{"action":"created","issue":{"url":"https://api.github.com/repos/stnava/ANTsR/issues/8","labels_url":"https://api.github.com/repos/stnava/ANTsR/issues/8/labels{/name}","comments_url":"https://api.github.com/repos/stnava/ANTsR/issues/8/comments","events_url":"https://api.github.com/repos/stnava/ANTsR/issues/8/events","html_url":"https://github.com/stnava/ANTsR/issues/8","id":55495708,"number":8,"title":"ANTsR: towards CRAN & standardization of development","user":{"login":"stnava","id":324222,"avatar_url":"https://avatars.githubusercontent.com/u/324222?v=3","gravatar_id":"","url":"https://api.github.com/users/stnava","html_url":"https://github.com/stnava","followers_url":"https://api.github.com/users/stnava/followers","following_url":"https://api.github.com/users/stnava/following{/other_user}","gists_url":"https://api.github.com/users/stnava/gists{/gist_id}","starred_url":"https://api.github.com/users/stnava/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/stnava/subscriptions","organizations_url":"https://api.github.com/users/stnava/orgs","repos_url":"https://api.github.com/users/stnava/repos","events_url":"https://api.github.com/users/stnava/events{/privacy}","received_events_url":"https://api.github.com/users/stnava/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":156,"created_at":"2015-01-26T15:32:26Z","updated_at":"2015-03-23T16:30:17Z","closed_at":null,"body":"@ntustison , @bkandel , @dorianps, @jeffduda , @cookpa , @armaneshaghi, @muschellij2 \r\n\r\nhoping to work toward a CRAN submission for ANTsR - some updates on this topic:\r\n\r\ni ran rd2roxygen and dealt with most of the issues.  hopefully wont have \r\n\r\nto do that again ... so, in the future, we should write documentation \r\n\r\nusing the roxygen2 style and just roxygenize() regularly.  \r\n\r\na couple other changes\r\n\r\n* enabled plot( antsImage ) so we dont need to type plotANTsImage \r\n\r\n*  added resampleImage \r\n\r\n*  updated invariantImageSimilarity to use reflection as well as rotation, only tested in 2D so far\r\n\r\n*  added CreateJacobianDeterminantImage\r\n\r\n*   added a simple kmeansSegmentation filter ...\r\n\r\n*  would like to start running R  CMD CHECK and get failures to a minimum ...\r\n\r\n*  need to write a quick vignette, possibly based on the README.md ...\r\n\r\n@muschellij2  - would appreciate any advice / help on this .... \r\n\r\nsome advice from wickham: http://www.rstudio.com/products/rpackages/devtools/\r\n\r\nit's a very good page with strategies that will help with most of the issues we've had in the past ...\r\n\r\nany thoughts appreciated."},"comment":{"url":"https://api.github.com/repos/stnava/ANTsR/issues/comments/85079500","html_url":"https://github.com/stnava/ANTsR/issues/8#issuecomment-85079500","issue_url":"https://api.github.com/repos/stnava/ANTsR/issues/8","id":85079500,"user":{"login":"bkandel","id":606089,"avatar_url":"https://avatars.githubusercontent.com/u/606089?v=3","gravatar_id":"","url":"https://api.github.com/users/bkandel","html_url":"https://github.com/bkandel","followers_url":"https://api.github.com/users/bkandel/followers","following_url":"https://api.github.com/users/bkandel/following{/other_user}","gists_url":"https://api.github.com/users/bkandel/gists{/gist_id}","starred_url":"https://api.github.com/users/bkandel/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bkandel/subscriptions","organizations_url":"https://api.github.com/users/bkandel/orgs","repos_url":"https://api.github.com/users/bkandel/repos","events_url":"https://api.github.com/users/bkandel/events{/privacy}","received_events_url":"https://api.github.com/users/bkandel/received_events","type":"User","site_admin":false},"created_at":"2015-03-23T16:30:17Z","updated_at":"2015-03-23T16:30:17Z","body":"I think doing our own advertising would be more important than CRAN.\nSpecifically:\n1) Nice vignettes that show non-trivial examples of how ANTsR can be useful\n2) JSS submission, once we reach stability.\n\nOnce we have that, install.github should be fine, I think.