R Under development (unstable) (2024-01-26 r85832 ucrt) -- "Unsuffered Consequences"
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> 
> library( colorSpec )
Attaching colorSpec.  Version: 1.5-0.  Author: Glenn Davis [aut, cre].  Built: R 4.4.0; ; 2024-01-28 04:15:05 UTC; windows
> 
> cs.options( loglevel='TRACE' )
$colorSpec.loglevel
[1] "TRACE"

$colorSpec.logformat
[1] "%t{%H:%M:%OS3} %l %n::%f(). %m"

$colorSpec.stoponerror
[1] TRUE

> 
> testCGATS <- function()
+     {
+     mess    = sprintf( "in testCGATS().  getwd() = '%s'", getwd() )
+     cat( mess, '\n', file=stderr() )
+     
+     #   find the extdata folder
+     if( grepl( "[..]Rcheck", getwd() ) )
+         extdata = "../colorSpec/extdata"
+     else
+         extdata = "inst/extdata"
+         
+     #   extdata = system.file( "extdata", package="colorSpec" )    # override
+     extdata  = '.'
+ 
+     
+     if( ! file.exists( extdata ) )
+         {
+         print( getwd() )    
+         print( extdata )
+         cat( "Cannot find the extdata folder !\n", file=stderr() )
+         return(FALSE)
+         }
+         
+ 
+         
+     #   test-CGATS-2-2S.txt 2 tables, both are spectral
+     path    =   file.path( extdata, "test-CGATS-2-2S.txt" )    
+     junk    = readCGATS(path)   # should be 2 tables
+     if( length(junk) != 2 )
+         return(FALSE)
+     junk    = readSpectraCGATS(path)  # should be 2 tables
+     if( length(junk) != 2 )
+         return(FALSE)
+         
+     #   test-CGATS-2-1S.txt 2 tables, only the 1st one is spectral
+     path    =   file.path( extdata, "test-CGATS-2-1S.txt" )    
+     junk    = readCGATS(path)           # should be 2 tables
+     if( length(junk) != 2 )
+         return(FALSE)
+     junk    = readSpectraCGATS(path)    # should be 1 table 
+     if( length(junk) != 1 )
+         return(FALSE)
+         
+     #   test-CGATS-2-1S-swap.txt 2 tables, only the 2nd one is spectral
+     path    =   file.path( extdata, "test-CGATS-2-1S-swap.txt" )    
+     junk    = readCGATS(path)           # should be 2 tables
+     if( length(junk) != 2 )
+         return(FALSE)
+     junk    = readSpectraCGATS(path)    # should be 1 table 
+     if( length(junk) != 1 )
+         return(FALSE)
+         
+         
+ 
+     #   A70.ti3 has 2 tables, both non-spectral
+     path    =   file.path( extdata, "A70.ti3" )
+     junk    = readCGATS(path)   # should be 2 tables
+     if( length(junk) != 2 )
+         return(FALSE)
+         
+     #   the final call should generate an ERROR and return NULL, so disable stopping
+     cs.options( stoponerror=FALSE )
+     junk    = readSpectraCGATS(path) 
+     if( ! is.null(junk) )
+         return(FALSE)
+         
+     return(TRUE)
+     }
>     
> 
>     
> if( ! testCGATS() )  stop( "testCGATS() failed !" )
in testCGATS().  getwd() = 'd:/RCompile/CRANincoming/R-devel/colorSpec.Rcheck/tests' 
05:16:09.671 INFO  colorSpec::extractTableCGATS(). In table 1, using CGATS-standard white-space specification. 
05:16:09.771 INFO  colorSpec::extractTableCGATS(). In table 2, using CGATS-standard white-space specification. 
05:16:09.781 INFO  colorSpec::readCGATS(). 2 tables read from './test-CGATS-2-2S.txt'. 
05:16:09.812 INFO  colorSpec::extractTableCGATS(). In table 1, using CGATS-standard white-space specification. 
05:16:09.821 INFO  colorSpec::extractTableCGATS(). In table 2, using CGATS-standard white-space specification. 
05:16:09.832 INFO  colorSpec::readCGATS(). 2 tables read from './test-CGATS-2-2S.txt'. 
05:16:09.833 INFO  colorSpec::spectralColumns(). In file './test-CGATS-2-2S.txt' and table 2, using non-standard convention for spectral data. 
05:16:09.835 DEBUG colorSpec::guessSpectrumQuantity(). guessed type=NA 
05:16:09.837 WARN  colorSpec::colorSpecFromDF(). Perturbed wavelengths in './test-CGATS-2-2S.txt' to have equal increments of 3.33333 nm [380 to 730 nm] 
