R Development Page

moveBB log file (check_x86_64_linux)

Wed Sep  6 11:25:25 2017: Checking package moveBB (SVN revision 33) ...
* using log directory ‘/mnt/building/build_2017-09-06-11-24/RF_PKG_CHECK/PKGS/moveBB.Rcheck’
* using R version 3.4.1 Patched (2017-09-04 r73206)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘moveBB/DESCRIPTION’ ... OK
* this is package ‘moveBB’ version ‘0.7.11’
* checking CRAN incoming feasibility ...Warning: /mnt/building/build_2017-09-06-11-24/RF_PKG_CHECK/PKGS/moveBB.Rcheck/00_pkg_src/moveBB/man/statistics.Rd:15: unknown macro '\const'
Warning: /mnt/building/build_2017-09-06-11-24/RF_PKG_CHECK/PKGS/moveBB.Rcheck/00_pkg_src/moveBB/man/statistics.Rd:15: unknown macro '\const'
 NOTE
Maintainer: ‘Stef Sijben ’

New submission

The Date field is not in ISO 8601 yyyy-mm-dd format.
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘OpenCL’
* 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 ‘moveBB’ can be installed ... [8s/8s] WARNING
Found the following significant warnings:
  Warning: /mnt/building/build_2017-09-06-11-24/RF_PKG_CHECK/PKGS/moveBB.Rcheck/00_pkg_src/moveBB/man/statistics.Rd:15: unknown macro '\const'
See ‘/mnt/building/build_2017-09-06-11-24/RF_PKG_CHECK/PKGS/moveBB.Rcheck/00install.out’ for details.
* 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 ... NOTE
'library' or 'require' call to ‘OpenCL’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘parallel’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
package 'methods' is used but not declared
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  barplot.encounterDuration contour.ud
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [15s/14s] NOTE
Found the following possibly unsafe calls:
File ‘moveBB/R/OpenCL.r’:
  unlockBinding(".OpenCL_kernels", loadNamespace(getPackageName()))

