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 <andr...@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
