Re: [sage-devel] Re: C build problems on MacOS 10.7 Lion.

2012-05-24 Thread Georg S. Weber


On Tuesday, 22 May 2012 23:26:52 UTC+2, Jason Ekstrand wrote:

 On Tue, May 22, 2012 at 2:53 PM, Jason Grout 
 jason-s...@creativetrax.com wrote: 
  Sorry I haven't got back to you on this.  Is XCode installed on the 10.7 
  laptop?  Also, I notice that the error messages seem to indicate that 
 you're 
  using the 10.6 binary; I wonder if that might be part of the problem? 
  Did 
  you compile 5.0 on the 10.7 machine, or did you download a binary? 

 I'm not sitting at the machine right now, but I believe that XCode was 
 installed. The command line tools are, however, NOT installed. But I 
 believe the point of bundling GCC in with sage was to get rid of this 
 problem, wasn't it? 

  Also, Jason, can you try executing the above?  I think the file you are 
 using 
  is version 1.0.0 of the library, but the above code loads version 1.1.0. 
  I 
  doubt it will make a difference in the limits.h problem, but who knows. 

 That was the first thing I tried. It gives the exact same error. 

 --Jason Ekstrand 



 Hi Jason,

the Sage README.txt says:


QUICK INSTRUCTIONS TO BUILD FROM SOURCE
---

The following steps briefly outline the process of building Sage from
source. More detailed instructions, including how to build faster on
multicore machines are contained later in this README and in the
Installation Guide:

http://www.sagemath.org/doc/installation

1. Make sure you have the dependencies and 3 GB of free disk space.

   Linux: gcc, make, m4, perl, ranlib, and tar.
   (install these using your package manager)
   On recent Debian or Ubuntu systems (in particular Ubuntu 12.04
   Precise), you need the dpkg-dev package.

   OS X: Xcode. Make sure you have installed the most recent version
   of Xcode. For pre-Lion versions of OS X, you can download Xcode
   from http://developer.apple.com/downloads/. For OS X Lion, you can
   install it using the App Store. With Xcode 4.3 or later, you need
   to install the Command Line Tools: from the File menu, choose
   Preferences, then the Downloads tab, and then Install the
   Command Line Tools.



As mentioned in this thread, one can install those (e.g. late march) 
command line tools independently of XCode, but they are indispensable. They 
install (amongst other stuff) what in Linux land would be called kernel 
headers and C library/runtime headers, in OS X nomenclature this is 
named SDK. Sage does bundle GCC now, but not some C library/runtime --- 
nor, what is more important, any respective system headers. In Debian 
Linux, the couterpart of these command line tools would be the 
build-essential (AFAIR) metabundle, so the requirement to have this 
available when trying to build C sources, is not really OS X specific. (But 
with XCode 4.2 and earlier, this came more or less automatically as a part 
of XCode, which is no longer the case with the fully application-like 
XCode 4.3 and younger).
Hope that helps!

Cheers,
Georg
 

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Re: [sage-devel] Re: C build problems on MacOS 10.7 Lion.

2012-05-24 Thread Jason Ekstrand
I appreciate all the help people have been trying to give me
concerning building sage from source. Unfortunately, this is not the
problem. I understand build systems and have done a fair amount of
software development on my own, and I know where to go to get the mac
build tools.

Here is the problem: Sage 5 ships with GCC bundled in so that mac
users can install sage and build sage packages without having to have
the mac build toolchain (It makes sage much easier to install for the
end user). There is a problem in the way it was bundled (specifically
regarding limits.h and possibly others) that prevents it from building
certain C extensions (i.e. Jason Grout's Minimum Rank library). These
problems probably have not come into light before because everyone who
has tested the bundle is a developer and so they already have the dev
tools installed. If I'm misunderstanding the purpose of bundling GCC
into sage 5, please let me know.

