Re: [Gmod-gbrowse] Bio::DB::BigFile

[Nathaniel S. <nat...@pl...>]

Thanks for the reply. I discovered my problem and, of course, I was being stupid - so here's where I went wrong in case anyone else makes the same mistake.

I compiled the kent source as 'me' i.e. not sudo so MACHTYPE was set only for me. I then ran sudo ./build and of course MACHTYPE was no longer set.

I also found that I had to compile the kent source using 'make CXXFLAGS=-fPIC CFLAGS=-fPIC CPPFLAGS=-fPIC' because otherwise I got an error about shared libraries. 

This was all on Ubuntu (10.1)

Nat

On Sep 29, 2010, at 5:59 PM, Chris Fields wrote:

> Make sure to export MACHTYPE to match whatever you compiled the kent source tree into (generally, something like 'x86', 'x86_64', etc).  See here (under TROUBLESHOOTING).  
> 
> http://cpansearch.perl.org/src/LDS/Bio-BigFile-1.03/README
> 
> In the kent source tree, the instructions for building are in src/product/README.building.source.
> 
> chris
> 
> On Sep 29, 2010, at 2:32 AM, Nathaniel Street wrote:
> 
>> Hi
>> 
>> I'm having problems installing Bio::DB::BigFile. I have downloaded and compiled the kent source as in the instructions. I can see bigWig.h in the src/inc directory and I have jkweb.a in src/lib/i686. When prompted for the kent src location for the BigFile install I enter the path (/home/nat/work/software/kent/src) but get the error 
>> 
>> Can't find the bigWig.h and jkweb.a files at this location.
>> 
>> I've tried other paths e.g. src/lib src/lib/i686 etc but nothing works.
>> 
>> I'm obviously doing somthing stupid but I can't see what it is. Can anyone help?
>> 
>> Thanks
>> 
>> Nathaniel
>> --
>> Nathaniel Street
>> Umeå Plant Science Centre
>> Department of Plant Physiology
>> Umeå University
>> SE901-87 Umeå
>> SWEDEN
>> 
>> email: nat...@pl...
>> skype: nathaniel_street
>> tel: 0046907865473
>> fax:  0046907866676
>> 
>> www.popgenie.org
>> 
>> 
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--
Nathaniel Street
Umeå Plant Science Centre
Department of Plant Physiology
Umeå University
SE901-87 Umeå
SWEDEN

email: nat...@pl...
skype: nathaniel_street
tel: 0046907865473
fax:  0046907866676

www.popgenie.org