Package: cifti
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘cifti_work.Rmd’ using rmarkdown
  
  Quitting from cifti_work.Rmd:20-92 [unnamed-chunk-1]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error in `rgl.triangles()`:
  ! 'rgl.triangles' is defunct.
  Use 'triangles3d' instead.
  See help("Defunct")
  ---
  Backtrace:
      ▆
   1. └─rgl::rgl.triangles(left_surf$pointset, color = colors)
   2.   └─base::.Defunct("triangles3d")
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'cifti_work.Rmd' failed with diagnostics:
  'rgl.triangles' is defunct.
  Use 'triangles3d' instead.
  See help("Defunct")
  --- failed re-building ‘cifti_work.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘cifti_work.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: gifti
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘Reading_GIFTI_Files.Rmd’ using rmarkdown
  trying URL 'http://johnmuschelli.com/gifti/BV_GIFTI.tar.gz'
  Content type 'application/gzip' length 11249990 bytes (10.7 MB)
  ==================================================
  downloaded 10.7 MB
  
  
  Quitting from Reading_GIFTI_Files.Rmd:75-105 [unnamed-chunk-6]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error in `rgl::rgl.open()`:
  ! 'rgl.open' is defunct.
  Use 'open3d' instead.
  See help("Defunct")
  ---
  Backtrace:
      ▆
   1. └─rgl::rgl.open()
   2.   └─base::.Defunct("open3d")
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'Reading_GIFTI_Files.Rmd' failed with diagnostics:
  'rgl.open' is defunct.
  Use 'open3d' instead.
  See help("Defunct")
  --- failed re-building ‘Reading_GIFTI_Files.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘Reading_GIFTI_Files.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: hyperoverlap
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘hyperoverlap-vignette.Rmd’ using rmarkdown
  
  Quitting from hyperoverlap-vignette.Rmd:91-94 [unnamed-chunk-7]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error in `rgl.close()`:
  ! 'rgl.close' is defunct.
  Use 'close3d' instead.
  See help("Defunct")
  ---
  Backtrace:
      ▆
   1. └─rgl::rgl.close()
   2.   └─base::.Defunct("close3d")
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'hyperoverlap-vignette.Rmd' failed with diagnostics:
  'rgl.close' is defunct.
  Use 'close3d' instead.
  See help("Defunct")
  --- failed re-building ‘hyperoverlap-vignette.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘hyperoverlap-vignette.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: msir
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘msir.Rmd’ using rmarkdown
  
  Quitting from msir.Rmd:100-103 [unnamed-chunk-5]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error in `rgl::rgl.open()`:
  ! 'rgl.open' is defunct.
  Use 'open3d' instead.
  See help("Defunct")
  ---
  Backtrace:
      ▆
   1. ├─base::plot(MSIR, type = "spinplot")
   2. └─msir::plot.msir(MSIR, type = "spinplot")
   3.   └─msir::spinplot(...)
   4.     └─rgl::rgl.open()
   5.       └─base::.Defunct("open3d")
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Error: processing vignette 'msir.Rmd' failed with diagnostics:
  'rgl.open' is defunct.
  Use 'open3d' instead.
  See help("Defunct")
  --- failed re-building ‘msir.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘msir.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted

Package: nat.nblast
Check: tests
New result: ERROR
    Running ‘spelling.R’ [0s/0s]
    Running ‘test-all.R’ [4s/4s]
  Running the tests in ‘tests/test-all.R’ failed.
  Complete output:
    > library(testthat)
    > library(nat.nblast)
    Loading required package: rgl
    Loading required package: nat
    Some nat functions depend on a CMTK installation. See ?cmtk and README.md for details.
    
    Attaching package: 'nat'
    
    The following objects are masked from 'package:base':
    
        intersect, setdiff, union
    
    > 
    > test_check("nat.nblast")
    Saving _problems/test-clustering-31.R
    [ FAIL 1 | WARN 0 | SKIP 0 | PASS 65 ]
    
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Error ('test-clustering.r:31:3'): plot3d.hclust ─────────────────────────────
    <defunctError/error/condition>
    Error in `rgl.close()`: 'rgl.close' is defunct.
    Use 'close3d' instead.
    See help("Defunct")
    Backtrace:
        ▆
     1. └─rgl::rgl.close() at test-clustering.r:31:3
     2.   └─base::.Defunct("close3d")
    
    [ FAIL 1 | WARN 0 | SKIP 0 | PASS 65 ]
    Error:
    ! Test failures.
    Execution halted

Package: radviz3d
Check: examples
New result: ERROR
  Running examples in ‘radviz3d-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: radialvis3d
  > ### Title: 3D Radial Visualization function
  > ### Aliases: radialvis3d
  > 
  > ### ** Examples
  > 
  > radialvis3d(data = iris[,-5], cl = iris[,5], domrp = TRUE)
  cumulative variance explained: 0.9588083 1 1 1 
  Error in rgl.lines(rbind(rep(0, 3), radius * anchors[p, ]), col = "gray40",  : 
    'rgl.lines' is defunct.
  Use 'segments3d' instead.
  See help("Defunct")
  Calls: radialvis3d -> rgl.lines -> .Defunct
  Execution halted

Package: SimCop
Check: examples
New result: ERROR
  Running examples in ‘SimCop-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: GetApprox
  > ### Title: Approximate a copula by a histogram density
  > ### Aliases: GetApprox
  > 
  > ### ** Examples
  > 
  > Cop <- NewMEVGumbelCopula(3)
  > CopApprox <- GetApprox(Cop, dim=2)
  > plot(CopApprox)
  Error in rgl::rgl.quads(x1, y1, z1, col = rep(sidecol, each = 4), alpha = alpha) : 
    'rgl.quads' is defunct.
  Use 'quads3d' instead.
  See help("Defunct")
  Calls: plot ... plot.CopApprox -> SimCop_binplot_3d -> <Anonymous> -> .Defunct
  Execution halted