I haven't been able to provide any feedback yet because the machine
having the problem is not my own (I'm a linux user). Our IT guy is
going to be getting me a mac in the next few days so that I can have
one sitting on my desk to do some testing to try and find more details
about the problem. Once I get a chance to sit down at a mac and build
some things, I'll get back to you all and let you know what I've
found.
--Jason Ekstrand

On Thu, May 24, 2012 at 7:48 AM, Georg S. Weber
georgswe...@googlemail.com wrote:


 On Tuesday, 22 May 2012 23:26:52 UTC+2, Jason Ekstrand wrote:

 On Tue, May 22, 2012 at 2:53 PM, Jason Grout
 jason-s...@creativetrax.com wrote:
  Sorry I haven't got back to you on this.  Is XCode installed on the 10.7
  laptop?  Also, I notice that the error messages seem to indicate that
  you're
  using the 10.6 binary; I wonder if that might be part of the problem?
   Did
  you compile 5.0 on the 10.7 machine, or did you download a binary?

 I'm not sitting at the machine right now, but I believe that XCode was
 installed. The command line tools are, however, NOT installed. But I
 believe the point of bundling GCC in with sage was to get rid of this
 problem, wasn't it?

  Also, Jason, can you try executing the above?  I think the file you are
  using
  is version 1.0.0 of the library, but the above code loads version 1.1.0.
   I
  doubt it will make a difference in the limits.h problem, but who knows.

 That was the first thing I tried. It gives the exact same error.

 --Jason Ekstrand



  Hi Jason,

 the Sage README.txt says:
 

 QUICK INSTRUCTIONS TO BUILD FROM SOURCE
 ---

 The following steps briefly outline the process of building Sage from
 source. More detailed instructions, including how to build faster on
 multicore machines are contained later in this README and in the
 Installation Guide:

 http://www.sagemath.org/doc/installation

 1. Make sure you have the dependencies and 3 GB of free disk space.

Linux: gcc, make, m4, perl, ranlib, and tar.
(install these using your package manager)
On recent Debian or Ubuntu systems (in particular Ubuntu 12.04
Precise), you need the dpkg-dev package.

OS X: Xcode. Make sure you have installed the most recent version
of Xcode. For pre-Lion versions of OS X, you can download Xcode
from http://developer.apple.com/downloads/. For OS X Lion, you can
install it using the App Store. With Xcode 4.3 or later, you need
to install the Command Line Tools: from the File menu, choose
Preferences, then the Downloads tab, and then Install the
Command Line Tools.

 

 As mentioned in this thread, one can install those (e.g. late march)
 command line tools independently of XCode, but they are indispensable. They
 install (amongst other stuff) what in Linux land would be called kernel
 headers and C library/runtime headers, in OS X nomenclature this is named
 SDK. Sage does bundle GCC now, but not some C library/runtime --- nor,
 what is more important, any respective system headers. In Debian Linux, the
 couterpart of these command line tools would be the build-essential
 (AFAIR) metabundle, so the requirement to have this available when trying to
 build C sources, is not really OS X specific. (But with XCode 4.2 and
 earlier, this came more or less automatically as a part of XCode, which is
 no longer the case with the fully application-like XCode 4.3 and younger).
 Hope that helps!

 Cheers,
 Georg


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Re: [sage-devel] Re: C build problems on MacOS 10.7 Lion.

2012-05-24 Thread Jason Ekstrand
Jason,
I'll get back to you on the details in a few days when I actually have
a mac sitting on my desk to test with. I guess the next question is,
If you have to have command line tools installed anyway, why are we
bundling gcc?
--Jason



On Thu, May 24, 2012 at 10:32 AM, Jason Grout
jason-s...@creativetrax.com wrote:
 On 5/24/12 9:45 AM, Jason Ekstrand wrote:

 Here is the problem: Sage 5 ships with GCC bundled in so that mac
 users can install sage and build sage packages without having to have
 the mac build toolchain (It makes sage much easier to install for the
 end user). There is a problem in the way it was bundled (specifically
 regarding limits.h and possibly others) that prevents it from building
 certain C extensions (i.e. Jason Grout's Minimum Rank library). These
 problems probably have not come into light before because everyone who
 has tested the bundle is a developer and so they already have the dev
 tools installed. If I'm misunderstanding the purpose of bundling GCC
 into sage 5, please let me know.



