Error in pathology.lookup.table(group_name_in) : 
  object 'group_name_out' not found 

if (identical(group_name_in,'POAG') |
      identical(group_name_in,'NTG') |
      identical(group_name_in,'DISC SUSPECT')) {
    
    group_name_out = 'Glaucoma'

 .. Removed total of " 92 " rows from Control Excel sheet
 .. Removed total of " 58 " rows from Glaucoma Excel sheet
 .. Removed total of " 78 " rows from Diabetes Excel sheet
 .. Removed total of " 96 " rows from Exceptional Cases (Neuro) Excel sheet
Error in rbind(deparse.level, ...) : 
  numbers of columns of arguments do not match

6. stop("numbers of columns of arguments do not match") 
5. rbind(deparse.level, ...) 
4. rbind(comb1, df_diabetes2) at combine_excelDataFramesToOne.R#28
3. combine.excelDataFramesToOne(df_control, df_glaucoma, df_diabetes, 
    df_neuro, vars_to_keep) at read_theMasterExcel.R#40
2. read.theMasterExcel(masterXLS_data_path, XLS_filename) at import_computedFeats.R#9
1. import.computedFeats(data_path_feats, pattern_to_find, dataset_type, 
    masterXLS_data_path, XLS_filename) 

Your sheets are not the same length! Fix your Master Data Sheet!
  no of columns in Control sheet =  63 
  no of columns in Glaucoma sheet =  63 
  no of columns in Diabetes sheet =  62 
  no of columns in Neuro sheet =  62 

warning('Petteri: Inspect the imputation now manually, \n
          or change the path from next block if you do not want to do it \n
          Eyeball the details from the GITHUB WIKI if this does not make sense to you')

Warning in file(file, "rt") :
  cannot open file 'C:/Users/User/Desktop/RPLR/TEST_OUT/imputation_final/NA': No such file or directory
Warning: Error in file: cannot open the connection
  50: file
  49: read.table
  48: read.csv
  47: server [C:\Users\User\Desktop\RPLR\R-PLR\Apps_Shiny\inspect_outliers/server.R#105]
Error in file(file, "rt") : cannot open the connection

DATA IN:  C:/Users/User/Desktop/RPLR/TEST_IN/recon_EMD 

> runApp('Apps_Shiny/inspect_EMD')

Listening on http://127.0.0.1:7682
   --- just_the_file =  server.R 
   --- --- full_path_script =  C:/Users/User/Desktop/RPLR/R-PLR/Apps_Shiny/inspect_EMD/server.R 


DATA IN:  C:/Users/User/Desktop/RPLR/TEST_IN/recon_EMD
DATA OUT:  C:/Users/User/Desktop/RPLR/TEST_IN/recon_EMD/IMF_fusion
... moving done files to:  C:/Users/User/Desktop/RPLR/TEST_IN/recon_EMD/DONE 

Warning in server(...) :
  No input files were found from DATA IN = "C:/Users/User/Desktop/RPLR/TEST_IN/recon_EMD"
 .... There are no done files from your "check path" =  C:/Users/User/Desktop/RPLR/TEST_IN/recon_EMD/IMF_fusion 
        -> in other we assume now that you have not yet processed any of the input files
         EXPLANATION #2: Why we are checking from "Reconstructed path"? As that is the end point of this script

Warning in check.for.done.filecodes(files_fullpath, path_out) :
  There are no done files from your "input path"
  -> now we cannot processing anything now!!!
  .. found 0 unprocessed input files
Input file: NA 
Warning in server(...) :
  Well we have no input filename to open as no files were found from input path
Warning in file(file, "rt") :
  cannot open file 'NA': No such file or directory
Warning: Error in file: cannot open the connection
  50: file
  49: read.table
  48: read.csv
  47: server [C:\Users\User\Desktop\RPLR\R-PLR\Apps_Shiny\inspect_EMD/server.R#95]
Error in file(file, "rt") : cannot open the connection

Error in library(pracma) : there is no package called ‘pracma’ 

# Finally compute the hand-crafted features here
  batch.PLR.analyze.reconstructions(data_path =  paths[['data_in']][['features']], 
                                     data_path_out = paths[['data_out']][['features']],
                                     RPLR_analysis_path = paths[['analysis']],
                                     parameters, RPLR_paths, masterExcel,
                                     process_only_unprocessed = TRUE,
                                     path_check_for_done = paths[['data_out']][['features']], 
                                     no_of_cores_to_use = detectCores(),
                                     pupil_col = 'pupil')

