* using log directory ‘/home/rstudio/webpages/books/GIS_course/giscourse.Rcheck’ * using R version 3.5.1 (2018-07-02) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using options ‘--no-manual --as-cran’ * checking for file ‘giscourse/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘giscourse’ version ‘0.1.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking serialization versions ... OK * checking whether package ‘giscourse’ can be installed ... OK * checking installed package size ... NOTE installed size is 5.6Mb sub-directories of 1Mb or more: doc 5.5Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. Non-standard license specification: What license is it under? Standardizable: FALSE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘dismo’ A package should be listed in only one of these fields. * checking top-level files ... NOTE Non-standard files/directories found at top level: ‘git_code’ ‘mymap.html’ * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... WARNING 'library' or 'require' calls not declared from: ‘RPostgreSQL’ ‘climatol’ ‘dismo’ ‘dplyr’ ‘leaflet.extras’ ‘mapedit’ ‘maptools’ ‘mapview’ ‘raster’ ‘rpostgis’ ‘sf’ ‘tmap’ ‘tmaptools’ 'library' or 'require' calls in package code: ‘RPostgreSQL’ ‘climatol’ ‘dismo’ ‘dplyr’ ‘leaflet.extras’ ‘mapedit’ ‘maptools’ ‘mapview’ ‘raster’ ‘rpostgis’ ‘sf’ ‘tmap’ ‘tmaptools’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Unexported object imported by a ':::' call: ‘mapview:::mapViewLayersControl’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE connect: no visible global function definition for ‘dbConnect’ disconnect: no visible binding for global variable ‘conn’ disconnect: no visible global function definition for ‘dbDisconnect’ dquery: no visible global function definition for ‘st_crs’ dquery: no visible global function definition for ‘st_read’ dquery: no visible binding for global variable ‘conn’ dquery: no visible global function definition for ‘geocode_OSM’ draw: no visible global function definition for ‘%>%’ draw: no visible global function definition for ‘addDrawToolbar’ draw: no visible global function definition for ‘editToolbarOptions’ draw: no visible global function definition for ‘selectedPathOptions’ draw: no visible global function definition for ‘addLayersControl’ draw: no visible global function definition for ‘layersControlOptions’ draw: no visible global function definition for ‘addStyleEditor’ emap: no visible global function definition for ‘%>%’ emap: no visible global function definition for ‘mapview’ emap: no visible global function definition for ‘geocode_OSM’ emap: no visible global function definition for ‘editMap’ emap: no visible global function definition for ‘st_write’ emap: no visible binding for global variable ‘conn’ extras: no visible global function definition for ‘%>%’ extras: no visible global function definition for ‘addSearchOSM’ extras: no visible global function definition for ‘searchOptions’ extras: no visible global function definition for ‘addFullscreenControl’ extras: no visible global function definition for ‘addMiniMap’ extras: no visible global function definition for ‘addMeasure’ getwclim: no visible global function definition for ‘getData’ getwclim: no visible global function definition for ‘as’ getwclim: no visible global function definition for ‘geocode_OSM’ hansen_wms: no visible global function definition for ‘%>%’ hansen_wms: no visible global function definition for ‘addFullscreenControl’ hansen_wms: no visible global function definition for ‘addMiniMap’ hansen_wms: no visible global function definition for ‘addWMSTiles’ hansen_wms: no visible global function definition for ‘WMSTileOptions’ landcover: no visible global function definition for ‘st_read’ landcover: no visible binding for global variable ‘conn’ landcover: no visible global function definition for ‘dbSendQuery’ merge_rasters: no visible binding for global variable ‘db’ mkpnt: no visible global function definition for ‘geocode_OSM’ mkpnt: no visible global function definition for ‘st_as_sf’ mkpnt: no visible global function definition for ‘st_transform’ mksite: no visible global function definition for ‘st_buffer’ mksite: no visible global function definition for ‘write_sf’ mksite: no visible binding for global variable ‘conn’ os5km: no visible global function definition for ‘write_sf’ os5km: no visible binding for global variable ‘conn’ os5km: no visible global function definition for ‘st_read’ osm: no visible global function definition for ‘st_read’ osm: no