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Fix compiler and linker warnings #1605

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@betatim betatim commented Feb 1, 2017

Some trivial fix ups to reduce the number of compiler warnings generated by khmer.

@luizirber do you know what the -mmacosx-version-min=10.7 really does? I don't really know more than what you can deduce from the name, which makes me wonder if adding it breaks something (we aren't testing for)?

  • Is it mergeable?
  • make test Did it pass the tests?

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codecov-io commented Feb 2, 2017

Codecov Report

Merging #1605 into master will not change coverage.
The diff coverage is 0%.

Impacted file tree graph

@@          Coverage Diff           @@
##           master   #1605   +/-   ##
======================================
  Coverage    0.06%   0.06%           
======================================
  Files          78      78           
  Lines        9792    9792           
  Branches     2457    2457           
======================================
  Hits            6       6           
  Misses       9786    9786
Impacted Files Coverage Δ
src/oxli/assembler.cc 0% <0%> (ø) ⬆️
src/oxli/traversal.cc 0% <0%> (ø) ⬆️

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betatim commented Feb 14, 2017

Ready for review! @luizirber, @camillescott, @standage , or @ctb

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betatim commented Feb 14, 2017

Somewhat related, my terminal is filling up with large number of copies of this warning. It has "always" been there but usually only once, is the duplication related to the multiple template instantiations we do for the read parser?

In file included from third-party/seqan/core/include/seqan/basic.h:62:0,
                 from third-party/seqan/core/include/seqan/seq_io.h:44,
                 from lib/read_parsers.hh:41,
                 from lib/hashtable.hh:57,
                 from lib/kmer_filters.cc:40:
third-party/seqan/core/include/seqan/basic/test_system.h:92:10: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     std::auto_ptr<Test> instance;
          ^~~~~~~~
In file included from /usr/include/c++/6.3.1/bits/locale_conv.h:41:0,
                 from /usr/include/c++/6.3.1/locale:43,
                 from /usr/include/c++/6.3.1/iomanip:43,
                 from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46,
                 from third-party/seqan/core/include/seqan/basic/basic_debug.h:52,
                 from third-party/seqan/core/include/seqan/basic.h:52,
                 from third-party/seqan/core/include/seqan/seq_io.h:44,
                 from lib/read_parsers.hh:41,
                 from lib/hashtable.hh:57,
                 from lib/kmer_filters.cc:40:
/usr/include/c++/6.3.1/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~

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is the duplication related to the multiple template instantiations we do for the read parser?

SeqAn is heavily templated as well, so that may also be a factor. There are some warnings I see duplicated several times during compilation, but I haven't kept track of which they were and haven't seen a substantial increase since introducing templating to the read parser.

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👍

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betatim commented Feb 14, 2017

Ok. For sure the original sin comes from seqan being a bit old, hence the warnings. Downside to all the "visual noise" is that I train myself to ignore it all which means sometimes you miss a new warning :-/

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Downside to all the "visual noise" is that I train myself to ignore it all which means sometimes you miss a new warning :-/

Yep, the struggle is real

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betatim commented Feb 20, 2017

@standage this can be merged right?

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"Yes", given the caveats in our current #khmer@slack discussion.

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betatim commented Feb 20, 2017

Had forgotten about that, let's wait for a decision re: merging into feature/cython_all_the_things

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betatim commented Jul 27, 2017

I am impressed merging master just worked. 😀

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betatim commented Jul 27, 2017

From scrolling through the travis output there are less warnings, I think. Merge first, squash more warnings later?

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standage commented Jul 27, 2017 via email

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standage commented Jul 27, 2017 via email

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3 participants