Your message dated Mon, 08 Nov 2021 17:38:08 +0000 with message-id <e1mk8au-000b8a...@fasolo.debian.org> and subject line Bug#984243: fixed in mothur 1.46.1-1 has caused the Debian Bug report #984243, regarding mothur: ftbfs with GCC-11 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.) -- 984243: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=984243 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Package: src:mothur Version: 1.44.3-2 Severity: normal Tags: sid bookworm User: debian-...@lists.debian.org Usertags: ftbfs-gcc-11 [This bug is not targeted to the upcoming bullseye release] Please keep this issue open in the bug tracker for the package it was filed for. If a fix in another package is required, please file a bug for the other package (or clone), and add a block in this package. Please keep the issue open until the package can be built in a follow-up test rebuild. The package fails to build in a test rebuild on at least amd64 with gcc-11/g++-11, but succeeds to build with gcc-10/g++-10. The severity of this report will be raised before the bookworm release, so nothing has to be done for the bullseye release. The full build log can be found at: http://people.debian.org/~doko/logs/20210228/filtered/gcc11/mothur_1.44.3-2_unstable_gcc11.log The last lines of the build log are at the end of this report. To build with GCC 11, either set CC=gcc-11 CXX=g++-11 explicitly, or install the gcc, g++, gfortran, ... packages from experimental. apt-get -t=experimental install g++ Common build failures are new warnings resulting in build failures with -Werror turned on, or new/dropped symbols in Debian symbols files. For other C/C++ related build failures see the porting guide at http://gcc.gnu.org/gcc-11/porting_to.html GCC 11 defaults to the GNU++17 standard. If your package installs header files in /usr/include, please don't work around C++17 issues by choosing a lower C++ standard for the package build, but fix these issues to build with the C++17 standard. [...] from source/datastructures/counttable.h:58, from source/datastructures/optidata.hpp:15, from source/datastructures/optimatrix.h:12, from source/cluster.hpp:5, from source/averagelinkage.cpp:5: source/writer.h:19:34: error: expected ‘)’ before ‘<’ token 19 | OutputWriter (std::shared_ptr<SynchronizedOutputFile> s) : sf(s) {} | ~ ^ | ) source/writer.h:24:10: error: ‘shared_ptr’ in namespace ‘std’ does not name a template type 24 | std::shared_ptr<SynchronizedOutputFile> sf; | ^~~~~~~~~~ source/writer.h:13:1: note: ‘std::shared_ptr’ is defined in header ‘<memory>’; did you forget to ‘#include <memory>’? 12 | #include "sharedwriter.hpp" +++ |+#include <memory> 13 | In file included from source/datastructures/sequence.hpp:22, from source/datastructures/counttable.h:58, from source/datastructures/optidata.hpp:15, from source/datastructures/optimatrix.h:12, from source/cluster.hpp:5, from source/cluster.cpp:10: source/writer.h:19:34: error: expected ‘)’ before ‘<’ token 19 | OutputWriter (std::shared_ptr<SynchronizedOutputFile> s) : sf(s) {} | ~ ^ | ) source/writer.h:24:10: error: ‘shared_ptr’ in namespace ‘std’ does not name a template type 24 | std::shared_ptr<SynchronizedOutputFile> sf; | ^~~~~~~~~~ source/writer.h:13:1: note: ‘std::shared_ptr’ is defined in header ‘<memory>’; did you forget to ‘#include <memory>’? 12 | #include "sharedwriter.hpp" +++ |+#include <memory> 13 | source/writer.h: In member function ‘void OutputWriter::write(const string&)’: source/writer.h:21:46: error: ‘sf’ was not declared in this scope 21 | void write (const string& dataToWrite) { sf->write(dataToWrite); } | ^~ In file included from source/datastructures/sequence.hpp:22, from source/datastructures/counttable.h:58, from source/clusterclassic.h:9, from source/clusterclassic.cpp:10: source/writer.h:19:34: error: expected ‘)’ before ‘<’ token 19 | OutputWriter (std::shared_ptr<SynchronizedOutputFile> s) : sf(s) {} | ~ ^ | ) source/writer.h:24:10: error: ‘shared_ptr’ in namespace ‘std’ does not name a template type 24 | std::shared_ptr<SynchronizedOutputFile> sf; | ^~~~~~~~~~ source/writer.h:13:1: note: ‘std::shared_ptr’ is defined in header ‘<memory>’; did you forget to ‘#include <memory>’? 