CRAN Package Check Results for Package sclero

Last updated on 2021-04-08 10:51:27 CEST.

Check Details

Version: 0.2
Check: R code for possible problems
Result: NOTE
    assign.size : <anonymous>: no visible global function definition for
     'centroid.owin'
    assign.size : <anonymous>: no visible global function definition for
     'ppp'
    assign.size : <anonymous> : <anonymous>: no visible global function
     definition for 'nncross'
    assign.size : <anonymous>: no visible global function definition for
     'marks'
    assign.size : <anonymous> : <anonymous>: no visible global function
     definition for 'area.owin'
    assign.size : <anonymous> : <anonymous>: no visible global function
     definition for 'diameter'
    assign.size : <anonymous>: no visible global function definition for
     'hyperframe'
    assign.size : <anonymous>: no visible global function definition for
     'marks<-'
    assign.size : <anonymous>: no visible global function definition for
     'superimpose'
    assign.value : <anonymous>: no visible global function definition for
     'marks'
    assign.value : <anonymous>: no visible global function definition for
     'npoints'
    convert.ijdata: no visible global function definition for 'ppp'
    convert.ijdata: no visible global function definition for 'psp'
    convert.ijdata: no visible global function definition for 'superimpose'
    create.rawDist: no visible global function definition for 'marks'
    create.rawDist: no visible global function definition for 'marks<-'
    create.rawDist : <anonymous>: no visible global function definition for
     'marks'
    create.rawDist : <anonymous>: no visible global function definition for
     'marks<-'
    create.rawDist: no visible global function definition for 'owin'
    create.rawDist: no visible global function definition for 'ppp'
    plot.spotDist: no visible global function definition for 'coords'
    plot.spotDist : <anonymous>: no visible global function definition for
     'crossdist'
    plot.spotDist : <anonymous>: no visible global function definition for
     'coords'
    samplemap: no visible global function definition for 'marks'
    samplemap: no visible global function definition for 'colourmap'
    samplemap : <anonymous>: no visible global function definition for
     'coords'
    samplemap : <anonymous>: no visible global function definition for
     'marks'
    samplemap: no visible global function definition for 'coords'
    spot.dist : seg.fun: no visible global function definition for
     'npoints'
    spot.dist : seg.fun: no visible global function definition for 'coords'
    spot.dist : seg.fun: no visible global function definition for 'psp'
    spot.dist : spot.dist.calculation: no visible global function
     definition for 'nncross'
    spot.dist : spot.dist.calculation : <anonymous>: no visible global
     function definition for 'nncross'
    spot.dist : spot.dist.calculation : <anonymous>: no visible global
     function definition for 'npoints'
    spot.dist : spot.dist.calculation : <anonymous>: no visible global
     function definition for 'superimpose'
    spot.dist : spot.dist.calculation : <anonymous>: no visible global
     function definition for 'project2segment'
    spot.dist : spot.dist.calculation : <anonymous> : <anonymous>: no
     visible global function definition for 'nncross'
    spot.dist: no visible global function definition for 'crossing.psp'
    spot.dist: no visible global function definition for 'superimpose'
    spot.dist: no visible global function definition for 'endpoints.psp'
    spot.dist: no visible global function definition for 'npoints'
    spot.dist: no visible global function definition for 'nncross'
    spot.dist: no visible global function definition for 'marks<-'
    spot.dist: no visible global function definition for 'project2segment'
    spot.dist: no visible global function definition for 'ppp'
    spot.dist: no visible global function definition for 'crossdist'
    spot.dist: no visible global function definition for 'lengths.psp'
    spot.dist: no visible global function definition for 'marks'
    spot.dist : <anonymous> : <anonymous>: no visible global function
     definition for 'edges'
    spot.dist : <anonymous> : <anonymous>: no visible global function
     definition for 'marks<-'
    spot.dist : <anonymous> : <anonymous> : <anonymous>: no visible global
     function definition for 'npoints'
    spot.dist : <anonymous> : <anonymous> : <anonymous>: no visible global
     function definition for 'crossing.psp'
    spot.dist : <anonymous> : <anonymous> : <anonymous>: no visible global
     function definition for 'marks'
    spot.dist : <anonymous> : <anonymous>: no visible global function
     definition for 'as.ppp'
    spot.dist : <anonymous> : <anonymous>: no visible global function
     definition for 'nncross'
    spot.dist : <anonymous> : <anonymous>: no visible global function
     definition for 'marks'
    spot.dist : <anonymous>: no visible global function definition for
     'superimpose'
    Undefined global functions or variables:
     area.owin as.ppp centroid.owin colourmap coords crossdist
     crossing.psp diameter edges endpoints.psp hyperframe lengths.psp
     marks marks<- nncross npoints owin ppp project2segment psp
     superimpose
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-devel-windows-x86_64-gcc10-UCRT, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.2
Check: Rd cross-references
Result: WARN
    Missing link or links in documentation object 'assign.size.Rd':
     'ppp' 'hyperframe'
    
    Missing link or links in documentation object 'create.rawDist.Rd':
     '[spatstat]{ppp}' '[spatstat]{marks}' '[spatstat]{psp}'
    
