Your message dated Thu, 07 Mar 2019 18:19:29 +0000 with message-id <[email protected]> and subject line Bug#923954: fixed in libbpp-seq 2.4.1-3 has caused the Debian Bug report #923954, regarding libbpp-seq: FTBFS (dh_makeshlibs fails) 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 [email protected] immediately.) -- 923954: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=923954 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---Package: src:libbpp-seq Version: 2.4.1-2 Severity: serious Tags: ftbfs Dear maintainer: I tried to build this package in buster but it failed: -------------------------------------------------------------------------------- [...] debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a cd obj-x86_64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu .. -- The CXX compiler identification is GNU 8.2.0 -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- bpp-core 4.1.0 found: [... snipped ...] _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN3bpp8SequenceEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS7_EESM_IJEEEEESt17_Rb_tree_iteratorISB_ESt23_Rb_tree_const_iteratorISB_EDpOT_@Base 2.4.1 _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN3bpp8SequenceEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE24_M_get_insert_unique_posERS7_@Base 2.4.1 @@ -1851,6 +1853,7 @@ _ZNSt8_Rb_treeIcSt4pairIKcdESt10_Select1stIS2_ESt4lessIcESaIS2_EE24_M_get_insert_unique_posERS1_@Base 2.4.1 _ZNSt8_Rb_treeIcSt4pairIKcdESt10_Select1stIS2_ESt4lessIcESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_@Base 2.4.1 _ZNSt8_Rb_treeIcSt4pairIKcdESt10_Select1stIS2_ESt4lessIcESaIS2_EE8_M_eraseEPSt13_Rb_tree_nodeIS2_E@Base 2.4.1 + _ZNSt8_Rb_treeIdSt4pairIKdmESt10_Select1stIS2_ESt4lessIdESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_@Base 2.4.1-2 _ZNSt8_Rb_treeIdSt4pairIKdmESt10_Select1stIS2_ESt4lessIdESaIS2_EE24_M_get_insert_unique_posERS1_@Base 2.4.1 _ZNSt8_Rb_treeIdSt4pairIKdmESt10_Select1stIS2_ESt4lessIdESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_@Base 2.4.1 _ZNSt8_Rb_treeIdSt4pairIKdmESt10_Select1stIS2_ESt4lessIdESaIS2_EE7_M_copyINS8_11_Alloc_nodeEEEPSt13_Rb_tree_nodeIS2_EPKSC_PSt18_Rb_tree_node_baseRT_@Base 2.4.1 @@ -1873,6 +1876,7 @@ _ZNSt8_Rb_treeIiSt4pairIKiiESt10_Select1stIS2_ESt4lessIiESaIS2_EE7_M_copyINS8_11_Alloc_nodeEEEPSt13_Rb_tree_nodeIS2_EPKSC_PSt18_Rb_tree_node_baseRT_@Base 2.4.1 _ZNSt8_Rb_treeIiSt4pairIKiiESt10_Select1stIS2_ESt4lessIiESaIS2_EE8_M_eraseEPSt13_Rb_tree_nodeIS2_E@Base 2.4.1 _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE14_M_insert_nodeEPSt18_Rb_tree_node_baseSA_PSt13_Rb_tree_nodeIS2_E@Base 2.4.1 + _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJOiEESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_@Base 2.4.1-2 _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_@Base 2.4.1 _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE24_M_get_insert_unique_posERS1_@Base 2.4.1 _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_@Base 2.4.1 @@ -1884,10 +1888,11 @@ _ZNSt8_Rb_treeImSt4pairIKmPN3bpp13SiteContainerEESt10_Select1stIS5_ESt4lessImESaIS5_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS5_ERS1_@Base 2.4.1 _ZNSt8_Rb_treeImSt4pairIKmPN3bpp13SiteContainerEESt10_Select1stIS5_ESt4lessImESaIS5_EE8_M_eraseEPSt13_Rb_tree_nodeIS5_E@Base 2.4.1 _ZNSt8_Rb_treeImSt4pairIKmmESt10_Select1stIS2_ESt4lessImESaIS2_EE14_M_insert_nodeEPSt18_Rb_tree_node_baseSA_PSt13_Rb_tree_nodeIS2_E@Base 2.4.1 + _ZNSt8_Rb_treeImSt4pairIKmmESt10_Select1stIS2_ESt4lessImESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJOmEESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_@Base 2.4.1-2 _ZNSt8_Rb_treeImSt4pairIKmmESt10_Select1stIS2_ESt4lessImESaIS2_EE24_M_get_insert_unique_posERS1_@Base 2.4.1 _ZNSt8_Rb_treeImSt4pairIKmmESt10_Select1stIS2_ESt4lessImESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_@Base 2.4.1 _ZNSt8_Rb_treeImSt4pairIKmmESt10_Select1stIS2_ESt4lessImESaIS2_EE8_M_eraseEPSt13_Rb_tree_nodeIS2_E@Base 2.4.1 - _ZSt11__remove_ifIN9__gnu_cxx17__normal_iteratorIPiSt6vectorIiSaIiEEEENS0_5__ops16_Iter_equals_valIKiEEET_SB_SB_T0_@Base 2.4.1 +#MISSING: 