Your message dated Thu, 21 May 2020 02:36:31 +0000 with message-id <e1jbb4r-000bhm...@fasolo.debian.org> and subject line Bug#952623: fixed in ncbi-vdb 2.10.6+dfsg-2 has caused the Debian Bug report #952623, regarding libncbi-vdb2 uses undefined symbols to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 952623: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=952623 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---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.
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--- Begin Message ---Source: ncbi-vdb Source-Version: 2.10.6+dfsg-2 Done: u...@debian.org (Aaron M. Ucko) We believe that the bug you reported is fixed in the latest version of ncbi-vdb, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 952...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Aaron M. Ucko <u...@debian.org> (supplier of updated ncbi-vdb package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Wed, 20 May 2020 22:13:24 -0400 Source: ncbi-vdb Architecture: source Version: 2.10.6+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Aaron M. Ucko <u...@debian.org> Closes: 952623 952627 953897 Changes: ncbi-vdb (2.10.6+dfsg-2) unstable; urgency=medium . * Install libs/vfs/services-priv.h as .../services-priv-internal.h to distinguish it from interfaces/vfs/services-priv.h. (Neither can stand in for the other.) * Formally refresh patches that developed offsets. * Factor out a new DSLMFLAGS macro for common d-shlibmove flags; include the libmbedx509-0 quirk there since it will soon be needed everywhere. * Address remaining underlinkage of system libraries (mbed*, z, bz2). At this point, the only remaining unresolved references are of libkdf5 against symbols that could come from either libncbi-vdb or libncbi-wvdb. (Closes: #952623, #952627, #953897.) * Copy headers rather than moving them to allow for consecutive builds. * Fix typo in override_dh_missing name; supply debian/not-installed. * Add myself to Uploaders. Checksums-Sha1: ed8d69b9c4c30d07c1bb2b7c645dbbc64b5393e7 2671 ncbi-vdb_2.10.6+dfsg-2.dsc 9b364204d73ede879411b6ad48782408ea09a93d 20804 ncbi-vdb_2.10.6+dfsg-2.debian.tar.xz 869fafe96f9a01ae6b5dd20b1f1e1039e2b345c2 11727 ncbi-vdb_2.10.6+dfsg-2_source.buildinfo Checksums-Sha256: 66dbfa5717affc164d86c35edda3ae73b542e18184b40a7a5b3e06aed3ee345c 2671 ncbi-vdb_2.10.6+dfsg-2.dsc 7ff00fdfb0142bf7db2b60dbe26d2663a2bbf428d5a4bd6f19d38e6337d1f38c 20804 ncbi-vdb_2.10.6+dfsg-2.debian.tar.xz 1bad6e0be5e6fa5b14a1e82c8f0c8901b6580bfa191696e62217a8bb8bb6cbd6 11727 ncbi-vdb_2.10.6+dfsg-2_source.buildinfo Files: b175225c15b9ca765d538456401d9140 2671 science optional ncbi-vdb_2.10.6+dfsg-2.dsc 97ac4d8b0012a7cab71a964dd76ca54d 20804 science optional ncbi-vdb_2.10.6+dfsg-2.debian.tar.xz 878bb6cb13000ed7eadd182bc2b0f3a3 11727 science optional ncbi-vdb_2.10.6+dfsg-2_source.buildinfo -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEfDq5z9IwvTDdAJxZHnCRsfFKZKIFAl7F5BcACgkQHnCRsfFK ZKK5DxAAgv+ofQsLx4D/cw/c/vlI2sePh0mzyGFfTsY5g17+o50A5fguV0+4qQqN Z1EE8x/77MUBOtG2G39WAjdsFv1Pk4oZZsaLTit4Iujnxq3LPPUFlQe2KN57mBE/ /YilBlftAtNHcVv4lctqNUjP35dIJmYuRVhIQ76cOY+N9zBbKujLjqfFBGoKl7fa TgoXxmMJSwOaUrk668wtDggNl8LDfwrpFYWSA8QZrM/8aF2f2Gg69lSDQ2mY1ujT K/jVipzgnbAWTjMpRc7U/DdrrtA6jBWBv0iI4c4UAii6JyWsDYxC01W9UWdQ/FBc b75vNqalDMaU7+eh9Qdh673SjnaPAIZx0QF/u+x2C++RtjUOmi5eOD1BnabcQadY h4dJ6+iCvjcFEOao3VmIfxfGm/rEIrNpRsbjDgURp74FrcnmccCuiQwmxK1PfFHy /VTYqEPp/Uwmv1JRY83AULWSI17ZNsaj5bh5RNxxfIVG3GwDMLsvqiItolYdh6sO By2S4pv32ObwU2y+t2GiI7fDNYFDMC4uOKlPf4w+3NV4812M1lu8mTU3J/toZYfF 8FxD4lbjS1Fp1v1LEIO72j6dXYDlBIWw09kLz/lKfZZZo86WBXW7fJibT6h4ky/1 BKMcoiuJrMZ5Mu8w8K24RsEH/PK5QcO3lAHW2oz4LJm5/Mhy4T8= =hf8V -----END PGP SIGNATURE-----
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