bioseg installation

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bioseg installation

Vallejos, Andrew

I cannot get BioSeg to install on my Mac.  I have a full installation of postgres and I have updated the configuration file with the suggestions found on Intermine.org.

 

Thanks,

 

Andrew

 

======================

Andrew Vallejos

Web Developer II

Biotechnology and Bioengineering Center

Medical College of Wisconsin

414-955-4104

[hidden email]

 


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Re: bioseg installation

Richard Smith
Hi Andrew,
Matthew points out that the error trace says gcc can't find stdio.h
which means it is failing to compile the bioseg C code.

I'm not sure we've ever installed BioSeg on a mac - I'll have a go
on mine and let you know how I get on.  For most development work
you shouldn't need BioSeg.

Cheers,
Richard.



Vallejos, Andrew wrote:

> I cannot get BioSeg to install on my Mac.  I have a full installation of
> postgres and I have updated the configuration file with the suggestions
> found on Intermine.org.
>
>  
>
> Thanks,
>
>  
>
> Andrew
>
>  
>
> ======================
>
> Andrew Vallejos
>
> Web Developer II
>
> Biotechnology and Bioengineering Center
>
> Medical College of Wisconsin
>
> 414-955-4104
>
> [hidden email]
>
>  
>
>
>
> ------------------------------------------------------------------------
>
> This body part will be downloaded on demand.


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[hidden email]
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Re: bioseg installation

Richard Smith
I just installed Bioseg on Tiger (10.5.8) and it worked first time.

I originally installed postgres with this:

        http://www.postgresqlformac.com/


For more recent installations on Snow Leopard I've used this;
       
        http://www.enterprisedb.com/products/pgdownload.do#osx

Which has worked really well.  Is re-installing postgres an option?

I can try also on a Snow Leopard mac soon.

Cheers,
Richard.




Vallejos, Andrew wrote:

