can't build Bio-BigFile about kent

[maximilianh]

I haven't redirected the issue, I just CC'ed someone over there. I don't know how the other project works, so the best way forward would be if you open a ticket over there.

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On Mon, Jan 18, 2021 at 1:59 PM hkmztrk ***@***.***> wrote: Thanks a lot for your fast response @maximilianh <https://github.com/maximilianh>! Yes, I tried make clean && make afterwards but somehow it has no effect. Thanks for redirecting the issue. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#51 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AACL4TPK65PU5GOISE2QNFTS2QWEBANCNFSM4WHFIN2A> .

[maximilianh]

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

[hkmztrk]

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.

[braneyboo]

Hey @hkmztrk, what do you mean by "nothing works" or "somehow it has no effect". Are you able to recompile the library with -fPIC ?

[hkmztrk]

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

[braneyboo]

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.

[hkmztrk]

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?

[braneyboo]

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"