Re: undefined vdb_mbed functions in ncbi-vdb2 library - ran out of ideas
Hi Steffen,
On Mon, Mar 02, 2020 at 02:34:03AM +0100, Steffen Möller wrote:
> Hello,
>
> I am attempting to package igblast which I hoped to allow an optional
> dependency on the NCBI vdb library. This fails at config stage because of
> libncbi-vdb2.so* having undefined functions
>
> $ /usr/local/bin/g++ -std=gnu++14 -msse4.2 -o conftest -Wall
> -Wno-format-y2k -pthread -fopenmp -I/usr/include/ncbi-vdb -fPIC -g -O
> -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE
> -I/usr/include/ncbi-vdb -D_MT -D_REENTRANT -D_THREAD_SAFE -I/os/linux
> -I/os/unix -I/cc/gcc/x86_64 -I/cc/gcc -Wl,--enable-new-dtags
> -Wl,-export-dynamic -pthread -fopenmp -lmbedtls -g -O a.cc -ldl -lm
> -lpthread -lncbi-vdb -lxml2 -lmbedtls -lmbedx509 -lmbedcrypto -lz -lnsl
> -lbz2 -lz -ldl
> /usr/bin/ld:
> /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libncbi-vdb.so:
> undefined reference to `vdb_mbedtls_pk_decrypt'
> /usr/bin/ld:
> /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libncbi-vdb.so:
> undefined reference to `vdb_mbedtls_ctr_drbg_random'
> /usr/bin/ld:
> /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libncbi-vdb.so:
> undefined reference to `vdb_mbedtls_md_setup'
> /usr/bin/ld:
> /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libncbi-vdb.so:
> undefined reference to `vdb_mbedtls_pk_parse_public_key'
> /usr/bin/ld:
> /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libncbi-vdb.so:
> undefined reference to `vdb_mbedtls_pk_encrypt'
> /usr/bin/ld:
> /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libncbi-vdb.so:
> undefined reference to `vdb_mbedtls_aes_setkey_dec'
> /usr/bin/ld:
> /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libncbi-vdb.so:
> undefined reference to `vdb_mbedtls_md_hmac_update'
> /usr/bin/ld:
> /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libncbi-vdb.so:
> undefined reference to `vdb_mbedtls_ctr_drbg_seed'
> /usr/bin/ld:
> /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libncbi-vdb.so:
> undefined reference to `vdb_mbedtls_aes_crypt_cbc'
> /usr/bin/ld:
> /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libncbi-vdb.so:
> undefined reference to `vdb_mbedtls_md_hmac_starts'
> /usr/bin/ld:
> /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libncbi-vdb.so:
> undefined reference to `vdb_mbedtls_pk_parse_keyfile'
> /usr/bin/ld:
> /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libncbi-vdb.so:
> undefined reference to `vdb_mbedtls_md_hmac_finish'
> /usr/bin/ld:
> /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libncbi-vdb.so:
> undefined reference to `vdb_mbedtls_aes_setkey_enc'
> collect2: error: ld returned 1 exit status
>
> That is all a bit historic since vdb came with these flavours of the real
> mbedtls and of course Debian uses the real thing. When grepping through the
> source tree, none of these functions are found.
Hmmmm, I'm not sure whether vdb came with the original. I remember I
had to patch some stuff (specifically droping the 'vbd_' prefix). But
I do not remember and I have no spare cycles currently to dive into
this.
> Anyone with an idea where to look?
Contacting upstream?
Kind regards
Andreas.
--
http://fam-tille.de
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