 Georg's message indicates that you *do* need the OSX command line tools
 installed to get the system headers (which would be necessary for compiling
 extensions).  So then the question is: do you have the OSX command line
 tools installed (which is a different question than if you have XCode
 installed).

 In other words, if I understand Georg and Dima correctly, the answer to your
 original question:


 It appears as if the version of the limits.h file bundled in with sage
 depends on the system's limits.h file which does not exist on a standard
 MacOS 10.7 install. How do you recommend dealing with this?

 is: Install the OSX command line tools (not XCode), which include such a
 header file.

 Disclaimer: I don't have 10.7, so I can't test my answer above.

 Thanks,

 Jason



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Re: [sage-devel] Re: C build problems on MacOS 10.7 Lion.

2012-05-24 Thread William Stein
On Thu, May 24, 2012 at 8:38 AM, Jason Ekstrand ja...@jlekstrand.net wrote:
 Jason,
 I'll get back to you on the details in a few days when I actually have
 a mac sitting on my desk to test with. I guess the next question is,
 If you have to have command line tools installed anyway, why are we
 bundling gcc?

Apple's compilers are buggy.

Also, before I could install the OS X command line tools, I had to
first install XCode.   People keep suggesting on this thread that the
command line tools are currently an *alternative* to XCode, but for me
at least that did not seem to be the case.

 -- William

 --Jason



 On Thu, May 24, 2012 at 10:32 AM, Jason Grout
 jason-s...@creativetrax.com wrote:
 On 5/24/12 9:45 AM, Jason Ekstrand wrote:

 Here is the problem: Sage 5 ships with GCC bundled in so that mac
 users can install sage and build sage packages without having to have
 the mac build toolchain (It makes sage much easier to install for the
 end user). There is a problem in the way it was bundled (specifically
 regarding limits.h and possibly others) that prevents it from building
 certain C extensions (i.e. Jason Grout's Minimum Rank library). These
 problems probably have not come into light before because everyone who
 has tested the bundle is a developer and so they already have the dev
 tools installed. If I'm misunderstanding the purpose of bundling GCC
 into sage 5, please let me know.



 Georg's message indicates that you *do* need the OSX command line tools
 installed to get the system headers (which would be necessary for compiling
 extensions).  So then the question is: do you have the OSX command line
 tools installed (which is a different question than if you have XCode
 installed).

 In other words, if I understand Georg and Dima correctly, the answer to your
 original question:


 It appears as if the version of the limits.h file bundled in with sage
 depends on the system's limits.h file which does not exist on a standard
 MacOS 10.7 install. How do you recommend dealing with this?

 is: Install the OSX command line tools (not XCode), which include such a
 header file.

 Disclaimer: I don't have 10.7, so I can't test my answer above.

 Thanks,

 Jason



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-- 
William Stein
Professor of Mathematics
University of Washington
http://wstein.org

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Re: [sage-devel] Re: C build problems on MacOS 10.7 Lion.

2012-05-24 Thread Jason Ekstrand
Ok, that makes a lot more sense. I guess my next question would be, is
there a way we could bundle the whole thing so that users don't need
to download the command line tools? I know we have several users in
our department who use the minimum rank library and beyond that have
no reason to be doing development and don't even know what they're
installing. It would make it much nicer for the end-user.
--Jason


On Thu, May 24, 2012 at 10:42 AM, William Stein wst...@gmail.com wrote:
 On Thu, May 24, 2012 at 8:38 AM, Jason Ekstrand ja...@jlekstrand.net wrote:
 Jason,
 I'll get back to you on the details in a few days when I actually have
 a mac sitting on my desk to test with. I guess the next question is,
 If you have to have command line tools installed anyway, why are we
 bundling gcc?

 Apple's compilers are buggy.

 Also, before I could install the OS X command line tools, I had to
 first install XCode.   People keep suggesting on this thread that the
 command line tools are currently an *alternative* to XCode, but for me
 at least that did not seem to be the case.