> So it seems like my Postgres installation was installed with the
> CPPFLAGS set to 'usr/local/include/', rather than '/usr/include/'.  I
> made a symbolic link so that Postgres now uses the correct directory,
> however I am still getting errors...new errors, but still error.
>
> net-250-50:release-0.8 andrew$ sudo make USE_PGXS=t
> gcc -no-cpp-precomp -isysroot /Developer/SDKs/MacOSX10.4u.sdk
> -mmacosx-version-min=10.4 -headerpad_max_install_names -arch ppc -arch
> i386 -Wall -Wmissing-prototypes -Wpointer-arith
> -Wdeclaration-after-statement -Wendif-labels -fno-strict-aliasing
> -fwrapv  -I. -I. -I/usr/local/PostgreSQL/8.4/include/postgresql/server
> -I/usr/local/PostgreSQL/8.4/include/postgresql/internal
> -I/usr/include/libxml2  -I/usr/local/include/libxml2
> -I/usr/local/include  -c -o bioseg.o bioseg.c
>
> ## Error Message Follows ##
> In file included from
> /usr/local/PostgreSQL/8.4/include/postgresql/server/c.h:71,
>                  from
> /usr/local/PostgreSQL/8.4/include/postgresql/server/postgres.h:47,
>                  from bioseg.c:13:
> /usr/local/include/stdarg.h:4:25: error: no include path in which to
> search for stdarg.h
> In file included from
> /usr/local/PostgreSQL/8.4/include/postgresql/server/utils/timestamp.h:18
> ,
>                  from
> /usr/local/PostgreSQL/8.4/include/postgresql/server/access/xlog.h:19,
>                  from
> /usr/local/PostgreSQL/8.4/include/postgresql/server/access/gist.h:19,
>                  from bioseg.c:19:
> /usr/local/include/float.h:8:24: error: no include path in which to
> search for float.h
> In file included from
> /usr/local/PostgreSQL/8.4/include/postgresql/server/c.h:71,
>                  from
> /usr/local/PostgreSQL/8.4/include/postgresql/server/postgres.h:47,
>                  from bioseg.c:13:
> /usr/local/include/stdarg.h:4:25: error: no include path in which to
> search for stdarg.h
> In file included from
> /usr/local/PostgreSQL/8.4/include/postgresql/server/utils/timestamp.h:18
> ,
>                  from
> /usr/local/PostgreSQL/8.4/include/postgresql/server/access/xlog.h:19,
>                  from
> /usr/local/PostgreSQL/8.4/include/postgresql/server/access/gist.h:19,
>                  from bioseg.c:19:
> /usr/local/include/float.h:8:24: error: no include path in which to
> search for float.h
> lipo: can't figure out the architecture type of: /var/tmp//ccZjtEJB.out
>
>
>
> -----Original Message-----
> From: Vallejos, Andrew
> Sent: Monday, July 12, 2010 1:35 PM
> To: 'Richard Smith'
> Subject: RE: [InterMine Dev] bioseg installation
>
> That does seem to be a key compenent.  Although, I am not sure why the
> complier cannot find those libraries.  I uninstalled and reinstalled the
> OS X developer tools, just to make sure everything was installed
> correctly.  And I do have all the libraries installed in /usr/include/.
>
> I wrote a simple Hello World GCC file with #include <stdio.h> at the
> top.  The "program" compiles and executes perfectly.
>
> -Andrew
>
> -----Original Message-----
> From: Richard Smith [mailto:[hidden email]]
> Sent: Monday, July 12, 2010 10:58 AM
> To: Vallejos, Andrew
> Cc: [hidden email]
> Subject: Re: [InterMine Dev] bioseg installation
>
> Hi Andrew,
> Matthew points out that the error trace says gcc can't find stdio.h
> which means it is failing to compile the bioseg C code.
>
> I'm not sure we've ever installed BioSeg on a mac - I'll have a go
> on mine and let you know how I get on.  For most development work
> you shouldn't need BioSeg.
>
> Cheers,
> Richard.
>
>
>
> Vallejos, Andrew wrote:
>> I cannot get BioSeg to install on my Mac.  I have a full installation
> of
>> postgres and I have updated the configuration file with the
> suggestions
>> found on Intermine.org.
>>
>>  
>>
>> Thanks,
>>
>>  
>>
>> Andrew
>>
>>  
>>
>> ======================
>>
>> Andrew Vallejos
>>
>> Web Developer II
>>
>> Biotechnology and Bioengineering Center
>>
>> Medical College of Wisconsin
>>
>> 414-955-4104
>>
>> [hidden email]
>>
>>  
>>
>>
>>
>>
> ------------------------------------------------------------------------
>> This body part will be downloaded on demand.
>
>


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dev mailing list
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Re: bioseg installation

Vallejos, Andrew
Definitely, I've reinstalled it a couple times already. :-)

I also use the one click installer.  The problem, in at least what I
see, is that postgres was compiled with '-I/usr/local/include', but my
gcc libraries are installed to '-I/usr/include'.  

-----Original Message-----
From: Richard Smith [mailto:[hidden email]]
Sent: Tuesday, July 13, 2010 11:58 AM
To: Vallejos, Andrew
Cc: [hidden email]
Subject: Re: [InterMine Dev] bioseg installation

I just installed Bioseg on Tiger (10.5.8) and it worked first time.

I originally installed postgres with this:

        http://www.postgresqlformac.com/


For more recent installations on Snow Leopard I've used this;
       
        http://www.enterprisedb.com/products/pgdownload.do#osx

Which has worked really well.  Is re-installing postgres an option?

I can try also on a Snow Leopard mac soon.

Cheers,
Richard.




Vallejos, Andrew wrote:

