read.spc cannot handle spectra files with only one line in the audit log that ends with "\r\n"

[PAAC1984]

Hi,

I'm using hyperSpec to process Grams spectral data(*.spc files) and recently I received the following error:

Error in apply(pos, 1, function(p, x) substr(x, p[1], p[2]), x) : 
  dim(X) must have a positive length

After tracing down the function in the code, it looks like the origin is in the "hyperSpec:::split.string" function.
What happens is when variable "x" only has one line and ends with "\r\n\" (for example "myString\r\n\"), the pos matrix will turn into an array rather then a matrix and cause the error above.

Alternate versions of strings using "r\n\" like:

• "myString\r\n\test"
• "myString\r\n\test\r\n\"

Do seem to work.

Let me know if there are further questions on this.

Best regards,

Patrick

[GegznaV]

Hello, Patric (@PAAC1984),

Thanks for contacting us. It seems that the issue is OS-specific, as you indicate that it is related to \r\n. I have a few additional questions:

• what R version do you use?
• what hyperSpec version do you use?
• what operating system do you use?
• what operating system was used to create the data file?
• could you provide an example of a data file? You may zip it and drag-and-drop here.
• could you provide a minimal reproducible example of code (a.k.a, reprex) that reproduces the reproduction of the issue. I recommend using reprex package to generate a reprex.
• If possible, show us how the expected result should look like.

[PAAC1984]

• what R version do you use?
  

3.6.0 (2019-04-26)

• what hyperSpec version do you use?
  

hyperSpec_0.100.0

• what operating system do you use?
  

Windows 10 x64

• what operating system was used to create the data file?
  

Windows 10 x64

• could you provide an example of a data file? You may zip it and drag-and-drop here.
  

Example_spectra.zip

• could you provide a minimal reproducible example of code (a.k.a, reprex) that reproduces the reproduction of the issue. I recommend using reprex package to generate a reprex.
  

library(hyperSpec)
hyperSpec::read.spc("../Example_spectra.spc")

• If possible, show us how the expected result should look like.
  

In the function "hyperSpec:::string.split" adjust the following line:
x <- apply(pos, 1, function(p, x) substr(x, p[1], p[2]),
x)

To include a check whether the variable "pos" is a matrix(which has dimensions), otherwise it should be an array according on how the script acts:
if(!is.null(dim(pos))){
x <- apply(pos, 1, function(p, x) substr(x, p[1], p[2]),
x)
} else {
x <- substr(x, pos[1], pos[2])
return(x)
}

[GegznaV]

Thank you @PAAC1984.

@cbeleites, could you look into this? Does this issue belong to hyperSpec or to hySpc.read.spc?

[GegznaV]

I can reproduce the issue with hySpc.read.spc package:

hySpc.read.spc::read.spc("Example_spectra.spc")
## Error in apply(pos, 1, function(p, x) substr(x, p[1], p[2]), x) : 
## dim(X) must have a positive length

It seems that function read.spc() is not renamed into read_spc() yet. And internal function split.string() is now a part of hySpc.read.spc package (so I'll migrate the issue to the appropriate repo).

[GegznaV]

GitHub does not allow transferring the issue to the particular hySpc.read.spc repo. But the following discussion must continue there:

• read.spc cannot handle spectra files with only one line in the audit log that ends with "\r\n" hySpc.read.spc#15