org.uk
Subject: Re: [ome-users] Mcpp install failure during OMERO install attempt under Mac OS X 10.6

On 3 Jun 2010, at 01:58, Taylor, Ronald C wrote:

> 
> Hello folks,

Hi Ron.

> 
> Haven't heard back yet on the two questions I sent last Tuesday to the list on my not-yet-completed OMERO install under Red Hat Linux. In the meantime, I thought I would try an entirely separate installation of OMERO on my Mac laptop, using Ken Arcieri's instructions on how to install under OS X 10.6.
> 
> Things were going smoothly - I installed Postgres, then many of the libraries. And then I got to mcpp (ver  2.7.2)  in the ThirdParty software download.

Did you perform the edits to the MCPP source outlined in Ken's document?

> 
> That mcpp install fails when I try to install according to the ThirdParty directory's  README.
> 
> I run configure like this:
> 
> ./configure  CFLAGS=fno-common  --enable-mcpplib  --disable-shared  --prefix=/Library/mcpp/Versions/2.7.2
> 
> and it appears to run OK.
> 
> But I then run "make" and get error msgs:
> 
> In file included from main.c:42:
> Internal.H:561: error  expected declaration specifiers or '...' before numeric constant
>  ...  followed by a couple more errors reported on line 561
> 
> Looking up mcpp at SourceForge, I found this note:
>  "On Linux ... and Mac OS X the system's standard headers have certain defects, and some workarounds are necessary for mcpp. Refer to section 3.9.9. in the manual"
> 
> I checked the HTML manual. From what I gather, the problems relate to stddef.h and limits.h? And to a compiler independent build? Not sure if I have that right. In any event, the manual does not tell you how to fix the install. But the SourceForge site says that there is a Mac disk image file available for the mcpp install. Though if I want to make sure I can uninstall it, I have to use the associated "port" file to install it - which will mean installing MacPorts on my laptop. Which I'm willing to do, if the Mac  disk image version of mcpp will work for Ice and Omero. Will it?

Presumably, you'd have to try it. Those of us here who are on 10.6 have either compiled it manually (using our own or Ken's suggested patch) or used MacPorts. 

> 
> Also: I found another web page at http://mcpp.darwinports.com that describes a Portfile for mcpp and says that there is a known set of patch files for mcpp 2.7.2. The page lists three:
>   patch-src__internal.H
>   patch-scr__system.H
>   fix-core-dumps.patch
> 
> Since one of the patch files has the same name as where the error appeared in the "make" run, I presume that that patch and maybe the others are needed in order for the "make" to work OK. However, I haven't been able to find the patch files themselves. Does anybody know how I should best proceed (and where the patch files are)?

A suggested patch is in Ken's document.

> (I did not have to deal with this in my Linux install - I ran an RPM to install mcpp  that our local sysadmin people had already downloaded into our AFS file system.) If the three patch files are available someplace, should I try patching with them, and then rerunning "make"? Or should I try the Mac disk image?

All of those options should work, really it's up to you as to what you feel most comfortable deploying.

> 
> Cheers,
>   Ron

-Chris

> 
> ___________________________________________
> Ronald Taylor, Ph.D.
> Computational Biology & Bioinformatics Group
> Pacific Northwest National Laboratory
> 902 Battelle Boulevard
> P.O. Box 999, Mail Stop J4-33
> Richland, WA  99352 USA
> Office:  509-372-6568
> Email: ronald.taylor at pnl.gov
> 
> 
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