Re: Packaging BLAT for Debian
Hi again,
after droping the -O2 compiler option I was able to run
$ cd blat/test ; make
blat -verbose=0 throwback/target1.fa throwback/query1.fa throwback/test.psl
Loaded 129433 letters in 1 sequences
Searched 2050 bases in 1 sequences
pslCheck -verbose=0 throwback/test.psl
blat -verbose=0 v29skips/ex1_database.fa v29skips/ex1_query.fa v29skips/ex1.psl
Loaded 4481 letters in 1 sequences
Searched 4484 bases in 1 sequences
diff v29skips/ex1_reference.psl v29skips/ex1.psl
blat -verbose=0 v29skips/ex2_database.fa v29skips/ex2_query.fa v29skips/ex2.psl
Loaded 4186 letters in 1 sequences
Searched 4185 bases in 1 sequences
diff v29skips/ex2_reference.psl v29skips/ex2.psl
mkdir -p intron50k/out
blat -verbose=0 intron50k/target.fa intron50k/query.fa intron50k/out/test1.psl -minScore=190
Loaded 100000 letters in 1 sequences
Searched 600 bases in 1 sequences
diff intron50k/expected/test1.psl intron50k/out/test1.psl
blat -verbose=0 intron50k/target.fa intron50k/query.fa intron50k/out/test2.psl -minScore=190 -maxIntron=40000
Loaded 100000 letters in 1 sequences
Searched 600 bases in 1 sequences
diff intron50k/expected/test2.psl intron50k/out/test2.psl
blat -verbose=0 intron50k/target.fa intron50k/query.fa intron50k/out/test3.psl -minScore=190 -maxIntron=5000
Loaded 100000 letters in 1 sequences
Searched 600 bases in 1 sequences
diff intron50k/expected/test3.psl intron50k/out/test3.psl
rm -rf intron50k/out
So probably -O2 is causing the trouble I faced running the test.
Now since I figured out this I need to decide how I reaonably get
pslCheck included as source to be able to run the full test. I realised
that several other parts of jksrc are involved. Any hint?
Kind regards
Andreas.
On Wed, Feb 26, 2014 at 10:14:01AM +0100, Andreas Tille wrote:
> Hi Jim,
>
> On Wed, Feb 26, 2014 at 12:40:56AM -0800, Jim Kent wrote:
> > No problem about the users not necessarily respecting the license. We
> > already have the source code up on the net with no protection. We rely on
> > the honor system, and the business remains good enough at least to pay the
> > mortgage.
>
> :-)
>
> > I think there may be a problem with your build. I've got a _little_ time
> > to help you with this, but if I get too busy to answer all your email
> > please don't take it personally.
>
> I'm far away from taking this personally. Considering your past response
> time I'm pretty sure that you might have more urgent things to do if we
> need to wait a bit longer.
>
> > Here's the output I get from the make
> > test in our main source tree.
> >
> > blat -verbose=0 hCrea.geno hCrea.mrna testRna.psl
> > ...
> > diff intron50k/expected/test3.psl intron50k/out/test3.psl
> >
> > rm -rf intron50k/out
> >
> > make[1]: Leaving directory `/cluster/home/kent/kent/src/blat/test'
>
> This looks like a perfect test result and we definitely need to reach
> this state with the Debian package before this will be published. The
> only vague idea I have is that some compiler options might lead to the
> wrong result. I attached a build log for blat and I wonder whether you
> might like to have a short look whether some of the options might look
> suspiciouos to you. This could give some hint where to switch the lever
> next time.
>
> Thanks a lot for your kind cooperation
>
> Andreas.
>
> --
> http://fam-tille.de
--
http://fam-tille.de
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