  -- William

 --Jason



 On Thu, May 24, 2012 at 10:32 AM, Jason Grout
 jason-s...@creativetrax.com wrote:
 On 5/24/12 9:45 AM, Jason Ekstrand wrote:

 Here is the problem: Sage 5 ships with GCC bundled in so that mac
 users can install sage and build sage packages without having to have
 the mac build toolchain (It makes sage much easier to install for the
 end user). There is a problem in the way it was bundled (specifically
 regarding limits.h and possibly others) that prevents it from building
 certain C extensions (i.e. Jason Grout's Minimum Rank library). These
 problems probably have not come into light before because everyone who
 has tested the bundle is a developer and so they already have the dev
 tools installed. If I'm misunderstanding the purpose of bundling GCC
 into sage 5, please let me know.



 Georg's message indicates that you *do* need the OSX command line tools
 installed to get the system headers (which would be necessary for compiling
 extensions).  So then the question is: do you have the OSX command line
 tools installed (which is a different question than if you have XCode
 installed).

 In other words, if I understand Georg and Dima correctly, the answer to your
 original question:


 It appears as if the version of the limits.h file bundled in with sage
 depends on the system's limits.h file which does not exist on a standard
 MacOS 10.7 install. How do you recommend dealing with this?

 is: Install the OSX command line tools (not XCode), which include such a
 header file.

 Disclaimer: I don't have 10.7, so I can't test my answer above.

 Thanks,

 Jason



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 William Stein
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 University of Washington
 http://wstein.org

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Re: [sage-devel] Re: C build problems on MacOS 10.7 Lion.

2012-05-24 Thread William Stein
On Thu, May 24, 2012 at 8:55 AM, Jason Ekstrand ja...@jlekstrand.net wrote:
 Ok, that makes a lot more sense. I guess my next question would be, is
 there a way we could bundle the whole thing so that users don't need
 to download the command line tools? I know we have several users in
 our department who use the minimum rank library and beyond that have
 no reason to be doing development and don't even know what they're
 installing. It would make it much nicer for the end-user.
 --Jason

Install any optional packages you want into your copy of Sage, then do

   ./sage -bdist 5.0-ekstrand

wait a while, and give them the .dmg that is in the dist/
subdirectory.  It will contain everything.

William



 On Thu, May 24, 2012 at 10:42 AM, William Stein wst...@gmail.com wrote:
 On Thu, May 24, 2012 at 8:38 AM, Jason Ekstrand ja...@jlekstrand.net wrote:
 Jason,
 I'll get back to you on the details in a few days when I actually have
 a mac sitting on my desk to test with. I guess the next question is,
 If you have to have command line tools installed anyway, why are we
 bundling gcc?

 Apple's compilers are buggy.

 Also, before I could install the OS X command line tools, I had to
 first install XCode.   People keep suggesting on this thread that the
 command line tools are currently an *alternative* to XCode, but for me
 at least that did not seem to be the case.

  -- William

 --Jason



 On Thu, May 24, 2012 at 10:32 AM, Jason Grout
 jason-s...@creativetrax.com wrote:
 On 5/24/12 9:45 AM, Jason Ekstrand wrote:

 Here is the problem: Sage 5 ships with GCC bundled in so that mac
 users can install sage and build sage packages without having to have
 the mac build toolchain (It makes sage much easier to install for the
 end user). There is a problem in the way it was bundled (specifically
 regarding limits.h and possibly others) that prevents it from building
 certain C extensions (i.e. Jason Grout's Minimum Rank library). These
 problems probably have not come into light before because everyone who
 has tested the bundle is a developer and so they already have the dev
 tools installed. If I'm misunderstanding the purpose of bundling GCC
 into sage 5, please let me know.



 Georg's message indicates that you *do* need the OSX command line tools
 installed to get the system headers (which would be necessary for compiling
 extensions).  So then the question is: do you have the OSX command line
 tools installed (which is a different question than if you have XCode
 installed).