.OpenCL: no visible global function definition for ‘oclRun’
.OpenCL: no visible global function definition for ‘getPackageName’
.OpenCL_getKernel: no visible global function definition for
  ‘getPackageName’
.OpenCL_getKernel: no visible global function definition for
  ‘oclSimpleKernel’
.OpenCL_init: no visible global function definition for
  ‘packageVersion’
.OpenCL_init: no visible global function definition for ‘oclPlatforms’
.OpenCL_init: no visible binding for global variable ‘oclDevices’
.OpenCL_init : : no visible global function definition for
  ‘oclInfo’
.OpenCL_init: no visible global function definition for ‘oclInfo’
.direction_cdf : : no visible global function definition for
  ‘integrate’
.direction_pdf: no visible global function definition for ‘pnorm’
.moveBB: no visible global function definition for ‘is’
.moveBB: no visible global function definition for ‘new’
.overlappingBursts: no visible global function definition for
  ‘bbFilterNA’
barplot.encounterDuration: no visible global function definition for
  ‘hcl’
contour.ud: no visible global function definition for ‘hcl’
.distance_statistic,MoveBBStack-numeric: no visible global function
  definition for ‘mclapply’
[,MoveBB-ANY-ANY: no visible global function definition for
  ‘callNextMethod’
[,MoveBBStack-ANY-ANY: no visible global function definition for
  ‘callNextMethod’
[[,UDStack-ANY-ANY: no visible global function definition for
  ‘callNextMethod’
[[,UDStack-ANY-ANY: no visible global function definition for ‘new’
contourPolygons,RasterLayer-numeric: no visible global function
  definition for ‘contourLines’
contourPolygons,RasterLayer-numeric: no visible global function
  definition for ‘SpatialPolygons’
contourPolygons,RasterLayer-numeric : : no visible global
  function definition for ‘Polygons’
contourPolygons,RasterLayer-numeric :  : : no
  visible global function definition for ‘Polygon’
moveBBStack,list: no visible binding for global variable ‘as’
moveBBStack,list: no visible binding for global variable ‘slot’
moveBBStack,list: no visible global function definition for ‘new’
position,MoveBB-numeric : : no visible global function
  definition for ‘integrate’
speedDistribution,.MoveTrack-RasterLayer-numeric-missing: no visible
  binding for global variable ‘time.scale’
split,MoveBBStack-missing: no visible binding for global variable ‘as’
summary,.MoveTrackSingle: no visible global function definition for
  ‘distanceSummary’
summary,.MoveTrackSingle: no visible global function definition for
  ‘timeSummary’
summary,.MoveTrackSingle: no visible global function definition for
  ‘speedSummary’
summary,.MoveTrackSingle: no visible global function definition for
  ‘angleSummary’
summary,.MoveTrackSingle: no visible global function definition for
  ‘Line’
summary,.MoveTrackSingle: no visible global function definition for
  ‘SpatialLinesDataFrame’
summary,.MoveTrackSingle: no visible global function definition for
  ‘SpatialLines’
summary,.MoveTrackSingle: no visible global function definition for
  ‘Lines’
summary,.MoveTrackStack : : no visible global function
  definition for ‘spChFIDs’
unstack,UDStack: no visible global function definition for
  ‘callNextMethod’
unstack,UDStack : : no visible global function definition
  for ‘new’
utilizationDistribution,MoveBB-RasterLayer-numeric: no visible global
  function definition for ‘new’
utilizationDistribution,MoveBBStack-RasterLayer-numeric: no visible
  global function definition for ‘new’
velocity,MoveBB-numeric-numeric : : no visible global
  function definition for ‘integrate’
Undefined global functions or variables:
  Line Lines Polygon Polygons SpatialLines SpatialLinesDataFrame
  SpatialPolygons angleSummary as bbFilterNA callNextMethod
  contourLines distanceSummary getPackageName hcl integrate is mclapply
  new oclDevices oclInfo oclPlatforms oclRun oclSimpleKernel
  packageVersion pnorm slot spChFIDs speedSummary time.scale
  timeSummary
Consider adding
  importFrom("grDevices", "contourLines", "hcl")
  importFrom("methods", "as", "callNextMethod", "getPackageName", "is",
             "new", "slot")
  importFrom("stats", "integrate", "pnorm")
  importFrom("utils", "packageVersion")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... WARNING
prepare_Rd: MoveBBStack-class.Rd:73-75: Dropping empty section \note
prepare_Rd: MoveBBStack-class.Rd:70-72: Dropping empty section \author
prepare_Rd: MoveBBStack-class.Rd:67-69: Dropping empty section \references
prepare_Rd: MoveBBStack-class.Rd:79-82: Dropping empty section \seealso
prepare_Rd: monkey.data.Rd:24-26: Dropping empty section \source
prepare_Rd: monkey.tr.Rd:17-19: Dropping empty section \source
prepare_Rd: moveBBStack.Rd:7-9: Dropping empty section \description
prepare_Rd: moveBBStack.Rd:15-17: Dropping empty section \details
prepare_Rd: moveBBStack.Rd:18-20: Dropping empty section \source
prepare_Rd: moveBBStack.Rd:21-23: Dropping empty section \references
checkRd: (5) moveBBStack.Rd:0-29: Must have a \description
prepare_Rd: statistics.Rd:15: unknown macro '\const'
prepare_Rd: statistics.Rd:5-8: Dropping empty section \description
checkRd: (5) statistics.Rd:0-38: Must have a \description
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'encounterDuration.Rd':
  \usage lines wider than 90 characters:
     encounterDuration(tr, threshold, model = c("BBMM", "linear"), byburst = FALSE, timestepSize = 60)

Rd file 'speedDistribution.Rd':
  \usage lines wider than 90 characters:
     speedDistribution(tr, grid = NULL, timestepSize = 60, time.scale = timestepSize, xc = NULL, yc = NULL, grid.dim = 100, grid.pad = 0.2)

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'MoveBB-class.Rd':
  ‘move:Move-class’

Missing link or links in documentation object 'MoveBBStack-class.Rd':
  ‘.BBInfo-class’ ‘SpatialPointsDataFrame-class’ ‘SpatialPoints-class’
  ‘Spatial-class’

