[Debian-med-packaging] Bug#952623: sra-sdk: FTBFS: ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_entropy_init'

Lucas Nussbaum lucas at debian.org
Wed Feb 26 16:10:09 GMT 2020


Source: sra-sdk
Version: 2.9.3+dfsg-1
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):
> gcc -static-libgcc -o /<<PKGBUILDDIR>>/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/bin/rcexplain.2.9.3 -DNDEBUG -m64 -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 -lxml2 -Wl,-Bdynamic -lm -lz -lbz2 -lsz -lmbedx509 -lmbedtls -lmbedcrypto
> 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/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_entropy_init'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_pk_decrypt'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_base64_encode'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_ctr_drbg_random'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_aes_free'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_ctr_drbg_free'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_pk_free'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_md_update'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_md_init'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_aes_init'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_pk_parse_key'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_md_hmac'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_md_setup'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_pk_parse_public_key'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_pk_encrypt'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_aes_setkey_dec'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_pk_init'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_pk_get_len'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_md_hmac_update'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_ctr_drbg_init'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_ctr_drbg_seed'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_x509_crt_parse_path'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_md_free'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_aes_crypt_cbc'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_pk_rsa'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_x509_crt_parse_file'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_md'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_md_finish'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_md_hmac_starts'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_entropy_free'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_pk_parse_keyfile'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_md_info_from_type'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_rsa_rsassa_pkcs1_v15_sign'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_md_get_size'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_md_hmac_finish'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_rsa_rsassa_pkcs1_v15_verify'
> /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `vdb_mbedtls_aes_setkey_enc'
> /usr/bin/ld: /usr/lib/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/sra-sdk_2.9.3+dfsg-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.



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