 In other words, if I understand Georg and Dima correctly, the answer to 
 your
 original question:


 It appears as if the version of the limits.h file bundled in with sage
 depends on the system's limits.h file which does not exist on a standard
 MacOS 10.7 install. How do you recommend dealing with this?

 is: Install the OSX command line tools (not XCode), which include such a
 header file.

 Disclaimer: I don't have 10.7, so I can't test my answer above.

 Thanks,

 Jason



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 University of Washington
 http://wstein.org

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University of Washington
http://wstein.org

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Re: [sage-devel] Re: C build problems on MacOS 10.7 Lion.

2012-05-23 Thread Jeroen Demeyer
On 2012-05-23 03:14, John H Palmieri wrote:
 Try installing the command line tools and see if that helps. Sage
 bundles GCC, but it doesn't necessarily include everything which is
 installed with the command line tools, so the machine might be missing
 some important component.
What are these command line tools?  The problem is a missing include file.

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Re: [sage-devel] Re: C build problems on MacOS 10.7 Lion.

2012-05-23 Thread John H Palmieri


On Tuesday, May 22, 2012 11:50:26 PM UTC-7, Jeroen Demeyer wrote:

 On 2012-05-23 03:14, John H Palmieri wrote: 
  Try installing the command line tools and see if that helps. Sage 
  bundles GCC, but it doesn't necessarily include everything which is 
  installed with the command line tools, so the machine might be missing 
  some important component. 
 What are these command line tools?  The problem is a missing include 
 file. 


They are an optional part of Xcode: they allow you to run gcc and other 
programs from the command-line, rather than just through Apple's Xcode app. 
So installing them puts various files into standard places (e.g., gcc goes 
into /usr/bin). I don't know if it also puts libraries or headers in 
standard places.

-- 
John

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Re: [sage-devel] Re: C build problems on MacOS 10.7 Lion.

2012-05-23 Thread Dima Pasechnik


On Wednesday, 23 May 2012 16:42:24 UTC+2, John H Palmieri wrote:



 On Tuesday, May 22, 2012 11:50:26 PM UTC-7, Jeroen Demeyer wrote:

 On 2012-05-23 03:14, John H Palmieri wrote: 
  Try installing the command line tools and see if that helps. Sage 
  bundles GCC, but it doesn't necessarily include everything which is 
  installed with the command line tools, so the machine might be missing 
  some important component. 
 What are these command line tools?  The problem is a missing include 
 file. 


 They are an optional part of Xcode: they allow you to run gcc and other 
 programs from the command-line, rather than just through Apple's Xcode app. 
 So installing them puts various files into standard places (e.g., gcc goes 
 into /usr/bin). I don't know if it also puts libraries or headers in 
 standard places.

 As far as I know, you do not need Xcode app any more! See 
http://kennethreitz.com/xcode-gcc-and-homebrew.html
So you can download these command line tools for free 
from http://developer.apple.com/downloads
(with a free registration)
With this, why would one need Xcode app for Sage any more?
(well, this is getting slightly off-topic ––  so why won't we require these 
tools for installing Sage from Source on OSX 10.7 ?)

Dima

 

 -- 
 John



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Re: [sage-devel] Re: C build problems on MacOS 10.7 Lion.

2012-05-22 Thread Justin C. Walker

On May 22, 2012, at 12:59 , Jason Grout wrote:

 On 5/22/12 2:53 PM, Jason Grout wrote:
 Can anyone else evaluate this in Sage 5.0 on OSX 10.7?
 
 Just as a data point, this works fine for me in Sage 5.0 on OSX 10.6.8:
 
 sage: URL='http://github.com/jasongrout/minimum_rank/raw/minimum_rank_1_1_0/'
 sage: 
 files=['Zq_c.pyx','Zq.py','zero_forcing_64.pyx','zero_forcing_wavefront.pyx','minrank.py']
 sage: for f in files:
 : load(URL+f)
 :
 Compiling /Users/grout/.sage//temp/tiny.local/77075//tmp_0.pyx...
 Compiling /Users/grout/.sage//temp/tiny.local/77075//tmp_2.pyx...
 Compiling /Users/grout/.sage//temp/tiny.local/77075//tmp_3.pyx...
 
