[Debian-med-packaging] Bug#952627: skesa: FTBFS: ld: /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_entropy_init'

[Lucas Nussbaum]

Source: skesa
Version: 2.3.0-2
Severity: serious
Justification: FTBFS on amd64
Tags: bullseye sid ftbfs
Usertags: ftbfs-20200225 ftbfs-bullseye

Hi,

During a rebuild of all packages in sid, your package failed to build on
amd64.

This rebuild was done by building only architecture:any binary packages
(binary-arch target of debian/rules).

Relevant part (hopefully):
> c++ -std=c++11 -o skesa skesa.o glb_align.o -L /<<PKGBUILDDIR>>/NGS/vdb_out/lib64 -lncbi-ngs-c++ -lncbi-vdb -L /<<PKGBUILDDIR>>/NGS/ngs_out/lib64 -lngs-c++-static -Wl,-Bstatic  -lboost_program_options -lboost_iostreams -lboost_regex -lboost_timer -lboost_chrono -lboost_system -Wl,-Bdynamic -lrt -ldl -lm  -lpthread -lz -Wl,-z,relro
> /usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_entropy_init'
> /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_base64_encode'
> /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_aes_free'
> /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_free'
> /usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_pk_free'
> /usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_md_update'
> /usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_md_init'
> /usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_aes_init'
> /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_key'
> /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'
> /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_pk_init'
> /usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_pk_get_len'
> /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_init'
> /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_x509_crt_parse_path'
> /usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_md_free'
> /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_pk_rsa'
> /usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_x509_crt_parse_file'
> /usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_md'
> /usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_md_finish'
> /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_entropy_free'
> /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_info_from_type'
> /usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_rsa_rsassa_pkcs1_v15_sign'
> /usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_md_get_size'
> /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_rsa_rsassa_pkcs1_v15_verify'
> /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'
> /usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_md_starts'
> collect2: error: ld returned 1 exit status

The full build log is available from:
   http://qa-logs.debian.net/2020/02/25/skesa_2.3.0-2_unstable.log

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.