[From nobody Mon Sep 28 02:35:07 2026 Received: (at 1144917-close) by bugs.debian.org; 28 Sep 2026 01:34:17 +0000 X-Spam-Checker-Version: SpamAssassin 4.0.1-bugs.debian.org_2005_01_02 (2024-03-25) on buxtehude.debian.org X-Spam-Level: X-Spam-Status: No, score=-110.0 required=4.0 tests=BAYES_00,DKIM_SIGNED, DKIM_VALID,DKIM_VALID_AU,DKIM_VALID_EF,FOURLA,FVGT_m_MULTI_ODD, HAS_BUG_NUMBER,MD5_SHA1_SUM,MEDS2,PGPSIGNATURE,RCVD_IN_DNSWL_MED, SPF_HELO_PASS,SPF_PASS,USER_IN_DKIM_WELCOMELIST,WORD_WITHOUT_VOWELS autolearn=ham autolearn_force=no version=4.0.1-bugs.debian.org_2005_01_02 X-Spam-Bayes: score:0.0000 Tokens: new, 172; hammy, 150; neutral, 371; spammy, 0. spammytokens: hammytokens:0.000-+--HX-Debian:DAK, 0.000-+--H*rp:D*ftp-master.debian.org, 0.000-+--HX-DAK:process-upload, 0.000-+--UD:debian.tar.xz, 0.000-+--H*r:sk:fasolo. Return-path: <envelope@ftp-master.debian.org> Received: from mitropoulos.debian.org ([2001:648:2ffc:deb:216:61ff:fe9d:958d]:42012) by buxtehude.debian.org with esmtps (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <envelope@ftp-master.debian.org>) id 1xB0G1-006Dmb-1G for 1144917-close@bugs.debian.org; Mon, 28 Sep 2026 01:34:17 +0000 Received: via submission from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA, CN=fasolo.debian.org, EMAIL=hostmaster@fasolo.debian.org (verified) by mitropoulos.debian.org with esmtps (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <envelope@ftp-master.debian.org>) id 1xB0Fz-009YZ3-0v for 1144917-close@bugs.debian.org; Mon, 28 Sep 2026 01:34:15 +0000 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=ftp-master.debian.org; s=smtpauto.fasolo; h=Date:Message-Id:Content-Type: Subject:MIME-Version:To:Reply-To:From:Cc:Content-Transfer-Encoding:Content-ID :Content-Description:In-Reply-To:References; bh=xOCjj/BLwIWLSW488V59/f4YkvoC7uLKekSb2i6GM/4=; b=ITu3EHfOlVHDcy7ZlbQSjyAtgi jvtP/wIbGwWEA8bJtufT7rVqbcpJtTYBXiZoOCynyqCkXand42Cknl1QLFsQVvpgXW3owNYSg/NBD wCb0eerIYVvv8BUEl/odt2BRtpakiGDfnwqg9/U5rL1BkT6SHZE34ksHwx+1eXG4kbA3EpRf5QkRz DlhMiffifG5mLuYB50A+dsCsdHcooAeIt9XUrL9XO54SmCh936VEr0UTqcoU/Fs0chJRgS6OMXVTJ H1K5MwlYRmkPCAwrzZAa9eFsFam8EA1Gmox9hKZOtGoitFpPxDWGBbTbA4yncEDa//+3SUrowkUTZ 6owKnWnw==; Received: from dak by fasolo.debian.org with local (Exim 4.98.2) (envelope-from <envelope@ftp-master.debian.org>) id 1xB0Fy-00000001LyQ-0Ydb; Mon, 28 Sep 2026 01:34:14 +0000 From: Debian FTP Masters <ftpmaster@ftp-master.debian.org> Reply-To: ucko@debian.org (Aaron M. Ucko) To: 1144917-close@bugs.debian.org X-DAK: dak process-upload X-Debian: DAK X-Debian-Package: sra-sdk Debian: DAK Debian-Changes: sra-sdk_3.4.1+dfsg-1_source.changes Debian-Source: sra-sdk Debian-Version: 3.4.1+dfsg-1 Debian-Architecture: source Debian-Suite: unstable Debian-Archive-Action: accept MIME-Version: 1.0 Subject: Bug#1144917: fixed in sra-sdk 3.4.1+dfsg-1 Content-Type: multipart/signed; micalg="pgp-sha256"; protocol="application/pgp-signature"; boundary="===============2781294013448810244==" Message-Id: <E1xB0Fy-00000001LyQ-0Ydb@fasolo.debian.org> Date: Mon, 28 Sep 2026 01:34:14 +0000 --===============2781294013448810244== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Source: sra-sdk Source-Version: 3.4.1+dfsg-1 Done: Aaron M. Ucko <ucko@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 1144917@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Aaron M. Ucko <ucko@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 ftpmaster@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Sun, 27 Sep 2026 21:07:56 -0400 Source: sra-sdk Architecture: source Version: 3.4.1+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debi= an.org> Changed-By: Aaron M. Ucko <ucko@debian.org> Closes: 1144917 Changes: sra-sdk (3.4.1+dfsg-1) unstable; urgency=3Dmedium . * New upstream release. - test-sra no longer crashes under glibc 2.43. (Closes: #1144917.) * debian/control: - Bump libngs-c++-dev Breaks/Replaces on libncbi-vdb-dev to (<< 3.4) per libkapp.a takeover. (NB: sra-sdk took over the name and the main() wrapper, but ncbi-vdb retained the remaining content under the name libvdbapp.a.) - Bump B-D on libncbi-vdb-dev to (>=3D 3.4.1+dfsg~) and add one on python3-setuptools-whl to support Test_NGS_Python_install's patch. * debian/copyright: Revisit per licenserecon (lrc). - Add stanzas for bxzstr, rwqueue, SparkKMer.java, sse2neon.h, taskflow (complete with internal special cases), and tsl. - Wildcard (N. Lohmann's) json.hpp. - Extend BitMagic (libs/inc/bm) date range. - Formally rename BSD-3-clause-CLI11 to BSD-3-clause, uncontended. * debian/not-installed: Broaden lib*ngs*-static.a to lib*-static.a. * debian/patches: Update existing patches for new release. Notably: - bypass-libxml2-ATTRIBUTE_UNUSED.patch, fix_bm_for_gcc15.patch: Disable (fully superseded). - include_cstdint_for_gcc15.patch: Drop superseded portion. - label_online_tests.patch: Resync; leave out Test_NGS_Python_install. - link_vdb_dynamically.patch, prefer_dynamic_libraries.patch: Drop build/env.cmake changes; we can now set DYNAMIC_LINK=3DON instead. - setuptools.patch: Repurpose somewhat. (setup.py has already migrated to setuptools, but the new accompanying test-install.sh [Test_NGS_Python_install] uses pip and needs patching to take infrastructure wheels from the local filesystem rather than PyPI.) - support_libre2-11.patch, use_debian_packaged_*.patch: Resync. * debian/patches/not_just_ubuntu.patch (new): Don't use a build-wide Python virtual env. under Debian (or any other derivative) either. * debian/patches/public_version-hash.patch (new): In tools/loaders/sharq/version.h, #include <kapp/version-hash.h> without a leading ../libs/, which works only when building against uninstalled VDB. (As of 3.4.1, Debian's installation makes the header public.) * debian/patches/tiny_csra_shell.patch (new): Run test/external/fasterq-dump/tiny_csra.sh under bash per its use of [[. (As is, it could never officially fail. No further changes needed, though.) * debian/rules: - Don't clean "expected" (golden) *.orig files. To that end, move custom cleanup logic to override_dh_clean (vs. _autoclean). - override_dh_auto_install: Add libkapp.a* to libngs-c++-dev. - execute_after_dh_auto_build (new): Take over javadoc invocation from the upstream build system, which no longer ever runs javadoc itself. - override_dh_auto_configure: Set the new DYNAMIC_LINK option to ON, thereby linking dynamically against dependencies in most cases. (Some portions of the tree still need patching to do so.) * debian/tests/run-unit-test: Stop testing cache-mgr, retired upstream. * Standards-Version: 4.7.4 (routine-update) * Reflow Uploaders field (cme) * Remove Priority field (cme) * Drop 'Rules-Requires-Root: no' from d/control (routine-update) * Reformat the Last-Update date as ISO YYYY-MM-DD. * No tab in license text (routine-update) . sra-sdk (3.2.1+dfsg-7) UNRELEASED; urgency=3Dmedium . * Fix watch file Checksums-Sha1: 3bcf9527c866c4ff58447fec76ce5ae0c0b2f812 3036 sra-sdk_3.4.1+dfsg-1.dsc 15a020e8c65d4115f28d85703c3d531045161446 50290644 sra-sdk_3.4.1+dfsg.orig.ta= r.xz 4e010bfd54e18c033616a64a60acde4f55db9bbb 3798672 sra-sdk_3.4.1+dfsg-1.debian= .tar.xz Checksums-Sha256: e9ebcf5412fc1b8bc3f95a9a2a3ab136ff3bc69cd9de12f35d522d2d62872b39 3036 sra-sd= k_3.4.1+dfsg-1.dsc 658663be972005fbae4d6b53963fb1aff069a1d4c4c2a81c320910f40701f66c 50290644 sr= a-sdk_3.4.1+dfsg.orig.tar.xz 5015efbb2fd710377d940d614816a1c9010461c5cabc9bba73e9f6d728a74d86 3798672 sra= -sdk_3.4.1+dfsg-1.debian.tar.xz Files: 8df5493df73a2dea7728f5219363f60d 3036 science optional sra-sdk_3.4.1+dfsg-1.= dsc 37f30ef5d9a181d2881a833416a3036e 50290644 science optional sra-sdk_3.4.1+dfs= g.orig.tar.xz 1981d0b2c494ba60b5d8d0c7e5342505 3798672 science optional sra-sdk_3.4.1+dfsg= -1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEfDq5z9IwvTDdAJxZHnCRsfFKZKIFAmq5vnUACgkQHnCRsfFK ZKIwmxAAlEOCoGhnItVBW1hnf1vED/GxA9BNqzPPiWG5dxO+QTed824CfJ3j2OBS f0JTr6m+zPAXtbFMjd6330be9Cnwzy6Po2YCNEOmXuCG3EdO7CzElqRHbTDg5z0A mA/nYn2FG7AbwGQ0VL/TY9T2HKi7V3n476HuRgBmwe6huWmNHJzpX00YPtQCZu1Z Z7yGYRKgOpkXS3KKqfP2nxabdahNPMJZ1D+9/+pyWldSl1pO57p/TLcQUxHNUOdF uDwluvG4XFq4SkCmsjTAIYJSwEqkgosxO3w3jG9gZyserguRm3OvhVFl2ZNmIP/2 aBRz6LoBB0NlWVp758YWZj4e1pxx33omR4Zn8cW5Rrfu72YIy9kaziDpUZncTb84 Xusy0p4B2RaeCOfXl/QYLsUuqrPadpIg/0LGUuIdU7MizKJ9djHj29E4vZnM1fBD twxKwAIXyuvolxzubTV/W3S6w4IyV44YDsjVPbrmIVV0TpcPqkuPNHiSbU041cRv RnxFr0Ja6Nt3xyXnoOvRdZ3padmxmi1+rr+qmL4IDh21ky6kb+K1S02PcyIttCCA xy8V2lRjdUcpGqtYA+73kW7bapzbvVxRMWhyuyK1o/vHHKVgO0R2h+Mc/PeXOob/ uUNZgA45XZ1qMHr+1Huhy6Ieo3bRK1hsHtm/611PJgL8R6mFkwM=3D =3Dp8N0 -----END PGP SIGNATURE----- --===============2781294013448810244== Content-Type: application/pgp-signature -----BEGIN PGP SIGNATURE----- iHUEABYIAB0WIQTziqJOuF8J+ZI8pJSb9qggYcy5IQUCarnEFgAKCRCb9qggYcy5 IfDbAQD7EWb52EMnucB7JcFY4tQLoIh1DRkr7e/9Qhr9ba+FugD+ImEjgyZc+ypj LpzWAoslAzcfueFnLFwCxbwydZ6EoQA= =zZp9 -----END PGP SIGNATURE----- --===============2781294013448810244==-- ]