Running ‘testthat.R’ [48s/58s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(freesurferformats)
  > 
  > test_check("freesurferformats")
  [1] "Label table cdata (region names for the rows below):"
   [1] "unknown"                  "bankssts"                
   [3] "caudalanteriorcingulate"  "caudalmiddlefrontal"     
   [5] "corpuscallosum"           "cuneus"                  
   [7] "entorhinal"               "fusiform"                
   [9] "inferiorparietal"         "inferiortemporal"        
  [11] "isthmuscingulate"         "lateraloccipital"        
  [13] "lateralorbitofrontal"     "lingual"                 
  [15] "medialorbitofrontal"      "middletemporal"          
  [17] "parahippocampal"          "paracentral"             
  [19] "parsopercularis"          "parsorbitalis"           
  [21] "parstriangularis"         "pericalcarine"           
  [23] "postcentral"              "posteriorcingulate"      
  [25] "precentral"               "precuneus"               
  [27] "rostralanteriorcingulate" "rostralmiddlefrontal"    
  [29] "superiorfrontal"          "superiorparietal"        
  [31] "superiortemporal"         "supramarginal"           
  [33] "frontalpole"              "temporalpole"            
  [35] "transversetemporal"       "insula"                  
  [1] "Label table attribute columns:"
                           Red Green Blue Alpha      Key    Index
  unknown                   25     5   25     0  1639705  1639705
  bankssts                  25   100   40     0  2647065  2647065
  caudalanteriorcingulate  125   100  160     0 10511485 10511485
  caudalmiddlefrontal      100    25    0     0     6500     6500
  corpuscallosum           120    70   50     0  3294840  3294840
  cuneus                   220    20  100     0  6558940  6558940
  entorhinal               220    20   10     0   660700   660700
  fusiform                 180   220  140     0  9231540  9231540
  inferiorparietal         220    60  220     0 14433500 14433500
  inferiortemporal         180    40  120     0  7874740  7874740
  isthmuscingulate         140    20  140     0  9180300  9180300
  lateraloccipital          20    30  140     0  9182740  9182740
  lateralorbitofrontal      35    75   50     0  3296035  3296035
  lingual                  225   140  140     0  9211105  9211105
  medialorbitofrontal      200    35   75     0  4924360  4924360
  middletemporal           160   100   50     0  3302560  3302560
  parahippocampal           20   220   60     0  3988500  3988500
  paracentral               60   220   60     0  3988540  3988540
  parsopercularis          220   180  140     0  9221340  9221340
  parsorbitalis             20   100   50     0  3302420  3302420
  parstriangularis         220    60   20     0  1326300  1326300
  pericalcarine            120   100   60     0  3957880  3957880
  postcentral              220    20   20     0  1316060  1316060
  posteriorcingulate       220   180  220     0 14464220 14464220
  precentral                60    20  220     0 14423100 14423100
  precuneus                160   140  180     0 11832480 11832480
  rostralanteriorcingulate  80    20  140     0  9180240  9180240
  rostralmiddlefrontal      75    50  125     0  8204875  8204875
  superiorfrontal           20   220  160     0 10542100 10542100
  superiorparietal          20   180  140     0  9221140  9221140
  superiortemporal         140   220  220     0 14474380 14474380
  supramarginal             80   160   20     0  1351760  1351760
  frontalpole              100     0  100     0  6553700  6553700
  temporalpole              70    20  170     0 11146310 11146310
  transversetemporal       150   150  200     0 13145750 13145750
  insula                   255   192   32     0  2146559  2146559
  [ FAIL 3 | WARN 0 | SKIP 21 | PASS 715 ]
  
  ══ Skipped tests (21) ══════════════════════════════════════════════════════════
  • Freesurfer installation with GCA file available. (1):
    'test-read_fs_annot.R:175:3'
  • On CRAN (18): 'test-cifti.R:7:3', 'test-gifti_xml_tools.R:4:3',
    'test-read_fs_annot.R:78:3', 'test-read_fs_patch.R:6:3',
    'test-read_fs_patch.R:28:3', 'test-read_fs_surface.R:4:3',
    'test-read_fs_surface.R:36:3', 'test-read_fs_surface.R:60:3',
    'test-read_nifti1.R:2:3', 'test-read_nifti1.R:21:3',
    'test-read_nifti1.R:39:3', 'test-read_nifti1.R:57:3',
    'test-read_nifti1.R:77:3', 'test-read_nifti2.R:4:3',
    'test-read_nifti2.R:28:3', 'test-read_nifti2.R:44:3',
    'test-surface_dist.R:4:3', 'test-write_fs_surface.R:41:3'
  • Test data missing. (2): 'test-mgh2nii.R:8:33', 'test-read_fs_surface.R:89:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-nifti_to_mgh.R:6:3'): We can load a NIFTI volume file as an MGH instance ──
  Error in `read.fs.volume.nii(nii_file, with_header = TRUE)`: The 'oro.nifti' package is required to use this functionality.
  Backtrace:
      ▆
   1. └─freesurferformats::read.fs.volume.nii(nii_file, with_header = TRUE) at test-nifti_to_mgh.R:6:3
  ── Error ('test-nifti_to_mgh.R:29:3'): We can compute mghheader data from the q-form in a NIFTI volume file ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'oro.nifti'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-nifti_to_mgh.R:29:3
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-nifti_to_mgh.R:38:3'): Warnings are show if neither s-form nor  q-form are available in a NIFTI volume file ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'oro.nifti'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-nifti_to_mgh.R:38:3
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 3 | WARN 0 | SKIP 21 | PASS 715 ]
  Error: Test failures
  Execution halted