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

[Vincent Carey]

I can confirm that on a mingw build for windows, these computations do
not succeed as intended.  This is a situation where the testing and
error reporting of the software are not sufficient to allow our use of
R CMD check to identify nonportable code.  Somewhere in the package
man pages or obligatory test code the result of a computation should
be checked against its known value and an error thrown if a
discrepancy occurs.

Some of the computations in the examples seem solvable using Biostrings.

Solution for you at this moment is to use another platform.  I have
shown that it works on MacOSX, and just tested a linux machine, and
the intended results seem to come back.  But it is important for all
contributors to recognize that our multiplatform build/check system
cannot identify nonportability if erroneous calculations do not raise
error conditions in examples or tests.

On Fri, Oct 9, 2009 at 4:46 AM, avargas <avargas at lcg.unam.mx> wrote:
> I apreciate the quick response, here is my code:
>
>> library("GeneR")
>> s<-"gtcatgcatgctaggtgacagttaaaatgcgtctaggtgacagtctaacaa"
>> placeString(s)
> [1] 0
>>
>> getOrfs(phase = NULL,seqno=0)
> NULL
>> maxOrf()
> [1] -1
>>
>> #Problem with exact word
>
>> placeString("TTTTTTTTTTTT")
> [1] 0
>> exactWord("TTT")
> [[1]]
> [1] -1
>
>> sessionInfo()
> R version 2.10.0 Under development (unstable) (2009-08-15 r49252)
> i386-pc-mingw32
>
> locale:
> [1] LC_COLLATE=Spanish_Mexico.1252  LC_CTYPE=Spanish_Mexico.1252
> [3] LC_MONETARY=Spanish_Mexico.1252 LC_NUMERIC=C
> [5] LC_TIME=Spanish_Mexico.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] GeneR_2.15.0
>
> On Fri, 9 Oct 2009 04:21:58 -0400, Vincent Carey
> <stvjc at channing.harvard.edu> wrote:
>> 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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>
>