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
--
http://fam-tille.de