> So it seems like my Postgres installation was installed with the
> CPPFLAGS set to 'usr/local/include/', rather than '/usr/include/'.  I
> made a symbolic link so that Postgres now uses the correct directory,
> however I am still getting errors...new errors, but still error.
>
> net-250-50:release-0.8 andrew$ sudo make USE_PGXS=t
> gcc -no-cpp-precomp -isysroot /Developer/SDKs/MacOSX10.4u.sdk
> -mmacosx-version-min=10.4 -headerpad_max_install_names -arch ppc -arch
> i386 -Wall -Wmissing-prototypes -Wpointer-arith
> -Wdeclaration-after-statement -Wendif-labels -fno-strict-aliasing
> -fwrapv  -I. -I. -I/usr/local/PostgreSQL/8.4/include/postgresql/server
> -I/usr/local/PostgreSQL/8.4/include/postgresql/internal
> -I/usr/include/libxml2  -I/usr/local/include/libxml2
> -I/usr/local/include  -c -o bioseg.o bioseg.c
>
> ## Error Message Follows ##
> In file included from
> /usr/local/PostgreSQL/8.4/include/postgresql/server/c.h:71,
>                  from
> /usr/local/PostgreSQL/8.4/include/postgresql/server/postgres.h:47,
>                  from bioseg.c:13:
> /usr/local/include/stdarg.h:4:25: error: no include path in which to
> search for stdarg.h
> In file included from
>
/usr/local/PostgreSQL/8.4/include/postgresql/server/utils/timestamp.h:18

> ,
>                  from
> /usr/local/PostgreSQL/8.4/include/postgresql/server/access/xlog.h:19,
>                  from
> /usr/local/PostgreSQL/8.4/include/postgresql/server/access/gist.h:19,
>                  from bioseg.c:19:
> /usr/local/include/float.h:8:24: error: no include path in which to
> search for float.h
> In file included from
> /usr/local/PostgreSQL/8.4/include/postgresql/server/c.h:71,
>                  from
> /usr/local/PostgreSQL/8.4/include/postgresql/server/postgres.h:47,
>                  from bioseg.c:13:
> /usr/local/include/stdarg.h:4:25: error: no include path in which to
> search for stdarg.h
> In file included from
>
/usr/local/PostgreSQL/8.4/include/postgresql/server/utils/timestamp.h:18
> ,
>                  from
> /usr/local/PostgreSQL/8.4/include/postgresql/server/access/xlog.h:19,
>                  from
> /usr/local/PostgreSQL/8.4/include/postgresql/server/access/gist.h:19,
>                  from bioseg.c:19:
> /usr/local/include/float.h:8:24: error: no include path in which to
> search for float.h
> lipo: can't figure out the architecture type of:
/var/tmp//ccZjtEJB.out

>
>
>
> -----Original Message-----
> From: Vallejos, Andrew
> Sent: Monday, July 12, 2010 1:35 PM
> To: 'Richard Smith'
> Subject: RE: [InterMine Dev] bioseg installation
>
> That does seem to be a key compenent.  Although, I am not sure why the
> complier cannot find those libraries.  I uninstalled and reinstalled
the
> OS X developer tools, just to make sure everything was installed
> correctly.  And I do have all the libraries installed in
/usr/include/.

>
> I wrote a simple Hello World GCC file with #include <stdio.h> at the
> top.  The "program" compiles and executes perfectly.
>
> -Andrew
>
> -----Original Message-----
> From: Richard Smith [mailto:[hidden email]]
> Sent: Monday, July 12, 2010 10:58 AM
> To: Vallejos, Andrew
> Cc: [hidden email]
> Subject: Re: [InterMine Dev] bioseg installation
>
> Hi Andrew,
> Matthew points out that the error trace says gcc can't find stdio.h
> which means it is failing to compile the bioseg C code.
>
> I'm not sure we've ever installed BioSeg on a mac - I'll have a go
> on mine and let you know how I get on.  For most development work
> you shouldn't need BioSeg.
>
> Cheers,
> Richard.
>
>
>
> Vallejos, Andrew wrote:
>> I cannot get BioSeg to install on my Mac.  I have a full installation
> of
>> postgres and I have updated the configuration file with the
> suggestions
>> found on Intermine.org.
>>
>>  
>>
>> Thanks,
>>
>>  
>>
>> Andrew
>>
>>  
>>
>> ======================
>>
>> Andrew Vallejos
>>
>> Web Developer II
>>
>> Biotechnology and Bioengineering Center
>>
>> Medical College of Wisconsin
>>
>> 414-955-4104
>>
>> [hidden email]
>>
>>  
>>
>>
>>
>>
>
------------------------------------------------------------------------
>> This body part will be downloaded on demand.
>
>


_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
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Re: bioseg installation

Richard Smith
I just tried this on my Snow Leopard (10.6.3) laptop with postgres 8.4.1
and it also worked fine.  I installed this with the enterprisedb
installer.  Maybe it has broken in more recent versions?