Missing link or links in documentation object 'contourPolygons.Rd':
  ‘SpatialPolygons-class’ ‘Polygons-class’

Missing link or links in documentation object 'direction.Rd':
  ‘bbtraj’

Missing link or links in documentation object 'distance.Rd':
  ‘bbtraj’

Missing link or links in documentation object 'encounterDuration.Rd':
  ‘bbtraj’

Missing link or links in documentation object 'moveBB.Rd':
  ‘CRS-class’

Missing link or links in documentation object 'plot.utilizationDistribution.Rd':
  ‘SpatialPolygons’

Missing link or links in documentation object 'position.Rd':
  ‘bbtraj’

Missing link or links in documentation object 'speed.Rd':
  ‘bbtraj’

Missing link or links in documentation object 'speedDistribution.Rd':
  ‘bbtraj’

Missing link or links in documentation object 'velocity.Rd':
  ‘bbtraj’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘IDs’ ‘circumcircle.ct’ ‘circumcircle.ll’ ‘classify’ ‘contour.ud’
  ‘diffusion’ ‘diffusion.LL’ ‘diffusion.convert’ ‘diffusion<-’
  ‘diffusionCoefficient’ ‘displacement.direction’
  ‘displacement.distance’ ‘dist.ct’ ‘dist.ll’ ‘interpolate’ ‘ll2xyz’
  ‘midpoint.ct’ ‘midpoint.ll’ ‘moveBB’ ‘segment.cnt’ ‘segment.dscr’
  ‘statistics’ ‘xyz2ll’
Undocumented S4 classes:
  ‘UD’ ‘UDStack’
Undocumented S4 methods:
  generic '[[' and siglist 'UDStack,ANY,ANY'
  generic 'classify' and siglist 'MoveBBStack,matrix,missing'
  generic 'classify' and siglist 'MoveBBStack,matrix,numeric'
  generic 'classify' and siglist 'MoveBBStack,missing,ANY'
  generic 'classify' and siglist 'MoveBBStack,numeric,ANY'
  generic 'contourPolygons' and siglist 'ANY,missing'
  generic 'contourPolygons' and siglist 'RasterLayer,numeric'
  generic 'contourPolygons' and siglist 'RasterStack,numeric'
  generic 'diffusion.convert' and siglist 'dBMvariance'
  generic 'diffusion.convert' and siglist 'function'
  generic 'diffusion.convert' and siglist 'matrix'
  generic 'diffusion.convert' and siglist 'numeric'
  generic 'diffusion' and siglist '.BBInfo'
  generic 'diffusion<-' and siglist '.BBInfo'
  generic 'moveBB' and siglist
    '.MoveTrack,missing,numeric,missing,missing,missing'
  generic 'moveBB' and siglist 'ANY,ANY,missing,ANY,ANY,ANY'
  generic 'moveBB' and siglist 'ANY,ANY,numeric,ANY,missing,ANY'
  generic 'moveBB' and siglist
    'numeric,numeric,numeric,POSIXct,data.frame,ANY'
  generic 'moveBBStack' and siglist 'list'
  generic 'position' and siglist 'ANY,POSIXct'
  generic 'position' and siglist 'MoveBBStack,numeric'
  generic 'segment.cnt' and siglist 'MoveBB,function,missing'
  generic 'segment.cnt' and siglist 'MoveBB,function,numeric'
  generic 'segment.cnt' and siglist 'MoveBB,missing,ANY'
  generic 'speedDistribution' and siglist
    '.MoveTrack,RasterLayer,numeric,missing'
  generic 'speedDistribution' and siglist '.MoveTrack,missing,ANY,ANY'
  generic 'split' and siglist 'MoveBBStack,character'
  generic 'split' and siglist 'MoveBBStack,factor'
  generic 'statistics' and siglist '.MoveTrackSingle'
  generic 'statistics' and siglist '.MoveTrackStack'
  generic 'summary' and siglist '.MoveTrackSingle'
  generic 'summary' and siglist '.MoveTrackStack'
  generic 'unstack' and siglist 'UDStack'
  generic 'utilizationDistribution' and siglist
    '.MoveTrack,missing,ANY'
  generic 'velocity' and siglist 'ANY,POSIXct,numeric'
All user-level objects in a package (including S4 classes and methods)
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 'distance' but not in code:
  encounterIntervals

