Re: Finishing ncbi-vdb and sra-sdk

[Andreas Tille <andreas@an3as.eu>]

Hi Aaron,

Am Wed, Jul 27, 2022 at 10:29:38PM +0200 schrieb Andreas Tille:
> No real problem - the package will sit in NEW for some time.  I think I
> also stumbled upon the line-ending issue and solved it by excluding
> .gitattributes from upstream source tarball which makes the issue void
> (from my perspective).
> 
> > Does -DVDB_LIBDIR=/usr/lib/${DEB_HOST_MULTIARCH} help?
> 
> I'll check tomorrow.

Thanks for the hint.  This hurdle was taken but the next one is coming up.
  
> > Meanwhile, I'm concerned about how to handle ngs-sdk's incorporation
> > into sra-sdk 3.x, since sra-sdk needs ncbi-vdb libraries but ncbi-vdb at
> > least historically needed to build against ngs-sdk.
> 
> Upstream has not yet tagged any 3.0.0 release - so I simply assumed
> the current version is fine.

May be the issue I'm facing now is connected to this.  The next error
is:

-- Found Python3: /usr/bin/python3.10 (found version "3.10.5") found components: Interpreter.
Using ncbi-vdb interfaces: /usr/include/ncbi-vdb/interfaces
Using ncbi-vdb binary libraries: /usr/lib/x86_64-linux-gnu
-- Could NOT find JNI (missing: JAVA_AWT_LIBRARY JAVA_AWT_INCLUDE_PATH).


(which is probably caused at the end of file
   ngs/ncbi/ngs-jni/CMakeLists.txt )

But maybe that's not really critical but rather the next one:

-- Found Threads: TRUE..
-- Found HDF5: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so;/usr/lib/x86_64-linux-gnu/libcrypto.so;/usr/lib/x86_64-linux-gnu/libcurl.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib
HDF5_INCLUDE_DIRS=/usr/include/hdf5/serial
HDF5_LIBRARIES=/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so/usr/lib/x86_64-linux-gnu/libcrypto.so/usr/lib/x86_64-linux-gnu/libcurl.so/usr/lib/x86_64-linux-gnu/libpthread.so/usr/lib/x86_64-linux-gnu/libsz.so/usr/lib/x86_
CMake Error at /usr/share/cmake-3.23/Modules/ExternalProject.cmake:2540 (message):
  error: could not find git for clone of RE2_
Call Stack (most recent call first):
  /usr/share/cmake-3.23/Modules/ExternalProject.cmake:3640 (_ep_add_download_command)
  test/sharq/CMakeLists.txt:44 (ExternalProject_Add)


-- Configuring incomplete, errors occurred!


It seems the patch I tried[1] is not working as intended. :-(

Kind regards

      Andreas.


[1] https://salsa.debian.org/med-team/sra-sdk/-/blob/master/debian/patches/use_debian_packaged_re2.patch 

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