Re: Finishing ncbi-vdb and sra-sdk

[Andreas Tille <tille@debian.org>]

Hi Aaron,

thanks a lot for your iterative help which enables taking one hurdle
after the other.  Unfortunately there seem to be many of them. ;-)

Am Thu, Jul 28, 2022 at 11:41:18AM -0400 schrieb Aaron M. Ucko:
> Andreas Tille <andreas@an3as.eu> writes:
> 
> > -- 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 )
> 
> More likely the find_package(Java ...) call on line 159 of
> build/env.cmake.  At any rate, it looks like CMake might want the full
> (non-headless) JDK; I don't see an obvious way around that requirement
> short of setting the relevant variables explicitly, so I'd suggest
> keeping it simple and upgrading the build dependency.

Seems this did the trick.

> >   test/sharq/CMakeLists.txt:44 (ExternalProject_Add)
> >
> > -- Configuring incomplete, errors occurred!
> >
> > It seems the patch I tried[1] is not working as intended. :-(
> 
> Please try patching test/sharq in addition to tools/sharq.

I pushed some change but I have no idea how to finalise this.  With the
latest commit I get:

...
-- 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_
-- Configuring done
CMake Warning (dev) at tools/sharq/CMakeLists.txt:92 (add_executable):
  Policy CMP0115 is not set: Source file extensions must be explicit.  Run
  "cmake --help-policy CMP0115" for policy details.  Use the cmake_policy
  command to set the policy and suppress this warning.

  File:

    /build/sra-sdk-3.0.0+dfsg/tools/sharq/fastq_parse.cpp
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Error at test/sharq/CMakeLists.txt:42 (add_dependencies):
  The dependency target "RE2_" of target "test-sharq-parser" does not exist.


-- Generating done


Any more help would be really appreciated.

Kind regards

     Andreas. 

-- 
http://fam-tille.de