 It would be great if someone else could try OSX 10.7...

I get the same, using Mac OS X, 10.7.4, with Xcode 4.2.1

Justin

--
Justin C. Walker, Curmudgeon-At-Large, Director
Institute for the Enhancement of the Director's Income

The path of least resistance:
it's not just for electricity any more.




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Re: [sage-devel] Re: C build problems on MacOS 10.7 Lion.

2012-05-22 Thread Justin C. Walker

On May 22, 2012, at 13:08 , Justin C. Walker wrote:

 
 On May 22, 2012, at 12:59 , Jason Grout wrote:
 
 On 5/22/12 2:53 PM, Jason Grout wrote:
 Can anyone else evaluate this in Sage 5.0 on OSX 10.7?
 
 Just as a data point, this works fine for me in Sage 5.0 on OSX 10.6.8:
 
 sage: URL='http://github.com/jasongrout/minimum_rank/raw/minimum_rank_1_1_0/'
 sage: 
 files=['Zq_c.pyx','Zq.py','zero_forcing_64.pyx','zero_forcing_wavefront.pyx','minrank.py']
 sage: for f in files:
 : load(URL+f)
 :
 Compiling /Users/grout/.sage//temp/tiny.local/77075//tmp_0.pyx...
 Compiling /Users/grout/.sage//temp/tiny.local/77075//tmp_2.pyx...
 Compiling /Users/grout/.sage//temp/tiny.local/77075//tmp_3.pyx...
 
 It would be great if someone else could try OSX 10.7...
 
 I get the same, using Mac OS X, 10.7.4, with Xcode 4.2.1

...and Sage 5.0, as well.

Justin

--
Justin C. Walker, Curmudgeon-At-Large
Institute for the Enhancement of the Director's Income

Experience is what you get
  when you don't get what you want.




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Re: [sage-devel] Re: C build problems on MacOS 10.7 Lion.

2012-05-22 Thread Jason Ekstrand
On Tue, May 22, 2012 at 2:53 PM, Jason Grout
jason-s...@creativetrax.com wrote:
 Sorry I haven't got back to you on this.  Is XCode installed on the 10.7
 laptop?  Also, I notice that the error messages seem to indicate that you're
 using the 10.6 binary; I wonder if that might be part of the problem?  Did
 you compile 5.0 on the 10.7 machine, or did you download a binary?

I'm not sitting at the machine right now, but I believe that XCode was
installed. The command line tools are, however, NOT installed. But I
believe the point of bundling GCC in with sage was to get rid of this
problem, wasn't it?

 Also, Jason, can you try executing the above?  I think the file you are using
 is version 1.0.0 of the library, but the above code loads version 1.1.0.  I
 doubt it will make a difference in the limits.h problem, but who knows.

That was the first thing I tried. It gives the exact same error.

--Jason Ekstrand

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Re: [sage-devel] Re: C build problems on MacOS 10.7 Lion.

2012-05-22 Thread John H Palmieri


On Tuesday, May 22, 2012 2:26:52 PM UTC-7, Jason Ekstrand wrote:

 On Tue, May 22, 2012 at 2:53 PM, Jason Grout wrote: 
  Sorry I haven't got back to you on this.  Is XCode installed on the 10.7 
  laptop?  Also, I notice that the error messages seem to indicate that 
 you're 
  using the 10.6 binary; I wonder if that might be part of the problem? 
  Did 
  you compile 5.0 on the 10.7 machine, or did you download a binary? 

 I'm not sitting at the machine right now, but I believe that XCode was 
 installed. The command line tools are, however, NOT installed. But I 
 believe the point of bundling GCC in with sage was to get rid of this 
 problem, wasn't it? 


Try installing the command line tools and see if that helps. Sage bundles 
GCC, but it doesn't necessarily include everything which is installed with 
the command line tools, so the machine might be missing some important 
component.

-- 
John

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