[R] incomplete final line found by readTableHeader

[David Winsemius]

On Apr 8, 2010, at 2:14 PM, Leonardo K. Shikida wrote:

> Hi
>
> I am trying this
>
>> x <- read.table("/home/kenji/1245/GDS1_2grps_.cls", header = F,  
>> skip = 2)
>> x <- read.table("/home/kenji/1246/MYCset.cls", header = F, skip = 2)
> Warning message:
> In read.table("/home/kenji/1246/MYCset.cls", header = F, skip = 2) :
>  incomplete final line found by readTableHeader on
> '/home/kenji/1246/MYCset.cls'
>
> Here are the hex's
>
> kenji at Yule:~$ hd 1245/GDS1_2grps_.cls
> 00000000  31 32 20 32 20 31 0a 23  20 43 44 31 39 2b 20 43  |12 2  
> 1.# CD19+ C|
> 00000010  44 34 30 4c 0a 30 20 30  20 30 20 30 20 30 20 30  |D40L.0  
> 0 0 0 0 0|
> 00000020  20 31 20 31 20 31 20 31  20 31 20 31 0a           | 1 1 1  
> 1 1 1.|
> 0000002d
> kenji at Yule:~$ hd 1246/
> job938_MYC_RMA.gct  MYCset.cls          .MYCset.cls.swp
> kenji at Yule:~$ hd 1246/MYCset.cls
> 00000000  31 32 20 32 20 31 0a 23  20 4d 59 43 20 4e 6f 74  |12 2  
> 1.# MYC Not|
> 00000010  0a 30 20 30 20 30 20 30  20 30 20 30 20 31 20 31  |.0 0 0  
> 0 0 0 1 1|
> 00000020  20 31 20 31 20 31 20 31                           | 1 1 1 1|
> 00000028
>
> So it seems the problem is the linefeed (0a) absent in the second
> file, probably generated by some evil excel or something like this.
>
> My question is: is there any simple way to make read.table robust to
> deal with this problem? I would like to avoid solutions such as
> re-implement using scan or asking the user to deal with this for me,
> changing himself the file.

Did the line get read?

(I have failed in my efforts on a Mac to create a file with a text  
editor that throws that warning.) In a sense it appears to already be  
"robust" , since it only generated a warning, rather than an error. If  
you want to programmatically turn off warnings, then:

?warnings
?options   # with a bunch of settings for warn

Perhaps inside your function you could call set warn = -1 the restore  
to =0 before exit.

options(warn=-1)
read.table( ...  )
options(warn=0)
>
> Thanks in advance
>
> Leonardo K. Shikida
> Vetta Labs
> +55(31)2551-6936 ext 203
> http://www.vettalabs.com
>
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David Winsemius, MD
West Hartford, CT