Cheers,
Richard.


On 13/07/2010 17:59, Vallejos, Andrew wrote:

> Definitely, I've reinstalled it a couple times already. :-)
>
> I also use the one click installer.  The problem, in at least what I
> see, is that postgres was compiled with '-I/usr/local/include', but my
> gcc libraries are installed to '-I/usr/include'.
>
> -----Original Message-----
> From: Richard Smith [mailto:[hidden email]]
> Sent: Tuesday, July 13, 2010 11:58 AM
> To: Vallejos, Andrew
> Cc: [hidden email]
> Subject: Re: [InterMine Dev] bioseg installation
>
> I just installed Bioseg on Tiger (10.5.8) and it worked first time.
>
> I originally installed postgres with this:
>
> http://www.postgresqlformac.com/
>
>
> For more recent installations on Snow Leopard I've used this;
>
> http://www.enterprisedb.com/products/pgdownload.do#osx
>
> Which has worked really well.  Is re-installing postgres an option?
>
> I can try also on a Snow Leopard mac soon.
>
> Cheers,
> Richard.
>
>
>
>
> Vallejos, Andrew wrote:
>> So it seems like my Postgres installation was installed with the
>> CPPFLAGS set to 'usr/local/include/', rather than '/usr/include/'.  I
>> made a symbolic link so that Postgres now uses the correct directory,
>> however I am still getting errors...new errors, but still error.
>>
>> net-250-50:release-0.8 andrew$ sudo make USE_PGXS=t
>> gcc -no-cpp-precomp -isysroot /Developer/SDKs/MacOSX10.4u.sdk
>> -mmacosx-version-min=10.4 -headerpad_max_install_names -arch ppc -arch
>> i386 -Wall -Wmissing-prototypes -Wpointer-arith
>> -Wdeclaration-after-statement -Wendif-labels -fno-strict-aliasing
>> -fwrapv  -I. -I. -I/usr/local/PostgreSQL/8.4/include/postgresql/server
>> -I/usr/local/PostgreSQL/8.4/include/postgresql/internal
>> -I/usr/include/libxml2  -I/usr/local/include/libxml2
>> -I/usr/local/include  -c -o bioseg.o bioseg.c
>>
>> ## Error Message Follows ##
>> In file included from
>> /usr/local/PostgreSQL/8.4/include/postgresql/server/c.h:71,
>>                   from
>> /usr/local/PostgreSQL/8.4/include/postgresql/server/postgres.h:47,
>>                   from bioseg.c:13:
>> /usr/local/include/stdarg.h:4:25: error: no include path in which to
>> search for stdarg.h
>> In file included from
>>
> /usr/local/PostgreSQL/8.4/include/postgresql/server/utils/timestamp.h:18
>> ,
>>                   from
>> /usr/local/PostgreSQL/8.4/include/postgresql/server/access/xlog.h:19,
>>                   from
>> /usr/local/PostgreSQL/8.4/include/postgresql/server/access/gist.h:19,
>>                   from bioseg.c:19:
>> /usr/local/include/float.h:8:24: error: no include path in which to
>> search for float.h
>> In file included from
>> /usr/local/PostgreSQL/8.4/include/postgresql/server/c.h:71,
>>                   from
>> /usr/local/PostgreSQL/8.4/include/postgresql/server/postgres.h:47,
>>                   from bioseg.c:13:
>> /usr/local/include/stdarg.h:4:25: error: no include path in which to
>> search for stdarg.h
>> In file included from
>>
> /usr/local/PostgreSQL/8.4/include/postgresql/server/utils/timestamp.h:18
>> ,
>>                   from
>> /usr/local/PostgreSQL/8.4/include/postgresql/server/access/xlog.h:19,
>>                   from
>> /usr/local/PostgreSQL/8.4/include/postgresql/server/access/gist.h:19,
>>                   from bioseg.c:19:
>> /usr/local/include/float.h:8:24: error: no include path in which to
>> search for float.h
>> lipo: can't figure out the architecture type of:
> /var/tmp//ccZjtEJB.out
>>
>>
>>
>> -----Original Message-----
>> From: Vallejos, Andrew
>> Sent: Monday, July 12, 2010 1:35 PM
>> To: 'Richard Smith'
>> Subject: RE: [InterMine Dev] bioseg installation
>>
>> That does seem to be a key compenent.  Although, I am not sure why the
>> complier cannot find those libraries.  I uninstalled and reinstalled
> the
>> OS X developer tools, just to make sure everything was installed
>> correctly.  And I do have all the libraries installed in
> /usr/include/.
>>
>> I wrote a simple Hello World GCC file with #include<stdio.h>  at the
>> top.  The "program" compiles and executes perfectly.
>>
>> -Andrew
>>
>> -----Original Message-----
>> From: Richard Smith [mailto:[hidden email]]
>> Sent: Monday, July 12, 2010 10:58 AM
>> To: Vallejos, Andrew
>> Cc: [hidden email]
>> Subject: Re: [InterMine Dev] bioseg installation
>>
>> Hi Andrew,
>> Matthew points out that the error trace says gcc can't find stdio.h
>> which means it is failing to compile the bioseg C code.
>>
>> I'm not sure we've ever installed BioSeg on a mac - I'll have a go
>> on mine and let you know how I get on.  For most development work
>> you shouldn't need BioSeg.
>>
>> Cheers,
>> Richard.
>>
>>
>>
>> Vallejos, Andrew wrote:
>>> I cannot get BioSeg to install on my Mac.  I have a full installation
>> of
>>> postgres and I have updated the configuration file with the
>> suggestions
>>> found on Intermine.org.
>>>
>>>
>>>
>>> Thanks,
>>>
>>>
>>>
>>> Andrew
>>>
>>>
>>>
>>> ======================
>>>
>>> Andrew Vallejos
>>>
>>> Web Developer II
>>>
>>> Biotechnology and Bioengineering Center
>>>
>>> Medical College of Wisconsin
>>>
>>> 414-955-4104
>>>
>>> [hidden email]
>>>
>>>
>>>
>>>
>>>
>>>
>>
> ------------------------------------------------------------------------
>>> This body part will be downloaded on demand.
>>
>>
>
>


