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spacetime log file (check_x86_64_linux)

Thu Aug 18 16:04:09 2016: Checking package spacetime (SVN revision 111) ...
* using log directory ‘/mnt/building/build_2016-08-18-12-24/RF_PKG_CHECK/PKGS/spacetime.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 ‘spacetime/DESCRIPTION’ ... OK
* this is package ‘spacetime’ version ‘1.0-10’
* checking CRAN incoming feasibility ... WARNING
Maintainer: ‘Edzer Pebesma ’

Insufficient package version (submitted: 1.0.10, existing: 1.1.5)

The Title field should be in title case, current version then in title case:
‘classes and methods for spatio-temporal data’
‘Classes and Methods for Spatio-Temporal Data’

The Date field is over a month old.
* 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 ‘spacetime’ can be installed ... [3s/3s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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' calls in package code:
  ‘raster’ ‘rgdal’ ‘rgeos’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
':::' calls which should be '::':
  ‘sp:::longlat.scales’ ‘sp:::sp.panel.layout’
  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
EOF: no visible global function definition for ‘prcomp’
EOF: no visible global function definition for ‘predict’
lines.STTDF: no visible global function definition for ‘lines’
read.tgrass: no visible global function definition for ‘untar’
read.tgrass: no visible global function definition for ‘read.table’
read.tgrass: no visible global function definition for ‘setZ’
stplot.STFDF: no visible global function definition for ‘as.formula’
stplot.STI: no visible global function definition for ‘as.formula’
stplot.STTDF: no visible global function definition for ‘as.formula’
unstack.STFDF: no visible global function definition for ‘as.formula’
write.tgrass: no visible global function definition for ‘nlayers’
write.tgrass: no visible global function definition for ‘writeRaster’
write.tgrass: no visible global function definition for ‘raster’
write.tgrass: no visible global function definition for ‘write.table’
write.tgrass: no visible global function definition for ‘getZ’
coerce,RasterStackBrick-STFDF: no visible global function definition
  for ‘getZ’
coerce,RasterStackBrick-STFDF: no visible global function definition
  for ‘getValues’
coerce,STTDF-ltraj: no visible global function definition for
  ‘as.ltraj’
stplot,RasterStackBrick: no visible global function definition for
  ‘sampleRegular’
stplot,STFDF: no visible global function definition for ‘as.formula’
stplot,STI: no visible global function definition for ‘as.formula’
stplot,STTDF: no visible global function definition for ‘as.formula’
Undefined global functions or variables:
  as.formula as.ltraj getValues getZ lines nlayers prcomp predict
  raster read.table sampleRegular setZ untar write.table writeRaster
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "as.formula", "prcomp", "predict")
  importFrom("utils", "read.table", "untar", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'STF'
  generic '[' and siglist 'STI'
  generic '[' and siglist 'STS'
  generic 'geometry' and siglist 'ST'
  generic 'geometry' and siglist 'STFDF'
  generic 'geometry' and siglist 'STIDF'
  generic 'geometry' and siglist 'STSDF'
  generic 'geometry' and siglist 'STTDF'
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
Codoc mismatches from documentation object 'STFDF-class':
\S4method{[}{STFDF}
  Code: function(x, i, j, ..., drop = is(x, "STFDF"))
  Docs: function(x, i, j, ..., drop = TRUE)
  Mismatches in argument default values:
    Name: 'drop' Code: is(x, "STFDF") Docs: TRUE

Codoc mismatches from documentation object 'STSDF-class':
\S4method{[}{STSDF}
  Code: function(x, i, j, ..., drop = is(x, "STSDF"))
  Docs: function(x, i, j, ..., drop = TRUE)
  Mismatches in argument default values:
    Name: 'drop' Code: is(x, "STSDF") Docs: TRUE

* checking Rd \usage sections ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [12s/12s] WARNING
Found the following significant warnings:

  Warning: 'sp:::sp.panel.layout' is deprecated.
  Warning: 'sp:::sp.panel.layout' is deprecated.
  Warning: 'sp:::sp.panel.layout' is deprecated.
  Warning: 'sp:::sp.panel.layout' is deprecated.
  Warning: 'sp:::sp.panel.layout' is deprecated.
  Warning: 'sp:::sp.panel.layout' is deprecated.
  Warning: 'sp:::sp.panel.layout' is deprecated.
  Warning: 'sp:::sp.panel.layout' is deprecated.
  Warning: 'sp:::sp.panel.layout' is deprecated.
  Warning: 'sp:::sp.panel.layout' is deprecated.
  Warning: 'sp:::sp.panel.layout' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* checking differences from ‘spacetime-Ex.Rout’ to ‘spacetime-Ex.Rout.save’ ... OK

