R Development Page

MODIS log file (check_x86_64_linux)

Thu Aug 18 15:03:22 2016: Checking package MODIS (SVN revision 510) ...
* using log directory ‘/mnt/building/build_2016-08-18-12-24/RF_PKG_CHECK/PKGS/MODIS.Rcheck’
* using R version 3.3.1 Patched (2016-08-17 r71112)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘MODIS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MODIS’ version ‘0.10-34’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Matteo Mattiuzzi ’

New submission

Found the following (possibly) invalid URLs:
  URL: ftp://e4ftl01.cr.usgs.gov/
    From: man/getHdf.Rd
    Status: Error
    Message: libcurl error code 7
    	Failed to connect to e4ftl01.cr.usgs.gov port 21: Connection timed out
  URL: ftp://e4ftl01u.ecs.nasa.gov/
    From: man/getHdf.Rd
    Status: Error
    Message: libcurl error code 7
    	Failed to connect to e4ftl01u.ecs.nasa.gov port 21: Connection timed out
  URL: http://modis-land.gsfc.nasa.gov/MODLAND_grid.htm
    From: man/delHdf.Rd
          man/getHdf.Rd
    Status: 404
    Message: Not Found

The Title field starts with the package name.

The Date field is not in ISO 8601 yyyy-mm-dd format.
* 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 whether package ‘MODIS’ can be installed ... [8s/9s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* 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 use of S3 registration ... OK
* checking dependencies in R code ... WARNING
'library' or 'require' calls in package code:
  ‘RCurl’ ‘XML’ ‘bitops’ ‘mapdata’ ‘ptw’ ‘rgdal’ ‘rgeos’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
':::' call which should be '::': ‘parallel:::clusterEvalQ’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘parallel:::recvOneData’ ‘parallel:::sendCall’ ‘raster:::.doCluster’
  See the note in ?`:::` about the use of this operator.
  Including base/recommended package(s):
  ‘parallel’
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘filesUrl’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ModisFileDownloader: no visible global function definition for
  ‘download.file’
arcStats: no visible global function definition for ‘png’
arcStats: no visible global function definition for ‘map’
arcStats: no visible global function definition for ‘coordinates<-’
arcStats: no visible global function definition for ‘proj4string<-’
arcStats: no visible global function definition for ‘spTransform’
arcStats: no visible global function definition for ‘CRS’
arcStats: no visible global function definition for ‘as’
arcStats: no visible global function definition for ‘spplot’
arcStats: no visible global function definition for ‘dev.off’
arcStats: no visible global function definition for ‘write.csv’
checkDeps: no visible global function definition for
  ‘installed.packages’
checkOutProj: no visible global function definition for ‘CRS’
checksizefun: no visible global function definition for ‘xmlParse’
checksizefun: no visible global function definition for ‘getNodeSet’
checksizefun: no visible global function definition for ‘xmlValue’
extractBits: no visible global function definition for ‘bitAnd’
extractBits: no visible global function definition for ‘bitShiftR’
filesUrl: no visible global function definition for ‘getURLContent’
filesUrl: no visible global function definition for ‘htmlTreeParse’
filesUrl : : no visible global function definition for
  ‘xmlGetAttr’
getHdf: no visible global function definition for ‘download.file’
getHdf: no visible global function definition for ‘getURL’
getHdf: no visible global function definition for ‘write.table’
getHdf: no visible global function definition for ‘read.table’
getStruc: no visible global function definition for ‘na.omit’
getStruc: no visible global function definition for ‘read.table’
getStruc: no visible global function definition for ‘write.table’
getTile: no visible global function definition for ‘map’
getTile: no visible global function definition for ‘CRS’
getTile: no visible global function definition for ‘spTransform’
getTile: no visible global function definition for ‘proj4string’
getTile: no visible global function definition for ‘proj4string<-’
getTile: no visible global function definition for ‘gBuffer’
getTile: no visible global function definition for ‘Polygon’
