Very close there.
Please try "make libs" instead of "make lib".
Then you should be able to get raSqlQuery etc to compile.
-Galt
Gordon Robertson wrote:
> 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]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
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https://lists.soe.ucsc.edu/mailman/listinfo/genome