2.4.1-2# _ZSt11__remove_ifIN9__gnu_cxx17__normal_iteratorIPiSt6vectorIiSaIiEEEENS0_5__ops16_Iter_equals_valIKiEEET_SB_SB_T0_@Base 2.4.1 _ZSt13__adjust_heapIN9__gnu_cxx17__normal_iteratorIPPN3bpp5RangeImEESt6vectorIS5_SaIS5_EEEElS5_NS0_5__ops15_Iter_comp_iterINS2_10rangeComp_ImEEEEEvT_T0_SH_T1_T2_@Base 2.4.1 _ZSt16__insertion_sortIN9__gnu_cxx17__normal_iteratorIPPN3bpp5RangeImEESt6vectorIS5_SaIS5_EEEENS0_5__ops15_Iter_comp_iterINS2_10rangeComp_ImEEEEEvT_SG_T0_@Base 2.4.1 _ZSt16__introsort_loopIN9__gnu_cxx17__normal_iteratorIPPN3bpp5RangeImEESt6vectorIS5_SaIS5_EEEElNS0_5__ops15_Iter_comp_iterINS2_10rangeComp_ImEEEEEvT_SG_T0_T1_@Base 2.4.1 @@ -2460,7 +2465,7 @@ _ZTVN3bpp7ClustalE@Base 2.4.1 _ZTVN3bpp7GenBankE@Base 2.4.1 _ZTVN3bpp8BLOSUM50E@Base 2.4.1 - _ZTVN3bpp8ClonableE@Base 2.4.1 +#MISSING: 2.4.1-2# _ZTVN3bpp8ClonableE@Base 2.4.1 _ZTVN3bpp8DNAToRNAE@Base 2.4.1 _ZTVN3bpp8PhredPhdE@Base 2.4.1 _ZTVN3bpp9PhredPolyE@Base 2.4.1 dh_makeshlibs: failing due to earlier errors make[1]: *** [debian/rules:15: override_dh_makeshlibs] Error 2 make[1]: Leaving directory '/<<PKGBUILDDIR>>' make: *** [debian/rules:10: binary-arch] Error 2 dpkg-buildpackage: error: fakeroot debian/rules binary-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- (The above is just how the build ends and not necessarily the most relevant part) The build was made in my autobuilder with "dpkg-buildpackage -B" and it also fails here: https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/libbpp-seq.html where you can get a full build log if you need it. If this is really a bug in one of the build-depends, please use reassign and affects, so that this is still visible in the BTS web page for this package. Thanks.
--- End Message ---
--- Begin Message ---Source: libbpp-seq Source-Version: 2.4.1-3 We believe that the bug you reported is fixed in the latest version of libbpp-seq, 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 [email protected], and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Tille <[email protected]> (supplier of updated libbpp-seq 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 [email protected]) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Thu, 07 Mar 2019 18:56:16 +0100 Source: libbpp-seq Architecture: source Version: 2.4.1-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <[email protected]> Changed-By: Andreas Tille <[email protected]> Closes: 923954 Changes: libbpp-seq (2.4.1-3) unstable; urgency=medium . * Rebuild for new version of gcc to fix symbols Closes: #923954 * Standards-Version: 4.3.0 Checksums-Sha1: f2c791c0414b0bcc7bde4772107a978c71594054 2141 libbpp-seq_2.4.1-3.dsc 274f6682eb2eea90e0eb5f1d854897d0052938c6 28084 libbpp-seq_2.4.1-3.debian.tar.xz e71af4b57daf8a271731b8c1033936240ee52a57 7171 libbpp-seq_2.4.1-3_amd64.buildinfo Checksums-Sha256: 73a72c4d8e4706c9577f453551db01e6648b19cf6872e4a8f7aac6f3fe1fe984 2141 libbpp-seq_2.4.1-3.dsc 1d11a42d671f1ebe97f9f4047b69be9f1ab1ea017ec50c759916e55c911890e5 28084 libbpp-seq_2.4.1-3.debian.tar.xz 5df3bda913577cdf9667d8e86c32c155b0039149fe8fe9514e5a3b5f80f41047 7171 libbpp-seq_2.4.1-3_amd64.buildinfo Files: a28f768e32330308022862eaa45e2090 2141 science optional libbpp-seq_2.4.1-3.dsc 1a576939bb9922555819d6741ee04239 28084 science optional libbpp-seq_2.4.1-3.debian.tar.xz b4c6b4fa0808f462bd8ec079b65c5954 7171 science optional libbpp-seq_2.4.1-3_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlyBXV0RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFL5g/9Gf8iUsqJ2S22KnNqSz1vyaJy5e8nwNQ/ 0+EpD+DhVa7Qon91GrkrH5V305JVyzp8OXjqMWce2LG6W7Xf/pSaq09hA4uZQ88t dfsmqt1AMfc8v7nFWGZhQ7yApDIX2lx7fBszt3nsHGaEHWimZnAdcXGMPdglTjDG kyoqvQti3RfYXBLNop/X3xSDuSK28bPLmAmpA6RlMiEHyTm/r+quPWX8IzjG4aea +0j99316AIeqHOhpj/VjprrQMW2dZqbGeYQPcDoa5GJ3uomgA4ylXXUS9eGcqICR nGEvDknkOrnfR7+ry+UwjlGC1amMyZfIltEAmhveMaorq5Dwna0vkM4QFqC87uEN Doal58tjWqATNsaWyN1i4SsV2VaQTtKnD0kuaQNvzfzNlIp6+ZZyDcsCjbsw0V21 msyN8R/DbpGVJ3vRU9IHjf9yB/Uj5xhtvqJ31QNOzOk2d4l/w88ZGL2y5aascbZJ ZMfmIlq1hBFwij0N7vdRS16THDp5YwrUVrATG9QF1cRXUOkefpAL2C0/qXjBEq+Y 9rGqH0Z8TeR4ucgyh+AmqbqjNuqVbnrEfdmiJWymMD/jhG5k60npn8EBgLnfjeKn evFBtQyKvYFHTv7xgAq2EiZq42p9Xg4/sruJjmcOs4Pqtz0LON0mUdwzKPNm2LaX dJhdJAXJtUI= =ceg6 -----END PGP SIGNATURE-----
--- End Message ---
