Your message dated Tue, 26 Oct 2021 02:24:19 +0000 with message-id <e1mfc8r-0006he...@fasolo.debian.org> and subject line Bug#997280: fixed in sra-sdk 2.11.3+dfsg-1 has caused the Debian Bug report #997280, regarding sra-sdk: FTBFS: ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `ZSTD_freeDCtx' 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.) -- 997280: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=997280 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: sra-sdk Version: 2.10.9+dfsg-2 Severity: serious Justification: FTBFS Tags: bookworm sid ftbfs Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part (hopefully): > g++ -static-libgcc -o > /<<PKGBUILDDIR>>/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/bin/sratools.2.10.9 > -Wl,-z,relro -Wl,-z,now -DNDEBUG -m64 sratools.o sratools2.o > imp_fasterq_dump.o imp_fastq_dump.o imp_prefetch.o imp_sam_dump.o > imp_sra_pileup.o imp_srapath.o imp_vdb_dump.o cmdline.o config.o proc.o > run-source.o uuid.o service.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 -lncbi-vdb -ljson -Wl,-Bdynamic -ldl -lpthread > -lxml2 -Wl,-Bdynamic -lm -lz -lbz2 -lsz -lmbedx509 -lmbedtls -lmbedcrypto > /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to > `ZSTD_freeDCtx' > /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to > `ZSTD_decompressDCtx' > /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to > `ZSTD_createDCtx' > /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to > `ZSTD_isError' > /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to > `ZSTD_getErrorName' > collect2: error: ld returned 1 exit status The full build log is available from: http://qa-logs.debian.net/2021/10/23/sra-sdk_2.10.9+dfsg-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! If you reassign this bug to another package, please marking it as 'affects'-ing this package. See https://www.debian.org/Bugs/server-control#affects If you fail to reproduce this, please provide a build log and diff it with mine so that we can identify if something relevant changed in the meantime.
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--- Begin Message ---Source: sra-sdk Source-Version: 2.11.3+dfsg-1 Done: Aaron M. Ucko <u...@debian.org> We believe that the bug you reported is fixed in the latest version of sra-sdk, 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 997...@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 sra-sdk 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: SHA512 Format: 1.8 Date: Mon, 25 Oct 2021 18:29:10 -0400 Source: sra-sdk Architecture: source Version: 2.11.3+dfsg-1 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: 997280 Changes: sra-sdk (2.11.3+dfsg-1) unstable; urgency=medium . [ Andreas Tille ] * Fix watchfile to detect new versions on github * New upstream version 2.11.2. * Standards-Version: 4.6.0 (routine-update) * Bump versioned Build-Depends: libngs-sdk-dev (>= 2.11.2) * Skip test that test needs a *lot* of memory * Link against libzstd. (Closes: #997280.) . [ Aaron M. Ucko ] * d/p/fix_libngs_linkage.patch (new): Substitute ngs-c++ library for absent ngs library. * debian/rules: Stop renaming kget (to avoid a file conflict, #851219) now that it's retired altogether. * d/p/allow_multi_help.patch (new): Tolerate redundant --help declarations within tools/driver-tool. * d/p/run_unversioned_tools.patch (new): Look for tools by their unversioned names, per Debian's simplified installation arrangement. * debian/tests: Switch to modern encryption/decryption setup. - run-unit-test: Replace protected repository configuration (no longer supported as of ncbi-vdb 2.11.0) by --ngc [...].ngc. - test-data.tar.gz: Replace dbGaP-0.enc_key by a copy of upstream's test/prefetch/data/prj_phs710EA_test.ngc. * debian/watch: Look for tags rather than releases, as GitHub currently lists none(!) of the latter. * New upstream version 2.11.3. Checksums-Sha1: b8488308a93525a984403c9ff0bb4b1d2cbb46ce 2217 sra-sdk_2.11.3+dfsg-1.dsc 2231b643173ab4fc460ac5f1fb4457c2e2fce9a3 5842636 sra-sdk_2.11.3+dfsg.orig.tar.xz 271e46d326eebcb7546fc919e526c1b839f69fbc 3779492 sra-sdk_2.11.3+dfsg-1.debian.tar.xz 89f8c1118a46d3727701b9bcd61b2788d3003698 12401 sra-sdk_2.11.3+dfsg-1_source.buildinfo Checksums-Sha256: b212a12ebdfe609d8315e94f80cb39a73b929704f4334dd997934ae130e40cd2 2217 sra-sdk_2.11.3+dfsg-1.dsc f6a26bfbfda2f41a9be9b61963a20e5607127a9260d3984af1a747f8d5dbee76 5842636 sra-sdk_2.11.3+dfsg.orig.tar.xz 186ea0722bf5a78132a4525bb91022e4f6381f6e9ffa062e1f3a317fd1ac4174 3779492 sra-sdk_2.11.3+dfsg-1.debian.tar.xz c58fced7d214c14a1fa9a34f5d5e0e272953c6e849ef74ce45ec259b070d593b 12401 sra-sdk_2.11.3+dfsg-1_source.buildinfo Files: 93b9fe5ced1cda86a3377702cc087487 2217 science optional sra-sdk_2.11.3+dfsg-1.dsc 76b7d4e37c9009eeffac61a0c1f1aaff 5842636 science optional sra-sdk_2.11.3+dfsg.orig.tar.xz a31438d6d3ceb1202f551f938da429b1 3779492 science optional sra-sdk_2.11.3+dfsg-1.debian.tar.xz 85116eff1604bdd9ca13311ce44adcc7 12401 science optional sra-sdk_2.11.3+dfsg-1_source.buildinfo -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEfDq5z9IwvTDdAJxZHnCRsfFKZKIFAmF3RL4ACgkQHnCRsfFK ZKIdkBAAsP6iLklJxJrw9gPX7AFPeAY+z9qbGB7AK4O4r2qB1FPCKvDNk20kbp4y P1TAOrdoDCPwq8D5BBV6Pl+Dojw2/XHRccmcpHTKnWJD8Et9YFR5i4S97o/BlbG7 uDCP7/+HPyMFag9JIYw/QZdKdofdun9IX3it7hPyCeckhINubumh1VyKbYZAOaAw 1wjNwoEXgmvt+1wgO4bBtNHczcAAgSSyB6O/vOcvmhlrHqAfV8S+i8Tkn6yJNBhm SR+GngQkpzQC2SgUi3un4xLi2OSo8Q2MCbIX7om+g8ZORZjXAYbybiNzonp0dpvj 2t4Z+oo8cB4GEnAE5pgtXTUFObRtNnV++KB6XxdosTy4idYXbyw2umakC/l1iXZf IvAXqoyvPCoiZC5nBmIOfT9DertJt/utM/3ehHrpSwpbppY8nqFhMAO60d6Nr9xU 4c5dw1UMsXEKzaNBQpTzPS9bOr7dYZ0kPC4bXa97ZAEsoQILvxdHQzbDGqYSTa4d 9hHzTGQIFqw9KGeZC5WzGst+/+QccPODuUM5Io2/hgB0wv0S1SkRZqQm4GmhUYqV 1kw4VJR+QRwBvnsyxUuz0Rqp6aLCT6gKKqe303UsughcmEfobxbUzF3NjxfFIJ0F H1O8xwRzASzia2GCxu08LU5v2NoShl+pfhzWUs2JhrxDqPb1Pu4= =vKZV -----END PGP SIGNATURE-----
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