visible binding for global variable ‘conn’ osm: no visible global function definition for ‘dbSendQuery’ phabitat: no visible global function definition for ‘st_read’ phabitat: no visible binding for global variable ‘conn’ phabitat: no visible global function definition for ‘dbSendQuery’ qmap: no visible global function definition for ‘addFullscreenControl’ sconnect: no visible global function definition for ‘dbConnect’ sssi: no visible global function definition for ‘st_read’ sssi: no visible binding for global variable ‘conn’ sssi: no visible global function definition for ‘dbSendQuery’ uk_wms: no visible global function definition for ‘%>%’ uk_wms: no visible global function definition for ‘addFullscreenControl’ uk_wms: no visible global function definition for ‘addWMSTiles’ uk_wms: no visible global function definition for ‘WMSTileOptions’ wldiag: no visible global function definition for ‘diagwl’ xyquery: no visible global function definition for ‘st_read’ xyquery: no visible binding for global variable ‘conn’ Undefined global functions or variables: %>% WMSTileOptions addDrawToolbar addFullscreenControl addLayersControl addMeasure addMiniMap addSearchOSM addStyleEditor addWMSTiles as conn db dbConnect dbDisconnect dbSendQuery diagwl editMap editToolbarOptions geocode_OSM getData layersControlOptions mapview searchOptions selectedPathOptions st_as_sf st_buffer st_crs st_read st_transform st_write write_sf Consider adding importFrom("methods", "as") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE prepare_Rd: add_shp.Rd:19-21: Dropping empty section \examples prepare_Rd: osm.Rd:15-17: Dropping empty section \examples * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘draw’ ‘phabitat’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... WARNING Functions or methods with usage in documentation object 'hello' but not in code: hello * checking Rd \usage sections ... WARNING Undocumented arguments in documentation object 'add_shp' ‘flnm’ ‘pth’ ‘srid’ ‘tabnm’ Undocumented arguments in documentation object 'connect' ‘db’ Documented arguments not in \usage in documentation object 'connect': ‘No’ Undocumented arguments in documentation object 'dquery' ‘place’ ‘dist’ Undocumented arguments in documentation object 'landcover' ‘x’ ‘y’ Undocumented arguments in documentation object 'merge_rasters' ‘fls’ ‘tabnm’ ‘dbn’ Undocumented arguments in documentation object 'mksite' ‘x’ ‘y’ Undocumented arguments in documentation object 'os5km' ‘x’ Undocumented arguments in documentation object 'osm' ‘x’ ‘y’ Undocumented arguments in documentation object 'phab_choose' ‘place’ ‘phab’ Undocumented arguments in documentation object 'sssi' ‘x’ ‘y’ Undocumented arguments in documentation object 'xyquery' ‘x’ ‘y’ ‘dist’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... WARNING Argument items with no description in Rd object 'add_shp': ‘db’ Argument items with no description in Rd object 'disconnect': ‘con’ Argument items with no description in Rd object 'dquery': ‘query’ Argument items with no description in Rd object 'hansen_wms': ‘m’ Argument items with no description in Rd object 'landcover': ‘dist’ Argument items with no description in Rd object 'make_db': ‘db’ Argument items with no description in Rd object 'merge_rasters': ‘srid’ Argument items with no description in Rd object 'mksite': ‘dist’ Argument items with no description in Rd object 'os5km': ‘y’ Argument items with no description in Rd object 'osm': ‘dist’ Argument items with no description in Rd object 'phab_choose': ‘dist’ Argument items with no description in Rd object 'qmap': ‘place’ Argument items with no description in Rd object 'sssi': ‘dist’ Argument items with no description in Rd object 'uk_wms': ‘m’ Argument items with no description in Rd object 'wldiag': ‘df’ Argument items with no description in Rd object 'xyquery': ‘query’ * checking for unstated dependencies in examples ... WARNING Warning: parse error in file 'giscourse-Ex.R': 24: unexpected symbol 122: 123: landcover("Arne,Dorset"dist ^ WARNING ‘qpdf’ is needed for checks on size reduction of PDFs * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘giscourse-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: disconnect > ### Title: Quick type disconnect > ### Aliases: disconnect > > ### ** Examples > > disconnect() Loading required package: DBI Error in dbDisconnect(con) : object 'conn' not found Calls: disconnect -> dbDisconnect Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... OK * DONE Status: 1 ERROR, 7 WARNINGs, 5 NOTEs