{"action":"created","issue":{"url":"https://api.github.com/repos/PacificBiosciences/blasr/issues/192","repository_url":"https://api.github.com/repos/PacificBiosciences/blasr","labels_url":"https://api.github.com/repos/PacificBiosciences/blasr/issues/192/labels{/name}","comments_url":"https://api.github.com/repos/PacificBiosciences/blasr/issues/192/comments","events_url":"https://api.github.com/repos/PacificBiosciences/blasr/issues/192/events","html_url":"https://github.com/PacificBiosciences/blasr/issues/192","id":139300404,"number":192,"title":"Fix some warnings","user":{"login":"pb-cdunn","id":12086299,"avatar_url":"https://avatars.githubusercontent.com/u/12086299?v=3","gravatar_id":"","url":"https://api.github.com/users/pb-cdunn","html_url":"https://github.com/pb-cdunn","followers_url":"https://api.github.com/users/pb-cdunn/followers","following_url":"https://api.github.com/users/pb-cdunn/following{/other_user}","gists_url":"https://api.github.com/users/pb-cdunn/gists{/gist_id}","starred_url":"https://api.github.com/users/pb-cdunn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pb-cdunn/subscriptions","organizations_url":"https://api.github.com/users/pb-cdunn/orgs","repos_url":"https://api.github.com/users/pb-cdunn/repos","events_url":"https://api.github.com/users/pb-cdunn/events{/privacy}","received_events_url":"https://api.github.com/users/pb-cdunn/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2016-03-08T15:06:26Z","updated_at":"2016-03-08T15:54:46Z","closed_at":null,"body":"* One warning-suppression does not work with gcc-5.3.0. (In pitchfork, we can use 4.8.4 or 5.3.0, but not 4.9.2. So we want 5.3.0 to work.)\r\n\r\n```\r\nIn file included from /tmp/cdunn/pf/include/boost/scoped_ptr.hpp:14:0,\r\n/tmp/cdunn/pf/include/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]\r\n     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )\r\n```\r\nWe can fix that by switching from `boost::scoped_ptr<>` to `std::unique_ptr<> const`.\r\n```\r\nIn file included from /mnt/software/g/gcc/5.3.0/u1404/usr/include/c++/5/memory:81:0,\r\n/mnt/software/g/gcc/5.3.0/u1404/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here\r\n   template<typename> class auto_ptr;\r\n                            ^\r\n```\r\nSo there is a problem in gcc-5.3.0, which we cannot solve today. Oh, well.\r\n```\r\nIn file included from /tmp/cdunn/pf/include/boost/bind/mem_fn.hpp:25:0,\r\n                 from /tmp/cdunn/pf/include/boost/mem_fn.hpp:22,\r\n                 from /tmp/cdunn/pf/include/boost/bind/bind.hpp:26,\r\n                 from /tmp/cdunn/pf/include/boost/bind.hpp:22,\r\n                 from /tmp/cdunn/pf/include/boost/multi_index/sequenced_index.hpp:49,\r\n                 from /tmp/cdunn/pf/include/boost/property_tree/ptree.hpp:23,\r\n/tmp/cdunn/pf/include/boost/get_pointer.hpp:27:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]\r\n template<class T> T * get_pointer(std::auto_ptr<T> const& p)\r\n\r\n                                        ^\r\n```\r\nWe cannot fix that without changing boost versions."},"comment":{"url":"https://api.github.com/repos/PacificBiosciences/blasr/issues/comments/193835983","html_url":"https://github.com/PacificBiosciences/blasr/issues/192#issuecomment-193835983","issue_url":"https://api.github.com/repos/PacificBiosciences/blasr/issues/192","id":193835983,"user":{"login":"pb-cdunn","id":12086299,"avatar_url":"https://avatars.githubusercontent.com/u/12086299?v=3","gravatar_id":"","url":"https://api.github.com/users/pb-cdunn","html_url":"https://github.com/pb-cdunn","followers_url":"https://api.github.com/users/pb-cdunn/followers","following_url":"https://api.github.com/users/pb-cdunn/following{/other_user}","gists_url":"https://api.github.com/users/pb-cdunn/gists{/gist_id}","starred_url":"https://api.github.com/users/pb-cdunn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pb-cdunn/subscriptions","organizations_url":"https://api.github.com/users/pb-cdunn/orgs","repos_url":"https://api.github.com/users/pb-cdunn/repos","events_url":"https://api.github.com/users/pb-cdunn/events{/privacy}","received_events_url":"https://api.github.com/users/pb-cdunn/received_events","type":"User","site_admin":false},"created_at":"2016-03-08T15:54:46Z","updated_at":"2016-03-08T15:54:46Z","body":"Also, some gtest warnings:\r\n```\r\n/tmp/cdunn/pf/src/gtest/include/gtest/gtest.h: In instantiation