getTile: no visible global function definition for ‘Polygons’
getTile: no visible global function definition for ‘SpatialPolygons’
m2SL: no visible global function definition for ‘CRS’
m2SL: no visible global function definition for ‘Line’
m2SL: no visible global function definition for ‘Lines’
m2SL: no visible global function definition for ‘SpatialLines’
m2SP: no visible global function definition for ‘CRS’
m2SP: no visible global function definition for ‘Polygon’
m2SP: no visible global function definition for ‘Polygons’
m2SP: no visible global function definition for
  ‘as.SpatialPolygons.PolygonsList’
makeWeights: no visible global function definition for ‘bitAnd’
makeWeights: no visible global function definition for ‘bitShiftR’
mapSelect: no visible global function definition for ‘dev.new’
mapSelect: no visible global function definition for ‘map’
mapSelect: no visible global function definition for ‘map.axes’
mapSelect: no visible global function definition for ‘grid’
mapSelect: no visible global function definition for ‘abline’
mapSelect: no visible global function definition for ‘title’
mapSelect: no visible global function definition for ‘locator’
mapSelect: no visible global function definition for ‘dev.off’
miwhitatzb1: no visible global function definition for ‘whit1’
miwhitatzb2: no visible global function definition for ‘whit2’
search4map: no visible global function definition for ‘map’
search4map: no visible global function definition for ‘map.axes’
search4map: no visible global function definition for ‘box’
search4map: no visible global function definition for ‘grid’
search4map: no visible global function definition for ‘title’
smooth.spline.raster: no visible binding for global variable ‘opts’
smooth.spline.raster: no visible global function definition for
  ‘sendCall’
smooth.spline.raster: no visible global function definition for
  ‘recvOneData’
smooth.spline.raster: no visible global function definition for
  ‘clusterEvalQ’
smooth.spline.raster : clFun: no visible binding for global variable
  ‘vi’
smooth.spline.raster: no visible global function definition for
  ‘write.table’
smooth.splineMtr: no visible global function definition for
  ‘smooth.spline’
st1: no visible global function definition for ‘na.omit’
whittaker.raster : clFun : kickOutlier: no visible global function
  definition for ‘whit2’
whittaker.raster : clFun: no visible global function definition for
  ‘whit2’
writeStopMODIS: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  CRS Line Lines Polygon Polygons SpatialLines SpatialPolygons abline
  as as.SpatialPolygons.PolygonsList bitAnd bitShiftR box clusterEvalQ
  coordinates<- dev.new dev.off download.file gBuffer getNodeSet getURL
  getURLContent grid htmlTreeParse installed.packages locator map
  map.axes na.omit opts png proj4string proj4string<- read.table
  recvOneData sendCall smooth.spline spTransform spplot title vi whit1
  whit2 write.csv write.table xmlGetAttr xmlParse xmlValue
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "png")
  importFrom("graphics", "abline", "box", "grid", "locator", "title")
  importFrom("methods", "as")
  importFrom("stats", "na.omit", "smooth.spline")
  importFrom("utils", "download.file", "installed.packages",
             "read.table", "vi", "write.csv", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'smoothspline.Rd':
  \examples lines wider than 100 characters:
     # https://ivfl-rio.boku.ac.at/owncloud/public.php?service=files&t=2fdac3598dba8f5bd865b9dadd715e22&download

Rd file 'whittaker.raster.Rd':
  \usage lines wider than 90 characters:
     whittaker.raster(vi, w=NULL, t=NULL, timeInfo = orgTime(vi), lambda = 5000, nIter= 3, outputAs="single", collapse=FALSE, prefixSuffix=c ... [TRUNCATED]
  \examples lines wider than 100 characters:
     # https://ivfl-rio.boku.ac.at/owncloud/public.php?service=files&t=2fdac3598dba8f5bd865b9dadd715e22&download

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'whittaker.raster':
  ‘removeOutlier’

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 ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... [2s/2s] OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 3 NOTEs
See
  ‘/mnt/building/build_2016-08-18-12-24/RF_PKG_CHECK/PKGS/MODIS.Rcheck/00check.log’
for details.


Run time: 358.97 seconds.