Comments (8)
from kent.
Hi @hkmztrk, after some googling I found that you're using a Gbrowse adaptor for bigWig files that uses the public domain part of our source code. Your approach of adding CFLAGS=-fPIC sounds good to me (I imagine you did a "make clean" after this?) but how Gbrowse integrates our code is outside our domain of expertise. It sounds like you should contact the Gbrowse adapter maintainers for some ideas GMOD/GBrowse-Adaptors#19 I've CCed one of them here, but your problem should rather be handled in their issue tracker. We can also make small changes to makefile to make integrating our code easier @keiranmraine
from kent.
Thanks a lot for your fast response @maximilianh! Yes, I tried make clean && make
afterwards but somehow it has no effect. Thanks for redirecting the issue.
from kent.
Hey @hkmztrk, what do you mean by "nothing works" or "somehow it has no effect". Are you able to recompile the library with -fPIC ?
from kent.
Hi @braneyboo,
After updating this line CFLAGS
to CFLAGS=-fPIC
in kent/src/inc/common.mk
I run make clean && make
in kent/src/lib
. make command works fine. But when I go back to run ./Build
in Bio-BigFile-1.07 these changes have no effect and I receive the same error.
I also tested what's suggested here: http://seqanswers.com/forums/archive/index.php/t-70219.html
run make in Kent folders with following:
make CXXFLAGS=-fPIC CFLAGS=-fPIC CPPFLAGS=-fPIC
After this I'm finally passed ./Build
in Bio-BigFile-1.07 but this time ./Build test
fails,
Test Summary Report
-------------------
t/01.bigwig.t (Wstat: 512 Tests: 0 Failed: 0)
Non-zero exit status: 2
Parse errors: Bad plan. You planned 29 tests but ran 0.
t/02.bigbed.t (Wstat: 512 Tests: 0 Failed: 0)
Non-zero exit status: 2
Parse errors: Bad plan. You planned 15 tests but ran 0.
t/03.bigwig_high.t (Wstat: 512 Tests: 0 Failed: 0)
Non-zero exit status: 2
Parse errors: Bad plan. You planned 32 tests but ran 0.
t/04.bigbed_high.t (Wstat: 512 Tests: 0 Failed: 0)
Non-zero exit status: 2
Parse errors: Bad plan. You planned 35 tests but ran 0.
t/05.bigwig_set.t (Wstat: 512 Tests: 0 Failed: 0)
Non-zero exit status: 2
Parse errors: No plan found in TAP output
Files=5, Tests=0, 2 wallclock secs ( 0.07 usr 0.03 sys + 1.39 cusr 0.41 csys = 1.90 CPU)
Result: FAIL
Failed 5/5 test programs. 0/0 subtests failed.
I opened an issue here GMOD/GBrowse-Adaptors#22
from kent.
Yeah, this looks like something that they'll have to help you with. I'm going to close this, but do get back to us if it looks like something going haywire with our code.
from kent.
One final question @braneyboo, @maximilianh:
Make the directory ~/bin/$MACHTYPE which is
where the (non-web) executables will go.
Add this directory to your path to access the built binaries.
I realise that my ~/bin/$MACHTYPE
(~/bin/x86_64) is empty. Does this mean I somehow failed compiling Kent?
from kent.
From what you've said so far, @hkmztrk , it looks like you're only using the kent libraries. If those were missing, your compile/link would have failed, so I don't think that's your problem.
I don't know anything about GBrowse, but this error message seems to imply that some configuration file is missing.
"Parse errors: Bad plan"
from kent.
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from kent.