_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
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Re: bioseg installation

Vallejos, Andrew
RE: [InterMine Dev] bioseg installation

Perhaps...I am trying with Postgres 8.4.4, I don't remember having any trouble with bioseg in earlier versions.


-----Original Message-----
From: Richard Smith [[hidden email]]
Sent: Wed 7/14/2010 1:33 AM
To: Vallejos, Andrew
Cc: [hidden email]
Subject: Re: [InterMine Dev] bioseg installation

I just tried this on my Snow Leopard (10.6.3) laptop with postgres 8.4.1
and it also worked fine.  I installed this with the enterprisedb
installer.  Maybe it has broken in more recent versions?


Cheers,
Richard.


On 13/07/2010 17:59, Vallejos, Andrew wrote:
> Definitely, I've reinstalled it a couple times already. :-)
>
> I also use the one click installer.  The problem, in at least what I
> see, is that postgres was compiled with '-I/usr/local/include', but my
> gcc libraries are installed to '-I/usr/include'.
>
> -----Original Message-----
> From: Richard Smith [[hidden email]]
> Sent: Tuesday, July 13, 2010 11:58 AM
> To: Vallejos, Andrew
> Cc: [hidden email]
> Subject: Re: [InterMine Dev] bioseg installation
>
> I just installed Bioseg on Tiger (10.5.8) and it worked first time.
>
> I originally installed postgres with this:
>
>       http://www.postgresqlformac.com/
>
>
> For more recent installations on Snow Leopard I've used this;
>      
>       http://www.enterprisedb.com/products/pgdownload.do#osx
>
> Which has worked really well.  Is re-installing postgres an option?
>
> I can try also on a Snow Leopard mac soon.
>
> Cheers,
> Richard.
>
>
>
>
> Vallejos, Andrew wrote:
>> So it seems like my Postgres installation was installed with the
>> CPPFLAGS set to 'usr/local/include/', rather than '/usr/include/'.  I
>> made a symbolic link so that Postgres now uses the correct directory,
>> however I am still getting errors...new errors, but still error.
>>
>> net-250-50:release-0.8 andrew$ sudo make USE_PGXS=t
>> gcc -no-cpp-precomp -isysroot /Developer/SDKs/MacOSX10.4u.sdk
>> -mmacosx-version-min=10.4 -headerpad_max_install_names -arch ppc -arch
>> i386 -Wall -Wmissing-prototypes -Wpointer-arith
>> -Wdeclaration-after-statement -Wendif-labels -fno-strict-aliasing
>> -fwrapv  -I. -I. -I/usr/local/PostgreSQL/8.4/include/postgresql/server
>> -I/usr/local/PostgreSQL/8.4/include/postgresql/internal
>> -I/usr/include/libxml2  -I/usr/local/include/libxml2
>> -I/usr/local/include  -c -o bioseg.o bioseg.c
>>
>> ## Error Message Follows ##
>> In file included from
>> /usr/local/PostgreSQL/8.4/include/postgresql/server/c.h:71,
>>                   from
>> /usr/local/PostgreSQL/8.4/include/postgresql/server/postgres.h:47,
>>                   from bioseg.c:13:
>> /usr/local/include/stdarg.h:4:25: error: no include path in which to
>> search for stdarg.h
>> In file included from
>>
> /usr/local/PostgreSQL/8.4/include/postgresql/server/utils/timestamp.h:18
>> ,