\n\n2015-03-23 12:25 GMT-04:00 stnava <notifications@github.com>:\n\n> yes - that is a common complaint that, if lucky, one will benefit from:\n> i.e. CRAN package review is not actually objective.\n>\n> anyway, i think development will proceed more or less as is with the added\n> benefit that we now know what needs to be done to keep the package clean in\n> terms of documentation etc.\n>\n> primary barriers remain, maybe show-stoppers:\n>\n> * cmake dependency\n>\n> * unless someone wants to identify how to build all of ants/itk with\n> autoconf (definitely not me)\n>\n> * build time\n> * on the order of 10 minutes for itk, 12 or so for ants\n>\n> * package footprint - no real way to avoid numbers in this range\n> * cmaker (15MB minimum), itk (90MB), ants (66MB)\n>\n> maybe [drat](http://dirk.eddelbuettel.com/code/drat.html) would help\n> discoverability - not sure.\n>\n>\n> brian\n>\n>\n> On Mon, Mar 23, 2015 at 12:15 PM, John Muschelli <notifications@github.com\n> >\n> wrote:\n>\n>\n> > FSLR originally had 2 goals:\n> > 1) Wrap FSL commands\n> > 2) Expand functions of the oro.nifti package (these were testable)\n> >\n> > 1) I didn't have many tests - I wrote this over a year ago\n> > 2) Technically, CRAN checks get angry if you don't have ANY examples, but\n> > it counts an example even if wrapped in a \\dontrun{}\n> >\n> > It may have been a luck of the draw as I believe Kurt Hornik and Uwes\n> > Ligges were the main reviewers.\n> >\n> >\n> >\n> >\n> > On Mon, Mar 23, 2015 at 12:05 PM, bkandel <notifications@github.com>\n> > wrote:\n> >\n> > > I'm actually sort of shocked that you got FSLR accepted by CRAN if they\n> > > couldn't run any of your code or tests without having FSL installed.\n> Were\n> > > there any meaningful/helpful comments along the way?\n> > >\n> > > 2015-03-23 12:00 GMT-04:00 John Muschelli <notifications@github.com>:\n> > >\n> > >\n> > > > We've run into similar things. We have discussed creating\n> > > > Bioconductor-like alternative for imaging primarily on GitHub, but\n> > > haven't\n> > > > really gauged interest. It seems like there may be more and more of\n> > these\n> > > > cases.\n> > > >\n> > > > As of now though, I would say that I have had a few auto-rejects from\n> > > CRAN\n> > > > but they are still open (albeit maybe more critical) of submissions.\n> I\n> > > > haven't figured out the best way around CRAN's requirements\n> (especially\n> > > > file sizes).\n> > > >\n> > > > I would say just adding ITK and CMake to System Requirements (qtbase\n> > > req's\n> > > > CMake):\n> > > > http://cran.r-project.org/web/packages/qtbase/index.html\n> > > >\n> > > > I figure this was the only way I could figure to do fslr without\n> having\n> > > to\n> > > > install FSL (as it's like 5Gb):\n> > > > http://cran.r-project.org/web/packages/fslr/index.html\n> > > >\n> > > > Obviously this limits people to who can install ITK and CMake and is\n> > less\n> > > > packaged than your github install right now, but still would be\n> useful.\n> > > > Sorry I'm not more help.\n> > > >\n> > > >\n> > > >\n> > > >\n> > > >\n> > > >\n> > > > On Mon, Mar 23, 2015 at 11:49 AM, stnava <notifications@github.com>\n> > > wrote:\n> > > >\n> > > > > the non-transparent nature of the CRAN submission / rejection\n> process\n> > > is\n> > > > > particularly at issue. because it leads to a lack of accountability\n> > on\n> > > > > their side.\n> > > > >\n> > > > >\n> > > > > ​​\n> > > > >\n> > > > > —\n> > > > > Reply to this email directly or view it on GitHub\n> > > > > <https://github.com/stnava/ANTsR/issues/8#issuecomment-85057543>.\n> > > >\n> > > > >\n> > > >\n> > > > —\n> > > > Reply to this email directly or view it on GitHub\n> > > > <https://github.com/stnava/ANTsR/issues/8#issuecomment-85065648>.\n> > >\n> > > >\n> > >\n> > > —\n> > > Reply to this email directly or view it on GitHub\n> > > <https://github.com/stnava/ANTsR/issues/8#issuecomment-85067871>.\n> >\n> > >\n> >\n> > —\n> > Reply to this email directly or view it on GitHub\n> > <https://github.com/stnava/ANTsR/issues/8#issuecomment-85071637>.\n>\n> >\n>\n> —\n> Reply to this email directly or view it on GitHub\n> <https://github.com/stnava/ANTsR/issues/8#issuecomment-85076031>.\n>\n"}}