Hi Aaron,
On Thu, Jun 18, 2020 at 08:20:10AM -0400, Aaron M. Ucko wrote:
>
> Yes, that's probably what happened; AFAICT, we have the right thing on
> SALSA and the GH repository simply holds source for Magic-BLAST's
> external documentation https://boratyng.github.io/magicblast .
>
> Thanks for checking!
Thanks for your clarification. Thanks to your explanation I was able
to upate the magicblast repository[1] to the latest upstream version.
Unfortunately I get a linker error:
...
/usr/bin/g++ -std=gnu++11 -c -Wall -Wno-format-y2k -pthread -fopenmp -g
-fdebug-prefix-map=/build/ncbi-magicblast-1.5.0=. -fstack-protector-strong
-Wformat -Werror=format-security - fPIC -DNCBI_MODULE=BLAST -I/os/linux
-I/os/unix -I/cc/gcc/x86_64 -I/cc/gcc -D_DEBUGGING -D_DEBUG
-D_LARGEFILE_SO/usr/bin/ld: warning: size of symbol
`mbedtls_threading_readdir_mutex' changed from 8 in
/build/ncbi-magicblast-1.5.0/c++/GCC900-DebugMT64/lib/libxconnect-static.a(threading.o)
to 48 in /usr/lib/x86_64-linux-gnu/libmbedcrypto.so.3
/usr/bin/ld:
/build/ncbi-magicblast-1.5.0/c++/GCC900-DebugMT64/lib/libxconnect-static.a(threading.o):
undefined reference to symbol 'mbedtls_threading_readdir_mutex'
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/libmbedcrypto.so.3: error adding
symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
...
Symbol mbedtls_threading_readdir_mutex can be found in libmbedcrypto but
the linker flags are missing -lmbedcrypto. Since I know you have some
insight into NCBI's own build system I wonder whether you might manage
to sneak this in. May be its even an issue in libncbi-vdb-dev since I
remember an issue with these symbols when I dealt with libncbi-vdb-dev.
So any help for this packaging that looks promising in principle would
be really welcome.
Kind regards
Andreas.
[1] https://salsa.debian.org/med-team/ncbi-magicblast
--
http://fam-tille.de
