[BioC] snapCGH: T instead of TRUE, etc

ma3mls at bath.ac.uk ma3mls at bath.ac.uk
Fri Mar 16 17:41:01 CET 2007


Hi Ramon,

I've made and uploaded the changes you suggested.  All instances of T 
have been changed to TRUE in the appropriate source files.

It's not an issue I've ever seen before.

Mike Smith


Quoting Ramon Diaz-Uriarte <rdiaz at cnio.es>:

> Sorry, I forgot to say I am seeing this with versions 1.2.0 (BioC 1.9) and
> 1.3.2 (BioC 2.0) of snapCGH (R-2.4., under Debian GNU/Linux).
>
> R.
>
> On Friday 16 March 2007 14:29, Ramon Diaz-Uriarte wrote:
>> Dear All,
>>
>> Somewhat similar to what I reported before, with snapCGH I am getting
>> errors, when building a package, that can be traced to errors in snapCGH.
>> Specifically:
>>
>> The functions "find.param.{two.three..}" lead to errors such as
>>
>> Error in matrix(c(1 - p1, p1, p2, 1 - p2), ncol = 2, b = T) :
>>          T used instead of TRUE
>> Error in matrix(c(1 - p1, p1, p2, 1 - p2), ncol = 2, b = T) :
>>          recursive default argument reference
>>
>>
>>
>>
>> And the functions Viterbi.{two.three..} also show similar problems, as in
>>
>> Error in matrix(nrow = K, ncol = n, b = T) :
>>          T used instead of TRUE
>> Error in matrix(nrow = K, ncol = n, b = T) :
>>          recursive default argument referenc
>>
>> max(-1e+05, log(BFGS.output$prior[i]), na.rm = T)
>>          T used instead of TRUE
>>
>>
>>
>>
>> Once all the appropriate T are replaced by TRUE things are OK again.
>>
>>
>>
>> Best,
>>
>>
>> R.
>
> --
> Ramón Díaz-Uriarte
> Statistical Computing Team
> Centro Nacional de Investigaciones Oncológicas (CNIO)
> (Spanish National Cancer Center)
> Melchor Fernández Almagro, 3
> 28029 Madrid (Spain)
> Fax: +-34-91-224-6972
> Phone: +-34-91-224-6900
>
> http://ligarto.org/rdiaz
> PGP KeyID: 0xE89B3462
> (http://ligarto.org/rdiaz/0xE89B3462.asc)
>
>
>
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