{"action":"created","issue":{"url":"https://api.github.com/repos/dib-lab/khmer/issues/1387","repository_url":"https://api.github.com/repos/dib-lab/khmer","labels_url":"https://api.github.com/repos/dib-lab/khmer/issues/1387/labels{/name}","comments_url":"https://api.github.com/repos/dib-lab/khmer/issues/1387/comments","events_url":"https://api.github.com/repos/dib-lab/khmer/issues/1387/events","html_url":"https://github.com/dib-lab/khmer/issues/1387","id":160975858,"number":1387,"title":"`test_countgraph.py:test_load_truncated` core dumps in Fedora 23","user":{"login":"standage","id":566823,"avatar_url":"https://avatars.githubusercontent.com/u/566823?v=3","gravatar_id":"","url":"https://api.github.com/users/standage","html_url":"https://github.com/standage","followers_url":"https://api.github.com/users/standage/followers","following_url":"https://api.github.com/users/standage/following{/other_user}","gists_url":"https://api.github.com/users/standage/gists{/gist_id}","starred_url":"https://api.github.com/users/standage/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/standage/subscriptions","organizations_url":"https://api.github.com/users/standage/orgs","repos_url":"https://api.github.com/users/standage/repos","events_url":"https://api.github.com/users/standage/events{/privacy}","received_events_url":"https://api.github.com/users/standage/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2016-06-17T21:12:32Z","updated_at":"2016-06-20T13:49:34Z","closed_at":null,"body":"Walking through the function interactively, it's fine until the following.\r\n\r\n```\r\n>>> _ = khmer.load_countgraph(truncpath)\r\nterminate called after throwing an instance of 'std::ios_base::failure'\r\n  what():  basic_ios::clear\r\nAborted (core dumped)\r\n```\r\n\r\nI don't have much experience with C++ exception handling, and therefore not much intuition for what's happening at that level. At the Python level, it's clear that the the `load_countgraph` command is supposed to evoke some OS error, which Python is supposed to wrap and handle. Why this works on Jenkins and my laptop but not on Fedora is a mystery to me."},"comment":{"url":"https://api.github.com/repos/dib-lab/khmer/issues/comments/227147230","html_url":"https://github.com/dib-lab/khmer/issues/1387#issuecomment-227147230","issue_url":"https://api.github.com/repos/dib-lab/khmer/issues/1387","id":227147230,"user":{"login":"ctb","id":51016,"avatar_url":"https://avatars.githubusercontent.com/u/51016?v=3","gravatar_id":"","url":"https://api.github.com/users/ctb","html_url":"https://github.com/ctb","followers_url":"https://api.github.com/users/ctb/followers","following_url":"https://api.github.com/users/ctb/following{/other_user}","gists_url":"https://api.github.com/users/ctb/gists{/gist_id}","starred_url":"https://api.github.com/users/ctb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ctb/subscriptions","organizations_url":"https://api.github.com/users/ctb/orgs","repos_url":"https://api.github.com/users/ctb/repos","events_url":"https://api.github.com/users/ctb/events{/privacy}","received_events_url":"https://api.github.com/users/ctb/received_events","type":"User","site_admin":false},"created_at":"2016-06-20T13:49:34Z","updated_at":"2016-06-20T13:49:34Z","body":"@standage, I've noticed that more recent versions of gcc are better about\nflagging certain kinds of issues, including memory leaks.  In this case it\ndoesn't look like that kind of issue, but by analogy it's likely to be\nsomething version related :)\n\nWhat version of gcc are you using?\n\nDo you want some help tracking down the line number? You should be able to\ndo something like 'gdb python' and then 'python -m pytest ...', followed\nby a 'where' after the crash, to see which line, exactly, is triggering\nthe error.\n\nWherever the exception is being raised, it seems like it isn't being properly\ncaught and transformed into a khmer_file_exception in\nCountingHashFileReader::CountingHashFileReader in counting.cc.\n"}}
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