[Debian-med-packaging] Bug#844900: sra-sdk: FTBFS: libncbi-vdb.so: undefined reference to `mbedtls_x509_crt_parse_file'

[Lucas Nussbaum]

Source: sra-sdk
Version: 2.7.0-1
Severity: serious
Tags: stretch sid
User: debian-qa at lists.debian.org
Usertags: qa-ftbfs-20161118 qa-ftbfs
Justification: FTBFS on amd64

Hi,

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

Relevant part (hopefully):
> gcc -static-libstdc++ -static-libgcc -o /<<PKGBUILDDIR>>/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/bin/rcexplain.2.7.0 -DNDEBUG -m64 -specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,now rcexplain.o -L/<<PKGBUILDDIR>>/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/lib -L/<<PKGBUILDDIR>>/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/ilib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -lkapp -ltk-version -lncbi-vdb -Wl,-Bdynamic -ldl -lpthread -Wl,-Bdynamic -lm -lz -lbz2 -lsz
> ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
> ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
> ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
> /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `mbedtls_x509_crt_parse_file'
> /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `mbedtls_ctr_drbg_seed'
> /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `mbedtls_ssl_init'
> /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `mbedtls_strerror'
> /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `mbedtls_ssl_set_hostname'
> /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `mbedtls_ssl_config_init'
> /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `mbedtls_ssl_handshake'
> /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `mbedtls_ssl_conf_ca_chain'
> /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `mbedtls_entropy_init'
> /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `mbedtls_x509_crt_init'
> /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `mbedtls_ctr_drbg_init'
> /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `mbedtls_ssl_free'
> /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `mbedtls_ssl_config_free'
> /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `mbedtls_ssl_close_notify'
> /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `mbedtls_ssl_setup'
> /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `mbedtls_ssl_config_defaults'
> /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `mbedtls_ssl_conf_authmode'
> /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `mbedtls_ctr_drbg_random'
> /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `mbedtls_x509_crt_parse'
> /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `mbedtls_ctr_drbg_free'
> /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `mbedtls_ssl_set_bio'
> /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `mbedtls_ssl_get_verify_result'
> /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `mbedtls_entropy_free'
> /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `mbedtls_ssl_read'
> /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `mbedtls_x509_crt_free'
> /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `mbedtls_entropy_func'
> /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `mbedtls_ssl_conf_rng'
> /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `mbedtls_ssl_write'
> /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `mbedtls_x509_crt_verify_info'
> collect2: error: ld returned 1 exit status

The full build log is available from:
   http://aws-logs.debian.net/2016/11/18/sra-sdk_2.7.0-1_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.