{"action":"closed","number":9,"pull_request":{"url":"https://api.github.com/repos/vcftools/vcftools/pulls/9","id":41558833,"html_url":"https://github.com/vcftools/vcftools/pull/9","diff_url":"https://github.com/vcftools/vcftools/pull/9.diff","patch_url":"https://github.com/vcftools/vcftools/pull/9.patch","issue_url":"https://api.github.com/repos/vcftools/vcftools/issues/9","number":9,"state":"closed","locked":false,"title":"conformity in cpp/Makefile","user":{"login":"wookietreiber","id":827088,"avatar_url":"https://avatars.githubusercontent.com/u/827088?v=3","gravatar_id":"","url":"https://api.github.com/users/wookietreiber","html_url":"https://github.com/wookietreiber","followers_url":"https://api.github.com/users/wookietreiber/followers","following_url":"https://api.github.com/users/wookietreiber/following{/other_user}","gists_url":"https://api.github.com/users/wookietreiber/gists{/gist_id}","starred_url":"https://api.github.com/users/wookietreiber/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/wookietreiber/subscriptions","organizations_url":"https://api.github.com/users/wookietreiber/orgs","repos_url":"https://api.github.com/users/wookietreiber/repos","events_url":"https://api.github.com/users/wookietreiber/events{/privacy}","received_events_url":"https://api.github.com/users/wookietreiber/received_events","type":"User","site_admin":false},"body":"In general: CPP had been mistaken for CXX:\r\n\r\n- CC is the C compiler\r\n- CFLAGS for C compiler flags, used whenever $(CC) is used\r\n- CXX is the C++ compiler\r\n- CXXFLAGS for C++ compiler flags, used whenever $(CXX) is used\r\n- CPPFLAGS are for headers, e.g. -I/path/to/include, used whenever $(CC) -c or $(CXX) -c are used\r\n- LDFLAGS are for library locations, e.g. -L/path/to/lib, used whenever linking occurs\r\n- LIBS are for libs during linking, e.g. -lz (LIBS is more conform than LIB)\r\n\r\nThis commit adresses these issues. Other changes:\r\n\r\n- both CFLAGS and CXXFLAGS append, so the user can specify his/her own flags (like -Wall)\r\n- neither CPPFLAGS nor LDFLAGS are set in any way in the Makefile\r\n  - the defaults of /usr/include and /usr/lib are always included anyway\r\n  - the user only needs to set CPPFLAGS and LDFLAGS if there are libraries in non-standard locations\r\n- -m64 should not be hard-coded because this would *always* compile in 64-bit mode, even if on a 32-bit system\r\n  - -D_FILE_OFFSET_BITS=64 remains in both CFLAGS and CXXFLAGS to enable large-file operations, IIRC -m64 is not necessary for this to work\r\n- the bgzf target was actually never used, so I removed it for now, I hope this is OK","created_at":"2015-08-04T11:18:02Z","updated_at":"2015-08-04T18:39:52Z","closed_at":"2015-08-04T18:39:52Z","merged_at":"2015-08-04T18:39:52Z","merge_commit_sha":"d59547c26879d781d4c2d2d3df7bc57a88c3b884","assignee":null,"milestone":null,"commits_url":"https://api.github.com/repos/vcftools/vcftools/pulls/9/commits","review_comments_url":"https://api.github.com/repos/vcftools/vcftools/pulls/9/comments","review_comment_url":"https://api.github.com/repos/vcftools/vcftools/pulls/comments{/number}","comments_url":"https://api.github.com/repos/vcftools/vcftools/issues/9/comments","statuses_url":"https://api.github.com/repos/vcftools/vcftools/statuses/c850351ecf9cbfc9ecaf857fe6b4ba811bef1fd9","head":{"label":"wookietreiber:cpp-vs-cxx","ref":"cpp-vs-cxx","sha":"c850351ecf9cbfc9ecaf857fe6b4ba811bef1fd9","user":{"login":"wookietreiber","id":827088,"avatar_url":"https://avatars.githubusercontent.com/u/827088?v=3","gravatar_id":"","url":"https://api.github.com/users/wookietreiber","html_url":"https://github.com/wookietreiber","followers_url":"https://api.github.com/users/wookietreiber/followers","following_url":"https://api.github.com/users/wookietreiber/following{/other_user}","gists_url":"https://api.github.com/users/wookietreiber/gists{/gist_id}","starred_url":"https://api.github.com/users/wookietreiber/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/wookietreiber/subscriptions","organizations