>>                   from
>> /usr/local/PostgreSQL/8.4/include/postgresql/server/access/xlog.h:19,
>>                   from
>> /usr/local/PostgreSQL/8.4/include/postgresql/server/access/gist.h:19,
>>                   from bioseg.c:19:
>> /usr/local/include/float.h:8:24: error: no include path in which to
>> search for float.h
>> In file included from
>> /usr/local/PostgreSQL/8.4/include/postgresql/server/c.h:71,
>>                   from
>> /usr/local/PostgreSQL/8.4/include/postgresql/server/postgres.h:47,
>>                   from bioseg.c:13:
>> /usr/local/include/stdarg.h:4:25: error: no include path in which to
>> search for stdarg.h
>> In file included from
>>
> /usr/local/PostgreSQL/8.4/include/postgresql/server/utils/timestamp.h:18
>> ,
>>                   from
>> /usr/local/PostgreSQL/8.4/include/postgresql/server/access/xlog.h:19,
>>                   from
>> /usr/local/PostgreSQL/8.4/include/postgresql/server/access/gist.h:19,
>>                   from bioseg.c:19:
>> /usr/local/include/float.h:8:24: error: no include path in which to
>> search for float.h
>> lipo: can't figure out the architecture type of:
> /var/tmp//ccZjtEJB.out
>>
>>
>>
>> -----Original Message-----
>> From: Vallejos, Andrew
>> Sent: Monday, July 12, 2010 1:35 PM
>> To: 'Richard Smith'
>> Subject: RE: [InterMine Dev] bioseg installation
>>
>> That does seem to be a key compenent.  Although, I am not sure why the
>> complier cannot find those libraries.  I uninstalled and reinstalled
> the
>> OS X developer tools, just to make sure everything was installed
>> correctly.  And I do have all the libraries installed in
> /usr/include/.
>>
>> I wrote a simple Hello World GCC file with #include<stdio.h>  at the
>> top.  The "program" compiles and executes perfectly.
>>
>> -Andrew
>>
>> -----Original Message-----
>> From: Richard Smith [[hidden email]]
>> Sent: Monday, July 12, 2010 10:58 AM
>> To: Vallejos, Andrew
>> Cc: [hidden email]
>> Subject: Re: [InterMine Dev] bioseg installation
>>
>> Hi Andrew,
>> Matthew points out that the error trace says gcc can't find stdio.h
>> which means it is failing to compile the bioseg C code.
>>
>> I'm not sure we've ever installed BioSeg on a mac - I'll have a go
>> on mine and let you know how I get on.  For most development work
>> you shouldn't need BioSeg.
>>
>> Cheers,
>> Richard.
>>
>>
>>
>> Vallejos, Andrew wrote:
>>> I cannot get BioSeg to install on my Mac.  I have a full installation
>> of
>>> postgres and I have updated the configuration file with the
>> suggestions
>>> found on Intermine.org.
>>>
>>>
>>>
>>> Thanks,
>>>
>>>
>>>
>>> Andrew
>>>
>>>
>>>
>>> ======================
>>>
>>> Andrew Vallejos
>>>
>>> Web Developer II
>>>
>>> Biotechnology and Bioengineering Center
>>>
>>> Medical College of Wisconsin
>>>
>>> 414-955-4104
>>>
>>> [hidden email]
>>>
>>>
>>>
>>>
>>>
>>>
>>
> ------------------------------------------------------------------------
>>> This body part will be downloaded on demand.
>>
>>
>
>



