Thanks for your quick response, Galt.
I changed 'X*Y' to '(X*Y)', exported what worked in the past -
export MACHTYPE=x86_64
export MYSQLINC=-I/usr/include/mysql
export MYSQLLIBS='-L/usr/lib64/mysql -lmysqlclient -lz -lcrypt -lnsl -lm
-L/usr/lib64 -lssl -lcrypto'
...and ran 'make' from the src/utils folder. Many (!) tools compiled. The
following error was reported, probably because I've not done all earlier steps
correctly -
make[1]: *** No rule to make target `../../lib/x86_64/jkhgap.a', needed by
`raSqlQuery'. Stop.
make[1]: Leaving directory
`/home/grobertson/linux_x86_64/KentSourceTree/kent/src/utils/raSqlQuery'
make: *** [all] Error 2
Could you clarify this error? I'd compiled lib -
{xhost06}~/linux_x86_64/KentSourceTree/kent/src> make lib
make: Nothing to be done for `lib'.
...but jkjgap.a is not in this folder -
{xhost06}~/linux_x86_64/KentSourceTree/kent/src/lib/x86_64> ll
total 6284
-rw-rw-r-- 1 grobertson users 893 Jan 30 18:24 jkOwnLib.a
-rw-rw-r-- 1 grobertson users 5370 Jan 30 18:24 jkweb.a
-rwxrwxr-x 1 grobertson users 0 Dec 1 2006 placeHolder.c
---
I now have bedToBigBed, which was the original goal -
{xhost06}~/linux_x86_64/KentSourceTree/kent/src/utils/bedToBigBed> bedToBigBed
./test.bed ./chrom.sizes ./out.bb
pass1 - making usageList (3 chroms): 21 millis
pass2 - checking and writing primary data (12 records, 4 fields): 1 millis
index write: 0 millis
pass3 - writeReducedOnceReturnReducedTwice: 1 millis
further reductions: 0 millis
Thanks again.
G
On 2010-02-01, at 12:00 PM, [email protected] wrote:
>
> Message: 4
> Date: Mon, 01 Feb 2010 11:20:38 -0800
> From: Galt Barber <[email protected]>
> Subject: Re: [Genome] can't compile bedToBigBed on RHELinux 4.x?
> To: Gordon Robertson <[email protected]>
> Cc: [email protected]
> Message-ID: <[email protected]>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi, Gordon!
>
> Looks like you are using gcc 3.4
> and we are using gcc 4.1.2 on 64-bit linux.
>
> Either the gcc3.4 is more sensitive
> and gcc4 has a bug in not showing the
> warning; or, perhaps the gcc developers
> decided that this shouldn't be a warning after all.
>
> In any case, simply adding parentheses around the
> argument made both compilers happy.
>
> bits64 is definted as unsigned long long.
>
> In effect we had this:
>
> printf("%llu", (bits64)X*Y);
>
> and both versions of gcc are happy when we changed it to
>
> printf("%llu", (bits64)(X*Y));
>
> This change has been commmitted.
> You can either update this file from CVS
> or else you can just add the parentheses yourself.
>
> -Galt
>
> Gordon Robertson wrote:
>> Is there a problem with the current Kent source tree bedToBigBed?
>>
>> I downloaded jksrc.zip tonight to 64-bit Red Hat Enterprise Linux 4.x. I'd
>> been using wigToBigWig for some time on that machine, but wanted to ensure
>> that I was using the latest version. I recompiled it after cd'ing to the
>> src/utils/wigToBigWig folder -
>> {xhost06}~/linux_x86_64/KentSourceTree/kent/src/utils/wigToBigWig> make
>> gcc -O -g -Wall -Werror -Wformat -Wimplicit -Wreturn-type -Wuninitialized
>> -o /home/grobertson/bin/x86_64/wigToBigWig wigToBigWig.o
>> ../../lib/x86_64/jkweb.a -lm -lz
>> {xhost06}~/linux_x86_64/KentSourceTree/kent/src/utils/wigToBigWig>
>> wigToBigWig
>> wigToBigWig v 3 - Convert ascii format wig file (in fixedStep, variableStep
>> or bedGraph format) to binary big wig format.
>> ...
>>
>> I want to start to use bedToBigBed. When I ran make from the src/utils
>> folder, a number of folders were processed (aNotB, addCols, ave, aveCols,
>> bedClip, bedGraphToBigWig) but there was an error message for bedToBigBed -
>>
>> make[1]: Entering directory
>> `/home/grobertson/linux_x86_64/KentSourceTree/kent/src/utils/bedToBigBed'
>> gcc -O -g -Wall -Werror -Wformat -Wimplicit -Wreturn-type -Wuninitialized
>> -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64
>> -Wall -Werror -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc
>> -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o
>> bedToBigBed.o -c bedToBigBed.c
>> bedToBigBed.c: In function `bbFileCreate':
>> bedToBigBed.c:537: warning: long long unsigned int format, long unsigned int
>> arg (arg 4)
>> make[1]: *** [bedToBigBed.o] Error 1
>> make[1]: Leaving directory
>> `/home/grobertson/linux_x86_64/KentSourceTree/kent/src/utils/bedToBigBed'
>> make: *** [all] Error 2
>>
>> If I'm missing something simple I apologize for wasting the list's time.
>>
>> Thanks for your help with this.
>>
>> Gordon
--
Gordon Robertson
BC Cancer Agency Genome Sciences Centre
Vancouver BC Canada
_______________________________________________
Genome maillist - [email protected]
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