[BioC] The funcion getOrfs, doesn`t works, package: GeneR

[Vincent Carey]

Please give sessionInfo() result.  Here are my results, installing
GeneR from source a moment ago

> s<-"gtcatgcatgctaggtgacagttaaaatgcgtctaggtgacagtctaacaa"
> placeString(s)
[1] 0
> s
[1] "gtcatgcatgctaggtgacagttaaaatgcgtctaggtgacagtctaacaa"
> ?placeString
>    getSeq(seqno=0)
[1] "GTCATGCATGCTAGGTGACAGTTAAAATGCGTCTAGGTGACAGTCTAACAA"
> getOrfs(phase = NULL,seqno=0)
     start stop
[1,]     4   18
[2,]     8   25
> maxOrf()
[1] 18
> ?maxOrf
> ?getOrfs
> getOrfs(phase = NULL,seqno=0)
     start stop
[1,]     4   18
[2,]     8   25
> placeString("TTTTTTTTTTTT")
[1] 0
> exactWord("TTT")
[[1]]
 [1]  1  2  3  4  5  6  7  8  9 10

> sessionInfo()
R version 2.10.0 Under development (unstable) (2009-09-09 r49642)
i386-apple-darwin9.8.0

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices datasets  tools     utils     methods
[8] base

other attached packages:
[1] GeneR_2.15.0    weaver_1.11.1   codetools_0.2-2 digest_0.3.1



On Fri, Oct 9, 2009 at 1:04 AM, avargas <avargas at lcg.unam.mx> wrote:
> Dear list, i have some troubles with the GeneR package, it seems that
> getOrfs is not working. I already try to use it with the example info of
> the help:
>
> library("GeneR")
> s<-"gtcatgcatgctaggtgacagttaaaatgcgtctaggtgacagtctaacaa"
> placeString(s)
>
> getOrfs(phase = NULL,seqno=0)
> maxOrf()
>
> But returns:
>> getOrfs(phase = NULL,seqno=0)
> NULL
>> maxOrf()
> [1] -1
> I have the version 2.10 of R and the Package GeneR version 2.15.0
> I mean, the examples of
> http://rss.acs.unt.edu/Rdoc/library/GeneR/doc/GeneR.pdf at page 5 are not
> reproducible, so, which is the problem?
> In advance, thanks.
>
> Amhed Missael Vargas Velàzquez
> avargas at lcg.unam.mx
> LCG,UNAM
>
> Pd: I think that the problem is with another function named, exact word,
> that does not work too.
> i.e.
> library("GeneR")
> placeString("TTTTTTTTTTTT")
> exactWord("TTT")
>
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