_url":"https://api.github.com/users/wookietreiber/orgs","repos_url":"https://api.github.com/users/wookietreiber/repos","events_url":"https://api.github.com/users/wookietreiber/events{/privacy}","received_events_url":"https://api.github.com/users/wookietreiber/received_events","type":"User","site_admin":false},"repo":{"id":40131724,"name":"vcftools","full_name":"wookietreiber/vcftools","owner":{"login":"wookietreiber","id":827088,"avatar_url":"https://avatars.githubusercontent.com/u/827088?v=3","gravatar_id":"","url":"https://api.github.com/users/wookietreiber","html_url":"https://github.com/wookietreiber","followers_url":"https://api.github.com/users/wookietreiber/followers","following_url":"https://api.github.com/users/wookietreiber/following{/other_user}","gists_url":"https://api.github.com/users/wookietreiber/gists{/gist_id}","starred_url":"https://api.github.com/users/wookietreiber/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/wookietreiber/subscriptions","organizations_url":"https://api.github.com/users/wookietreiber/orgs","repos_url":"https://api.github.com/users/wookietreiber/repos","events_url":"https://api.github.com/users/wookietreiber/events{/privacy}","received_events_url":"https://api.github.com/users/wookietreiber/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/wookietreiber/vcftools","description":"A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project. ","fork":true,"url":"https://api.github.com/repos/wookietreiber/vcftools","forks_url":"https://api.github.com/repos/wookietreiber/vcftools/forks","keys_url":"https://api.github.com/repos/wookietreiber/vcftools/keys{/key_id}","collaborators_url":"https://api.github.com/repos/wookietreiber/vcftools/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/wookietreiber/vcftools/teams","hooks_url":"https://api.github.com/repos/wookietreiber/vcftools/hooks","issue_events_url":"https://api.github.com/repos/wookietreiber/vcftools/issues/events{/number}","events_url":"https://api.github.com/repos/wookietreiber/vcftools/events","assignees_url":"https://api.github.com/repos/wookietreiber/vcftools/assignees{/user}","branches_url":"https://api.github.com/repos/wookietreiber/vcftools/branches{/branch}","tags_url":"https://api.github.com/repos/wookietreiber/vcftools/tags","blobs_url":"https://api.github.com/repos/wookietreiber/vcftools/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/wookietreiber/vcftools/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/wookietreiber/vcftools/git/refs{/sha}","trees_url":"https://api.github.com/repos/wookietreiber/vcftools/git/trees{/sha}","statuses_url":"https://api.github.com/repos/wookietreiber/vcftools/statuses/{sha}","languages_url":"https://api.github.com/repos/wookietreiber/vcftools/languages","stargazers_url":"https://api.github.com/repos/wookietreiber/vcftools/stargazers","contributors_url":"https://api.github.com/repos/wookietreiber/vcftools/contributors","subscribers_url":"https://api.github.com/repos/wookietreiber/vcftools/subscribers","subscription_url":"https://api.github.com/repos/wookietreiber/vcftools/subscription","commits_url":"https://api.github.com/repos/wookietreiber/vcftools/commits{/sha}","git_commits_url":"https://api.github.com/repos/wookietreiber/vcftools/git/commits{/sha}","comments_url":"https://api.github.com/repos/wookietreiber/vcftools/comments{/number}","issue_comment_url":"https://api.github.com/repos/wookietreiber/vcftools/issues/comments{/number}","contents_url":"https://api.github.com/repos/wookietreiber/vcftools/contents/{+path}","compare_url":"https://api.github.com/repos/wookietreiber/vcftools/compare/{base}...