{"push_id":677192758,"size":1,"distinct_size":1,"ref":"refs/heads/sim-env","head":"f7211a2c024e0f2805de81247e2f8f20ba5078b1","before":"18c6e5d6122bf8ee2584a77d152fd3c7e2d71a5a","commits":[{"sha":"f7211a2c024e0f2805de81247e2f8f20ba5078b1","author":{"email":"93bb28885269e4acd7ddc153f25cd47df18370b5@gmail.com","name":"Alex Chubaty"},"message":"partial fix of `R CMD check` documentation problems\n\n* added params for `[[` and `$`\n\nstill complains about:\n\n```r\n==> devtools::check(args = c('--as-cran'), build_args = c('--md5'))\n\nUpdating SpaDES documentation\nLoading SpaDES\nLoading required package: data.table\nLoading required package: grid\nLoading required package: raster\nLoading required package: sp\nWriting spadesEnv.Rd\nWriting loadFiles.Rd\n'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file\n--no-environ  \\\n  --no-save --no-restore CMD build\n'/Users/achubaty/Documents/GitHub/SpaDES'  \\\n  --md5 --no-resave-data --no-manual\n\n* checking for file\n‘/Users/achubaty/Documents/GitHub/SpaDES/DESCRIPTION’ ... OK\n* preparing ‘SpaDES’:\n* checking DESCRIPTION meta-information ... OK\n* installing the package to build vignettes\n* creating vignettes ... OK\n* checking for LF line-endings in source and make files\n* checking for empty or unneeded directories\n* adding MD5 file\n* building ‘SpaDES_1.0.0.9000.tar.gz’\n\n'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file\n--no-environ  \\\n  --no-save --no-restore CMD check  \\\n\n'/var/folders/l2/hy6b0sl977bcd8695nt6j7s80000gn/T//RtmpwaaR2V/SpaDES_1.0\n.0.9000.tar.gz'  \\\n  --timings --as-cran\n\n* using log directory ‘/Users/achubaty/Documents/GitHub/SpaDES.Rcheck’\n* using R version 3.2.0 (2015-04-16)\n* using platform: x86_64-apple-darwin13.4.0 (64-bit)\n* using session charset: UTF-8\n* using option ‘--as-cran’\n* checking for file ‘SpaDES/DESCRIPTION’ ... OK\n* checking extension type ... Package\n* this is package ‘SpaDES’ version ‘1.0.0.9000’\n* checking CRAN incoming feasibility ... NOTE\nMaintainer: ‘Alex M Chubaty <achubaty@NRCan.gc.ca>’\nNew submission\n\nSuggests or Enhances not in mainstream repositories:\n  fastshp\n\nAvailability using Additional_repositories specification:\n  fastshp   yes   http://rforge.net\nFound the following (possibly) invalid URLs:\n  URL: http://cran.r-project.org/web/packages/SpaDES\n    From: README.md\n    Status: 404\n    Message: Not Found\n* checking package namespace information ... OK\n* checking package dependencies ... NOTE\n  No repository set, so cyclic dependency check skipped\n* checking if this is a source package ... OK\n* checking if there is a namespace ... OK\n* checking for executable files ... OK\n* checking for hidden files and directories ... OK\n* checking for portable file names ... OK\n* checking for sufficient/correct file permissions ... OK\n* checking whether package ‘SpaDES’ can be installed ... [18s/18s] OK\n* checking installed package size ... OK\n* checking package directory ... OK\n* checking ‘build’ directory ... OK\n* checking DESCRIPTION meta-information ... OK\n* checking top-level files ... OK\n* checking for left-over files ... OK\n* checking index information ... OK\n* checking package subdirectories ... OK\n* checking R files for non-ASCII characters ... OK\n* checking R files for syntax errors ... OK\n* checking whether the package can be loaded ... OK\n* checking whether the package can be loaded with stated dependencies\n... OK\n* checking whether the package can be unloaded cleanly ... OK\n* checking whether the namespace can be loaded with stated dependencies\n... OK\n* checking whether the namespace can be unloaded cleanly ... OK\n* checking loading without being on the library search path ... OK\n* checking use of S3 registration ... OK\n* checking dependencies in R code ... OK\n* checking S3 generic/method consistency ... OK\n* checking replacement functions ... OK\n* checking foreign function calls ... OK\n* checking R code for possible problems ... OK\n* checking Rd files ... OK\n* checking Rd metadata ... OK\n* checking Rd line widths ... OK\n* checking Rd cross-references ... OK\n* checking for missing documentation entries ... WARNING\nUndocumented S4 methods:\n  generic '[[' and siglist 'simList,ANY,ANY'\n  generic '[[<-' and siglist 'simList,ANY,ANY'\nAll user-level objects in a package (including S4 classes and methods)\nshould have documentation entries.\nSee chapter ‘Writing R documentation files’ in the ‘Writing R\nExtensions’ manual.\n```\n\nand\n\n```r\n* checking Rd \\usage sections ... WARNING\nObjects in \\usage without \\alias in documentation object '[[':\n  ‘\\S4method{[[}{simList,ANY,ANY}’ ‘\\S4method{[[<-}{simList,ANY,ANY}’\n\nFunctions with \\usage entries need to have the appropriate \\alias\nentries, and all their arguments documented.\nThe \\usage entries must correspond to syntactically valid R code.\nSee chapter ‘Writing R documentation files’ in the ‘Writing R\nExtensions’ manual.\n```","distinct":true,"url":"https://api.github.com/repos/PredictiveEcology/SpaDES/commits/f7211a2c024e0f2805de81247e2f8f20ba5078b1"}]}