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Re: bioseg installation

Richard Smith
Do you need Bioseg on the mac?  Without it you can run all other
postprocess steps quite happily, you can ignore any warnings in the log.

You only need to install Bioseg if you actually want to query overlaps.

Richard.



Vallejos, Andrew wrote:

> Perhaps...I am trying with Postgres 8.4.4, I don't remember having any trouble with bioseg in earlier versions.
>
>
> -----Original Message-----
> From: Richard Smith [mailto:[hidden email]]
> Sent: Wed 7/14/2010 1:33 AM
> To: Vallejos, Andrew
> Cc: [hidden email]
> Subject: Re: [InterMine Dev] bioseg installation
>  
> I just tried this on my Snow Leopard (10.6.3) laptop with postgres 8.4.1
> and it also worked fine.  I installed this with the enterprisedb
> installer.  Maybe it has broken in more recent versions?
>
>
> Cheers,
> Richard.
>
>
> On 13/07/2010 17:59, Vallejos, Andrew wrote:
>> Definitely, I've reinstalled it a couple times already. :-)
>>
>> I also use the one click installer.  The problem, in at least what I
>> see, is that postgres was compiled with '-I/usr/local/include', but my
>> gcc libraries are installed to '-I/usr/include'.
>>
>> -----Original Message-----
>> From: Richard Smith [mailto:[hidden email]]
>> Sent: Tuesday, July 13, 2010 11:58 AM
>> To: Vallejos, Andrew
>> Cc: [hidden email]
>> Subject: Re: [InterMine Dev] bioseg installation
>>
>> I just installed Bioseg on Tiger (10.5.8) and it worked first time.
>>
>> I originally installed postgres with this:
>>
>> http://www.postgresqlformac.com/
>>
>>
>> For more recent installations on Snow Leopard I've used this;
>>
>> http://www.enterprisedb.com/products/pgdownload.do#osx
>>
>> Which has worked really well.  Is re-installing postgres an option?
>>
>> I can try also on a Snow Leopard mac soon.
>>
>> Cheers,
>> Richard.
>>
>>
>>
>>
>> Vallejos, Andrew wrote:
>>> So it seems like my Postgres installation was installed with the
>>> CPPFLAGS set to 'usr/local/include/', rather than '/usr/include/'.  I
>>> made a symbolic link so that Postgres now uses the correct directory,
>>> however I am still getting errors...new errors, but still error.
>>>
>>> net-250-50:release-0.8 andrew$ sudo make USE_PGXS=t
>>> gcc -no-cpp-precomp -isysroot /Developer/SDKs/MacOSX10.4u.sdk
>>> -mmacosx-version-min=10.4 -headerpad_max_install_names -arch ppc -arch
>>> i386 -Wall -Wmissing-prototypes -Wpointer-arith
>>> -Wdeclaration-after-statement -Wendif-labels -fno-strict-aliasing
>>> -fwrapv  -I. -I. -I/usr/local/PostgreSQL/8.4/include/postgresql/server
>>> -I/usr/local/PostgreSQL/8.4/include/postgresql/internal
>>> -I/usr/include/libxml2  -I/usr/local/include/libxml2
>>> -I/usr/local/include  -c -o bioseg.o bioseg.c
>>>
>>> ## Error Message Follows ##
>>> In file included from
>>> /usr/local/PostgreSQL/8.4/include/postgresql/server/c.h:71,
>>>                   from
>>> /usr/local/PostgreSQL/8.4/include/postgresql/server/postgres.h:47,
>>>                   from bioseg.c:13:
>>> /usr/local/include/stdarg.h:4:25: error: no include path in which to
>>> search for stdarg.h
>>> In file included from
>>>
>> /usr/local/PostgreSQL/8.4/include/postgresql/server/utils/timestamp.h:18