05:16:09.915 INFO  colorSpec::spectralColumns(). In file './test-CGATS-2-2S.txt' and table 1, using non-standard convention for spectral data. 
05:16:09.916 INFO  colorSpec::colorSpecFromDF(). Dividing spectral values by SPECTRAL_NORM=1923.81. 
05:16:09.962 DEBUG colorSpec::guessSpectrumQuantity(). guessed type=NA 
05:16:10.000 WARN  colorSpec::colorSpecFromDF(). Perturbed wavelengths in './test-CGATS-2-2S.txt' to have equal increments of 3.33333 nm [380 to 730 nm] 
05:16:10.012 INFO  colorSpec::extractTableCGATS(). In table 1, using CGATS-standard white-space specification. 
05:16:10.021 INFO  colorSpec::extractTableCGATS(). In table 2, using CGATS-standard white-space specification. 
05:16:10.023 INFO  colorSpec::readCGATS(). 2 tables read from './test-CGATS-2-1S.txt'. 
05:16:10.033 INFO  colorSpec::extractTableCGATS(). In table 1, using CGATS-standard white-space specification. 
05:16:10.043 INFO  colorSpec::extractTableCGATS(). In table 2, using CGATS-standard white-space specification. 
05:16:10.045 INFO  colorSpec::readCGATS(). 2 tables read from './test-CGATS-2-1S.txt'. 
05:16:10.045 DEBUG colorSpec::is.colorSpec(). 'obj' class 'logical' is invalid. 
05:16:10.045 INFO  colorSpec::spectralColumns(). In file './test-CGATS-2-1S.txt' and table 1, using non-standard convention for spectral data. 
05:16:10.047 INFO  colorSpec::colorSpecFromDF(). Dividing spectral values by SPECTRAL_NORM=1923.81. 
05:16:10.047 DEBUG colorSpec::guessSpectrumQuantity(). guessed type=NA 
05:16:10.048 WARN  colorSpec::colorSpecFromDF(). Perturbed wavelengths in './test-CGATS-2-1S.txt' to have equal increments of 3.33333 nm [380 to 730 nm] 
05:16:10.050 INFO  colorSpec::extractTableCGATS(). In table 1, using CGATS-standard white-space specification. 
05:16:10.051 INFO  colorSpec::extractTableCGATS(). In table 2, using CGATS-standard white-space specification. 
05:16:10.061 INFO  colorSpec::readCGATS(). 2 tables read from './test-CGATS-2-1S-swap.txt'. 
05:16:10.062 INFO  colorSpec::extractTableCGATS(). In table 1, using CGATS-standard white-space specification. 
05:16:10.063 INFO  colorSpec::extractTableCGATS(). In table 2, using CGATS-standard white-space specification. 
05:16:10.074 INFO  colorSpec::readCGATS(). 2 tables read from './test-CGATS-2-1S-swap.txt'. 
05:16:10.074 INFO  colorSpec::spectralColumns(). In file './test-CGATS-2-1S-swap.txt' and table 2, using non-standard convention for spectral data. 
05:16:10.076 INFO  colorSpec::colorSpecFromDF(). Dividing spectral values by SPECTRAL_NORM=1923.81. 
05:16:10.076 DEBUG colorSpec::guessSpectrumQuantity(). guessed type=NA 
05:16:10.077 WARN  colorSpec::colorSpecFromDF(). Perturbed wavelengths in './test-CGATS-2-1S-swap.txt' to have equal increments of 3.33333 nm [380 to 730 nm] 
05:16:10.078 DEBUG colorSpec::is.colorSpec(). 'obj' class 'logical' is invalid. 
05:16:10.079 INFO  colorSpec::extractTableCGATS(). In table 1, using CGATS-standard white-space specification. 
05:16:10.081 INFO  colorSpec::extractTableCGATS(). In table 2, using CGATS-standard white-space specification. 
05:16:10.083 INFO  colorSpec::readCGATS(). 2 tables read from './A70.ti3'. 
05:16:10.103 INFO  colorSpec::extractTableCGATS(). In table 1, using CGATS-standard white-space specification. 
05:16:10.106 INFO  colorSpec::extractTableCGATS(). In table 2, using CGATS-standard white-space specification. 
05:16:10.108 INFO  colorSpec::readCGATS(). 2 tables read from './A70.ti3'. 
05:16:10.108 DEBUG colorSpec::is.colorSpec(). 'obj' class 'logical' is invalid. 
05:16:10.108 DEBUG colorSpec::is.colorSpec(). 'obj' class 'logical' is invalid. 
05:16:10.108 ERROR colorSpec::readSpectraCGATS(). Found no tables with spectral data in './A70.ti3'. 
> 
> cat( "Passed all CGATS read tests !\n", file=stderr() )
Passed all CGATS read tests !
> 
> proc.time()
   user  system elapsed 
   0.59    0.09    0.67