  }

_Checking the LIBRARIESCreating the directory for DATA Recon outputCreating the directory for DATA Imputed outputCreating the directory for DATA Trimmed outputCreating the directory for DATA Recon EMD output

Warning messages:
1: In dir.create(data_path_out, showWarnings = TRUE, recursive = FALSE,  :
  cannot create dir 'C:\Users\Ray-Najjar\Desktop\GitPLR\R-PLR\..\TEST_OUT\outlier_free\outlier_free_corrected\..\recon', reason 'No such file or directory'
2: In dir.create(data_resampled_path_out, showWarnings = TRUE, recursive = FALSE,  :
  cannot create dir 'C:\Users\Ray-Najjar\Desktop\GitPLR\R-PLR\..\TEST_OUT\outlier_free\outlier_free_corrected\..\recon_resampled', reason 'No such file or directory'
3: In dir.create(data_trimmed_path_out, showWarnings = TRUE, recursive = FALSE,  :
  cannot create dir 'C:\Users\Ray-Najjar\Desktop\GitPLR\R-PLR\..\TEST_OUT\outlier_free\outlier_free_corrected\..\recon_trimmed', reason 'No such file or directory'
4: In dir.create(data_temp_path_out, showWarnings = TRUE, recursive = FALSE,  :
  cannot create dir 'C:\Users\Ray-Najjar\Desktop\GitPLR\R-PLR\..\TEST_OUT\outlier_free\outlier_free_corrected\..\recon_EMD', reason 'No such file or directory'_

 Error: package or namespace load failed for ‘forecast’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/petteri/R/x86_64-pc-linux-gnu-library/3.4/uroot/libs/uroot.so':
  libcudart.so.8.0: cannot open shared object file: No such file or directory 

=  C:/Users/User/Desktop/RPLR/TEST_OUT/PLR_feat 
        -> in other we assume now that you have not yet processed any of the input files
         EXPLANATION #2: Why we are checking from "Reconstructed path"? As that is the end point of this script

  .. found 3 unprocessed input files
 Analyzing file =  PLR2076_reconstruction.csv  
  Traditional time domain features: BLUE RED
    Fractal features
      Time-Frequency features
[1] "IMF 1 COMPLETE!"
[1] "IMF 2 COMPLETE!"
[1] "IMF 3 COMPLETE!"
[1] "IMF 4 COMPLETE!"
[1] "IMF 5 COMPLETE!"
[1] "IMF 6 COMPLETE!"
[1] "IMF 7 COMPLETE!"
[1] "IMF 8 COMPLETE!"
[1] "IMF 9 COMPLETE!"
Error: Unknown graphics device ''

# Finally compute the hand-crafted features here
  batch.PLR.analyze.reconstructions(data_path =  paths[['data_in']][['features']], 
                                     data_path_out = paths[['data_out']][['features']],
                                     RPLR_analysis_path = paths[['analysis']],
                                     parameters, RPLR_paths, masterExcel,
                                     process_only_unprocessed = TRUE,
                                     path_check_for_done = paths[['data_out']][['features']], 
                                     no_of_cores_to_use = detectCores(),
                                     pupil_col = 'pupil')

  }

Error in mclapply(files_to_process, function(files_to_process) { : 
 'mc.cores' > 1 is not supported on Windows 

 # Do some semi-intelligent decompositions for machine learning data augmentation purposes
  # Computes as well 1st and 2nd derivatives (i.e. velocity and acceleration) from the smoothed PLRs
  batch.data.decompose.for.augmentation(data_path = paths[['data_out']][['reconstructed']], 
                                        data_path_out = paths[['data_out']][['FinalOUT']],
                                        RPLR_recon_path = paths[['recon']],
                                        parameters = param[['decomp_augm']],
                                        RPLR_paths = paths[['RPLR']],
                                        masterExcel = paths[['data_in']][['excelMasterPath']],
                                        process_only_unprocessed = TRUE,
                                        path_check_for_done = paths[['data_out']][['FinalOUT']],
                                        pupil_col = 'denoised')