Dear all,
 
I am wondering does anybody know has there been any progress in fixing the problem with the getOrfs() function in the GeneR library, using R on a Windows computer?
 
I have just tried this function on my Windows PC, and get the error described below.
 
I would like to use this function to teach gene-finding for a bioinformatics practical class, so would be grateful if anybody could tell me if this problem with the function on Windows is likely to be fixed soon?
 
Kind Regards,
Avril
 
Avril Coghlan
University College Cork, Ireland
 
 
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 <https://stat.ethz.ch/mailman/listinfo/bioconductor> > 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 <https://stat.ethz.ch/mailman/listinfo/bioconductor> > 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 <https://stat.ethz.ch/mailman/listinfo/bioconductor> > 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 <https://stat.ethz.ch/mailman/listinfo/bioconductor> 
>>> 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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>>> Bioconductor at stat.math.ethz.ch <https://stat.ethz.ch/mailman/listinfo/bioconductor> 
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> 
> 
 

 


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