Functions or methods with usage in documentation object 'encounterDistribution' but not in code:
  encounterDistribution

Functions or methods with usage in documentation object 'plot.utilizationDistribution' but not in code:
  plot.utilizationDistribution contour.utilizationDistribution

Functions or methods with usage in documentation object 'utilizationDistribution' but not in code:
  utilizationDistribution.byID

Data with usage in documentation object 'moveBBStack' but not in code:
  moveBBStack

Codoc mismatches from documentation object 'contourPolygons':
contourPolygons
  Code: function(ud, levels = 0.99, ...)
  Docs: function(ud, levels = 0.99)
  Argument names in code not in docs:
    ...

Codoc mismatches from documentation object 'direction':
direction
  Code: function(tr, time, time.scale = NA, groupBy = NULL)
  Docs: function(tr, time, time.scale = NA)
  Argument names in code not in docs:
    groupBy
ddirection
  Code: function(d, tr, time, time.scale = NA, groupBy = NULL)
  Docs: function(d, tr, time, time.scale = NA)
  Argument names in code not in docs:
    groupBy
pdirection
  Code: function(d, tr, time, time.scale = NA, groupBy = NULL, lower =
                 0)
  Docs: function(d, tr, time, time.scale = NA, lower = 0)
  Argument names in code not in docs:
    groupBy
  Mismatches in argument names:
    Position: 5 Code: groupBy Docs: lower

Codoc mismatches from documentation object 'distance':
distance
  Code: function(tr, time, groupBy = NULL)
  Docs: function(tr, time)
  Argument names in code not in docs:
    groupBy
ddistance
  Code: function(d, tr, time, groupBy = NULL)
  Docs: function(d, tr, time)
  Argument names in code not in docs:
    groupBy
pdistance
  Code: function(d, tr, time, groupBy = NULL)
  Docs: function(d, tr, time)
  Argument names in code not in docs:
    groupBy
qdistance
  Code: function(p, tr, time, groupBy = NULL)
  Docs: function(p, tr, time)
  Argument names in code not in docs:
    groupBy
encounter
  Code: function(d, tr, time, groupBy = NULL)
  Docs: function(d, tr, time)
  Argument names in code not in docs:
    groupBy

Codoc mismatches from documentation object 'encounterDuration':
encounterDuration
  Code: function(tr, threshold, model = c("BBMM", "Linear"), groupBy =
                 NULL, timestepSize = 60)
  Docs: function(tr, threshold, model = c("BBMM", "linear"), byburst =
                 FALSE, timestepSize = 60)
  Argument names in code not in docs:
    groupBy
  Argument names in docs not in code:
    byburst
  Mismatches in argument names:
    Position: 4 Code: groupBy Docs: byburst
  Mismatches in argument default values:
    Name: 'model' Code: c("BBMM", "Linear") Docs: c("BBMM", "linear")
encounterDurationById
  Code: function(encounterDuration, groupBy = NULL)
  Docs: function(encounterDurationByBurst)
  Argument names in code not in docs:
    encounterDuration groupBy
  Argument names in docs not in code:
    encounterDurationByBurst
  Mismatches in argument names:
    Position: 1 Code: encounterDuration Docs: encounterDurationByBurst

Codoc mismatches from documentation object 'position':
position
  Code: function(object, time, groupBy = NULL)
  Docs: function(tr, time)
  Argument names in code not in docs:
    object groupBy
  Argument names in docs not in code:
    tr
  Mismatches in argument names:
    Position: 1 Code: object Docs: tr