>>> ,
>>>                   from
>>> /usr/local/PostgreSQL/8.4/include/postgresql/server/access/xlog.h:19,
>>>                   from
>>> /usr/local/PostgreSQL/8.4/include/postgresql/server/access/gist.h:19,
>>>                   from bioseg.c:19:
>>> /usr/local/include/float.h:8:24: error: no include path in which to
>>> search for float.h
>>> In file included from
>>> /usr/local/PostgreSQL/8.4/include/postgresql/server/c.h:71,
>>>                   from
>>> /usr/local/PostgreSQL/8.4/include/postgresql/server/postgres.h:47,
>>>                   from bioseg.c:13:
>>> /usr/local/include/stdarg.h:4:25: error: no include path in which to
>>> search for stdarg.h
>>> In file included from
>>>
>> /usr/local/PostgreSQL/8.4/include/postgresql/server/utils/timestamp.h:18
>>> ,
>>>                   from
>>> /usr/local/PostgreSQL/8.4/include/postgresql/server/access/xlog.h:19,
>>>                   from
>>> /usr/local/PostgreSQL/8.4/include/postgresql/server/access/gist.h:19,
>>>                   from bioseg.c:19:
>>> /usr/local/include/float.h:8:24: error: no include path in which to
>>> search for float.h
>>> lipo: can't figure out the architecture type of:
>> /var/tmp//ccZjtEJB.out
>>>
>>>
>>> -----Original Message-----
>>> From: Vallejos, Andrew
>>> Sent: Monday, July 12, 2010 1:35 PM
>>> To: 'Richard Smith'
>>> Subject: RE: [InterMine Dev] bioseg installation
>>>
>>> That does seem to be a key compenent.  Although, I am not sure why the
>>> complier cannot find those libraries.  I uninstalled and reinstalled
>> the
>>> OS X developer tools, just to make sure everything was installed
>>> correctly.  And I do have all the libraries installed in
>> /usr/include/.
>>> I wrote a simple Hello World GCC file with #include<stdio.h>  at the
>>> top.  The "program" compiles and executes perfectly.
>>>
>>> -Andrew
>>>
>>> -----Original Message-----
>>> From: Richard Smith [mailto:[hidden email]]
>>> Sent: Monday, July 12, 2010 10:58 AM
>>> To: Vallejos, Andrew
>>> Cc: [hidden email]
>>> Subject: Re: [InterMine Dev] bioseg installation
>>>
>>> Hi Andrew,
>>> Matthew points out that the error trace says gcc can't find stdio.h
>>> which means it is failing to compile the bioseg C code.
>>>
>>> I'm not sure we've ever installed BioSeg on a mac - I'll have a go
>>> on mine and let you know how I get on.  For most development work
>>> you shouldn't need BioSeg.
>>>
>>> Cheers,
>>> Richard.
>>>
>>>
>>>
>>> Vallejos, Andrew wrote:
>>>> I cannot get BioSeg to install on my Mac.  I have a full installation
>>> of
>>>> postgres and I have updated the configuration file with the
>>> suggestions
>>>> found on Intermine.org.
>>>>
>>>>
>>>>
>>>> Thanks,
>>>>
>>>>
>>>>
>>>> Andrew
>>>>
>>>>
>>>>
>>>> ======================
>>>>
>>>> Andrew Vallejos
>>>>
>>>> Web Developer II
>>>>
>>>> Biotechnology and Bioengineering Center
>>>>
>>>> Medical College of Wisconsin
>>>>
>>>> 414-955-4104
>>>>
>>>> [hidden email]
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>> ------------------------------------------------------------------------
>>>> This body part will be downloaded on demand.
>>>
>>
>
>
>


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