12 | #include "sharedwriter.hpp" +++ |+#include <memory> 13 | source/writer.h: In member function ‘void OutputWriter::write(const string&)’: source/writer.h:21:46: error: ‘sf’ was not declared in this scope 21 | void write (const string& dataToWrite) { sf->write(dataToWrite); } | ^~ source/writer.h: In member function ‘void OutputWriter::write(const string&)’: source/writer.h:21:46: error: ‘sf’ was not declared in this scope 21 | void write (const string& dataToWrite) { sf->write(dataToWrite); } | ^~ make[2]: *** [<builtin>: source/averagelinkage.o] Error 1 make[2]: *** Waiting for unfinished jobs.... make[2]: *** [Makefile:143: source/cluster.o] Error 1 make[2]: *** [Makefile:141: source/clusterclassic.o] Error 1 make[2]: Leaving directory '/<<PKGBUILDDIR>>' dh_auto_build: error: make -j4 "INSTALL=install --strip-program=true" 64BIT_VERSION=yes returned exit code 2 make[1]: *** [debian/rules:22: override_dh_auto_build] Error 25 make[1]: Leaving directory '/<<PKGBUILDDIR>>' make: *** [debian/rules:19: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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--- Begin Message ---Source: mothur Source-Version: 1.46.1-1 Done: Andreas Tille <ti...@debian.org> We believe that the bug you reported is fixed in the latest version of mothur, 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 984...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Tille <ti...@debian.org> (supplier of updated mothur 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, 08 Nov 2021 18:08:09 +0100 Source: mothur Architecture: source Version: 1.46.1-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Andreas Tille <ti...@debian.org> Closes: 984243 Changes: mothur (1.46.1-1) unstable; urgency=medium . [ Andreas Tille ] * New upstream version * Standards-Version: 4.6.0 (routine-update) * Fix build with gcc-11 Closes: #984243 * Follow parts of the hints by Aaron M. Ucko * Fix linking . [ Hamid Nassiby ] * Fix linking Checksums-Sha1: a32de483dfb2a701c55d07ce6b9601cfc317b9ca 2075 mothur_1.46.1-1.dsc 25b8bb38be632969fc4d126f1ba3e7ca82afeae4 1637738 mothur_1.46.1.orig.tar.gz e234e56feaaf7226231730ccf73ff962223c3984 21124 mothur_1.46.1-1.debian.tar.xz 0a17cd8a7595a0c94afe1cec16c831b1127e6fef 6626 mothur_1.46.1-1_amd64.buildinfo Checksums-Sha256: d42ee584fbc3b4893e1701606a2f07a4bb6a8786f78627ba2880946db3a29ce7 2075 mothur_1.46.1-1.dsc 29b500b3c92d726cde34922f697f2e47f0b7127d76d9a6fb167cc2b8ba3d00fd 1637738 mothur_1.46.1.orig.tar.gz cdc22f6e4e2d30942f9034512069f2611698dc3b9dbb390daa8e0c045cbee3ab 21124 mothur_1.46.1-1.debian.tar.xz 7c8b257c5a990cacf5fdfd765333b7feb089961111a569afabe82a76a87c7543 6626 mothur_1.46.1-1_amd64.buildinfo Files: bf78f5ff94a905a9e185baa3533c559f 2075 science optional mothur_1.46.1-1.dsc 17f47e9ac850791e5f9e4143c218ca69 1637738 science optional mothur_1.46.1.orig.tar.gz ebb76436280a486b60c5789682a96107 21124 science optional mothur_1.46.1-1.debian.tar.xz 01417d183057cc774a13446e825d5a8b 6626 science optional mothur_1.46.1-1_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmGJXPQRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGCzg//XyNHD3/b14sGJqsDsHXO5UEN8dOng21a FlArKyrMA6ApW2X2YurtMNhnzHZk5tBWg+UeUlvuDoXdrzNlRbZEHQQYG8xaKvyM FvurzOnNXZu2pmpXw6Xb0ucPjm3dFI5LEZZ94h/52vTW9ri405UwUoTH0SNCprgD cc2NlOupMmTrJiDj0flWIpgX7kOhj4I5MGqufcX68AL+OnDDoRfbRwzupesWSXU6 Ooa0y7ZEE5Eo7UekvtR0amQdAqODs9jIzcl1qkYFn72rJsa3YETKSTYbDW2sOIfF lT1ISi7iTD5bHTrmzUqunQHSIGtkYRueBLd8loq8TU0nJLMnPENTaZR3PMdQJiEa eJ+dKtb+e8NslzKDVA7DGOvcvEPW9KPpV2L5emjEoDeBTRQ7ajlm79BYOuA/kgz1 Lx8m/XK4mjtM8KI3tFxFCHJvHmkyt6zkXPK3EkJ2THTU/m0XZn4pR76Px4DtWE+f 1s4IvNoJoI9W0c1DE0oM4FLvP6RIqwkUh3f31+ZYcR8FmViTerm1c+3acEMTmfjg oqhieBd/tK/51HteOM8OOTd9O5iwsccW39qgTm/OYxR9pdmeALzu7+A42EGBi4pf GsepSmE4+kqj7aVsuv3SwUhg0DMHncL+zHSLpgBxb7KMSZ6gZzJ6qFsbumVU46yi 83mCALwpV/s= =AWno -----END PGP SIGNATURE-----
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