{"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":53,"created_at":"2015-01-26T15:32:26Z","updated_at":"2015-02-09T18:15:04Z","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/73559395","html_url":"https://github.com/stnava/ANTsR/issues/8#issuecomment-73559395","issue_url":"https://api.github.com/repos/stnava/ANTsR/issues/8","id":73559395,"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},"created_at":"2015-02-09T18:15:04Z","updated_at":"2015-02-09T18:15:04Z","body":"am embarrassed to say i never read these directions before:\n\nThe general rules are\n\n   - A package should be listed in only one of these fields.\n   - Packages whose namespace only is needed to load the package using\n   library(pkgname) should be listed in the ‘Imports’ field and not in the ‘\n   Depends’ field. Packages listed in imports or importFrom directives in\n   the NAMESPACE file should almost always be in ‘Imports’ and not ‘Depends\n   ’.\n   - Packages that need to be attached to successfully load the package\n   using library(pkgname) must be listed in the ‘Depends’ field.\n   - All packages that are needed7\n   <http://cran.r-project.org/doc/manuals/r-release/R-exts.html#FOOT7> to\n   successfully run R CMD check on the package must be listed in one of ‘\n   Depends’ or ‘Suggests’ or ‘Imports’. Packages used to run examples or\n   tests conditionally (e.g. *via* if(require(pkgname))) should be listed\n   in ‘Suggests’ or ‘Enhances’. (This allows checkers to ensure that all\n   the packages needed for a complete check are installed.)\n\nIn particular, packages providing “only” data for examples or vignettes\nshould be listed in ‘Suggests’ rather than ‘Depends’ in order to make lean\ninstallations possible.\n\n\nbrian\n\n\n\nOn Mon, Feb 9, 2015 at 1:06 PM, bkandel <notifications@github.com> wrote:\n\n> If we go with '::' calls, is a global import performed on the package or is\n> only that specific function imported?\n>\n> On 9 February 2015 at 13:02, John Muschelli <notifications@github.com>\n> wrote:\n>\n>\n> > Overall, in any of my packages, I use\n> > @importFrom package functiona functionb\n> > and so forth so that I do not have to load all the functionality of a\n> > package\n> >\n> > This can limit what you need and speed up time. Using :: is fine, (\":::\"\n> > is an auto-reject from CRAN), especially when there are multiple\n> functions\n> > of the same name that are hidden.\n> >\n> >\n> >\n> >\n> > On Mon, Feb 9, 2015 at 12:46 PM, bkandel <notifications@github.com>\n> wrote:\n> >\n> > > OK, I'll try that.\n> > >\n> > >\n> > > On 9 February 2015 at 12:43, stnava <notifications@github.com> wrote:\n> > >\n> > > > yes - maybe you are right .... definitely ::: is prohibited ...\n> > > >\n> > > > if you want to pursue this, then you can try the following:\n> > > >\n> > > > (1) change imports to suggests\n> > > >\n> > > > (2) using NAMESPACE as a guide, identify all the functions that need\n> ::\n> > > > and then fix them ...\n> > > >\n> > > > (3) test with\n> > > >\n> > > > R CMD INSTALL ANTsR\n> > > > R CMD build ANTsR\n> > > > R CMD check ANTsR_1.0.tar.gz --as-cran\n> > > >\n> > > > i am making progress with the operators but not there yet ...\n> > > >\n> > > >\n> > > > brian\n> > > >\n> > > >\n> > > >\n> > > > On Mon, Feb 9, 2015 at 12:39 PM, bkandel <notifications@github.com>\n> > > wrote:\n> > > >\n> > > > > The R extension manual (\n> > > > >\n> > > > >\n> > > >\n> > >\n> >\n> http://cran.r-project.org/doc/manuals/r-release/R-exts.html#Package-Dependencies\n> > > > > )\n> > > > > says:\n> > > > > R code in the package should call library or require only\n> > > exceptionally.\n> > > > > Such calls are never needed for packages listed in ‘Depends’ as\n> they\n> > > will\n> > > > > already be on the search path. It used to be common practice to use\n> > > > require\n> > > > > calls for packages listed in ‘suggests’ in functions which used\n> their\n> > > > > functionality, but nowadays it is better to access such\n> functionality\n> > > via\n> > > > > :: calls.\n> > > > >\n> > > > > Doesn't this imply that Suggests + :: calls are acceptable? (Or,\n> > > > > 'exceptionally', to use require, but in any case Suggests + using\n> > > > external\n> > > > > packages should be allowed.)\n> > > > >\n> > > > >\n> > > > > On 9 February 2015 at 12:20, stnava <notifications@github.com>\n> > wrote:\n> > > > >\n> > > > > > yes - those are prohibited\n> > > > > >\n> > > > > >\n> > > > > > brian\n> > > > > >\n> > > > > >\n> > > > > >\n> > > > > > On Mon, Feb 9, 2015 at 12:14 PM, bkandel <\n> notifications@github.com\n> > >\n> > > > > wrote:\n> > > > > >\n> > > > > > > Would using \"suggests\" also trigger failures if all the\n> functions\n> > > > were\n> > > > > > > accessed via '::' calls?\n> > > > > > >\n> > > > > > > On 9 February 2015 at 12:05, stnava <notifications@github.com>\n> > > > wrote:\n> > > > > > >\n> > > > > > > > \"Suggests\" contributes to the problem - names of functions\n> dont\n> > > get\n> > > > > > > > imported thus triggering several different types of check\n> > > failures.\n> > > > > > > > Importing is what's time consuming on startup.\n> > > > > > > >\n> > > > > > > > —\n> > > > > > > > Reply to this email directly or view it on GitHub\n> > > > > > > > <\n> > https://github.com/stnava/ANTsR/issues/8#issuecomment-73546722\n> > > >.\n> > > > > > >\n> > > > > > > >\n> > > > > > >\n> > > > > > > —\n> > > > > > > Reply to this email directly or view it on GitHub\n> > > > > > > <\n> https://github.com/stnava/ANTsR/issues/8#issuecomment-73548262\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-73549557\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-73553075>.\n> > > >\n> > > > >\n> > > >\n> > > > —\n> > > > Reply to this email directly or view it on GitHub\n> > > > <https://github.com/stnava/ANTsR/issues/8#issuecomment-73553932>.\n> > >\n> > > >\n> > >\n> > > —\n> > > Reply to this email directly or view it on GitHub\n> > > <https://github.com/stnava/ANTsR/issues/8#issuecomment-73554291>.\n> >\n> > >\n> >\n> > —\n> > Reply to this email directly or view it on GitHub\n> > <https://github.com/stnava/ANTsR/issues/8#issuecomment-73557141>.\n>\n> >\n>\n> —\n> Reply to this email directly or view it on GitHub\n> <https://github.com/stnava/ANTsR/issues/8#issuecomment-73557901>.\n>\n"}}