of ‘testing::AssertionResult testing::internal::CmpHelperGT(const char*, const char*, const T1&, const T2&) [with T1 = unsigned int; T2 = int]’:\r\n/tmp/cdunn/pf/src/gtest/include/gtest/gtest.h: In instantiation of ‘testing::AssertionResult testing::internal::CmpHelperGT(const char*, const char*, const T1&, const T2&) [with T1 = long unsigned int; T2 = int]’:\r\n/tmp/cdunn/pitchfork/workspace/blasr/utils/bax2bam/tests/src/test_ccs.cpp:98:25851:   required from here\r\n/tmp/cdunn/pf/src/gtest/include/gtest/gtest.h:1585:145: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]\r\n\r\n/tmp/cdunn/pf/src/gtest/include/gtest/gtest.h: In instantiation of ‘testing::AssertionResult testing::internal::CmpHelperEQ(const char*, const char*, const T1&, const T2&) [with T1 = int; T2 = unsigned int]’:\r\n/tmp/cdunn/pf/src/gtest/include/gtest/gtest.h:1484:23:   required from ‘static testing::AssertionResult testing::internal::EqHelper<lhs_is_null_literal>::Compare(const char*, const char*, const T1&, const T2&) [with T1 = int; T2 = unsigned int; bool lhs_is_null_literal = false]’\r\n/tmp/cdunn/pitchfork/workspace/blasr/utils/bax2bam/tests/src/test_ccs.cpp:98:15387:   required from here\r\n/tmp/cdunn/pf/src/gtest/include/gtest/gtest.h:1448:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]\r\n   if (expected == actual) {\r\n                ^\r\n/tmp/cdunn/pf/src/gtest/include/gtest/gtest.h: In instantiation of ‘testing::AssertionResult testing::internal::CmpHelperEQ(const char*, const char*, const T1&, const T2&) [with T1 = int; T2 = unsigned int]’:\r\n/tmp/cdunn/pf/src/gtest/include/gtest/gtest.h:1484:23:   required from ‘static testing::AssertionResult testing::internal::EqHelper<lhs_is_null_literal>::Compare(const char*, const char*, const T1&, const T2&) [with T1 = int; T2 = unsigned int; bool lhs_is_null_literal = false]’\r\n/tmp/cdunn/pitchfork/workspace/blasr/utils/bax2bam/tests/src/test_hqregions.cpp:101:17889:   required from here\r\n/tmp/cdunn/pf/src/gtest/include/gtest/gtest.h:1448:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]\r\n   if (expected == actual) {\r\n                ^\r\n/tmp/cdunn/pf/src/gtest/include/gtest/gtest.h: In instantiation of ‘testing::AssertionResult testing::internal::CmpHelperGT(const char*, const char*, const T1&, const T2&) [with T1 = long unsigned int; T2 = int]’:\r\n/tmp/cdunn/pitchfork/workspace/blasr/utils/bax2bam/tests/src/test_subreads.cpp:195:31507:   required from here\r\n/tmp/cdunn/pf/src/gtest/include/gtest/gtest.h:1585:145: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]\r\nIn file included from /tmp/cdunn/pitchfork/workspace/blasr/utils/bax2bam/tests/src/test_subreads.cpp:10:0:\r\n/tmp/cdunn/pf/src/gtest/include/gtest/gtest.h: In instantiation of ‘testing::AssertionResult testing::internal::CmpHelperEQ(const char*, const char*, const T1&, const T2&) [with T1 = int; T2 = unsigned int]’:\r\n/tmp/cdunn/pf/src/gtest/include/gtest/gtest.h:1484:23:   required from ‘static testing::AssertionResult testing::internal::EqHelper<lhs_is_null_literal>::Compare(const char*, const char*, const T1&, const T2&) [with T1 = int; T2 = unsigned int; bool lhs_is_null_literal = false]’\r\n/tmp/cdunn/pitchfork/workspace/blasr/utils/bax2bam/tests/src/test_subreads.cpp:195:17651:   required from here\r\n/tmp/cdunn/pf/src/gtest/include/gtest/gtest.h:1448:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]\r\n   if (expected == actual) {\r\n                ^\r\n/tmp/cdunn/pf/src/gtest/include/gtest/gtest.h: In instantiation of ‘testing::AssertionResult testing::internal::CmpHelperEQ(const char*, const char*, const T1&, const T2&) [with T1 = unsigned int; T2 = int]’:\r\n/tmp/cdunn/pf/src/gtest/include/gtest/gtest.h:1484:23:   required from ‘static testing::AssertionResult testing::internal::EqHelper<lhs_is_null_literal>::Compare(const char*, const char*, const T1&, const T2&) [with T1 = unsigned int; T2 = int; bool lhs_is_null_literal = false]’\r\n/tmp/cdunn/pitchfork/workspace/blasr/utils/bax2bam/tests/src/test_subreads.cpp:195:29142:   required from here\r\n\r\nblasr/utils/bam2bax/tests/src/test_Bam2BaxConverter.cpp:36:268:   required from here\r\ngtest/include/gtest/gtest.h:1448:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]\r\n   if (expected == actual) {\r\n                ^\r\n\r\ncc1plus: warning: unrecognized command line option ‘-Wno-unused-private-field’"}}