{"action":"created","issue":{"url":"https://api.github.com/repos/rqtl/qtl2geno/issues/35","labels_url":"https://api.github.com/repos/rqtl/qtl2geno/issues/35/labels{/name}","comments_url":"https://api.github.com/repos/rqtl/qtl2geno/issues/35/comments","events_url":"https://api.github.com/repos/rqtl/qtl2geno/issues/35/events","html_url":"https://github.com/rqtl/qtl2geno/issues/35","id":108661093,"number":35,"title":"iron dataset: warning followed by segfault ","user":{"login":"simecek","id":359539,"avatar_url":"https://avatars.githubusercontent.com/u/359539?v=3","gravatar_id":"","url":"https://api.github.com/users/simecek","html_url":"https://github.com/simecek","followers_url":"https://api.github.com/users/simecek/followers","following_url":"https://api.github.com/users/simecek/following{/other_user}","gists_url":"https://api.github.com/users/simecek/gists{/gist_id}","starred_url":"https://api.github.com/users/simecek/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/simecek/subscriptions","organizations_url":"https://api.github.com/users/simecek/orgs","repos_url":"https://api.github.com/users/simecek/repos","events_url":"https://api.github.com/users/simecek/events{/privacy}","received_events_url":"https://api.github.com/users/simecek/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/rqtl/qtl2geno/labels/bug","name":"bug","color":"fc2929"}],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2015-09-28T13:45:17Z","updated_at":"2015-09-29T01:21:16Z","closed_at":"2015-09-29T01:21:16Z","body":"Both\r\n\r\niron <- read_cross2(\"http://kbroman.org/qtl2/assets/sampledata/iron/iron.zip\")\r\n\r\nand\r\n\r\niron2 <- read_cross2(system.file(\"extdata\", \"iron.zip\", package=\"qtl2geno\"))\r\n\r\ngive me the following warning I do not understand\r\n\r\nWarning message:\r\nIn data.table::fread(filename, na.strings = na.strings, sep = sep,  :\r\n  Bumped column 2 to type character on data row 65, field contains 'X'. Coercing previously read values in this column from logical, integer or numeric back to character which may not be lossless; e.g., if '00' and '000' occurred before they will now be just '0', and there may be inconsistencies with treatment of ',,' and ',NA,' too (if they occurred in this column before the bump). If this matters please rerun and set 'colClasses' to 'character' for this column. Please note that column type detection uses the first 5 rows, the middle 5 rows and the last 5 rows, so hopefully this message should be very rare. If reporting to datatable-help, please rerun and include the output from verbose=TRUE.\r\n\r\nWhen I try to estimate the map, I get segmentation fault \r\n\r\n> est_map(iron)\r\n\r\n*** caught segfault ***\r\naddress (nil), cause 'unknown'\r\nSegmentation fault (core dumped)\r\n\r\nThe error is iron dataset specific, grav2 works fine.\r\n\r\nR version 3.1.2 (2014-10-31)\r\nPlatform: x86_64-unknown-linux-gnu (64-bit)\r\n\r\nlocale:\r\n [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C\r\n [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8\r\n [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8\r\n [7] LC_PAPER=en_US.UTF-8       LC_NAME=C\r\n [9] LC_ADDRESS=C               LC_TELEPHONE=C\r\n[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C\r\n\r\nattached base packages:\r\n[1] stats     graphics  grDevices utils     datasets  methods   base\r\n\r\nother attached packages:\r\n[1] qtl2geno_0.3-12\r\n\r\nloaded via a namespace (and not attached):\r\n[1] Rcpp_0.11.4"},"comment":{"url":"https://api.github.com/repos/rqtl/qtl2geno/issues/comments/143917129","html_url":"https://github.com/rqtl/qtl2geno/issues/35#issuecomment-143917129","issue_url":"https://api.github.com/repos/rqtl/qtl2geno/issues/35","id":143917129,"user":{"login":"kbroman","id":53972,"avatar_url":"https://avatars.githubusercontent.com/u/53972?v=3","gravatar_id":"","url":"https://api.github.com/users/kbroman","html_url":"https://github.com/kbroman","followers_url":"https://api.github.com/users/kbroman/followers","following_url":"https://api.github.com/users/kbroman/following{/other_user}","gists_url":"https://api.github.com/users/kbroman/gists{/gist_id}","starred_url":"https://api.github.com/users/kbroman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kbroman/subscriptions","organizations_url":"https://api.github.com/users/kbroman/orgs","repos_url":"https://api.github.com/users/kbroman/repos","events_url":"https://api.github.com/users/kbroman/events{/privacy}","received_events_url":"https://api.github.com/users/kbroman/received_events","type":"User","site_admin":false},"created_at":"2015-09-29T01:21:16Z","updated_at":"2015-09-29T01:21:16Z","body":"Fixed in PR #38."}}