{"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":134,"created_at":"2015-01-26T15:32:26Z","updated_at":"2015-03-17T16:58:00Z","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/82479249","html_url":"https://github.com/stnava/ANTsR/issues/8#issuecomment-82479249","issue_url":"https://api.github.com/repos/stnava/ANTsR/issues/8","id":82479249,"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":"2015-03-17T16:58:00Z","updated_at":"2015-03-17T16:58:00Z","body":"The rcmdcheck branch is up and running.  For some reason, the installation\nis failing, which I'm working on debugging now.  Current theory is that\ninstallation of dependencies changes compile flags.\n\nIf you want to get automated R CMD CHECK results for your commits too, do\nthe following:\n1) Add to your ANTsR/.git/hooks a file called \"post-commit\" that contains:\n#!/bin/bash\ngit checkout rcmdcheck\ngit merge master\ngit checkout master\n\nand make this file executable.\n\n2) Go into the ANTsR dir and type:\ngit config push.default matching\n\nOnce you've done these two things, the rcmdcheck branch will automatically\nmerge the master whenever you commit and push changes to rcmdcheck when you\nrun git push.\n\nAll these changes must be done on the client side (i.e. on your computer);\nthey are not pushed to github.\n\n2015-03-16 13:47 GMT-04:00 Ben Kandel <ben.kandel@sbcglobal.net>:\n\n> OK, started.  Looks like it should be working correctly.\n>\n> 2015-03-16 13:12 GMT-04:00 stnava <notifications@github.com>:\n>\n> that is fine with me\n>>\n>>\n>> brian\n>>\n>>\n>>\n>> On Mon, Mar 16, 2015 at 1:08 PM, bkandel <notifications@github.com>\n>> wrote:\n>>\n>> > It looks to me like making an R CMD CHECK branch makes the most sense.\n>> > This will involve:\n>> > 1) On branch rcmdcheck: Changing the travis yml to install all needed\n>> > packages and run R CMD CHECK instead of R CMD INSTALL\n>> > 2) On master: Setting up the travis yml to build master, cran, and\n>> > rcmdcheck branches on commit\n>> > 3) On local repo: If desired, add the following to\n>> .git/hooks/post-commit:\n>> > #!/bin/bash\n>> > git checkout rcmdcheck\n>> > git merge master\n>> > git checkout master\n>> >\n>> > and make executable.\n>> >\n>> > I think this will be the cleanest way to automate r cmd checking on\n>> travis,\n>> > and I think that the time is counted separately per branch, so the\n>> > 50-minute rule should not stop us.\n>> >\n>> > @stnava -- if you're good with this, I'll implement this approach.\n>> >\n>> > 2015-03-16 12:33 GMT-04:00 stnava <notifications@github.com>:\n>> >\n>> >\n>> > > yes ... i agree that splitting up may ultimately be necessary.\n>> > >\n>> > > however, i think it's probably worth trying the long (current)\n>> approach\n>> > > first to gauge reaction.\n>> > >\n>> > > now that i've studied this more, i think itkr would not be too\n>> difficult.\n>> > > just need to install the 35MB include directory and the 51MB library\n>> ( in\n>> > > form of itkr.so ) within the R package library system. this could be\n>> done\n>> > > by cannibalizing the ANTsRCran package as it stands today ... other\n>> > tricks\n>> > > likely necessary. this appears to be related:\n>> > >\n>> > > https://github.com/jyypma/nloptr\n>> > >\n>> > > ie relatively little functionality from the R source, mostly from the\n>> > > (powerful) library underneath. key things being to compile the library\n>> > > into a .so and write the include flags etc ...\n>> > >\n>> > > a (relatively) low cost experiment to try would be to write a very\n>> simple\n>> > > .cpp in a new Rcpp package skeleton that attempts to make use of\n>> ANTsR.so\n>> > > objects / symbols.\n>> > >\n>> > > this would reveal whatever magic is needed ... sure to be something\n>> about\n>> > > either (a) building both .so and static version or (b) converting (on\n>> the\n>> > > fly) the .so to a static library ....\n>> > >\n>> > > of course with all above passing R CMD check ....\n>> > >\n>> > >\n>> > > brian\n>> > >\n>> > >\n>> > > On Mon, Mar 16, 2015 at 11:58 AM, bkandel <notifications@github.com>\n>> > > wrote:\n>> > >\n>> > > > Working on this...trying to figure out the most efficient way to set\n>> > this\n>> > > > up.\n>> > > >\n>> > > > Either way, I don't see a way to get installation/check down below 7\n>> > > > minutes without splitting into a itkr and ANTsR repos.\n>> > > >\n>> > > > 2015-03-16 10:43 GMT-04:00 stnava <notifications@github.com>:\n>> > > >\n>> > > > > timing using:\n>> > > > >\n>> > > > > time R CMD check ANTsR_1.0.tar.gz --as-cran --no-build-vignettes\n>> > > > >\n>> > > > > on my laptop (recent macbook pro) resulted in about 20 minutes of\n>> > check\n>> > > > > time while running off battery:\n>> > > > >\n>> > > > > real 19m49.732s\n>> > > > > user 23m10.074s\n>> > > > > sys 3m25.180s\n>> > > > >\n>> > > > > so @bkandel <https://github.com/bkandel> - it would be good to\n>> have\n>> > > some\n>> > > > > number from travis ...\n>> > > > >\n>> > > > > —\n>> > > > > Reply to this email directly or view it on GitHub\n>> > > > > <https://github.com/stnava/ANTsR/issues/8#issuecomment-81706686>.\n>> > > >\n>> > > > >\n>> > > >\n>> > > > —\n>> > > > Reply to this email directly or view it on GitHub\n>> > > > <https://github.com/stnava/ANTsR/issues/8#issuecomment-81758798>.\n>> > >\n>> > > >\n>> > >\n>> > > —\n>> > > Reply to this email directly or view it on GitHub\n>> > > <https://github.com/stnava/ANTsR/issues/8#issuecomment-81779570>.\n>> >\n>> > >\n>> >\n>> > —\n>> > Reply to this email directly or view it on GitHub\n>> > <https://github.com/stnava/ANTsR/issues/8#issuecomment-81813483>.\n>>\n>> >\n>>\n>> —\n>> Reply to this email directly or view it on GitHub\n>> <https://github.com/stnava/ANTsR/issues/8#issuecomment-81814788>.\n>>\n>\n>\n"}}