{head}","merges_url":"https://api.github.com/repos/wookietreiber/vcftools/merges","archive_url":"https://api.github.com/repos/wookietreiber/vcftools/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/wookietreiber/vcftools/downloads","issues_url":"https://api.github.com/repos/wookietreiber/vcftools/issues{/number}","pulls_url":"https://api.github.com/repos/wookietreiber/vcftools/pulls{/number}","milestones_url":"https://api.github.com/repos/wookietreiber/vcftools/milestones{/number}","notifications_url":"https://api.github.com/repos/wookietreiber/vcftools/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/wookietreiber/vcftools/labels{/name}","releases_url":"https://api.github.com/repos/wookietreiber/vcftools/releases{/id}","created_at":"2015-08-03T15:16:21Z","updated_at":"2015-08-03T15:16:22Z","pushed_at":"2015-08-04T14:31:33Z","git_url":"git://github.com/wookietreiber/vcftools.git","ssh_url":"git@github.com:wookietreiber/vcftools.git","clone_url":"https://github.com/wookietreiber/vcftools.git","svn_url":"https://github.com/wookietreiber/vcftools","homepage":"https://vcftools.github.io/","size":1436,"stargazers_count":0,"watchers_count":0,"language":"C++","has_issues":false,"has_downloads":true,"has_wiki":false,"has_pages":false,"forks_count":0,"mirror_url":null,"open_issues_count":0,"forks":0,"open_issues":0,"watchers":0,"default_branch":"master"}},"base":{"label":"vcftools:master","ref":"master","sha":"990bc01cdc189d730f26210eec370f4353a6efac","user":{"login":"vcftools","id":13243179,"avatar_url":"https://avatars.githubusercontent.com/u/13243179?v=3","gravatar_id":"","url":"https://api.github.com/users/vcftools","html_url":"https://github.com/vcftools","followers_url":"https://api.github.com/users/vcftools/followers","following_url":"https://api.github.com/users/vcftools/following{/other_user}","gists_url":"https://api.github.com/users/vcftools/gists{/gist_id}","starred_url":"https://api.github.com/users/vcftools/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/vcftools/subscriptions","organizations_url":"https://api.github.com/users/vcftools/orgs","repos_url":"https://api.github.com/users/vcftools/repos","events_url":"https://api.github.com/users/vcftools/events{/privacy}","received_events_url":"https://api.github.com/users/vcftools/received_events","type":"Organization","site_admin":false},"repo":{"id":38052058,"name":"vcftools","full_name":"vcftools/vcftools","owner":{"login":"vcftools","id":13243179,"avatar_url":"https://avatars.githubusercontent.com/u/13243179?v=3","gravatar_id":"","url":"https://api.github.com/users/vcftools","html_url":"https://github.com/vcftools","followers_url":"https://api.github.com/users/vcftools/followers","following_url":"https://api.github.com/users/vcftools/following{/other_user}","gists_url":"https://api.github.com/users/vcftools/gists{/gist_id}","starred_url":"https://api.github.com/users/vcftools/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/vcftools/subscriptions","organizations_url":"https://api.github.com/users/vcftools/orgs","repos_url":"https://api.github.com/users/vcftools/repos","events_url":"https://api.github.com/users/vcftools/events{/privacy}","received_events_url":"https://api.github.com/users/vcftools/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/vcftools/vcftools","description":"A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project. ","fork":false,"url":"https://api.github.com/repos/vcftools/vcftools","forks_url":"https://api.github.com/repos/vcftools/vcftools/forks","keys_url":"https://api.github.com/repos/vcftools/vcftools/keys{/key_id}","collaborators_url":"https://api.github.com/repos/vcftools/vcftools/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/vcftools/vcftools/teams","hooks_url":"https://api.github.com/repos/vcftools/vcftools/hooks","issue_events_url":"https://api.github.com/repos/vcftools/vcftools/issues/events{/number}","events_url":"https://api.github.com/repos/vcftools/vcftools/events","assignees_url":"https://api.github.com/repos/vcftools/vcftools/assignees{/user}","branches_url":"https://api.github.com/repos/vcftools/vcftools/branches{/branch}","tags_url":"https://api.github.com/repos/vcftools/vcftools/tags","blobs_url":"https://api.github.com/repos/vcftools/vcftools/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/vcftools/vcftools/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/vcftools/vcftools/git/refs{/sha}","trees_url":"https://api.github.com/repos