[R] incomplete final line found by readTableHeader

[Leonardo K. Shikida]

sorry, it was read, indeed.

TIA

Leonardo K. Shikida
Vetta Labs
+55(31)2551-6936 ext 203
http://www.vettalabs.com




On Thu, Apr 8, 2010 at 3:43 PM, David Winsemius <dwinsemius at comcast.net> wrote:
>
> 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
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
> David Winsemius, MD
> West Hartford, CT
>
>