[Debian-med-packaging] Bug#984243: mothur: ftbfs with GCC-11

[Matthias Klose]

Package: src:mothur
Version: 1.44.3-2
Severity: normal
Tags: sid bookworm
User: debian-gcc at 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