/vcftools/vcftools/git/trees{/sha}","statuses_url":"https://api.github.com/repos/vcftools/vcftools/statuses/{sha}","languages_url":"https://api.github.com/repos/vcftools/vcftools/languages","stargazers_url":"https://api.github.com/repos/vcftools/vcftools/stargazers","contributors_url":"https://api.github.com/repos/vcftools/vcftools/contributors","subscribers_url":"https://api.github.com/repos/vcftools/vcftools/subscribers","subscription_url":"https://api.github.com/repos/vcftools/vcftools/subscription","commits_url":"https://api.github.com/repos/vcftools/vcftools/commits{/sha}","git_commits_url":"https://api.github.com/repos/vcftools/vcftools/git/commits{/sha}","comments_url":"https://api.github.com/repos/vcftools/vcftools/comments{/number}","issue_comment_url":"https://api.github.com/repos/vcftools/vcftools/issues/comments{/number}","contents_url":"https://api.github.com/repos/vcftools/vcftools/contents/{+path}","compare_url":"https://api.github.com/repos/vcftools/vcftools/compare/{base}...{head}","merges_url":"https://api.github.com/repos/vcftools/vcftools/merges","archive_url":"https://api.github.com/repos/vcftools/vcftools/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/vcftools/vcftools/downloads","issues_url":"https://api.github.com/repos/vcftools/vcftools/issues{/number}","pulls_url":"https://api.github.com/repos/vcftools/vcftools/pulls{/number}","milestones_url":"https://api.github.com/repos/vcftools/vcftools/milestones{/number}","notifications_url":"https://api.github.com/repos/vcftools/vcftools/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/vcftools/vcftools/labels{/name}","releases_url":"https://api.github.com/repos/vcftools/vcftools/releases{/id}","created_at":"2015-06-25T13:48:11Z","updated_at":"2015-08-04T18:08:18Z","pushed_at":"2015-08-04T18:39:53Z","git_url":"git://github.com/vcftools/vcftools.git","ssh_url":"git@github.com:vcftools/vcftools.git","clone_url":"https://github.com/vcftools/vcftools.git","svn_url":"https://github.com/vcftools/vcftools","homepage":"https://vcftools.github.io/","size":1436,"stargazers_count":17,"watchers_count":17,"language":"C++","has_issues":true,"has_downloads":true,"has_wiki":false,"has_pages":false,"forks_count":6,"mirror_url":null,"open_issues_count":4,"forks":6,"open_issues":4,"watchers":17,"default_branch":"master"}},"_links":{"self":{"href":"https://api.github.com/repos/vcftools/vcftools/pulls/9"},"html":{"href":"https://github.com/vcftools/vcftools/pull/9"},"issue":{"href":"https://api.github.com/repos/vcftools/vcftools/issues/9"},"comments":{"href":"https://api.github.com/repos/vcftools/vcftools/issues/9/comments"},"review_comments":{"href":"https://api.github.com/repos/vcftools/vcftools/pulls/9/comments"},"review_comment":{"href":"https://api.github.com/repos/vcftools/vcftools/pulls/comments{/number}"},"commits":{"href":"https://api.github.com/repos/vcftools/vcftools/pulls/9/commits"},"statuses":{"href":"https://api.github.com/repos/vcftools/vcftools/statuses/c850351ecf9cbfc9ecaf857fe6b4ba811bef1fd9"}},"merged":true,"mergeable":null,"mergeable_state":"unknown","merged_by":{"login":"amarcket","id":5130425,"avatar_url":"https://avatars.githubusercontent.com/u/5130425?v=3","gravatar_id":"","url":"https://api.github.com/users/amarcket","html_url":"https://github.com/amarcket","followers_url":"https://api.github.com/users/amarcket/followers","following_url":"https://api.github.com/users/amarcket/following{/other_user}","gists_url":"https://api.github.com/users/amarcket/gists{/gist_id}","starred_url":"https://api.github.com/users/amarcket/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/amarcket/subscriptions","organizations_url":"https://api.github.com/users/amarcket/orgs","repos_url":"https://api.github.com/users/amarcket/repos","events_url":"https://api.github.com/users/amarcket/events{/privacy}","received_events_url":"https://api.github.com/users/amarcket/received_events","type":"User","site_admin":false},"comments":1,"review_comments":0,"commits":3,"additions":18,"deletions":22,"changed_files":1}}