    See section 'Cross-references' in the 'Writing R Extensions' manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-devel-windows-x86_64-gcc10-UCRT, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.2
Check: examples
Result: ERROR
    Running examples in 'sclero-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: assign.value
    > ### Title: Assign values to 'rawDist' objects for plotting.
    > ### Aliases: assign.value
    >
    > ### ** Examples
    >
    > data(barium)
    > data(shellsizes)
    >
    > ## rawDist
    > shellvalues <- assign.value(shellsizes, barium, value.name = "Ba/Ca")
    > plot(shellvalues, spot.size = "actual", spot.type = "value", main.type = "none")
    >
    > ## spotDist
    > shellvalues.aligned <- spot.dist(shellvalues)
    Error in lengths.psp(tmp) : could not find function "lengths.psp"
    Calls: spot.dist -> data.frame
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building 'sclero_tutorial.Rnw' using Sweave
    Loading required package: RImageJROI
    Loading required package: spatstat
    Loading required package: spatstat.data
    Loading required package: spatstat.geom
    spatstat.geom 2.0-1
    Loading required package: spatstat.core
    Loading required package: nlme
    Loading required package: rpart
    spatstat.core 2.0-0
    Loading required package: spatstat.linnet
    spatstat.linnet 2.1-1
    
    spatstat 2.1-0 (nickname: 'Comedic violence')
    For an introduction to spatstat, type 'beginner'
    
    Loading required package: plyr
    
    Error: processing vignette 'sclero_tutorial.Rnw' failed with diagnostics:
     chunk 10 (label = plot2)
    Error in lengths.psp(tmp) : could not find function "lengths.psp"
    
    --- failed re-building 'sclero_tutorial.Rnw'
    
    SUMMARY: processing the following file failed:
     'sclero_tutorial.Rnw'
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64

Version: 0.2
Check: examples
Result: ERROR
    Running examples in ‘sclero-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: assign.value
    > ### Title: Assign values to 'rawDist' objects for plotting.
    > ### Aliases: assign.value
    >
    > ### ** Examples
    >
    > data(barium)
    > data(shellsizes)
    >
    > ## rawDist
    > shellvalues <- assign.value(shellsizes, barium, value.name = "Ba/Ca")
    > plot(shellvalues, spot.size = "actual", spot.type = "value", main.type = "none")
    >
    > ## spotDist
    > shellvalues.aligned <- spot.dist(shellvalues)
    Error in lengths.psp(tmp) : could not find function "lengths.psp"
    Calls: spot.dist -> data.frame
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-devel-windows-x86_64-gcc10-UCRT, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘sclero_tutorial.Rnw’ using Sweave
    Loading required package: RImageJROI
    Loading required package: spatstat
    Loading required package: spatstat.data
    Loading required package: spatstat.geom
    spatstat.geom 2.0-1
    Loading required package: spatstat.core
    Loading required package: nlme
    Loading required package: rpart
    spatstat.core 2.0-0
    Loading required package: spatstat.linnet
    spatstat.linnet 2.1-1
    
    spatstat 2.1-0 (nickname: ‘Comedic violence’)
    For an introduction to spatstat, type ‘beginner’
    
    Loading required package: plyr
    
    Error: processing vignette 'sclero_tutorial.Rnw' failed with diagnostics:
     chunk 10 (label = plot2)
    Error in lengths.psp(tmp) : could not find function "lengths.psp"
    
    --- failed re-building ‘sclero_tutorial.Rnw’
    
    SUMMARY: processing the following file failed:
     ‘sclero_tutorial.Rnw’
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-release-windows-ix86+x86_64

Version: 0.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building 'sclero_tutorial.Rnw' using Sweave
    Loading required package: RImageJROI
    Loading required package: spatstat
    Loading required package: spatstat.data
    Loading required package: spatstat.geom
    spatstat.geom 2.0-1
    Loading required package: spatstat.core
    Loading required package: nlme
    Loading required package: rpart
    spatstat.core 2.0-0
    Loading required package: spatstat.linnet
    spatstat.linnet 2.1-1
    
    spatstat 2.0-1 (nickname: 'Caution: contains small parts')
    For an introduction to spatstat, type 'beginner'
    
    Loading required package: plyr
    
    Error: processing vignette 'sclero_tutorial.Rnw' failed with diagnostics:
     chunk 10 (label = plot2)
    Error in lengths.psp(tmp) : could not find function "lengths.psp"
    
    --- failed re-building 'sclero_tutorial.Rnw'
    
    SUMMARY: processing the following file failed:
     'sclero_tutorial.Rnw'
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-devel-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.2
Check: running R code from vignettes
Result: ERROR
    Errors in running code in vignettes:
    when running code in 'sclero_tutorial.Rnw'
     ...
    
    > shell <- convert.ijdata(dat)
    
    > plot(shell)
    
    > aligned <- spot.dist(shell)
    
     When sourcing 'sclero_tutorial.R':
    Error: could not find function "lengths.psp"
    Execution halted
    
     'sclero_tutorial.Rnw'... failed
Flavor: r-devel-windows-x86_64-gcc10-UCRT

Version: 0.2
Check: re-building of vignette outputs
Result: NOTE
    Error(s) in re-building vignettes:
    --- re-building 'sclero_tutorial.Rnw' using Sweave
    Loading required package: RImageJROI
    Loading required package: spatstat
    Loading required package: spatstat.data
    Loading required package: spatstat.geom
    spatstat.geom 2.0-1
    Loading required package: spatstat.core
    Loading required package: nlme
    Loading required package: rpart
    spatstat.core 2.0-0
    Loading required package: spatstat.linnet
    spatstat.linnet 2.1-1
    
    spatstat 2.1-0 (nickname: 'Comedic violence')
    For an introduction to spatstat, type 'beginner'
    
    Loading required package: plyr
    
    Error: processing vignette 'sclero_tutorial.Rnw' failed with diagnostics:
     chunk 10 (label = plot2)
    Error in lengths.psp(tmp) : could not find function "lengths.psp"
    
    --- failed re-building 'sclero_tutorial.Rnw'
    
    SUMMARY: processing the following file failed:
     'sclero_tutorial.Rnw'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-windows-x86_64-gcc10-UCRT