338c338
< The following objects are masked from 'package:base':
---
> The following object is masked from 'package:base':
677,679d676
< Warning: 'sp:::sp.panel.layout' is deprecated.
< Use 'sppanel' instead.
< See help("Deprecated")
681,689d677
< Warning: 'sp:::sp.panel.layout' is deprecated.
< Use 'sppanel' instead.
< See help("Deprecated")
< Warning: 'sp:::sp.panel.layout' is deprecated.
< Use 'sppanel' instead.
< See help("Deprecated")
< Warning: 'sp:::sp.panel.layout' is deprecated.
< Use 'sppanel' instead.
< See help("Deprecated")
691,693d678
< Warning: 'sp:::sp.panel.layout' is deprecated.
< Use 'sppanel' instead.
< See help("Deprecated")
695,697d679
< Warning: 'sp:::sp.panel.layout' is deprecated.
< Use 'sppanel' instead.
< See help("Deprecated")
703,705d684
< Warning: 'sp:::sp.panel.layout' is deprecated.
< Use 'sppanel' instead.
< See help("Deprecated")
709,711d687
< Warning: 'sp:::sp.panel.layout' is deprecated.
< Use 'sppanel' instead.
< See help("Deprecated")
713,715d688
< Warning: 'sp:::sp.panel.layout' is deprecated.
< Use 'sppanel' instead.
< See help("Deprecated")
717,719d689
< Warning: 'sp:::sp.panel.layout' is deprecated.
< Use 'sppanel' instead.
< See help("Deprecated")
721,723d690
< Warning: 'sp:::sp.panel.layout' is deprecated.
< Use 'sppanel' instead.
< See help("Deprecated")
850c817
< rgdal: version: 1.1-10, (SVN revision 622)
---
> rgdal: version: 0.8-11, (SVN revision 479M)
852,853c819,820
<  Loaded GDAL runtime: GDAL 1.10.1, released 2013/08/26
<  Path to GDAL shared files: /usr/share/gdal/1.10
---
> Loaded GDAL runtime: GDAL 1.9.2, released 2012/10/08
> Path to GDAL shared files: /usr/share/gdal/1.9
856d822
<  Linking to sp version: 1.2-3 
1048a1015,1028
> 
> Attaching package: 'bdsmatrix'
> 
> The following object is masked from 'package:base':
> 
>     backsolve
> 
> 
> Attaching package: 'zoo'
> 
> The following object is masked from 'package:base':
> 
>     as.Date, as.Date.numeric
> 
1128,1129c1108,1110
< detaching 'package:gstat', 'package:plm', 'package:Formula',
<   'package:maptools', 'package:sp', 'package:maps'
---
> detaching 'package:gstat', 'package:plm', 'package:sandwich',
>   'package:zoo', 'package:MASS', 'package:Formula', 'package:nlme',
>   'package:bdsmatrix', 'package:maptools', 'package:sp', 'package:maps'
1340c1321
< The following objects are masked from 'package:base':
---
> The following object is masked from 'package:base':
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘basic.R’
  Comparing ‘basic.Rout’ to ‘basic.Rout.save’ ...329,337c329,337
< point1 1 1
< point2 2 1
< point3 3 1
< point4 1 2
< point5 2 2
< point6 3 2
< point7 1 3
< point8 2 3
< point9 3 3
---
>  [1,] 1 1
>  [2,] 2 1
>  [3,] 3 1
>  [4,] 1 2
>  [5,] 2 2
>  [6,] 3 2
>  [7,] 1 3
>  [8,] 2 3
>  [9,] 3 3
374,375c374,375
< point1 1 1
< point2 2 1
---
> [1,] 1 1
> [2,] 2 1
454,456d453
< Warning message:
< In validityMethod(object) :
<   duplicate rownames are interpreted by rgeos as MultiPoints; use SpatialMultiPoints to define these; in future sp versions this warning will become an error
461,463d457
< Warning message:
< In validityMethod(object) :
<   duplicate rownames are interpreted by rgeos as MultiPoints; use SpatialMultiPoints to define these; in future sp versions this warning will become an error
468,470d461
< Warning message:
< In validityMethod(object) :
<   duplicate rownames are interpreted by rgeos as MultiPoints; use SpatialMultiPoints to define these; in future sp versions this warning will become an error
472,474d462
< Warning message:
< In validityMethod(object) :
<   duplicate rownames are interpreted by rgeos as MultiPoints; use SpatialMultiPoints to define these; in future sp versions this warning will become an error
1090c1078
< The following objects are masked from 'package:base':
---
> The following object is masked from 'package:base':
  Running ‘over.R’
  Comparing ‘over.Rout’ to ‘over.Rout.save’ ... OK
  Running ‘raster.R’
  Comparing ‘raster.Rout’ to ‘raster.Rout.save’ ... OK
  Running ‘rw.R’
  Running ‘stconstruct.R’
  Comparing ‘stconstruct.Rout’ to ‘stconstruct.Rout.save’ ...9c9
< The following objects are masked from 'package:base':
---
> The following object is masked from 'package:base':
24a25,31
> 
> Attaching package: 'bdsmatrix'
> 
> The following object is masked from 'package:base':
> 
>     backsolve
> 
  Running ‘traj.R’
  Comparing ‘traj.Rout’ to ‘traj.Rout.save’ ...9a10,16
> 
> Attaching package: 'ade4'
> 
> The following object is masked from 'package:base':
> 
>     within
> 
24d30
< There were 24 warnings (use warnings() to see them)
  Running ‘wind.R’
  Comparing ‘wind.Rout’ to ‘wind.Rout.save’ ...97c97
< rgdal: version: 1.1-10, (SVN revision 622)
---
> rgdal: version: 0.8-11, (SVN revision 479M)
99,100c99,100
<  Loaded GDAL runtime: GDAL 1.10.1, released 2013/08/26
<  Path to GDAL shared files: /usr/share/gdal/1.10
---
> Loaded GDAL runtime: GDAL 1.9.2, released 2012/10/08
> Path to GDAL shared files: /usr/share/gdal/1.9
103d102
<  Linking to sp version: 1.2-3 
 [16s/17s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [32s/34s] OK
* checking PDF version of manual ... OK
* DONE

Status: 4 WARNINGs, 2 NOTEs
See
  ‘/mnt/building/build_2016-08-18-12-24/RF_PKG_CHECK/PKGS/spacetime.Rcheck/00check.log’
for details.


Run time: 125.4 seconds.