{"action":"created","issue":{"url":"https://api.github.com/repos/vegandevs/vegan/issues/194","repository_url":"https://api.github.com/repos/vegandevs/vegan","labels_url":"https://api.github.com/repos/vegandevs/vegan/issues/194/labels{/name}","comments_url":"https://api.github.com/repos/vegandevs/vegan/issues/194/comments","events_url":"https://api.github.com/repos/vegandevs/vegan/issues/194/events","html_url":"https://github.com/vegandevs/vegan/issues/194","id":172629756,"number":194,"title":"bug fix release 2.4-1?","user":{"login":"jarioksa","id":1432933,"avatar_url":"https://avatars.githubusercontent.com/u/1432933?v=3","gravatar_id":"","url":"https://api.github.com/users/jarioksa","html_url":"https://github.com/jarioksa","followers_url":"https://api.github.com/users/jarioksa/followers","following_url":"https://api.github.com/users/jarioksa/following{/other_user}","gists_url":"https://api.github.com/users/jarioksa/gists{/gist_id}","starred_url":"https://api.github.com/users/jarioksa/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jarioksa/subscriptions","organizations_url":"https://api.github.com/users/jarioksa/orgs","repos_url":"https://api.github.com/users/jarioksa/repos","events_url":"https://api.github.com/users/jarioksa/events{/privacy}","received_events_url":"https://api.github.com/users/jarioksa/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2016-08-23T07:26:45Z","updated_at":"2016-08-29T08:59:15Z","closed_at":null,"body":"It may be that we should have a minor release 2.4-1 in September. For a while this looked necessary because **R-devel**  commit 71113 on 18-Aug changed  `droplevels()` behaviour so that `betadisper()` failed. However, the behaviour was again modified in commit 71129 ( 22-Aug) and old `betadisper()` again works. These changes are discussed in issues #192 and #193. New release is no longer absolutely necessary, but there are some glitches that could be fixed, and we could quite well have a September release. Here some points:\r\n\r\n* Current **CRAN** tests with `R-devel` [WARN](https://cran.r-project.org/web/checks/check_results_vegan.html) on GNU extensions in Fortran files. I have now fixed all these warnings in `cepin.f`, `decorana.f` , `monoMDS.f` and `ordering.f`. None of these fixes changes the behaviour of these functions: they just remove the warnings.\r\n*  `goodness.cca` failed with rank=1 models and had lost `choices` argument. There were also some other glitches that needed fixes. These bugs were introduced with the complete re-writing of the function for the 2.4-0 release. Issues #189 and #190.\r\n* Checking problems in `goodness.cca` also radiated to fixes in some other functions with similar problem, and the work still continues here. Typical case is that we cast a vector to a diagonal matrix with `diagmat <- diag(vec)` which fails if `vec` has only one element (`diag` is one developer biting function that can take a scalar, a vector or a matrix as its first argument -- and works differently in all these cases). Other affected functions are `stressplot.rda`, `stressplot.cca`, `fitted.dbrda`, `inertcomp`, and the search continues. Function `meandist` also failed if the first or the last group had only one item (but worked if one-item groups were in other positions).\r\n* `as.mcmc.oecosimu` failed when there is only one chain (that is, it usually fails). Function is rarely used, and the bug was introduced in 2.4-0 release when `as.mcmc` gained the ability to handle multiple chains.\r\n* `nestedbetajac` and `nestedbetasor` did not cope with quantitative input data. \r\n* although **R** again works with `betadisper` and other `droplevels()` utilizing functions, the fixes made improve robustness and should be published.\r\n\r\nIn addition, there are some new features that could be safely ported: \r\n\r\n* `monoMDS` gained `points` and `text` after a query in [StackOverflow](http://stackoverflow.com/questions/38968880/vegan-package-point-colour). \r\n* `diversity` checks its input and works with `NA`  (issue #187).  \r\n* `ordixyplot` can draw polygons. \r\n* `tabasco` is more configurable. \r\n*  There is a non-merged pull request #184 to change scaling of biplot arrows in `rda` and friends that Daniel Borcard requested for the next edition of their book."},"comment":{"url":"https://api.github.com/repos/vegandevs/vegan/issues/comments/243070357","html_url":"https://github.com/vegandevs/vegan/issues/194#issuecomment-243070357","issue_url":"https://api.github.com/repos/vegandevs/vegan/issues/194","id":243070357,"user":{"login":"jarioksa","id":1432933,"avatar_url":"https://avatars.githubusercontent.com/u/1432933?v=3","gravatar_id":"","url":"https://api.github.com/users/jarioksa","html_url":"https://github.com/jarioksa","followers_url":"https://api.github.com/users/jarioksa/followers","following_url":"https://api.github.com/users/jarioksa/following{/other_user}","gists_url":"https://api.github.com/users/jarioksa/gists{/gist_id}","starred_url":"https://api.github.com/users/jarioksa/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jarioksa/subscriptions","organizations_url":"https://api.github.com/users/jarioksa/orgs","repos_url":"https://api.github.com/users/jarioksa/repos","events_url":"https://api.github.com/users/jarioksa/events{/privacy}","received_events_url":"https://api.github.com/users/jarioksa/received_events","type":"User","site_admin":false},"created_at":"2016-08-29T08:59:15Z","updated_at":"2016-08-29T08:59:15Z","body":"Kurt Hornik approached us with this message on Sunday Aug-28, 2016:\r\n\r\n> Using gfortran with options -Wall -pedantic to compile your package\r\nFortran code finds important problems, see your package check pages for\r\nmore information. \r\n\r\n> Can you please fix these problems as quickly as possible?\r\n\r\nThis means that we need to release 2.4-1. "}}
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