Codoc mismatches from documentation object 'speed':
speed
  Code: function(tr, time, time.scale = NA, groupBy = NULL)
  Docs: function(tr, time, time.scale = NA)
  Argument names in code not in docs:
    groupBy
mu.speed
  Code: function(tr, time, time.scale = NA, groupBy = NULL)
  Docs: function(tr, time, time.scale = NA)
  Argument names in code not in docs:
    groupBy
pspeed
  Code: function(v, tr, time, time.scale = NA, groupBy = NULL)
  Docs: function(v, tr, time, time.scale = NA)
  Argument names in code not in docs:
    groupBy
dspeed
  Code: function(v, tr, time, time.scale = NA, groupBy = NULL)
  Docs: function(v, tr, time, time.scale = NA)
  Argument names in code not in docs:
    groupBy
qspeed
  Code: function(p, tr, time, time.scale = NA, groupBy = NULL)
  Docs: function(p, tr, time, time.scale = NA)
  Argument names in code not in docs:
    groupBy

Codoc mismatches from documentation object 'speedDistribution':
speedDistribution
  Code: function(object, raster = NULL, timestepSize = 60, time.scale =
                 timestepSize, grid.dim = 100, grid.pad = 0.2, groupBy
                 = NULL)
  Docs: function(tr, grid = NULL, timestepSize = 60, time.scale =
                 timestepSize, xc = NULL, yc = NULL, grid.dim = 100,
                 grid.pad = 0.2)
  Argument names in code not in docs:
    object raster groupBy
  Argument names in docs not in code:
    tr grid xc yc
  Mismatches in argument names (first 3):
    Position: 1 Code: object Docs: tr
    Position: 2 Code: raster Docs: grid
    Position: 5 Code: grid.dim Docs: xc

Codoc mismatches from documentation object 'utilizationDistribution':
utilizationDistribution
  Code: function(object, raster = NULL, timestepSize = 60, grid.dim =
                 100, grid.pad = 0.2, groupBy = NULL, cutoff.level = 1)
  Docs: function(tr, grid = NULL, timestepSize = 60, xc = NULL, yc =
                 NULL, grid.dim = 100, grid.pad = 0.2, byburst = FALSE,
                 cutoff.level = 1)
  Argument names in code not in docs:
    object raster groupBy
  Argument names in docs not in code:
    tr grid xc yc byburst
  Mismatches in argument names (first 3):
    Position: 1 Code: object Docs: tr
    Position: 2 Code: raster Docs: grid
    Position: 4 Code: grid.dim Docs: xc

Codoc mismatches from documentation object 'velocity':
velocity
  Code: function(object, time, time.scale = NA, groupBy = NULL)
  Docs: function(tr, time, time.scale = NA)
  Argument names in code not in docs:
    object groupBy
  Argument names in docs not in code:
    tr
  Mismatches in argument names:
    Position: 1 Code: object Docs: tr

S4 class codoc mismatches from documentation object 'MoveBB-class':
Slots for class 'MoveBB'
  Code: bbox citation coords coords.nrs data dataUnUsedRecords
        dateCreation diffusion idData license proj4string sensor
        sensorUnUsedRecords study timestamps timestampsUnUsedRecords
        variance
  Inherited: timestamps idData sensor data coords.nrs coords bbox
        proj4string timestampsUnUsedRecords sensorUnUsedRecords
        dataUnUsedRecords dateCreation study citation license variance
        diffusion
  Docs: bbox citation coords coords.nrs data dateCreation diffusion
        idData license proj4string study timesMissedFixes timestamps
        variance

* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'moveBB':
  ‘\S4method{moveBB}{ANY,ANY,missing,ANY,ANY,ANY}’
  ‘\S4method{moveBB}{ANY,ANY,numeric,ANY,missing,ANY}’
  ‘\S4method{moveBB}{numeric,numeric,numeric,POSIXct,data.frame,ANY}’

Objects in \usage without \alias in documentation object 'statistics':
  ‘statistics’

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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
File ‘moveBB/libs/moveBB.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking examples ... [15s/15s] NOTE
Examples with CPU or elapsed time > 5s
                              user system elapsed
plot.utilizationDistribution 5.488  0.004   5.492
* checking PDF version of manual ... OK
* DONE

Status: 6 WARNINGs, 8 NOTEs
See
  ‘/mnt/building/build_2017-09-06-11-24/RF_PKG_CHECK/PKGS/moveBB.Rcheck/00check.log’
for details.


Run time: 94.36 seconds.